Modification of Salmonella phage φSan23 using BRED

Foodborne illnesses caused by Salmonella species are common and represent a significant public health challenge. Identifying the sources of contamination by these microorganisms is crucial for controlling and preventing infections. While various tests have been proposed for this purpose, many requir...

Full description

Autores:
Fajardo Poveda, Johan David
Tipo de recurso:
Trabajo de grado de pregrado
Fecha de publicación:
2025
Institución:
Universidad de los Andes
Repositorio:
Séneca: repositorio Uniandes
Idioma:
eng
OAI Identifier:
oai:repositorio.uniandes.edu.co:1992/75938
Acceso en línea:
https://hdl.handle.net/1992/75938
Palabra clave:
Salmonella
Biosensors
Bacteriophage
φSan23
Genetics
BRED
Microbiología
Rights
openAccess
License
Attribution 4.0 International
id UNIANDES2_6fdd132b2534776c1939378299edf2a0
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dc.title.eng.fl_str_mv Modification of Salmonella phage φSan23 using BRED
title Modification of Salmonella phage φSan23 using BRED
spellingShingle Modification of Salmonella phage φSan23 using BRED
Salmonella
Biosensors
Bacteriophage
φSan23
Genetics
BRED
Microbiología
title_short Modification of Salmonella phage φSan23 using BRED
title_full Modification of Salmonella phage φSan23 using BRED
title_fullStr Modification of Salmonella phage φSan23 using BRED
title_full_unstemmed Modification of Salmonella phage φSan23 using BRED
title_sort Modification of Salmonella phage φSan23 using BRED
dc.creator.fl_str_mv Fajardo Poveda, Johan David
dc.contributor.advisor.none.fl_str_mv Vives Flórez, Martha Josefina
dc.contributor.author.none.fl_str_mv Fajardo Poveda, Johan David
dc.contributor.researchgroup.none.fl_str_mv Facultad de Ciencias::Microbiologia Ambiental y Bioprospeccion
dc.subject.keyword.eng.fl_str_mv Salmonella
Biosensors
Bacteriophage
φSan23
Genetics
BRED
topic Salmonella
Biosensors
Bacteriophage
φSan23
Genetics
BRED
Microbiología
dc.subject.themes.spa.fl_str_mv Microbiología
description Foodborne illnesses caused by Salmonella species are common and represent a significant public health challenge. Identifying the sources of contamination by these microorganisms is crucial for controlling and preventing infections. While various tests have been proposed for this purpose, many require complex and time-consuming procedures. Although in-situ tests exist, they often lack the capacity for quantitative detection. Phage-based biosensors have been proposed as a promising alternative for identifying pathogens causing these foodborne diseases. However, they face technical limitations, such as the difficulty in properly attaching bacteriophages to the biosensor. Genetically modified bacteriophages have been suggested as a potential solution to overcome these limitations. In this work, we explore the genetic modification of the bacteriophage φSan23 using the BRED technique. To achieve this, we aimed to identify structural proteins of the bacteriophage head and fuse them with a His-tag and a marker protein, such as GFP. Additionally, we sought to produce this GFP marker protein inside the bacterial host. We were able to annotate and model the structural and non-structural proteins of the bacteriophage and found an efficient method for electroporating exogenous DNA into Salmonella. However, the modification of the bacteriophage φSan23 using the BRED technique was not successful. Additional approaches are needed to achieve this goal in future studies.
publishDate 2025
dc.date.accessioned.none.fl_str_mv 2025-01-31T19:56:26Z
dc.date.available.none.fl_str_mv 2025-01-31T19:56:26Z
dc.date.issued.none.fl_str_mv 2025-01-29
dc.type.none.fl_str_mv Trabajo de grado - Pregrado
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dc.language.iso.none.fl_str_mv eng
language eng
dc.relation.references.none.fl_str_mv Al-Hindi, R. R. et al. (2022). Bacteriophage-based biosensors: A platform for detection of foodborne bacterial pathogens from food and environment. Biosensors, 12(10), 905.
Andes, U. (2015). Composition comprising bacteriophage for reducing, eliminating and/or preventing Salmonella enteritidis, Salmonella typhimurium and Salmonella paratyphi b. Colombia.
Bernardinelli, G., & Högberg, B. (2017). Entirely enzymatic nanofabrication of DNA-protein conjugates. Nucleic Acids Research, 45(18), e160. https://doi.org/10.1093/nar/gkx707
Bio-Rad. (n.d.-a). Micropulser electroporator: Instruction manual and applications guide [Catalog #1652100]. https://www.bio-rad.com/sites/default/files/2022-01/10000148532.pdf
Bio-Rad. (n.d.-b). Pglo plasmid map resources [Accessed: 2025-01-25]. https://www.bio-rad.com/es-co/applications-technologies/pglo-plasmid-map-resources?ID=NISQOC15
Chinchilla Sarmiento, S. (2023). Aproximaciones al desarrollo de un bacteriófago recombinante reportero de Salmonella enteritidis y Salmonella typhimurium, mediante la refactorización in-vitro del genoma de φSan23.
Comeau, A. M., & Krisch, H. M. (2008). The capsid of the T4 phage superfamily: The evolution, diversity, and structure of some of the most prevalent proteins in the biosphere. Molecular Biology and Evolution, 25(7), 1321–1332.
Costa, A. R., Azeredo, J., & Pires, D. P. (2023). Synthetic biology to engineer bacteriophage genomes. In Bacteriophage therapy: From lab to clinical practice (pp. 261–277). Springer US.
Datsenko, K. A., & Wanner, B. L. (2000). One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proceedings of the National Academy of Sciences, 97(12), 6640–6645.
Dong, X. et al. (2022). Genetic manipulation of the human gut bacterium Eggerthella lenta reveals a widespread family of transcriptional regulators. Nature Communications, 13(1), 7624. https://doi.org/10.1038/s41467-022-33576-3
Fang, Z., Feng, T., Zhou, H., & Chen, M. (2022). DeepVP: Identification and classification of phage virion proteins using deep learning. Gigascience, 11, giac076.
Farooq, U., Yang, Q., Ullah, M. W., & Wang, S. (2019). Principle and development of phage-based biosensors. Biosens. Environ. Monit, 1, 1–18.
Flamholz, Z. N., Li, C., & Kelly, L. (2024). Improving viral annotation with artificial intelligence. mBio, 15(10), e03206–23.
Jensen, S. I. et al. (2015). Seven gene deletions in seven days: Fast generation of Escherichia coli strains tolerant to acetate and osmotic stress. Scientific Reports, 5, 17874. https://doi.org/10.1038/srep17874
Jiménez Sánchez, A. (2015). Caracterización y evaluación de la eficiencia in vitro de bacteriófagos nativos contra Salmonella, causante de salmonelosis en Colombia. Universidad de los Andes.
Khambhati, K. et al. (2023). Phage engineering and phage-assisted CRISPR-Cas delivery to combat multidrug-resistant pathogens. Bioengineering Translational Medicine, 8(2), e10381.
Kim, S., Kim, M., & Ryu, S. (2014). Development of an engineered bioluminescent reporter phage for the sensitive detection of viable Salmonella typhimurium. Analytical Chemistry, 86(12), 5858–5864.
Klucar, L., Stano, M., & Hajduk, M. (2010). Phisite: Database of gene regulation in bacteriophages. Nucleic Acids Research, 38(suppl1), D366–D370.
Lamas, A. et al. (2018). A comprehensive review of non-enterica subspecies of Salmonella enterica. Microbiological Research, 206, 60–73.
McNair, K. et al. (2019). PHANOTATE: A novel approach to gene identification in phage genomes. Bioinformatics, 35(22), 4537–4542.
Paczesny, J., Richter, L., & Hołyst, R. (2020). Recent progress in the detection of bacteria using bacteriophages: A review. Viruses, 12(8), 845.
Paddison, P. et al. (1998). The roles of the bacteriophage T4 r genes in lysis inhibition and fine-structure genetics: A new perspective. Genetics, 148(4), 1539–1550.
Pires, D. P. et al. (2016). Genetically engineered phages: A review of advances over the last decade. Microbiology and Molecular Biology Reviews, 80(3), 523–543.
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dc.publisher.none.fl_str_mv Universidad de los Andes
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dc.publisher.faculty.none.fl_str_mv Facultad de Ciencias
dc.publisher.department.none.fl_str_mv Departamento de Ciencias Biológicas
publisher.none.fl_str_mv Universidad de los Andes
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spelling Vives Flórez, Martha Josefinavirtual::23022-1Fajardo Poveda, Johan DavidFacultad de Ciencias::Microbiologia Ambiental y Bioprospeccion2025-01-31T19:56:26Z2025-01-31T19:56:26Z2025-01-29https://hdl.handle.net/1992/75938instname:Universidad de los Andesreponame:Repositorio Institucional Sénecarepourl:https://repositorio.uniandes.edu.co/Foodborne illnesses caused by Salmonella species are common and represent a significant public health challenge. Identifying the sources of contamination by these microorganisms is crucial for controlling and preventing infections. While various tests have been proposed for this purpose, many require complex and time-consuming procedures. Although in-situ tests exist, they often lack the capacity for quantitative detection. Phage-based biosensors have been proposed as a promising alternative for identifying pathogens causing these foodborne diseases. However, they face technical limitations, such as the difficulty in properly attaching bacteriophages to the biosensor. Genetically modified bacteriophages have been suggested as a potential solution to overcome these limitations. In this work, we explore the genetic modification of the bacteriophage φSan23 using the BRED technique. To achieve this, we aimed to identify structural proteins of the bacteriophage head and fuse them with a His-tag and a marker protein, such as GFP. Additionally, we sought to produce this GFP marker protein inside the bacterial host. We were able to annotate and model the structural and non-structural proteins of the bacteriophage and found an efficient method for electroporating exogenous DNA into Salmonella. However, the modification of the bacteriophage φSan23 using the BRED technique was not successful. Additional approaches are needed to achieve this goal in future studies.PregradoBacteriofagos30 páginasapplication/pdfengUniversidad de los AndesMicrobiologíaFacultad de CienciasDepartamento de Ciencias BiológicasAttribution 4.0 Internationalhttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Modification of Salmonella phage φSan23 using BREDTrabajo de grado - Pregradoinfo:eu-repo/semantics/bachelorThesisinfo:eu-repo/semantics/acceptedVersionhttp://purl.org/coar/resource_type/c_7a1fTexthttp://purl.org/redcol/resource_type/TPSalmonellaBiosensorsBacteriophageφSan23GeneticsBREDMicrobiologíaAl-Hindi, R. R. et al. (2022). Bacteriophage-based biosensors: A platform for detection of foodborne bacterial pathogens from food and environment. Biosensors, 12(10), 905.Andes, U. (2015). Composition comprising bacteriophage for reducing, eliminating and/or preventing Salmonella enteritidis, Salmonella typhimurium and Salmonella paratyphi b. Colombia.Bernardinelli, G., & Högberg, B. (2017). Entirely enzymatic nanofabrication of DNA-protein conjugates. Nucleic Acids Research, 45(18), e160. https://doi.org/10.1093/nar/gkx707Bio-Rad. (n.d.-a). Micropulser electroporator: Instruction manual and applications guide [Catalog #1652100]. https://www.bio-rad.com/sites/default/files/2022-01/10000148532.pdfBio-Rad. (n.d.-b). Pglo plasmid map resources [Accessed: 2025-01-25]. https://www.bio-rad.com/es-co/applications-technologies/pglo-plasmid-map-resources?ID=NISQOC15Chinchilla Sarmiento, S. (2023). Aproximaciones al desarrollo de un bacteriófago recombinante reportero de Salmonella enteritidis y Salmonella typhimurium, mediante la refactorización in-vitro del genoma de φSan23.Comeau, A. M., & Krisch, H. M. (2008). The capsid of the T4 phage superfamily: The evolution, diversity, and structure of some of the most prevalent proteins in the biosphere. Molecular Biology and Evolution, 25(7), 1321–1332.Costa, A. R., Azeredo, J., & Pires, D. P. (2023). Synthetic biology to engineer bacteriophage genomes. In Bacteriophage therapy: From lab to clinical practice (pp. 261–277). Springer US.Datsenko, K. A., & Wanner, B. L. (2000). One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proceedings of the National Academy of Sciences, 97(12), 6640–6645.Dong, X. et al. (2022). Genetic manipulation of the human gut bacterium Eggerthella lenta reveals a widespread family of transcriptional regulators. Nature Communications, 13(1), 7624. https://doi.org/10.1038/s41467-022-33576-3Fang, Z., Feng, T., Zhou, H., & Chen, M. (2022). DeepVP: Identification and classification of phage virion proteins using deep learning. Gigascience, 11, giac076.Farooq, U., Yang, Q., Ullah, M. W., & Wang, S. (2019). Principle and development of phage-based biosensors. Biosens. Environ. Monit, 1, 1–18.Flamholz, Z. N., Li, C., & Kelly, L. (2024). Improving viral annotation with artificial intelligence. mBio, 15(10), e03206–23.Jensen, S. I. et al. (2015). Seven gene deletions in seven days: Fast generation of Escherichia coli strains tolerant to acetate and osmotic stress. Scientific Reports, 5, 17874. https://doi.org/10.1038/srep17874Jiménez Sánchez, A. (2015). Caracterización y evaluación de la eficiencia in vitro de bacteriófagos nativos contra Salmonella, causante de salmonelosis en Colombia. Universidad de los Andes.Khambhati, K. et al. (2023). Phage engineering and phage-assisted CRISPR-Cas delivery to combat multidrug-resistant pathogens. Bioengineering Translational Medicine, 8(2), e10381.Kim, S., Kim, M., & Ryu, S. (2014). Development of an engineered bioluminescent reporter phage for the sensitive detection of viable Salmonella typhimurium. Analytical Chemistry, 86(12), 5858–5864.Klucar, L., Stano, M., & Hajduk, M. (2010). Phisite: Database of gene regulation in bacteriophages. Nucleic Acids Research, 38(suppl1), D366–D370.Lamas, A. et al. (2018). A comprehensive review of non-enterica subspecies of Salmonella enterica. Microbiological Research, 206, 60–73.McNair, K. et al. (2019). PHANOTATE: A novel approach to gene identification in phage genomes. Bioinformatics, 35(22), 4537–4542.Paczesny, J., Richter, L., & Hołyst, R. (2020). Recent progress in the detection of bacteria using bacteriophages: A review. Viruses, 12(8), 845.Paddison, P. et al. (1998). The roles of the bacteriophage T4 r genes in lysis inhibition and fine-structure genetics: A new perspective. Genetics, 148(4), 1539–1550.Pires, D. P. et al. (2016). Genetically engineered phages: A review of advances over the last decade. 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