Ciencia e Ingeniería en Alimentos y Biotecnología

URI permanente para esta comunidadhttp://repositorio.uta.edu.ec/handle/123456789/412

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Análisis de variantes genéticas asociadas al cáncer de mama y su impacto en la prevalencia de la enfermedad estudiando diferentes poblaciones
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología, 2026-07)
Mesias Barreno, Joel Esteban
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Galarza Galarza, Cristian Fernando
Breast cancer is a clinically relevant neoplasm due to its marked molecular heterogeneity, reflected in transcriptomic, regulatory, and genetic differences that influence tumor progression, therapeutic response, prognosis, and biological behavior of the disease. Therefore, its characterization using bioinformatics approaches allows for a more precise understanding of the variability among tumor subtypes, the recognition of mechanisms associated with aggressiveness, and provides useful information for the identification of potential biomarkers. Samples corresponding to the estrogen receptor-positive, progesterone receptor-positive, human epidermal growth factor receptor type 2- positive, and triple-negative breast cancer subtypes, obtained from NCBI, were analyzed using a bioinformatics workflow that included quality control, read preprocessing, alignment to the reference human genome, gene quantification, differential expression analysis, functional enrichment, detection of alternative splicing events, identification of genetic variants, functional annotation, and complementary review of prioritized candidate genes. The results showed that triple-negative breast cancer presented the most divergent transcriptomic profile, with a greater number of differentially expressed genes and processes associated with cell proliferation, DNA repair, RNA processing, extracellular matrix, tumor metabolism, and alternative splicing. The integration of differential expression, splicing, and variants allowed prioritizing genes such as QSOX1, MTCH2, and PTPRN2, providing relevant bioinformatics evidence for future research aimed at the experimental validation of biomarkers and the development of precision medicine strategies with possible application in the personalized management of breast cancer.
Evaluación de la diversidad genómica y las relaciones filogenéticas de Salmonella enterica aislada a partir de pollo comercializado en mercados de la ciudad de Ambato mediante secuenciación de Tercera Generación
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología, 2026-07)
Constante Chimborazo, Sasha Carolina
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Calero Cáceres, William Ricardo
Salmonellosis is one of the most important foodborne diseases worldwide, with S. enterica being one of the main pathogens associated with the poultry production chain. In Ecuador, the commercialization of chicken in traditional markets constitutes a potential source of exposure, especially in cities such as Ambato, where information on the genomic characterization of circulating strains is limited. The present study evaluated the genetic diversity and phylogenetic relationships of 12 S. enterica strains isolated from chicken carcasses and giblets marketed in Ambato markets. The strains were sequenced using Oxford Nanopore technology and characterized through bioinformatics tools to determine serotypes, sequence types, virulence genes, antimicrobial resistance genes, plasmids, and prophages. Phylogenetic relationships were established through comparative analysis of single nucleotide polymorphisms with reference strains. The genomes showed completeness levels ranging from 95.52 percent to 100 percent. Eleven isolates belonged to the Infantis serotype and one to the Kentucky serotype. All strains carried genes associated with resistance to aminoglycosides and sulfonamides, whereas blaCTX-M-65 was detected in seven isolates. Phylogenetic analysis revealed the circulation of a predominant clonal lineage of S. Infantis related to poultry isolates previously reported in Ecuador. The results demonstrate the presence of multidrug-resistant strains of epidemiological importance and highlight the value of third-generation sequencing for strengthening genomic surveillance under the One Health approach.
Evaluación de la diversidad genómica y las relaciones filogenéticas de Salmonella enterica aislada a partir de pollo comercializado en mercados de la ciudad de Ambato mediante secuenciación de Tercera Generación
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología, 2026-07)
Castelo Fiallos, Yajaira Ivanova
;
Calero Cáceres, William Ricardo
Salmonellosis is one of the most important foodborne diseases worldwide, with S. enterica being one of the main pathogens associated with the poultry production chain. In Ecuador, the commercialization of chicken in traditional markets constitutes a potential source of exposure, especially in cities such as Ambato, where information on the genomic characterization of circulating strains is limited. The present study evaluated the genetic diversity and phylogenetic relationships of 12 S. enterica strains isolated from chicken carcasses and giblets marketed in Ambato markets. The strains were sequenced using Oxford Nanopore technology and characterized through bioinformatics tools to determine serotypes, sequence types, virulence genes, antimicrobial resistance genes, plasmids, and prophages. Phylogenetic relationships were established through comparative analysis of single nucleotide polymorphisms with reference strains. The genomes showed completeness levels ranging from 95.52 percent to 100 percent. Eleven isolates belonged to the Infantis serotype and one to the Kentucky serotype. All strains carried genes associated with resistance to aminoglycosides and sulfonamides, whereas blaCTX-M-65 was detected in seven isolates. Phylogenetic analysis revealed the circulation of a predominant clonal lineage of S. Infantis related to poultry isolates previously reported in Ecuador. The results demonstrate the presence of multidrug-resistant strains of epidemiological importance and highlight the value of third-generation sequencing for strengthening genomic surveillance under the One Health approach.
Ensamblaje de genoma completo de la cepa 19 Lactobacillus Plantarum
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología, 2026-01)
Tapia Romero, David Eliseo
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Garcés Moncayo, María Daniela
The genomic characterization of Lactobacillus plantarum is a significant contribution to the development of biotechnological and probiotic applications, due to its adaptability, broad metabolic repertoire, and frequent presence in fermented foods and the human microbiota. In this context, the study of the genome of strain 19 is important for determining its functional potential and safety profile, essential aspects for its future implementation in the food industry or in products with health-promoting properties. The research was conducted by extracting genomic DNA using the MpBio kit and subsequently sequencing it on the Illumina NovaSeq platform. The data obtained underwent quality control, de novo assembly with SPAdes, and structural annotation with tools such as Prokka, PGAP, and RASTtk. Furthermore, a phylogenomic analysis based on conserved orthologs and a functional characterization were performed using specialized databases, complemented by the identification of resistance genes, non-pathogenic virulence genes, and metabolic subsystems. The results showed a complete and stable genome with high-quality sequencing, an abundance of genes associated with metabolism, stress, and transport, and a resistance profile comprised mainly of intrinsic mechanisms not associated with mobile elements. The functional distribution and the absence of plasmids indicate a safe and versatile genome, compatible with the strain's potential use as a probiotic or as a microorganism of biotechnological interest. Overall, strain exhibits genetic characteristics that support its future applicability in diverse areas.
Caracterización de genomas completos de aislamientos de Salmonella spp. aisladas de muestras de agua del canal de riego Mocha-Quero-Ladrillos mediante secuenciación de tercera generación
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología, 2026-01)
Portero Regalado, María José
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Arancibia Soria, Mirari Yosune
The presence of Salmonella enterica in the Mocha-Quero-Ladrillos irrigation canal represents a significant public health risk, as this water resource is used in agricultural activities and can serve as a vehicle for the transfer of pathogens to plant-based food products. The detection of the microorganism at multiple points along the system revealed that the canal functions as a reservoir capable of supporting the survival and dispersion of this pathogen in non-clinical environments, thereby increasing its potential impact on food safety and public health. To characterize the isolates, microbiological techniques and biochemical verification were applied, complemented by third-generation sequencing using Oxford Nanopore and specialized bioinformatic pipelines. This approach enabled the generation of complete genome assemblies and the identification of coding regions, mobile genetic elements, virulence factors, and intrinsic resistance determinants, including an aminoglycoside acetyltransferase conferring resistance to tobramycin and kanamycin. In silico serotyping confirmed that all isolates corresponded to the serovar Salmonella Typhimurium, while genomic parameters described their organization, variability, and degree of fragmentation. The phylogenetic analysis, integrating forty-nine isolates from different sources, demonstrated that the nine environmental strains from the canal exhibit a close evolutionary relationship with zoonotic sublineages ST19 and ST1649 associated with animal and food-related matrices in Ecuador. These findings indicate that the genotypes present in the canal are not exclusive aquatic variants but rather lineages circulating across multiple ecological niches.
Análisis metagenómico de la microbiota gástrica de ratones con diabetes mellitus tipo 2 inducida
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología, 2026-01)
Peralvo Valverde, Joselyn Katherine
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Garcés Moncayo, María Daniela
This research arises in response to the increasing prevalence of type 2 diabetes mellitus in Ecuador and the growing evidence linking the gastrointestinal microbiota with metabolic diseases. Unlike the intestinal microbiota, the gastric microbiota has been scarcely explored, despite its involvement in early digestion, local immune regulation, and the initial interaction with diet and drugs. In this context, the gastric bacterial community of healthy and diabetic BALB/c mice fed a high-carbohydrate diet was characterized, comparing animals without supplementation and animals receiving a commercial probiotic. Gastric content was processed for metagenomic DNA extraction and sequencing of the V3–V4 region of the 16S rRNA gene. Bioinformatic analysis using tools such as QIIME2 allowed the estimation of alpha and beta diversity indices, as well as relative abundances and taxonomic profiles. The communities were dominated by the phyla Bacillota and Bacteroidota, with a predominance of the genus Lactobacillus in all groups and additional enrichment of Bifidobacterium in supplemented animals. The Shannon and Chao1 indices showed a trend toward greater diversity and richness in the diabetic group receiving probiotics, whereas the Simpson index remained stable, indicating similar evenness among communities. Beta-diversity analyses using NMDS and PCoA revealed a partial separation between supplemented and non-supplemented diabetic mice. In summary, the results suggest that diabetes modifies the structure of the gastric microbiota and that probiotic supplementation promotes a more diverse and potentially protective microbial profile.
Análisis genómico comparativo de los bacteriófagos líticos F7M1, F4M1B y F8M2 de Salmonella enterica serovar Infantis. Articulado al proyecto de investigación aprobado mediante Resolución Nro. UTA-CONIN-2023 0294-R
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología, 2025-07)
Galarza Mayorga Priscila Jael
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Calero Cáceres William Ricardo
Poultry production represents a favorable environment for the spread of pathogenic bacteria such as S. enterica. The intensive use of antibiotics has contributed to the emergence of multidrug-resistant strains, making lytic bacteriophages a promising alternative. However, it is essential to analyze the complete genomes of bacteriophages to identify the presence of genes that may produce toxins, virulence factors, or antibiotic resistance. This study used Oxford Nanopore technology to sequence three lytic bacteriophages of S. enterica serovar Infantis named F7M1-Monchaphage, F4M1B-Cloudphage, and F8M2-Gilionphage. According to the genomic characterization, F7M1 encodes 41 functional proteins and has a length of 59,185 bp with a GC content of 56.46 percent, while F4M1B encodes 43 functional proteins and has a length of 38,972 bp with a GC content of 47.52 percent. Finally, F8M2 encodes 13 functional proteins and has a length of 17,011 bp with a GC content of 48.99 percent. Genetic comparison and phylogenetic analysis placed F7M1, F4M1B, and F8M2 within the genera Chivirus, Lederbergvirus, and Berlinvirus, respectively. In F7M1 and F8M2, no genes associated with toxin production or antibiotic resistance were detected. However, F4M1B contained lysogeny-related genes, confirming it as a temperate phage, and thus it was excluded as a candidate. In contrast, F7M1 and F8M2 are considered promising candidates for the biocontrol of Salmonella in Ecuador's poultry sector.
Análisis proteómico in silico en la ruta de flavonoides del cacao ecuatoriano (Theobroma Cacao)
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología, 2025-07)
Chamorro Sevilla Patricio Javier
;
Galarza Galarza Cristian Fernando
This study presents an in silico proteomic analysis of the flavonoid biosynthesis pathway in Theobroma cacao, focusing on the key enzymes involved in this process. Flavonoids are bioactive compounds in cacao that offer various health benefits, such as antioxidant, anti-inflammatory, and cardioprotective properties. The objective of this research is to understand the genetic and functional roles of enzymes such as Chalcone Synthase (CHS), Trans-cinnamate-4-monooxygenase (C4H), and Chalcone Isomerase (CHI) in the flavonoid biosynthetic pathway. Using bioinformatics tools like KEGG, UniProt, and STRING, enzyme sequences were identified, aligned, and analyzed for homology and protein-protein interactions. The research also utilized molecular modeling tools like AlphaFold to predict the 3D structures of these enzymes and AutoDock for docking simulations, aiming to identify potential enzyme-ligand interactions that could enhance flavonoid production. The study found that CHS, C4H, and CHI play critical roles in the conversion of precursor molecules into flavonoids and contribute to the antioxidant properties of cacao. Additionally, protein transmembrane prediction revealed specific regions involved in enzyme localization within cellular membranes. These findings provide insights into the biosynthesis of flavonoids in cacao, offering potential biotechnological applications for improving the production of bioactive compounds in cacao plants. The research contributes to the broader goal of optimizing cacao cultivation for higher nutritional value and health benefits, with implications for both agricultural practices and the food industry.
Análisis de variantes de splicing y factores de transcripción (HSF1, CBP y Sp1) en la evolución de la enfermedad de Huntington
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología, 2025-02)
Silva Gamboa, Christopher Joel
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Galarza Galarza, Cristian Fernando
Huntington's disease (HD) is a neurodegenerative disorder characterized by the expansion of CAG repeats in the HTT (Huntingtin) gene, leading to significant molecular dysfunctions. In the present study, the impact of splicing variants (SV) and transcription factors (TF) on disease progression was investigated using an in-silico approach with sequencing data based on RNA-seq technologies. Differential splicing variants were identified and their possible influence on the generation of aberrant HTT gene isoforms was analysed. Among these variants, the 109CAG condition showed a particularly severe impact on mRNA processing, primarily affecting huntingtin protein stability. In addition, the functional networks of the HSF1, CBP, and Sp1 factors were constructed and analysed. CBP and Sp1 emerged as central nodes, indicating that they play key roles in global epigenetic and genetic regulation, while HSF1 does not show significant connections with the others. These results suggest that interactions between SVs and TFs exacerbate cellular dysfunction, contributing to HD progression. Finally, the research concludes that both splicing variants and transcription factors represent critical components in HD pathogenesis. These findings provide a solid basis for exploring therapeutic interventions aimed at modulating these molecular processes.
Evaluación de un modelo de aprendizaje automático basado en redes neuronales para el diagnóstico temprano de la enfermedad de Alzheimer
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología, 2025-02)
Sarabia Ortiz, Lilián Catalina
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Galarza Galarza, Cristian Fernando
Alzheimer's disease, as the leading cause of dementia, poses a critical challenge in its early detection, where timely interventions can delay its progression. This issue is addressed by evaluating deep learning models based on neural networks to classify magnetic resonance imaging (MRI) scans into different stages of the disease using data from the OASIS and ADNI databases. The importance lies in the need for precise and automated tools to improve early diagnosis, particularly in stages such as mild cognitive impairment. The methodology included constructing a dataset from preprocessed images and applying it to the EfficientNet B7 and ResNet50 architectures. These were trained with advanced techniques such as data augmentation and validated across scenarios involving controlled data, modified images, and new data. Performance metrics such as precision, recall, specificity, F1-score, and ROC-AUC curves were analyzed. The results showed that the EfficientNet B7 architecture outperformed ResNet50 in precision, sensitivity, and specificity, especially in classifying early stages of Alzheimer's disease. EfficientNet B7 demonstrated greater generalization ability, achieving high precision with preprocessed and new images, while ResNet50 showed limitations when working with heterogeneous data. This highlights the importance of modern architectures in solving complex problems like early Alzheimer’s detection, although it also evidences that relying solely on controlled datasets like OASIS and ADNI may limit applicability in real clinical scenarios.

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