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
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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.
Optimización de un protocolo de extracción de ADN para la detección molecular de ooquistes de Toxoplasma gondii en coles verdes (Brassica oleracea var. Capitata) procedentes del mercado Central de Ambato
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología, 2026-07)
Barreno Vargas, Carlos Alexander
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De La Torre Olvera, Helena Maritza
Toxoplasmosis is a foodborne zoonosis of public health relevance, particularly in pregnant women, neonates, and immunocompromised individuals. Raw vegetables may act as vehicles for Toxoplasma gondii oocysts due to contact with contaminated water, soil, and handling practices. In this context, green cabbage marketed in Ambato represents a sanitary matrix of interest, since its compact leaf structure favors the retention of parasitic particles and hinders their removal through washing. This study was framed within the Microbiology and Biotechnology research line, linked to food safety, and was developed using an experimental approach. Green cabbage samples were analyzed through recovery with PBS 1X whit Tween® 80, concentration using the Ritchie technique, microscopic observation with Lugol and safranin staining, and molecular evaluation. To optimize DNA extraction, a 2 cubed factorial design was applied, considering thermal lysis, mechanical lysis, and proteinase K digestion. The recovered DNA was quantified by spectrophotometry, assessed using A260 out of 280 and A260 out of 230 ratios, and verified by conventional PCR and electrophoresis, amplifying a 196 bp fragment. The results showed structures compatible with oocysts in 8 of 21 samples using Lugol staining and in 6 samples using safranin staining. The treatment with 10 thermal shock cycles, 2 mechanical lysis cycles, and 20 microliter of proteinase K showed the best overall performance. The scientific novelty lies in proposing a combined, cost-efficient protocol adapted to plant matrices, achieving 100 percentage PCR detection compared with 50 percentage using the GeneJET® kit.
Desarrollo de formulaciones locales de tampón de carga y marcador de peso molecular de 100 pb para electroforesis en gel de agarosa
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología, 2026-07)
Avalos Chávez, Angie Valeria
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Calero Cáceres, William Ricardo
Irregular access to molecular biology reagents limits genetic research in Latin America due to high importation costs, dependence on international suppliers, and regulatory constraints that hinder scientific continuity in resource-limited settings. Natural pigments, including anthocyanins, betalains, chlorophylls, curcumin, capsanthin, and norbixin, as well as food-grade synthetic dyes, were evaluated through electrophoretic screening. Loading buffer formulations were prepared by combining two base buffer systems (60 mM Tris-HCl, pH 7.6, and 6X TE buffer) with different dye concentrations. Chemical stability was monitored by UV–Vis spectrophotometry over 120 days under three storage conditions. The molecular weight marker was generated from PCR products amplified from the rpoB gene of E. coli. The results showed that Brilliant Blue FCF (E133) and Tartrazine (E102) were colorants that showed compatibility with electrophoretic conditions. The T7 formulation, consisting of Tris-HCl without EDTA and a high concentration of both dyes, stored at 20 Celcius degree, exhibited the highest spectral and electrophoretic stability throughout the evaluation period. The developed molecular marker produced a reproducible banding pattern ranging from 400 to 2000 bp, with performance comparable to that of commercial references. These findings demonstrate that the local production of functional electrophoretic reagents is technically feasible using accessible and low-cost materials. This study provides a reproducible in-house methodology for the generation of electrophoresis reagents, with the potential to reduce the technological gap in laboratories located in low- and middle-income countries.
Caracterización cinética y estructural de la enzima ancestral N1 PETasa
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología, 2026-01)
Vallejo Espín, Diana Carolina
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Cerda Mejía, Liliana Alexandra
The contamination caused by polyethylene terephthalate (PET) represents one of the most critical environmental challenges today, due to its high global production, persistence, and the limited efficiency of conventional recycling methods. In this context, enzyme-based degradation strategies have emerged as sustainable and highly specific alternatives. The methodology included structural modeling using AlphaFold 3.0, multiple sequence alignments, comparative analysis with modern PETases, and the experimental evaluation of enzymatic activity on pNP-acetate, pNP-butyrate, and post-consumer PET. This research aligns with the development of biotechnologies applied to the enzymatic recycling of polymers. Structural analyses revealed that N1 PETase retains the α/β-hydrolase fold, the Ser–Asp–His catalytic triad, and functional motifs associated with polyester hydrolysis. The ancestral N1 PETase enzyme emerges as a promising candidate for designing optimized biocatalysts. It also provides evidence on the relationship between structural architecture, loop dynamics, and catalytic efficiency, contributing to the advancement of biotechnological solutions for the circular economy. In this context, the present study carried out the structural, functional, and kinetic characterization of the ancestral N1 PETase enzyme, reconstructed through phylogenetic methods, to determine its potential as a biocatalyst for PET depolymerization.
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 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 in silico de microbiomas intestinales para identificar biomarcadores específicos en enfermedades de Crohn y Celíaca usando técnicas de metagenómica comparativa
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología, 2025-02)
Lucero Chisaguano, Israel Joel
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Galarza Galarza, Cristian Fernando
Understanding the intestinal microbiota is crucial for advancing the diagnosis and treatment of inflammatory diseases such as Crohn's disease (CDr) and Celiac disease (CD). This study employs comparative metagenomics techniques to identify specific biomarkers to differentiate these pathologies. The results highlight the relevance of microbial dysbiosis as a common factor, but also highlight significant differences in the composition and functions of the intestinal microbiota in each disease, which will advance the understanding of these pathologies, and create opportunities for the development of diagnostic tools and innovative therapies. The analysis was performed using 16S rRNA gene samples, processed with the QIIME2 tool under strict sample quality criteria. In parallel, the impact of sex was evaluated by analyzing significant variations in beta microbial diversity in patients with CDr. Functional analysis performed with PICRUSt revealed specific metabolic pathways related to inflammation in CD and oxidative stress in rCD. Microbial differences observed showed an increase in Proteobacteria, along with reductions in Firmicutes and Actinobacteria. In addition, biomarkers were identified in common such as, Faecalibacterium and Lachnospiraceae, and specific ones such as Alistipes in CDr and Lachnoanaerobaculum in CD. These results validate metagenomics as a tool to explore the microbiome-disease relationship, facilitating early diagnosis and the design of personalized therapies aimed at restoring microbial balance, marking a significant milestone in the development of precision medicine for inflammatory bowel diseases.
Evaluación in silico de microbiomas intestinales para identificar biomarcadores específicos en enfermedades de Crohn y Celíaca usando técnicas de metagenómica comparativa
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología, 2025-02)
López Herrera, Alan Joshua
;
Galarza Galarza, Cristian Fernando
Understanding the intestinal microbiota is crucial for advancing the diagnosis and treatment of inflammatory diseases such as Crohn's disease (CDr) and Celiac disease (CD). This study employs comparative metagenomics techniques to identify specific biomarkers to differentiate these pathologies. The results highlight the relevance of microbial dysbiosis as a common factor, but also highlight significant differences in the composition and functions of the intestinal microbiota in each disease, which will advance the understanding of these pathologies, and create opportunities for the development of diagnostic tools and innovative therapies. The analysis was performed using 16S rRNA gene samples, processed with the QIIME2 tool under strict sample quality criteria. In parallel, the impact of sex was evaluated by analyzing significant variations in beta microbial diversity in patients with CDr. Functional analysis performed with PICRUSt revealed specific metabolic pathways related to inflammation in CD and oxidative stress in rCD. Microbial differences observed showed an increase in Proteobacteria, along with reductions in Firmicutes and Actinobacteria. In addition, biomarkers were identified in common such as, Faecalibacterium and Lachnospiraceae, and specific ones such as Alistipes in CDr and Lachnoanaerobaculum in CD. These results validate metagenomics as a tool to explore the microbiome-disease relationship, facilitating early diagnosis and the design of personalized therapies aimed at restoring microbial balance, marking a significant milestone in the development of precision medicine for inflammatory bowel diseases.

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