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  • PublicaciónAcceso abierto
    A step in biosafety: Genetic circuit design for the sabotage of sporulation capacity in Bacillus subtilis progeny
    (Universidad de los Andes, 2024-01-31) Pachón Dotor, Sergio Andrés
    Bacillus subtilis, a Gram-positive bacterium capable of sporulation through the activation of the spo0A gene, exhibits resilience against adverse conditions. This characteristic positions it as a candidate for hosting designed genetic circuits (DGC) with diverse applications. However, biosafety challenges arise due to the potential limitations of sporulation on disposal processes, despite its advantages in transportation and storage. Ideally, a variant allowing a single sporulation event is essential. Thus, understanding the effect of spo0A elimination during spore maturation in B. subtilis is crucial for safe utilization. Consequently, an in silico genetic circuit inhibiting sporulation in B. subtilis was designed using CRISPR-Cas9 to knock out the spo0A gene, laying the groundwork for future refinement and optimization. The circuit comprises an activation module based on the Lac operon, native to Escherichia coli, regulated by the lactose analog TMG to express Cas9. Another module is induced by sigma-G, a late-stage spore maturation transcription factor in B. subtilis, to express sgRNA targeting spo0A within the forespore. Once the active complex forms, it cuts the spo0A gene. Studies were conducted in both deterministic and stochastic contexts, analyzing the genetic circuit's behavior with or without inducers at different times. Deterministic solutions indicate that the DGC behavior is TMG dose dependent with TMG concentrations of 250 µM and 1000 sigma-G molecules, the circuit successfully sabotages the spo0A gene within 30 minutes. However, assessing the DGC robustness when not induced revealed spo0A cuts in the absence of TMG and sigma-G. Approximately 60% of the B. subtilis population cuts spo0A even when this behavior is not induced. To address this, a basal expression control module with RNA complementary to sgRNA (cRNA) was implemented, reducing undesired spo0A cut rates to less than 10% of the B. subtilis population. Nevertheless, it was demonstrated that the addition of cRNA module had no significative impact in the spo0A knockout time distribution. This study addressed the need for a Bacillus subtilis variant to sporulate only once, favoring disposal processes through CRISPR-Cas9 circuit design proposing that spo0A sabotaging efficacy is TMG dose dependent. An important challenge related to undesired cut rates in the absence of inducers was identified and resolved through a basal expression control module. Additionally, stochastic simulations highlighted noise influence on circuit behavior, emphasizing the significance of considering stochastic aspects in genetic circuit design. Finally, this study provides a solid foundation for future improvement and optimization of genetic circuits controlling sporulation in B. subtilis, with potential applications in synthetic biology and biosafety.
  • PublicaciónAcceso abierto
    Machine learning and software development to aid diagnosis of refractory epilepsy
    (Universidad de los Andes, 2023-12-11) Carvajal Dossman, Juan Pablo
    Epilepsy, as defined by the World Health Organization (WHO), is a chronic neurological disorder characterized by recurrent seizures. It is a non-transmissible condition that represents a significant proportion of the world's disease burden, affecting approximately 50 million people. Thus, investigating how to improve the different stages of diagnosis and prognosis is of great relevance. The aim of our study is to identify the varying needs in diagnosing and treating this condition. This thesis was conducted as part of a collaborative project between Los Andes university, the epileptology department of Fundacion Hospital Pediatrico de la Misericordia (HOMI) and Biotecgen S.A.S. The general project aims to design and develop a software solution for diagnosing refractory epilepsy. This includes predictive models that integrate information from different exams and analyze them individually. This thesis contributed to this project by establishing the requirements specification and software design. In addition, a classification model for epileptic seizures in EEG exams was developed, achieving high performance. Lastly, a bioinformatics pipeline was defined to extract the maximum possible miRNA information from raw sequencing reads.
  • PublicaciónRestringido
    Transposable element-rich regions in genomes of Neocosmospora clinical isolates
    (Universidad de los Andes, 2023-12-12) Lizcano Salas, Andrés Felipe
    Transposable elements (TEs) are repetitive DNA elements that can integrate into new genomic locations, contributing to the genome plasticity of fungi. Tes are classified into retrotransposons and DNA transposons based on their transposition intermediate. In some fungal pathogens, regions with a high proportion of TEs are associated with putative virulence factors. Neocosmospora is a trans-kingdom pathogen that can infect plants, animals, and humans. To our knowledge, no previous study has analyzed the genomes of Neocosmospora clinical isolates. For that reason, this project aimed to characterize transposable elements in the genomes of Neocosmospora spp. clinical isolates and compare them with non-clinical isolates. To achieve this goal, we sequenced and assembled genomes of Neocosmospora clinical isolates and used contiguous assemblies of other isolates available in GenBank. We identified and classified TEs on these genomes, and identified and characterized the genes associated with TE-rich regions. To the best of our knowledge, this is the first study that has sequenced and analyzed the genome assemblies of clinical isolates of Neocosmospora and provided the first genome assemblies of N. petroliphila and N. lichenicola. We found that there is a high variance in TEs content both within and between species. Also, TE-rich regions are associated with putative genes related to biosynthesis gene clusters (BGCs), azole resistance, and the acquisition of nitrogen, iron, zinc, and copper. Based on our results, we hypothesized that 1) compartmentalization of Neocosmospora core chromosomes based on changes in TEs distribution could be more relevant than LS-chromosomes in lifestyle adaptation; and 2) TE de-repression in Neocosmospora could be mediated by nutrient starvation.
  • PublicaciónAcceso abierto
    Analysis of ancient bacterial genomes from parchment manuscripts
    (Universidad de los Andes, 2023-12-12) Sacristán Carrillo, Luisa Fernanda
    Parchment, a material made from collagen extracted from animal hides, was the primary medium for manuscript production in the Middle Ages in Europe, and its manufacturing method depends on the geographical region and the era in which it was produced. Researchers have been able to reconstruct human history and study the culture of civilizations through the information contained in these ancient documents. However, thanks to Next-Generation Sequencing (NGS) techniques, a new field has emerged: biocodicology, which focuses on studying the biological information found in these manuscripts. In this study, the bacterial communities of 57 parchment manuscripts from Iceland, England, and Spain, spanning from the 10th to the 18th century, were analyzed and compared. We found that microbiome analysis serves as a reliable predictor of parchment-making methods and as a differentiator among parchments from various sources. The bacterial communities provide valuable insights into the parchment-making process, including the use of salt, evidence of manipulation, and distinctions in processing, while also indicating the potential presence of pathogens. Based on the analysis of all processed samples thus far, microbiome analysis seems to hold a promising future for advancing our understanding of parchment characteristics and origins.
  • PublicaciónRestringido
    Selección dirigida de comunidades microbianas provenientes de suelo de manglar capaces de prosperar en tereftalato de polietileno (PET)
    (Universidad de los Andes, 2023-12-12) Chaparro Avellaneda, Dayanne Paola
    Al año se genera una gran cantidad de plástico y entre los principales tipos de polímeros de este tipo que se producen a gran escala están el tereftalato de polietileno (PET). Sin embargo, su inadecuada disposición final ha causado que se acumule en diversos ambientes. El uso de enzimas microbianas capaces de degradar plástico a partir de microorganismos ha tomado gran fuerza en las investigaciones recientes y su búsqueda en ambientes con alto grado de contaminación ha arrojado resultados esperanzadores. Uno de los ecosistemas más afectados con la contaminación por plásticos son los bosques de manglar, donde se encuentran diversas comunidades de microorganismos tanto en las capas de sedimentos como en las columnas de agua. El objetivo principal de este estudio fue seleccionar un consorcio microbiano con una posible actividad degradadora de PET a partir de muestras de suelos de manglar de la costa caribe colombiana. Para conseguir el objetivo se utilizó un enfoque top-down mediante la estrategia de enriquecimiento dilution-to-stimulation usando micropartículas de PET como única fuente de carbono se realizó la construcción del consorcio. Igualmente, se realizó la secuenciación del gen ribosomal 16S rRNA para la caracterización taxonómica de los consorcios seleccionados. De manera particular, el consorcio seleccionado está compuesto principalmente por dos géneros bacterianos (Pseudoxanthomonas y Brevibacillus). Sin embargo, se recuperaron ocho metagenome-assembled genomes (MAGs) de buena calidad a partir de este consorcio estable. A partir de allí, se realizó la búsqueda de genes encargados de la degradación de PET mediante el uso de bases de datos específicas como la de PAZy. Se encontró genes asociados a diversos pasos de degradación del PET. En conclusión, sugerimos que la selección de microbiomas utilizando aproximaciones top-down (por ejemplo, enriquecimiento, selección artificial y evolución dirigida) son poderosas estrategias para recuperar nuevos microorganismos con un alto potencial para la degradación de plásticos sintéticos.
  • PublicaciónAcceso abierto
    Estudio de siRNA para la identificación de virus presentes en el banco de germoplasma de Achira (Canna edulis) Ker Gawl. (Cannaceae)
    (Universidad de los Andes, 2023-06-02) Rico Sierra, Edgar Mauricio
    En este estudio se analizó el banco de germoplasma de Achira (Canna edulis), una planta tropical utilizada para fines alimenticios y ornamentales en muchos países del mundo, el cual está a cargo de la corporación colombiana de investigación agropecuaria AGROSAVIA, localizado en centro de investigación La Selva (Rionegro - Antioquia) y con copia en centro de investigación Nataima (Espinal - Tolima). El objetivo fue detectar la presencia de virus en las diferentes accesiones de Achira mediante la secuenciación de siARN. Se identificaron virus previamente reportados como el Bean yellow mosaic virus (BYMV- Potyvirus), Canna yellow mosaic virus (CaYMV-Badnavirus) y Canna yellow streak virus (CaYSV-Potyvirus), siendo este último el más predominante y mostrando un porcentaje de identidad de aminoácido menor al 75% con respecto al genoma de referencia. Además, se detectó la posible infección con virus previamente no reportados, como el Lettuce chlorosis virus (LCV-Crinivirus) y Potato yellowing virus (PYV-Ilarvirus). LCV presentó patrones de alto mapeo o Hotspots en las accesiones de las dos localidades en regiones similares, mientras que el PYV solo se detectó en dos muestras en CI La selva. Estos hallazgos son importantes para la conservación y manejo de la variabilidad genética de la Achira y para la implementación de estrategias de control y prevención de la propagación de virus en las poblaciones.
  • PublicaciónAcceso abierto
    Towards an Ecological and Functional Framework for Modeling the Structure and Dynamics of the Human Gut Microbiome
    (Universidad de los Andes, 2023-06-02) Castellanos Sánchez, Alejandro
    The human gut microbiota is composed of complex communities of microorganisms, which are modulated by various factors including diet. It plays a fundamental role in human health and nutrition by metabolizing compounds that are not digestible by the human intestine. Understanding the mechanisms that regulate and modify the microbiota's structure under specific conditions is therefore essential. In this study, we used ecological dynamic modeling grounded on the generalized Lotka-Volterra (gLV) model, and comparative and functional genomics with time-course compositional and transcriptomic data of a representative human gut microbial community inoculated in two groups of gnotobiotic mice subjected to different dietary schemes; with the aim of determining the ecological interactions of the community species, the metabolic functions that mediate these interactions, and how diet influences these interactions. We found that in circumstances where bacteria are growing optimally, the community is enriched with negative interactions, particularly interspecies competition; whereas in circumstances where the community is not growing optimally, fewer interactions can be seen overall. Additionally, the order in which the bacteria are exposed to different diets influence the impact that the diet switch has over the species. Furthermore, bacteria belonging to the Bacteroidetes phylum, which in general dominated the system, present a generalist metabolism, showing a wide repertoire of mechanisms to digest both carbohydrates and amino acid from the diet; while bacteria belonging to other phyla, proved to be specialists, with more reduced and specific metabolic activities to metabolize certain components of the diet, in particular, amino acids. Overall, we present an ecological and functional modeling approach that elucidates relevant mechanisms of gut microbiota structure and dynamics that are hardly detectable using traditional methods of metagenomic analysis.
  • PublicaciónAcceso abierto
    Explorando el efecto de la introducción de polímeros en comunidades microbianas provenientes de suelos de manglares en el Caribe Colombiano: Un experimento con microcosmos
    (Universidad de los Andes, 2023-06-02) Sierra Alfonso, Felipe
    Los suelos de bosques de manglar albergan diversidad microbiana clave para algunos servicios ecosistémicos que prestan estos ambientes. Estos suelos se han convertido en sumidero de diferentes tipos de desechos, incluyendo los microplásticos. El objetivo de este estudio fue develar el impacto de la entrada de partículas de tereftalato de polietileno (PET) y de polímeros vegetales en la diversidad microbiana de los suelos de bosque de manglar en el caribe Colombiano. Para esto se llevó a cabo un experimento de microcosmos con los siguientes tratamientos: 1) Suelo + PET; 2) Suelo + cascarilla de arroz (principalmente lignocelulosa); 3) Suelo sin polímeros. Estos fueron incubados en presencia/ausencia de agua de mar a 30 ºC durante 30 y 90 días. Los resultados de secuenciación del gen ribosomal 16S y la región intergénica ITS2 mostraron que el factor más relevante en cuanto a su efecto en la estructura de la comunidad microbiana fue el uso de lignocelulosa, seguido por la presencia de agua de mar y el tiempo de incubación. En presencia de la cascarilla de arroz se incrementó la abundancia relativa de Firmicutes y algunos taxones (e.g., Blastopirullela) explicaron los cambios en la diversidad; además se observó una disminución de la riqueza de hongos debido a las condiciones impuestas después de 30 días. De manera particular observamos que la presencia de las partículas de PET generan cambios menores en la diversidad de los suelos (p 0,046). El análisis de los microorganismos menos abundantes (biosfera rara) mostró que las especies que explican los cambios en la beta diversidad fueron diferentes en comparación con todo el set de datos. Por otro lado, los microcosmos con ausencia de agua de mar e incubados durante 90 días mostraron una selección diferencial de especies de bacterias halófilas (e.g. Halobacillus), sugiriendo un aumento de la concentración de sales debido a la pérdida de humedad del microcosmo. Con estos resultados logramos identificar factores y taxones claves en la reestructuración de la diversidad microbiana de los suelos de manglar a causa de perturbaciones externas relacionadas con el impacto antropogénico (e.g. contaminación con polímeros) y el cambio climático (e.g. sequía) en estos ecosistemas.
  • PublicaciónAcceso abierto
    Population structure of the Piangua mollusk (Anadara tuberculosa): a tool to design conservation strategies
    (Universidad de los Andes, 2023-06-07) Fuentes Suarez, Luis Eduardo
    Piangua, Anadara tuberculosa, is a mollusk of the bivalve family. In Colombia, this mollusk has great importance in the economy of the population living on the Pacific Coast, a region with critical social indicators. In the last years, the demand and the exploitation of this mollusk have increased, putting the species at risk up to the point that nowadays, it is considered endangered. Therefore, knowing the organism's genetic information is essential to design conservation strategies. This research aim is to identify the genetic diversity and the population structure of the mollusk in two localities on the Pacific Coast of Colombia. For this, a genotyping analysis was performed with 89 samples using the DArT technology, and a raw genome was used as a reference, which was ensembled using Hifi reads. No geographical population structure was found between the two localities. However, there is a reduction in genetic diversity due to the loss of heterozygotes, which may be caused by the high level of inbreeding within localities. This is the first study in Colombia that gives information on the genetics of the piangua that can lay the foundations for conservation strategies.
  • PublicaciónAcceso abierto
    Genome-Scale Metabolic Reconstruction of the Phaseolus Genus: Insights into Cyanogenesis Metabolism
    (Universidad de los Andes, 2023-06-06) Duarte Torres, Erick Nicolas
    In this research, we present the first metabolic reconstruction of the Phaseolus genus, based on Phaseolus vulgaris metabolic data and incorporating cyanogenesis pathways from Phaseolus lunatus. Our model successfully simulates the plant cell metabolism under photoperiod conditions, making it a valuable tool for studying the metabolims of Phaseolus species. Additionally, we conducted a genomic comparison analysis between the two Phaseolus species to gather data for imposing contrainsts, enabling the simulation of linamarin and lotaustralin biosynthesis, both cyanogenic compounds. By studiyng these pathways, we gained insights into the genomic elements and metabolic mechanism responsible for the high production of linamarin in P. lunatus. In addition, we conducted an optimization analyses to identify metabolic differences that could explain the observed overproduction of linamarin compared to lotaustralin in P. lunatus.
  • PublicaciónAcceso abierto
    Breast cancer diagnosis and prognosis improvement based on a complete gene expression profile and ancestry
    (Universidad de los Andes, 2023-06-06) Stepanian Rozo, Johanna
    Breast cancer (BC) is the first leading cause of death in women around the world. Accurate subtyping of BC based on gene expression is crucial for optimizing treatment strategies. This study aims to improve BC subtyping by integrating comprehensive gene expression profiles and ancestry information. We acquired and analyzed a dataset of 406 RNA-Seq samples sequenced from patients with diverse ancestries, geographical origins, and ethnicities, combining 318 publicly available samples with 88 new samples. RNA-Seq from breast tumor data were used to genotype 10,397 SNPs and predict ancestries using the software ADMIXTURE, and combining the RNA-seq genotype calls with calls from the 1000 genomes project. We ran the genefu R package for predicting PAM50 subtypes, and recreated the results using the supervised machine learning algorithms random forest (RF) and support vector machine (SVM), achieving accuracy rates of 0.95 and 0.92, respectively. We integrated ancestry prediction to supervised machine learning experiments resulting in less favorable metrics, achieving accuracy values of 0.86 and 0.85 for RF and SVM, respectively. Additionally, we observed discrepancies between the assigned PAM50 subtypes, the gene expression patterns, and ancestry prediction. To overcome possible biases in the genefu predictions, we investigated the clusters obtained following an unsupervised machine learning strategy, based on the K-means algorithm. The results suggest novel gene expression-based subgroups within breast cancer tumors, where a part of the variance is explained by ancestry. In conclusion, this study highlights the importance of integrating gene expression profiles and ancestry information in BC clustering, contributing to understanding BC heterogeneity. The findings presented lay the groundwork for improved treatment decision-making in BC management.
  • PublicaciónAcceso abierto
    Development of a new structural variant detection software based on graph clustering machine learning algorithms from long reads
    (Universidad de los Andes, 2022-11-29) Gaitán Gómez, Nicolás Gustavo
    Structural variants (SV) are polymorphisms defined by their length (>50 bp). The usual types of SVs are deletions, insertions, translocations, inversions, and copy number variants. SV detection and genotyping is fundamental given the role of SVs in phenomena such as phenotypic variation and evolutionary events. Thus, methods to identify SVs using long-read sequencing data have been recently developed. We present an accurate and efficient algorithm to predict SVs from long-read sequencing data. The algorithm starts collecting evidence (Signatures) of SVs from read alignments. Then, signatures are clustered based on a Euclidean graph with coordinates calculated from lengths and genomic positions. Clustering is performed by the DBSCAN algorithm, which provides the advantage of delimiting clusters with high resolution. Clusters are transformed into SVs and a Bayesian model allows to precisely genotype SVs based on their supporting evidence. This algorithm is integrated into the single sample variants detector of the Next Generation Sequencing Experience Platform (NGSEP), which facilitates the integration with other functionalities for genomics analysis. For benchmarking, our algorithm is compared against different tools using VISOR for simulation and the GIAB SV dataset for real data. For indel calls in a 20x depth Nanopore simulated dataset, the DBSCAN algorithm performed better, achieving an F-score of 98%, compared to 97.8 for Dysgu, 97.8 for SVIM, 97.7 for CuteSV, and 96.8 for Sniffles. We believe that this work makes a significant contribution to the development of bioinformatic strategies to maximize the use of long-read sequencing technologies.
  • PublicaciónAcceso abierto
    Pipeline design for user-friendly viral metagenomic analysis
    (Universidad de los Andes, 2019) Forero Junco, Laura Milena
    "Cada vez se requieren más herramientas bioinformáticas y recursos computacionales para entender los amplios conjuntos de datos producidos por las tecnologías NGS. La curva de aprendizaje del uso de herramientas de bioinformática viene acompañada por sentimientos de frustración, quedándose así con opciones limitadas para avanzar en los análisis de sus datos. Así, el objetivo de este proyecto fue crear un software de fácil uso para el análisis de datos de metagenómica viral. Esta herramienta, Mosaic, está diseñada para el análisis de muestras enriquecidas por virus. Se basa en el uso de Snakemake como sistema de gestión de flujo de trabajo, junto con conda para la instalación de las dependencias requeridas. Así, este software utiliza datos de secuenciación crudos para generar la tabla de abundancia viral (vOTU). Además, este software de código abierto es compatible con lecturas largas, en concordancia con su prometedor futuro en el análisis metagenómico." -- Tomado del Formato de Documento de Grado.
  • PublicaciónAcceso abierto
    Assembly and annotation of phytophthora genome: looking for host specificity
    (Universidad de los Andes, 2016) Gonzalez Garcia, Laura Natalia
  • PublicaciónAcceso abierto
    Bioinformatics workflow and assessment of software to seek secondary metabolites in bacteria
    (Universidad de los Andes, 2017) Alzate Ocampo, José David
    "The potential to discover new Natural Products (NPs) from bacteria has evolved from an in-vitro test approach to a combination of in-vitro and in-silico processes. In particular, the exploration of novel species of microbes that have not previously been studied could signify an important pool of new de novo molecules. As the potential to find new products can be studied using new software tools, this project aims to define a pipeline that can help researchers foresee the potential that bacteria have to produce NPs." -- Tomado del Formato de Documento de Grado.
  • PublicaciónAcceso abierto
    Genome-Scale Metabolic Reconstruction of Cannabis sativa and validation with non-targeted LC-MS based leaf metabolomics data
    (Universidad de los Andes, 2022-06-16) González Camargo, Fidias David
    Here we would present a Genome-Scale Metabolic network model of Cannabis sativa with the analysis of non-targeted LC-MS based metabolomics data, which could help to understand their complex interactions toward applications in the anticancer, analgesic, and anti-inflammatory drug development, and other potential applications in food, cosmetic, textile and agrochemical industries. Starting from annotation reference genome avail in NCBI databank, we will create a semi-automated reconstruction of model using KEGG tools and ModelSEED respectively. Secondly, we will implement curation steps using gap-filling algorithms such as GapFind and GapFill, and manual curation supported by biochemical data reported in literature. Finally, we will obtain a first genome scale draft reconstruction of Cannabis sativa using constraint-based reconstruction and analysis.
  • PublicaciónAcceso abierto
    Diversity and evolution of Phaseolus lunatus L. (Lima bean) mobilome through comparative analysis of transposable elements against close species of the genus phaseolus
    (Universidad de los Andes, 2022) Daniela Alexandra, Lozano Arce
    Transposable elements (TEs) make up at least half of the genomes of complex plant species. Recent studies have shown that TEs can modify the expression of neighboring genes, producing a significant variability of different agronomically relevant traits. The current availability of TE data makes analysis within and between species difficult. Therefore, an effort was made in this work to identify and annotate the transposable element base of lima bean and common bean. The lima bean database contains 186,109 TE events and the common bean database was enhanced by annotation of TEs across the genome with a total of 185,060 TE events. In addition, we wanted to analyze the dynamics of these transposable elements by analyzing 60 accessions (WGS). We generated a variability matrix with 9,755 TE events, with which it was possible to differentiate the genetic pools (domesticated IM, wild IM and AI). Finally, TEs that were related to important genes in the lima bean domestication process were annotated and associations were detected in four important genes (PDH1, GIGANTEA, CYP83E47, UGT85K3). Given the importance of Lima bean as a current food security crop, we believe that both the databases and the compiled information will provide a basis for future studies on the evolution and function of TEs in different plant species, as well as applications to genetic improvement of Lima bean.
  • PublicaciónAcceso abierto
    Estimating the andean bear diet through DNA metabarcoding and its relationships to the gut microbiome
    (Universidad de los Andes, 2021-12-13) Chica Cardenas, Luis Alberto
    The Andean or spectacled bear, Tremarctos ornatus, is an endemic species of the tropical Andes and it is catalogued as Vulnerable by the International Union for the Conservation of Nature (IUCN). The methodologies to describe eating habits of Andean bears have been based traditionally on direct methods. In recent years, the possibility has emerged to analyze fecal samples through DNA approaches, making viable to characterize the Andean bear diet using metabarcoding. 4 different sets of primers designed to characterize plants, vertebrates, arthropods and bacteria were used. Amplicons were sequenced and an ASV (Amplicon sequence Variant) based workflow was applied. Bioinformatic analysis for 16S revealed a bacterial composition characterized by 8 phyla and 89 genera. Phyla Proteobacteria, Firmicutes and Bacteroidetes were found to have the highest prevalence. By characterizing the diet, Bromeliaceae family was found to be predominant in all samples, followed by Malvaceae and Ericaceae. Furthermore, no DNA from vertebrates was found on the samples, leading to assume that vertebrates are not part of the normal diet of this species. This study reports the first characterization of the Andean Bear diet via molecular methods in which new families of plants are reported as a food source.
  • PublicaciónAcceso abierto
    Estudio de la composición de comunidades bacterianas en aguas del distrito de riego La Ramada
    (Universidad de los Andes, 2022-02-10) Bautista Sánchez, Edwin Dwan
    El incremento de la población humano y su actividad asociada, han tenido impacto en la composición bacteriana de muchos ambientes, entre ellos los entornos acuáticos. Se ha reportado que en cuerpos de agua como ríos, lagos, lagunas y efluentes de plantas de tratamiento de aguas residuales, se presentan mayor abundancia bacterias presentes en el tracto gastrointestinal. Se han realizado trabajos donde han reportado la presencia de Salmonella, E. coli, Bacteroides, Bifiodobacterium y otros Bacteroidetes en el río Bogotá. En este trabajo se caracterizó la composición de la comunidad microbiana acuática de muestras tomadas en seis lugares en el distrito de riego La Ramada, a partir de secuenciación dirigida al gen del ARNr 16s. Las bacterias identificadas con las distintas herramientas dan cuenta que la actividad humana puede tener un impacto negativo en la calidad del agua, consistente con trabajos previos.
  • PublicaciónAcceso abierto
    Lipidomic profiling of bioactive lipids during spontaneous fermentation of fine-flavour cocoa
    (Universidad de los Andes, 2021) Herrera Rocha, Fabio Esteban
    Los lípidos son un ingrediente esencial del chocolate y otros productos de cacao, y representan más del 50% del peso seco de los granos de cacao. Aunque el efecto de los lípidos del cacao sobre el perfil de sabor aún no está caracterizado, se reconoce que los lípidos son fundamentales para la calidad de los productos de cacao. El contenido de lípidos del cacao influye en los factores de calidad del chocolate, como la textura, la fusión y el punto de cristalización. Sin embargo, sólo unos pocos estudios han diseccionado el perfil lipídico del cacao, pero se han centrado en la composición de los triglicéridos y los ácidos grasos en el cacao a granel y el chocolate negro. Además, la actividad biológica potencial de estos lípidos sigue siendo principalmente inexplorada. En este sentido, el presente estudio pretende analizar el lipidoma de las fermentaciones de cacao de sabor fino y el licor de cacao resultante utilizando LC-MS-QTOF. Nuestros resultados revelaron que el lipidoma del cacao está compuesto principalmente por acilos grasos, glicerofosfolípidos y otros pequeños grupos de lípidos como glicerolípidos, lípidos esteroles, esfingolípidos y lípidos prenoles. No se observaron variaciones significativas en estos grupos de lípidos durante las fermentaciones de cacao de sabor fino. Además, se exploró la potencial actividad biológica de los lípidos identificados mediante un enfoque de aprendizaje automático. Entrenamos varios algoritmos de aprendizaje automático utilizando un conjunto de datos con 493 compuestos bioactivos y no bioactivos. Después de optimizar y probar todos los algoritmos, descubrimos que K-Nearest Neighbors (KNN) tenía el mejor rendimiento. A continuación, utilizamos este modelo para clasificar los lípidos identificados. Así, nominamos 8 moléculas como potenciales lípidos bioactivos basándonos en sus descriptores moleculares. Hasta ahora, ninguno de estos compuestos tenía informes previos de actividad biológica. Hasta donde sabemos, este es el primer