Browsing by Autor "Silvia Restrepo"

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Análisis de ADNC-AFLP para la expresión diferencial de genes en la interacción Manihot esculenta Grantz (Yuca) Xanthomonas axonopodis pv. Manihotis
(LA Referencia, 2001) María L Santaella; Edward C. Suarez; Carolina González; Carolina López‐Cano; Silvia Restrepo; Alfredo Badillo; Valérie Verdier
Desarrollar patrones ADNc - AFLP, para identificar fragmentos expresados diferencialmente entre dos variedades de yuca, una resistente y una susceptible a la bacteriosis. Aislar, secuenciar y analizar los fragmentos seleccionados. Corroborar la expresión diferencial de estos fragmentos mediante "northern blots".
Changing a Generation’s Way of Thinking: Teaching Computational Thinking Through Programming
(SAGE Publishing, 2017) Francisco Buitrago Flórez; Rubby Casallas; Marcela Hernández; Alejandro Reyes; Silvia Restrepo; Giovanna Danies
Computational thinking (CT) uses concepts that are essential to computing and information science to solve problems, design and evaluate complex systems, and understand human reasoning and behavior. This way of thinking has important implications in computer sciences as well as in almost every other field. Therefore, we contend that CT should be taught in elementary schools and included in every university’s educational curriculum. Several studies that measure the impact of teaching programming, analytical thinking, and CT have been conducted. In this review, we analyze and discuss findings from these studies and highlight the importance of learning programming with a focus on the development of CT skills at a young age. We also describe the tools that are available to improve the teaching of CT and provide a state-of-the-art overview of how programming is being taught at schools and universities in Colombia and around the world.
Characterization of the First Batrachochytrium dendrobatidis Isolate from the Colombian Andes, an Amphibian Biodiversity Hotspot
(Springer Science+Business Media, 2013) Sandra V. Flechas; Edgar M. Medina; Andrew J. Crawford; Carolina Sarmiento; Martha Cárdenas; Adolfo Amézquita; Silvia Restrepo
Composición y función de la comunidad microbiana relacionada con el ciclaje de nitrógeno en la rizosfera de Solanum tuberosum (BAHUIN) grupo phureja
(2013) Nathalia Flórez-Zapata; Juan Carlos García; Patricia Del Portillo; Silvia Restrepo; Daniel Uribe-Vélez
COMPOSITION AND FUNCTION OF THE MICROBIAL COMMUNITY RELATED WITH THE NITROGEN CYCLING ON THE POTATO RHIZOSPHERE
(LA Referencia, 2013) Nathalia Flórez-Zapata; Juan Carlos García; Patricia Del Portillo; Silvia Restrepo; Daniel Uribe-Vélez
In the S. tuberosum group phureja crops, mineral fertilizer and organic amendments are applied to meet the plants’ nutritional demands, however the effect of such practices on the associated rizospheric microbial communities are still unknown. Nitrogen plays an important role in agricultural production, and a great diversity of microorganisms regulates its transformation in the soil, affecting its availability for the plant. The aim of this study was to assess the structure of microbal[trm1] communities related with the N cycle of S. tuberosum group phureja rizospheric soil samples, with contrasting physical-chemical properties and fertilization strategy. Few significant differences between the community composition at the phylum level were found, only Planctomycetes phylum was different between samples of different soil type and fertilization strategy. However, the analysis of nitrogen-associated functional groups made by ribotyping characterization, grouped soils in terms of such variables in a similar way to the physical-chemical properties. Major differences between soil samples were typified by higher percentages of the ribotypes from nitrite oxidation, nitrogen fixation and denitrification on organic amendment soils. Our results suggest that, the dominant rhizosphere microbial composition is very similar between soils, possibly as a result of population’s selection mediated by the rhizosphere effect. However, agricultural management practices in addition to edaphic properties of sampled areas, appear to affect some functional groups associated with the nitrogen cycling, due to differences found on soil’s physical-chemical properties, like the concentration of ammonium that seems to have an effect regulating the distribution and activity of nitrogen related functional groups in the S. tuberosum rhizosphere.
Deciphering the phenol degradation metabolic pathway in Scedosporium apiospermum HDO1
(American Society for Microbiology, 2025) Laura Ortiz; David Botero-Rozo; Natalia Vargas; Sagrario Ortiz; Silvia Restrepo; Martha J. Vives
The filamentous fungus Scedosporium apiospermum is a microorganism capable of phenol degradation. Phenol is a petroleum-derived pollutant and a compound widely used in several industries. As a result of its widespread use, phenol is commonly discarded and accumulated in soils and water bodies. In this study, overexpressed and repressed genes that produce enzymes involved in phenol metabolism were identified in S. apiospermum HDO1 when the fungus grows in the presence of phenol. The fungus was grown with either glucose (control) or phenol as the sole carbon source to achieve this. RNA from the mycelium was extracted and sequenced using the Illumina Hiseq-4000 platform, with paired-end libraries. Eighteen genes coding for enzymes related to catechol ortho-cleavage, catechol meta-cleavage, and hydroquinone pathways were annotated from the assembled transcriptome. In the differential gene expression analysis, 11 genes coding for phenol 2-monooxygenase, catechol 1,2-dioxygenase, 3-oxoadipate enol lactonase, hydroxyquinol 1,2-dioxygenase, and aldehyde dehydrogenase were overexpressed. In contrast, one gene coding for protocatechuate 3,4-dioxygenase was repressed. We show for the first time that phenol degradation in S. apiospermum occurs through one of the catechol routes, the catechol-ortho ring cleavage pathway, and through the hydroquinone A pathway. These findings are important because they improve the understanding of how eukaryotic microorganisms with the potential for bioremediation degrade organic pollutants such as phenol.IMPORTANCEIn recent years, bioremediation has emerged as one of the solutions to eliminate pollutants from the environment. Scedosporium apiospermum is one of the fungi capable of tolerating and degrading common pollutants such as phenol. This ability is of great interest as it highlights its potential for use, but also as an important eukaryotic model in contaminant metabolism. S. apiospermum has been widely studied for its clinical significance, but little is yet known about its role in natural environments and its capacity for removing organic pollutants. Using previously published biochemical data together with our differential gene expression results, we validated and completed the proposed phenol metabolic pathways.
Designing a Socio-Cultural Approachfor Teaching and Learning Computational Thinking
(Universitetsforlaget, 2020) Francisco Buitrago-Flórez; Giovanna Danies; Javier F. Tabima; Silvia Restrepo; Carola Hernández Hernández
In recent years, Computational Thinking (CT) has been claimed to be a powerful way for competencies and skill development for students at any stage. Programming has been the main tool for CT development; nevertheless, several issues associated with learning and teaching programming exist and have been widely described. In this study, we designed and tested in a qualitative way a set of active pedagogical strategies to implement an alternative way to immerse university students in the learning process of CT development. Such strategies were designed and analyzed under the socio-cultural vision of learning, in which individuals interact in communities to build significant knowledge. Results showed that our curriculum design engaged students in the active use of five key skills related to CT, which could be used as the base ground for further programming learning and high-level CT skills development. Additionally, data indicates that students were involved in reflective processes of learning, as well as in the development of key competencies such as teamwork, communication skills and creativity. Theoretical characteristics of the socio-cultural vision of education are subsequentially used to explain and discussed the scope and limitations of the implementation described herein.
El papel de la ingeniería en la pandemia de COVID-19
(Universidad de Los Andes, 2020) Paola Betancourt Ruiz; Marcela Guevara Suárez; Marylin Hidalgo; Silvia Restrepo; Erik Potdevin; Jorge A. Huertas; Andrés L. Medaglia; Juan Manuel Pedraza; Martha Cepeda; Pablo Arbeláez
Evaluation of small ncRNAs as a possible epigenetic mechanism mediating the transition from biotrophy to necrotrophy in the life cycle of Phytophthora infestans
(2019) Juliana González‐Tobón; Alejandra Rodríguez-Jaramillo; Laura Milena Forero; Laura Natalia González-García; Giovanna Danies; Silvia Restrepo
<title>Abstract</title> Background: Phytophthora infestans, the causal agent of late blight disease of potato and tomato, is responsible for billions of dollars in losses worldwide each year. This plant pathogen is a hemibiotroph, meaning that in the early stages of infection, it feeds on living host tissue, and later in the infection cycle, it kills the host. Even though the transcription dynamics of this transition are well characterized, information on the role of small noncoding RNAs (ncRNAs) during this process is still being obtained. Furthermore, a methodological pipeline useful for searching and analyzing small ncRNAs in this pathogen is needed. Results: Using the proposed pipeline, a set of 146 small ncRNAs were found to be significantly differentially expressed among the analyzed samples. From these, 100 small ncRNAs were successfully annotated to specific genes, some of them encoding effector proteins produced by the pathogen during its life cycle. Other molecular regulatory processes, mainly mediated by enzymes and transporters, were also identified. Conclusions: The pipeline presented here is an easy-to-use, comprehensive and efficient option for analyzing small ncRNA profiles of P. infestans small RNA-seq data sets. Additionally, the results presented here may further contribute to elucidating the specific molecular and epigenetic mechanisms controlling the life cycle of P. infestans.
Evaluation of small ncRNAs as a possible epigenetic mechanism mediating the transition from biotrophy to necrotrophy in the life cycle of Phytophthora infestans
(Research Square (United States), 2019) Juliana González‐Tobón; Alejandra Rodríguez-Jaramillo; Laura Milena Forero; Laura Natalia González-García; Giovanna Danies; Silvia Restrepo
Abstract Background Phytophthora infestans, the causal agent of late blight disease of potato and tomato, is responsible for billions of dollars in losses worldwide each year. This plant pathogen is a hemibiotroph, meaning that in the early stages of infection, it feeds on living host tissue, and later in the infection cycle, it kills the host. Even though the transcription dynamics of this transition are well characterized, information on the role of small noncoding RNAs (ncRNAs) during this process is still being obtained. Furthermore, a methodological pipeline useful for searching and analyzing small ncRNAs in this pathogen is needed. Results Using the proposed pipeline, a set of 146 small ncRNAs were found to be significantly differentially expressed among the analyzed samples. From these, 100 small ncRNAs were successfully annotated to specific genes, some of them encoding effector proteins produced by the pathogen during its life cycle. Other molecular regulatory processes, mainly mediated by enzymes and transporters, were also identified. Conclusions The pipeline presented here is an easy-to-use, comprehensive and efficient option for analyzing small ncRNA profiles of P. infestans small RNA-seq data sets. Additionally, the results presented here may further contribute to elucidating the specific molecular and epigenetic mechanisms controlling the life cycle of P. infestans.
Evolutionary history of the group formerly known as protists using a phylogenomics approach
(2016) Silvia Restrepo; Juan Enciso; Javier F. Tabima; Diego Mauricio Riaño‐Pachón
The lack of organisation of monophyletic lineages in the phylogeny and taxonomy of the group formerly known as protists has precluded the understanding of the group’s evolutionary history and trait comparison among members of the group. We used a phylogenomic approach to establish phylogenetic hypotheses of this group of organisms. We used an automatic orthologous clustering (OrthoMCL)-based strategy to recover 72 clusters of orthologues from 73 eukaryotic species. A maximum likelihood tree was inferred from the supermatrix. Overall, we obtained consistent inferences with previous published ones, but some unexpected phylogenetic relationships were poorly supported. Despite the large quantity of genes from the Opisthokonta groups, this clade was recovered as polyphyletic. We failed to recover a monophyletic Excavata group, most likely because of longbranch attraction artefacts. A second dataset was constructed after removing the fast-evolving/saturated sites, and a Shimodaira-Hasegawa test was performed to verify whether our data allowed us to reject relationships in previous hypotheses. The results of these tests suggested that the competing tree topologies were not significantly better than our recovered topologies. Novel relationships were shown inside the Opisthokonta, for two species, Thecamonas trahens and Capsaspora owczarzaki. Additionally, some controversial phylogenetic positions among several eukaryotic groups were found. We discuss the relative positions of the Alveolata and Stramenopila groups, the latter being of special interest in our research group. © 2016. Acad. Colomb. Cienc. Ex. Fis. Nat. All rights reserved.
Exploring the biocontrol potential of fungal endophytes from an Andean Colombian Paramo ecosystem
(Springer Science+Business Media, 2012) Laura A. Miles; Carolina Lopera; Segundo Leiva González; María Caridad Cepero de García; Alejandro Franco; Silvia Restrepo
Factors Associated with SARS-CoV-2 Infection in Bogotá, Colombia: Results from a Large Epidemiological Surveillance Study
(RELX Group (Netherlands), 2021) Andrea Ramírez Varela; Luis Jorge Hernández Flórez; Guillermo Tamayo Cabeza; Sandra Contreras‐Arrieta; Silvia Restrepo; Rachid Laajaj; Giancarlo Buitrago; Paola Rueda‐Guevara; Yuldor Caballero Diaz; Martha J. Vives
Fungal endophytes of cactus ( Stenocereus spp.) as a potential alternative to alleviate drought stress in juveniles of Theobroma cacao L. ICS95
(2025) Karen Sofia Trujillo Ortigoza; Angelis Marbello-Santrich; Fermín Rada; Marcela Guevara‐Suarez; Silvia Restrepo
Abstract Theobroma cacao , one of Colombia’s most economically and socially significant crops, faces productivity challenges due to drought. This stress can reduce growth, leaf area, and stomatal conductance (Ks), and generate reactive oxygen species (ROS). Therefore, exploring solutions to enhance drought tolerance is crucial. This study aimed to evaluate the use of fungal root endophytes from Stenocereus spp. to induce drought tolerance in T. cacao genotype ICS95. In vitro drought tolerance screening identified five fungal isolates that exhibited the highest biomass production and less than 20% biomass loss under drought compared to non-drought conditions. The soil of juvenile T. cacao plants was inoculated with these isolates, and physiological and morphological parameters were assessed, including leaf water potential (Ψ L ), stomatal conductance (Ks), proline content, and growth. The results showed a significant decrease in Ψ L and Ks in juveniles under drought stress, which was observed across all five fungal isolates tested. However, juveniles inoculated with Phoma sp. exhibited less negative Ψ L and lower Ks than non-inoculated controls, suggesting that this fungus may be a potential inducer of drought tolerance in T. cacao ICS95. One intriguing result was that plants inoculated with this fungus accumulated less proline during the drought treatment. Under non-drought conditions, juveniles inoculated with Acrophialophora sp., Ectophoma sp., Fusarium sp., and Phoma sp. exhibited an increase in mean leaf area. These findings suggest that fungal endophytes associated with Stenocereus spp. could provide a potential alternative for alleviating drought stress and may also mediate growth promotion under non-drought conditions in cacao. Importance Theobroma cacao is among the world’s most valuable crops, yet its productivity is increasingly threatened by fluctuating rainfall and prolonged drought. Identifying sustainable strategies to mitigate these impacts is therefore critical. Xerophilic plants, such as Stenocereus spp., harbor diverse fungal endophytes adapted to arid environments, representing a promising source of microorganisms capable of enhancing stress tolerance in commercial crops. Our study demonstrates that cactus-derived endophytes could improve drought resilience in juvenile cacao by modulating physiological responses such as stomatal conductance and leaf water potential. Furthermore, under favorable conditions, some endophytes could promote growth by increasing leaf area compared to non-inoculated plants. These findings underscore the potential of fungal endophytes from arid ecosystems as biotechnological tools for sustainable cacao production, offering an environmentally friendly alternative to mitigate drought stress while enhancing plant performance.
Hierarchical Bayesian classification methods to identify topics by journal quartile with an application in biological sciences
(IOS Press, 2021) Silvia Restrepo; Enrique ter Horst; Juan Diego Zambrano; Laura H. Gunn; Germán Molina; Carlos Andres Salazar
This manuscript builds on a novel, automatic, freely-available Bayesian approach to extract information in abstracts and titles to classify research topics by quartile. This approach is demonstrated for all N= 149,129 ISI-indexed publications in biological sciences journals during 2017. A Bayesian multinomial inverse regression approach is used to extract rankings of topics without the need of a pre-defined dictionary. Bigrams are used for extraction of research topics across manuscripts, and rankings of research topics are constructed by quartile. Worldwide and local results (e.g., comparison between two peer/aspirational research institutions in Colombia) are provided, and differences are explored both at the global and local levels. Some topics persist across quartiles, while the relevance of others is quartile-specific. Challenges in sustainable development appear as more prevalent in top quartile journals across institutions, while the two Colombian institutions favour plant and microorganism research. This approach can reduce information inequities, by allowing young/incipient researchers in biological sciences, especially within lower income countries or universities with limited resources, to freely assess the state of the literature and the relative likelihood of publication in higher impact journals by research topic. This can also serve institutions of higher education to identify missing research topics and areas of competitive advantage.
Fusarium species detected in onychomycosis in Colombia
(Wiley, 2008) Natalia Castro López; Clemencia Casas; Leticia Sopó; Alejandro Rojas; Patricia Del Portillo; María Caridad Cepero de García; Silvia Restrepo
Fusarium spp. have frequently been isolated from patients with onychomycosis. In Colombia, several studies have shown that Fusarium is the most common non-dermatophyte mould causing onychomycosis and its spread has increased in the past years. In this study, samples were collected in 2003 and 2004 from 137 patients who were diagnosed with onychomycosis caused by Fusarium spp. Three species of Fusarium were identified: Fusarium solani (64.9%), Fusarium oxysporum (32.8%) and Fusarium verticillioides (2.3%). The diseases were more common in women (73%) than in men (27%) and occurred mainly among adults between 31 and 40 years old. The percentage of patients who had received previous treatments was 63.5%. In the last years, new and improved antifungal agents like echinocandins or new triazoles like voriconazole have been developed. For this reason, susceptibility testing using voriconazole was performed, by broth microdilution and disk diffusion. The results showed that F. solani had the highest minimum inhibitory concentration. Using the disk diffusion test, many of the isolates showed variable susceptibility. Genetic diversity of F. oxysporum isolates was determined by random amplified polymorphic DNA. Twenty isolates belonging to different haplotypes were selected for PCR amplification of a region of the gene encoding α-l-arabinofuranosidase B, a specific test to determine if the isolates were F. oxysporum f. sp. dianthi. On the basis of these PCR results, we found that five out of the 20 F. oxysporum isolates corresponded to f. sp. dianthi.
Instructor practices and espoused beliefs about bilingual courses: the case of a Colombian university
(Routledge, 2021) Pablo Antonio Archila; Giovanna Danies; Anne‐Marie Truscott de Mejía; Silvia Restrepo
Recent studies show that English as the medium of instruction seems impractical and ineffective in countries where English is the second or foreign language. The situation becomes even more complicated because of students’ resistance to an English-only format. In response to this, universities around the world also offer first language-English bilingual courses. Although bilingual courses are a legitimate opportunity to achieve internationalization, very little is known about bilingual teaching practices (BTPs) and the instructors’ espoused beliefs about this type of practice. In this cross-sectional study, the twenty-eight-item questionnaire created by Archila and Truscott de Mejía (2020a) was adapted to explore the practices and espoused beliefs of three hundred eleven instructors from twelve schools at a Colombian university. Findings indicate that instructors used to include some BTPs in their courses. Nonetheless, there was evidence that they needed more preparation and support for the creation, implementation, and assessment of this type of practice. Most importantly, our results support the claim that bi/multilingual higher education policies should respond to the nature of each discipline. Relevant policy implications are discussed in light of the call of some authors to move towards university first language-English bilingual courses.
LA AGRICULTURA, COLOMBIA Y LA UNIVERSIDAD DE LOS ANDES
(Universidad de Los Andes, 2018) Silvia Restrepo
En la misión de la Universidad de los Andes se declara que somos una institución que imparte a sus estudiantes una formación crítica y ética para afianzar en ellos la conciencia de sus responsabilidades sociales y cívicas, así como su compromiso con el entorno. Dice además que apoya una actividad investigativa que contribuye al desarrollo del país. Es así que es difícil imaginar que la Universidad de los Andes sea indiferente al sector agrícola.
Malassezia spp. beyond The Mycobiota
(2017) Celis AM; Wösten HAB; Sergio Triana; Silvia Restrepo; de Cock H
Malassezia species are part of the normal mycobiota of skin of animals and humans but they can cause skin and blood stream infections as well. These yeasts are all lipid dependent explained by the absence of fatty acid synthase genes in their genome. At the same time, metabolic reconstruction revealed differences in the metabolism of fungal steroids and degradation of CoA-activated long-chain FAs, arachidonic acid, and butanoate metabolism between Malassezia yeasts. In addition, differences in the assimilation of palmitic acid were predicted. Indeed, M. furfur was able to metabolize palmitic acid but M. globosa, M. sympodialis, M. pachydermatis, and an atypical variant of M. furfur were not able to do so. Tools to genetically modify Malassezia have become available recently, which will speed up the process to decipher mechanisms underlying growth and pathogenicity of these yeasts. Here, we will provide an overview about the genus Malassezia and make an assessments to the new insights in this yeast.
Microscopical and molecular characterization of the infection cycle of Phytophthora betacei during disease development on tree tomato ( Solanum betaceum)
(2025) Natalia Guayazán Palacios; Juliana González‐Tobón; Maria Camila Buitrago Acosta; Daniel Bautista; Laura Natalia González-García; Martha Cárdenas; María Fernanda Mideros; Sebastián Schornack; Silvia Restrepo
Abstract Phytophthora betacei is a recently described oomycete plant pathogen closely related to Phytophthora infestans sensu stricto . This plant pathogen naturally infects tree tomato ( Solanum betaceum ) but has not been reported on tomatoes and potatoes, the primary hosts of P. infestans . The aim of this study was to characterize the infection cycle of P. betacei using microscopy and molecular approaches. Several strains were inoculated in susceptible tree tomato plants and disease progression was monitored via six epidemiological parameters. Although different P. betacei strains displayed a highly variable disease phenotype, the most aggressive one was chosen for further plant inoculations. Samples at different time points of the infection cycle were analyzed at the cellular level via light and scanning electron microscopy (SEM) and at the molecular level via qRT-PCR of infection-stage-specific markers. The infection cycle of P. betacei differed from that of P. infestans in having a longer biotrophic stage, larger lesions, and higher sporulation capacity. Additionally, P. betacei transcriptomic profiles were monitored along the infection cycle via RNAseq and evidenced a changing expression landscape that supports an elongated hemibiotrophic transition and a clear distinction from what is being expressed in the mycelium or the sporangia. This study provides novel insights into the interaction between P. betacei and S. betaceum .