Evaluación de la actividad y estabilidad de extractos enzimáticos obtenidos de hongos celulolíticos en fermentación líquida

El cultivo de arroz en Colombia es uno de los principales cultivos que se realizan en el país, y la generación de residuos derivados del arroz, como lo es el tamo, comprende problemas medio ambientales y debido a su gran cantidad el manejo de estos residuos muchas veces no es el adecuado. Es por esta razón que se han estudiado distintos tratamientos biológicos que puedan dar respuesta y solución a la disposición final de estos residuos. En este trabajo se evaluó la actividad enzimática de extractos crudos obtenidos de fermentación liquida de dos hongos con potencial celulolítico: Penicillium sp. MF 3-64 y Paecilomyces sp. MF 4-71, cada uno fue puesto en fermentación liquida sobre tamo de arroz durante 10 días, obteniéndose al final del proceso que la mayor actividad enzimática se observó con la cepa de Penicillium sp. MF 3-64 en el día 10 con valores de 16829,09 U/L para xilanasas, 6438,26 U/L para ?-glucosidasa, 896,94 U/L para endoglucanasa y 11049,3 U/L para celobiohidrolasa. De igual manera se evaluó el efecto de sulfato de amonio en la actividad enzimática de los hongos encontrando que este compuesto aumenta de manera significativa los valores de unidades enzimáticas para las 2 cepas de hongos estudiados. Se determinó la estabilidad frente a temperatura y pH de extractos la cepa Penicillium sp. MF 3-64, donde se encontró que la endoglucanasa tuvo mayor estabilidad a 30°C y a pH 7 con 106% y 96% de actividad residual respectivamente, la celobiohidrolasa fue más estable a 7°Cy pH 3 con 112% y 11% respectivamente, la ?-glucosidasa presento mayor estabilidad a 7°C y pH 7 con porcentajes de actividad residual de 100% y 35% cada una, en el caso de las xilanasas fueron estables a 40°C y a pH 7 con 113% y 122% de actividad residual. Las pruebas de estabilidad frente a temperatura se realizaron por 1 hora a pH 5 y las pruebas de estabilidad frente a pH se realizaron por 24 h a 25°C.Microbiólogo (a) IndustrialPregrad

Integration of RNA-Seq data with heterogeneous microarray data for breast cancer profiling

Background: Nowadays, many public repositories containing large microarray gene expression datasets are available. However, the problem lies in the fact that microarray technology are less powerful and accurate than more recent Next Generation Sequencing technologies, such as RNA-Seq. In any case, information from microarrays is truthful and robust, thus it can be exploited through the integration of microarray data with RNA-Seq data. Additionally, information extraction and acquisition of large number of samples in RNA-Seq still entails very high costs in terms of time and computational resources.This paper proposes a new model to find the gene signature of breast cancer cell lines through the integration of heterogeneous data from different breast cancer datasets, obtained from microarray and RNA-Seq technologies. Consequently, data integration is expected to provide a more robust statistical significance to the results obtained. Finally, a classification method is proposed in order to test the robustness of the Differentially Expressed Genes when unseen data is presented for diagnosis. Results: The proposed data integration allows analyzing gene expression samples coming from different technologies. The most significant genes of the whole integrated data were obtained through the intersection of the three gene sets, corresponding to the identified expressed genes within the microarray data itself, within the RNA-Seq data itself, and within the integrated data from both technologies. This intersection reveals 98 possible technology-independent biomarkers. Two different heterogeneous datasets were distinguished for the classification tasks: a training dataset for gene expression identification and classifier validation, and a test dataset with unseen data for testing the classifier. Both of them achieved great classification accuracies, therefore confirming the validity of the obtained set of genes as possible biomarkers for breast cancer. Through a feature selection process, a final small subset made up by six genes was considered for breast cancer diagnosis. Conclusions: This work proposes a novel data integration stage in the traditional gene expression analysis pipeline through the combination of heterogeneous data from microarrays and RNA-Seq technologies. Available samples have been successfully classified using a subset of six genes obtained by a feature selection method. Consequently, a new classification and diagnosis tool was built and its performance was validated using previously unseen samples.This work was supported by Project TIN2015-71873-R (Spanish Ministry of Economy and Competitiveness -MINECO- and the European Regional Development Fund -ERDF)

Programa de prácticas de bacteriología y micología

Conocer e identificar la morfología bacteriana y fungal, así como sus principios metabólicos, genéticos y taxonómicos

Leukemia multiclass assessment and classification from Microarray and RNA-seq technologies integration at gene expression level

In more recent years, a significant increase in the number of available biological experiments has taken place due to the widespread use of massive sequencing data. Furthermore, the continuous developments in the machine learning and in the high performance computing areas, are allowing a faster and more efficient analysis and processing of this type of data. However, biological information about a certain disease is normally widespread due to the use of different sequencing technologies and different manufacturers, in different experiments along the years around the world. Thus, nowadays it is of paramount importance to attain a correct integration of biologically-related data in order to achieve genuine benefits from them. For this purpose, this work presents an integration of multiple Microarray and RNA-seq platforms, which has led to the design of a multiclass study by collecting samples from the main four types of leukemia, quantified at gene expression. Subsequently, in order to find a set of differentially expressed genes with the highest discernment capability among different types of leukemia, an innovative parameter referred to as coverage is presented here. This parameter allows assessing the number of different pathologies that a certain gen is able to discern. It has been evaluated together with other widely known parameters under assessment of an ANOVA statistical test which corroborated its filtering power when the identified genes are subjected to a machine learning process at multiclass level. The optimal tuning of gene extraction evaluated parameters by means of this statistical test led to the selection of 42 highly relevant expressed genes. By the use of minimum- Redundancy Maximum-Relevance (mRMR) feature selection algorithm, these genes were reordered and assessed under the operation of four different classification techniques. Outstanding results were achieved by taking exclusively the first ten genes of the ranking into consideration. Finally, specific literature was consulted on this last subset of genes, revealing the occurrence of practically all of them with biological processes related to leukemia. At sight of these results, this study underlines the relevance of considering a new parameter which facilitates the identification of highly valid expressed genes for simultaneously discerning multiple types of leukemia.This work was supported by Project TIN2015-71873-R (Spanish Ministry of Economy and Competitiveness -MINECO- and the European Regional Development Fund -ERDF) and Junta de Andalucı´a (P12–TIC–2082)

Automation of functional annotation of genomes and transcriptomes

Functional annotation represents a means to investigate and classify genes and transcripts according to their function within a given organism.This paper presents Massive Automatic Functional Annotation (MAFA - Web), which is an online free bioinformatics tool that allows automation, unification and optimization of functional annotation processes when dealing with large volumes of sequences. MAFA includes tools for categorization and statistical analysis of associations between sequences. We have evaluated the performance of MAFA with a set of data taken from Diploria-Strigosatranscriptome (using an 8-core computer, namely E7450 @ 2,40GHZ with 256GB RAM), processing rates of 2,7 seconds per sequence (using Uniprot database) and 50,0 seconds per sequence (using Non-redundant from NCBI database) were found together with particular RAM usage patterns that depend on the database being processed (1GB for Uniprot database and 9GB for Non-redundant database).. Aviability: https://github.com/BioinfUD/MAFA. Functional annotation represents a means to investigate and classify genes and transcripts according to their function within a given organism.This paper presents Massive Automatic Functional Annotation (MAFA - Web), which is an online free bioinformatics tool that allows automation, unification and optimization of functional annotation processes when dealing with large volumes of sequences. MAFA includes tools for categorization and statistical analysis of associations between sequences. We have evaluated the performance of MAFA with a set of data taken from Diploria-Strigosatranscriptome (using an 8-core computer, namely E7450 @ 2,40GHZ with 256GB RAM), processing rates of 2,7 seconds per sequence (using Uniprot database) and 50,0 seconds per sequence (using Non-redundant from NCBI database) were found together with particular RAM usage patterns that depend on the database being processed (1GB for Uniprot database and 9GB for Non-redundant database). Aviability: https://github.com/BioinfUD/MAFA.

Diagnóstico del tratamiento de aguas residuales mediante los sistemas Cenicafé y Majavita del beneficio ecológico del café con módulo Becolsub en la Hacienda Majavita

Problema Central: En el proceso de beneficio del café se originan los subproductos pulpa y aguas mieles, los cuales contienen altas concentraciones de carga orgánica contaminante y pueden generar un impacto negativo al tener contacto con los recursos del medio ambiente debido al desecho indiscriminado sin previo tratamiento de estos. Objetivo: El objetivo de este proyecto consistió en el diagnóstico del manejo de las aguas residuales del beneficio ecológico del café con la tecnología Becolsub en la Hacienda Majavita, con el fin de mejorar la calidad del ambiente y garantizar la eficiencia en el tratamiento de estos subproductos. Metodología: Se desarrolló un proceso de cuantificación de los subproductos mediante el pesaje y monitoreo de las unidades que integran los dos sistemas. Para mejorar la remoción de material contaminante en los sistemas de tratamiento se diseñó, construyó e implementó una nueva unidad, reactor UASB (upflow anaerobic sludge blanket), el cual fue instalado al final de los dos sistemas de tratamiento y dispuesto para las futuras cosechas. Resultados: La evaluación de los sistemas de tratamiento mostró que el comportamiento de la materia orgánica varió de un sistema a otro, el sistema de tratamiento Cenicafé logro remoción total del 86,3% DQO y 89,7% DBO5. Se puso en operación el reactor anaerobio UASB, con el cual se incrementó la remoción de carga contaminante y se evaluó su comportamiento mediante el seguimiento de indicadores físico-químicos, también se diseñó el nuevo sistema de tratamiento para la Hacienda Majavita. Conclusión: La cuantificación de los subproductos generados en el proceso de beneficio de café permitió concluir que los sistemas de tratamiento existentes presentan una capacidad inferior a la requerida para el manejo de las aguas mieles, teniendo en cuenta que las producciones de café a futuro tienden a aumenta

Aislamiento e identificación fenotípica y genotípica de Moraxella ovis de casos clínicos de queratoconjuntivitis ovina en el Estado de México

La queratoconjuntivitis contagiosa ovina (QCO) es una enfermedad infectocontagiosa que produce ceguera temporal o permanente en ovinos y caprinos, se encuentra asociada a un conjunto de agentes infecciosos como Moraxella ovis, Mycoplasma conjunctivae y Chlamydia psittaci, el diagnóstico se realiza mediante un examen clínico y pruebas de laboratorio. De un total de 861 animales examinados, 209 presentaron algún tipo de lesión ocular resultando en una prevalencia del 24.27% de animales con lesiones compatibles con QCO. De las 209 muestras remitidas al laboratorio se lograron identificar 58 como Moraxella ovis mediante bacteriología y por la amplificación de los genes 16S rRNA y RxtA por PCR. En virtud de los resultados podemos concluir que Moraxella ovis esta involucrada en los casos de QCO en establecimientos productores de ovinos en el Estado de México

Aspergillus fumigatus Fumagillin Contributes to Host Cell Damage

The activity of fumagillin, a mycotoxin produced by Aspergillus fumigatus, has not been studied in depth. In this study, we used a commercial fumagillin on cultures of two cell types (A549 pneumocytes and RAW 264.7 macrophages). This toxin joins its target, MetAP2 protein, inside cells and, as a result, significantly reduces the electron chain activity, the migration, and the proliferation ability on the A549 cells, or affects the viability and proliferation ability of the RAW 264.7 macrophages. However, the toxin stimulates the germination and double branch hypha production of fungal cultures, pointing out an intrinsic resistant mechanism to fumagillin of fungal strains. In this study, we also used a fumagillin non-producer A. fumigatus strain (∆fmaA) as well as its complemented strain (∆fmaA::fmaA) and we tested the fumagillin secretion of the fungal strains using an Ultra High-Performance Liquid Chromatography (UHPLC) method. Furthermore, fumagillin seems to protect the fungus against phagocytosis in vitro, and during in vivo studies using infection of immunosuppressed mice, a lower fungal burden in the lungs of mice infected with the ∆fmaA mutant was demonstrated.This research was funded by the Basque Government: grant number IT1362-19. X.G. and S.C.-S. received a Ph.D. fellowship from the Basque Government; and U.P.-C. from the University of the Basque Country

Fitoperifiton asociado al río Acacias-Pajure en la Orinoquia colombiana

Phytoperiphyton refers to the autotrophic component belonging to the periphyton community, composed of aquatic microorganisms that have been monitored for their ecological importance and potential as bioindicators. Few investigations have been carried out on this community in the Colombian Orinoquia, a region with abundant water resources and multiple anthropic pressures, because it is the country’s main agricultural and energy source. Three monitorings were carried out at 12 points along the Acacias-Pajure River, where a total of 41 genera were identified. The highest records of richness were presented at monitoring points 6 and 7, associated with oil palm crops and livestock activity. Navicula (Ochrophyta) and Cosmarium (Charophyta) were the most frequent genera, Oedogonium (Chlorophyta) and Phormidium (Cyanobacteria) the most abundant along the river.El fitoperifiton hace referencia al componente autótrofo perteneciente a la comunidad del perifiton, compuesta por microorganismos acuáticos que han sido monitoreados por su importancia ecológica y potencial como bioindicadores. Son escasos los estudios que se han realizado sobre esta comunidad en la Orinoquia colombiana, región con un abundante recurso hídrico y con múltiples presiones antrópicas, debido a que es la principal despensa agrícola y energética del país. Se realizaron tres monitoreos en 12 puntos a lo largo del río Acacias-Pajure, en donde se identificaron un total de 41 géneros. Los mayores registros de riqueza se presentaron en los puntos de monitoreo 6 y 7, asociados a cultivos de palma de aceite y actividad ganadera. Navicula (Ochrophyta) y Cosmarium (Charophyta) fueron los géneros más frecuentes, Oedogonium (Chlorophyta) y Phormidium (Cyanobacteria) los más abundantes a lo largo del río

Recommendations for ophthalmologic practice during the easing of COVID-19 control measures

In the context of the COVID-19 pandemic, this paper provides recommendations for medical eye care during the easing of control measures after lockdown. The guidelines presented are based on a literature review and consensus among all Spanish Ophthalmology Societies regarding protection measures recommended for the ophthalmologic care of patients with or without confirmed COVID-19 in outpatient, inpatient, emergency and surgery settings. We recommend that all measures be adapted to the circumstances and availability of personal protective equipment at each centre and also highlight the need to periodically update recommendations as we may need to readopt more restrictive measures depending on the local epidemiology of the virus. These guidelines are designed to avoid the transmission of SARS-CoV-2 among both patients and healthcare staff as we gradually return to normal medical practice, to prevent postoperative complications and try to reduce possible deficiencies in the diagnosis, treatment and follow-up of the ophthalmic diseases. With this update (5th) the Spanish Society of Ophthalmology is placed as one of the major ophthalmology societies providing periodic and systematized recommendations for ophthalmic care during the COVID-19 pandemic