Shifts in leaf litter breakdown along a forest–pasture–urban gradient in Andean streams

Tropical montane ecosystems of the Andes are critically threatened by a rapid land-use change which can potentially affect stream variables, aquatic communities, and ecosystem processes such as leaf litter breakdown. However, these effects have not been sufficiently investigated in the Andean region and at high altitude locations in general. Here, we studied the influence of land use (forest–pasture–urban) on stream physico-chemical variables (e.g., water temperature, nutrient concentration, and pH), aquatic communities (macroinvertebrates and aquatic fungi) and leaf litter breakdown rates in Andean streams (southern Ecuador), and how variation in those stream physico-chemical variables affect macroinvertebrates and fungi related to leaf litter breakdown. We found that pH, water temperature, and nutrient concentration increased along the land-use gradient. Macroinvertebrate communities were significantly different between land uses. Shredder richness and abundance were lower in pasture than forest sites and totally absent in urban sites, and fungal richness and biomass were higher in forest sites than in pasture and urban sites. Leaf litter breakdown rates became slower as riparian land use changed from natural to anthropogenically disturbed conditions and were largely determined by pH, water temperature, phosphate concentration, fungal activity, and single species of leaf-shredding invertebrates. Our findings provide evidence that leaf litter breakdown in Andean streams is sensitive to riparian land-use change, with urban streams being the most affected. In addition, this study highlights the role of fungal biomass and shredder species (Phylloicus; Trichoptera and Anchytarsus; Coleoptera) on leaf litter breakdown in Andean streams and the contribution of aquatic fungi in supporting this ecosystem process when shredders are absent or present low abundance in streams affected by urbanization. Finally, we summarize important implications in terms of managing of native vegetation and riparian buffers to promote ecological integrity and functioning of tropical Andean stream ecosystems

DeepReGraph co-clusters temporal gene expression and cis-regulatory elements through heterogeneous graph representation learning

This work presents DeepReGraph, a novel method for co-clustering genes and cis-regulatory elements (CREs) into candidate regulatory networks. Gene expression data, as well as data from three CRE activity markers from a publicly available dataset of mouse fetal heart tissue, were used for DeepReGraph concept proofing. In this study we used open chromatin accessibility from ATAC-seq experiments, as well as H3K27ac and H3K27me3 histone marks as CREs activity markers. However, this method can be executed with other sets of markers. We modelled all data sources as a heterogeneous graph and adapted a state-of-the-art representation learning algorithm to produce a low-dimensional and easy-to-cluster embedding of genes and CREs. Deep graph auto-encoders and an adaptive-sparsity generative model are the algorithmic core of DeepReGraph. The main contribution of our work is the design of proper combination rules for the heterogeneous gene expression and CRE activity data and the computational encoding of well-known gene expression regulatory mechanisms into a suitable objective function for graph embedding. We showed that the co-clusters of genes and CREs in the final embedding shed light on developmental regulatory mechanisms in mouse fetal-heart tissue. Such clustering could not be achieved by using only gene expression data. Function enrichment analysis proves that the genes in the co-clusters are involved in distinct biological processes. The enriched transcription factor binding sites in CREs prioritize the candidate transcript factors which drive the temporal changes in gene expression. Consequently, we conclude that DeepReGraph could foster hypothesis-driven tissue development research from high-throughput expression and epigenomic data. Full source code and data are available on the DeepReGraph GitHub project

Micro momentos pedagógicos: ¿Cómo potenciar el aprendizaje colaborativo en programas de posgrado en línea?

El concepto de los micro momentos es quizás uno de los más revolucionarios en el tema de la psicología del comportamiento y está en el centro de la más reciente revolución del Marketing. En el contexto educativo un micro momento pedagógico se define como el conjunto de instrucciones que acompañadas de la información correcta inducen una reflexión profunda en el estudiante. El presente proyecto describe una estrategia innovadora para generar competencias de aprendizaje colaborativo (una debilidad actual con un impacto negativo en el éxito académico), en estudiantes de programas de posgrado en línea mediante la manipulación de micro momentos pedagógicos. Se diseñó una intervención educativa que consistió en la estructuración de sesiones síncronas de programas de posgrado en línea en cuatro micro momentos pedagógicos principales (activación, desarrollo, reflexión y conclusión). En la experiencia participaron 16 docentes y un total de 291 maestrantes: 154 en el grupo control (aprendizaje tradicional en línea) y 137 en el grupo experimental (aprendizaje en línea mediante la pedagogía de los micro momentos).  Al cabo de ocho semanas de trabajo se comprobó que los maestrantes del grupo experimental mostraron un nivel de desarrollo de competencias para el aprendizaje colaborativo significativamente mayor que aquellos en el grupo control. Dada la muestra utilizada consideramos que nuestra innovación es reproducible y que aportará al desarrollo de competencias para el aprendizaje en línea en programas de posgrado con un concomitante aumento en la tasa de éxito académico terminal de dichos programas

A network-based approach to identify substrate classes of bacterial glycosyltransferases

Background: Bacterial interactions with the environment-and/or host largely depend on the bacterial glycome. The specificities of a bacterial glycome are largely determined by glycosyltransferases (GTs), the enzymes involved in transferring sugar moieties from an activated donor to a specific substrate. Of these GTs their coding regions, but mainly also their substrate specificity are still largely unannotated as most sequence-based annotation flows suffer from the lack of characterized sequence motifs that can aid in the prediction of the substrate specificity. Results: In this work, we developed an analysis flow that uses sequence-based strategies to predict novel GTs, but also exploits a network-based approach to infer the putative substrate classes of these predicted GTs. Our analysis flow was benchmarked with the well-documented GT-repertoire of Campylobacter jejuni NCTC 11168 and applied to the probiotic model Lactobacillus rhamnosus GG to expand our insights in the glycosylation potential of this bacterium. In L. rhamnosus GG we could predict 48 GTs of which eight were not previously reported. For at least 20 of these GTs a substrate relation was inferred. Conclusions: We confirmed through experimental validation our prediction of WelI acting upstream of WelE in the biosynthesis of exopolysaccharides. We further hypothesize to have identified in L. rhamnosus GG the yet undiscovered genes involved in the biosynthesis of glucose-rich glycans and novel GTs involved in the glycosylation of proteins. Interestingly, we also predict GTs with well-known functions in peptidoglycan synthesis to also play a role in protein glycosylation

Erato polymnioides – A novel Hg hyperaccumulator plant in ecuadorian rainforest acid soils with potential of microbe-associated phytoremediation

Mercury (Hg) accumulation capacity was assessed in three plant species (Axonopus compressus, Erato polymnioides, and Miconia zamorensis) that grow on soils polluted by artisanal small-scale gold mines in the Ecuadorian rainforest. Individuals of three species were collected at two sampling zones: i) an intensive zone (IZ, 4.8 mg Hg kg−1 of soil) where gold extraction continues to occur, and ii) a natural zone (NZ, 0.19 mg Hg kg−1 of soil). In addition, the percentage of arbuscular mycorrhizal fungi (AMF) colonization was determined in plant roots and seven fungal morphotypes isolated from rhizospheric soil. Results suggest a facilitation role of native and pollution adapted AMF on Hg phytoaccumulation. E.g., E. polymnioides increased Hg accumulation when growing with greater AMF colonization. We concluded that E. polymnioides is a good candidate for the design of microbe-assisted strategies for Hg remediation at gold mining areas. The consortia between E. polymnioides and the AMF isolated in this study could be instrumental to get a deeper understanding of the AMF role in Hg phytoaccumulatio

Phylogenomics and Systematics of Overlooked Mesoamerican and South American Polyploid Broad-Leaved Festuca Grasses Differentiate F. sects. Glabricarpae and Ruprechtia and F. subgen. Asperifolia, Erosiflorae, Mallopetalon and Coironhuecu (subgen. nov.)

Allopolyploidy is considered a driver of diversity in subtribe Loliinae. We investigate the evolution and systematics of the poorly studied Mesoamerican and South American polyploid broad-leaved Festuca L. species of uncertain origin and unclear taxonomy. A taxonomic study of seven diagnostic morphological traits was conducted on a representation of 22 species. Phylogenomic analyses were performed on a representation of these supraspecific taxa and all other Loliinae lineages using separate data from the entire plastome, nuclear rDNA 45S and 5S genes, and repetitive DNA elements. F. subgen. Mallopetalon falls within the fine-leaved (FL) Loliinae clade, whereas the remaining taxa are nested within the broad-leaved (BL) Loliinae clade forming two separate Mexico–Central–South American (MCSAI, MCSAII) lineages. MCSAI includes representatives of F. sect. Glabricarpae and F. subgen. Asperifolia plus F. superba, and MCSAII of F. subgen. Erosiflorae and F. sect. Ruprechtia plus F. argentina. MCSAII likely had a BL Leucopoa paternal ancestor, MCSAI and MCSAII a BL Meso-South American maternal ancestor, and Mallopetalon FL, American I–II ancestors. Plastome vs. nuclear topological discordances corroborated the hybrid allopolyploid origins of these taxa, some of which probably originated from Northern Hemisphere ancestors. The observed data indicate rapid reticulate radiations in the Central–South American subcontinent. Our systematic study supports the reclassification of some studied taxa in different supraspecific Festuca ranks

Instant messaging to humanize online learning: lessons from the use of WhatsApp in a higher education context

La inclusión de herramientas tecnológicas es frecuente y un referente del sistema de estudios de educación superior en línea, aunque no garantiza el éxito estudiantil, son importantes la interacción y acompañamiento docente, la motivación y autonomía del estudiante. La finalidad del estudio es determinar factores de éxito académico e impacto del uso de mensajería instantánea (WhatsApp) como herramienta de apoyo académico para humanizar la experiencia de aprendizaje de estudiantes de educación superior, estudios en línea. Se utilizó el enfoque metodológico de orden cuantitativo. Los principales resultados dan cuenta que, el aprendizaje autónomo, la estructura del curso y la flexibilidad de la tutoría, son factores del éxito académico de mayor influencia. La interacción lograda (profesor estudiante) a través del WhatsApp, influye en la motivación, además, se evidenció mayor actividad en la utilización de contenidos auto dirigidos y actividades colaborativas que en conjunto, estimulan la humanización de la educación en línea.The inclusion of technological tools is frequently seen as a landmark of online study programs. However, the use of technological advancements per se does not guarantee students’ success. Interaction among peers and with the teacher are important success factors often linked to students’ motivation. Skills for autonomous learning are also crucial in the context of online learning. The purpose of this study was to highlight factors of academic success and to investigate the impact of instant messaging tools like WhatsApp, to humanize the learning experience of higher education students enrolled in online programs. Our results show that autonomous learning, the structure of the course, and the flexibility of mentoring sessions are key academic success factors. The amount of interaction student-student and student-teacher interaction favored by the use of WhatsApp influenced to a large degree students’ motivation. In addition, students showed a greater consumption of self-directed content and larger participation in collaborative activities. Altogether these factors contributed to the humanization of online education

Improved linkage analysis of Quantitative Trait Loci using bulk segregants unveils a novel determinant of high ethanol tolerance in yeast

Background: Bulk segregant analysis (BSA) coupled to high throughput sequencing is a powerful method to map genomic regions related with phenotypes of interest. It relies on crossing two parents, one inferior and one superior for a trait of interest. Segregants displaying the trait of the superior parent are pooled, the DNA extracted and sequenced. Genomic regions linked to the trait of interest are identified by searching the pool for overrepresented alleles that normally originate from the superior parent. BSA data analysis is non-trivial due to sequencing, alignment and screening errors. Results: To increase the power of the BSA technology and obtain a better distinction between spuriously and truly linked regions, we developed EXPLoRA (EXtraction of over-rePresented aLleles in BSA), an algorithm for BSA data analysis that explicitly models the dependency between neighboring marker sites by exploiting the properties of linkage disequilibrium through a Hidden Markov Model (HMM). Reanalyzing a BSA dataset for high ethanol tolerance in yeast allowed reliably identifying QTLs linked to this phenotype that could not be identified with statistical significance in the original study. Experimental validation of one of the least pronounced linked regions, by identifying its causative gene VPS70, confirmed the potential of our method. Conclusions: EXPLoRA has a performance at least as good as the state-of-the-art and it is robust even at low signal to noise ratio's i.e. when the true linkage signal is diluted by sampling, screening errors or when few segregants are available

Systematic review and a proposal for the implementation of active methodologies in STEM education

Este es un artículo de acceso abierto bajo la licencia Creative Commons 4.0 Atribución-No Comercial (CC By-NC 4.0 International)Attribution-NoDerivatives 4.0 InternacionalEl proceso requiere cambios continuos de acuerdo con las necesidades y demandas de la sociedad. Con la inclusión cada vez mayor de la tecnología en todos los ámbitos y niveles educativos, las estrategias didácticas han sufrido una transformación importante. La presente investigación se desarrolló con el fin de conocer y analizar los trabajos que desarrollan metodologías activas en la enseñanza de asignaturas STEM durante la educación básica y de bachillerato. Empleando una metodología mixta, en la que se usó la revisión sistemática y el análisis documental como técnicas de investigación. Los resultados muestran que existe un conjunto de factores clave que son comunes a la implementación de las cinco metodologías activas revisadas en nuestro trabajo: aula invertida, aprendizaje basado en proyectos, aprendizaje basado en problemas, aprendizaje cooperativo, gamificación. Se recomienda a los docentes de materias STEM emplear los recursos sugeridos para lograr una implementación efectiva de las metodologías activas propuestas.The educational process is not static and requires continuous changes according to the needs and demands of society. With the increasing inclusion of technology in all educational fields and levels, didactic strategies have undergone a major transformation. The present research was developed with the aim of learning about and analyzing the works that develop active methodologies in the teaching of STEM subjects during the basic education and high school stages. A mixed methodology was used with a convergent design, in which systematic review and documentary analysis were used as research techniques. The results show that there is a set of key factors that are common to the implementation of the five active methodologies reviewed in our work: flipped classroom, project-based learning, problembased learning, cooperative learning, gamification. It is recommended that teachers of STEM subjects use the suggested resources to achieve an effective implementation of the proposed active methodologies