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

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

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

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

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

Construcción y secuenciación parcial de una biblioteca sustractiva en Calcutta 4 (Musa AA) en estadio temprano de infección con Mycosphaerella fijiensis Morelet

The study of genes involved in plant defense response against pathogen attack, is one of most important steps leading to the elucidation of disease resistance molecular mechanisms. The generation of subtracted deoxyribonucleic acid libraries (cDNA), by means of suppression subtractive hybridization technique (SSH), has been used for this purpose. A subtractive hybridization was made between a cDNA population obtained from ‘Calcutta 4’ inoculated leaves with M. fijiensis (CCIBP-Pf83) and a mixture of cDNA from ‘Calcutta 4’ non inoculated leaves and mycelium. Leaves samples were taken at 6, 10 and 12 days after inoculation. The subtracted library was obtained by cloning and transformation of subtracted products and as a result, 600 recombinants clones were obtained. Sequence analysis of sixty nine clones, revealed redundancy of the expressed sequence tags and most of them showed no homology with reported sequences at databases and only 13 % had a high homology with metalothioneins. The results constitute a step in advance in the molecular study of Musa-Mycosphaerella fijiensis interaction. Key words: Banana-Mycosphaerella fijiensis interaction, BlackSigatoka, Musa spp., suppression subtractive hybridizationEl estudio de los genes involucrados en la respuesta de defensa en la planta contra el ataque de patógenos, es uno de los pasos más importantes para la elucidación de los mecanismos moleculares de resistencia a enfermedades. La generación de bibliotecas sustractivas de ácido desoxirribonucleico complementario (ADNc), por medio de la técnica de hibridación sustractiva por supresión, ha sido utilizada para este propósito. En este trabajo se realizó una hibridación sustractiva, entre el ADNc obtenido de hojas de ‘Calcutta 4’ inoculadas con M. fijiensis (CCIBP-Pf83) y una mezcla de ADNc de hojas de ‘Calcutta 4’ no inoculadas y del micelio del hongo. Las muestras de hojas se tomaron a los 6, 10 y 12 días posteriores a la inoculación. La biblioteca sustractiva se obtuvo por clonación y transformación de los productos sustraídos y como resultado se obtuvieron 600 clones recombinantes. El análisis de secuencia de 69 clones reveló redundancia de las secuencias blanco expresadas, la mayoría no mostró homología con secuencias en las bases de datos. El 13 % tuvo alta homología con metalotioninas. Los resultados constituyen un paso de avance en el estudio a nivel molecular de la interacción Musa- Mycosphaerella fijiensis. Palabras clave: hibridación sustractiva por supresión, interacción Banano-Mycosphaerella fijiensis, Musa spp., Sigatoka negr