Search

Abstract Background RNA sequencing (RNA-Seq) in its varied forms has become an indispensable tool for analyzing differential gene expression and thus characterization of specific tissues. Aiming to understand the brain barriers genetic signature, RNA seq has also been introduced in brain barriers research. This has led to availability of both, bulk and single-cell RNA-Seq datasets over the last few years. If appropriately performed, the RNA-Seq studies provide powerful datasets that allow for significant deepening of knowledge on the molecular mechanisms that establish the brain barriers. However, RNA-Seq studies comprise complex workflows that require to consider many options and variables before, during and after the proper sequencing process. Main body In the current manuscript, we build on the interdisciplinary experience of the European PhD Training Network BtRAIN ( https://www.btrain-2020.eu/ ) where bioinformaticians and brain barriers researchers collaborated to analyze and establish RNA-Seq datasets on vertebrate brain barriers. The obstacles BtRAIN has identified in this process have been integrated into the present manuscript. It provides guidelines along the entire workflow of brain barriers RNA-Seq studies starting from the overall experimental design to interpretation of results. Focusing on the vertebrate endothelial blood–brain barrier (BBB) and epithelial blood-cerebrospinal-fluid barrier (BCSFB) of the choroid plexus, we provide a step-by-step description of the workflow, highlighting the decisions to be made at each step of the workflow and explaining the strengths and weaknesses of individual choices made. Finally, we propose recommendations for accurate data interpretation and on the information to be included into a publication to ensure appropriate accessibility of the data and reproducibility of the observations by the scientific community. Conclusion Next generation transcriptomic profiling of the brain barriers provides a novel resource for understanding the development, function and pathology of these barrier cells, which is essential for understanding CNS homeostasis and disease. Continuous advancement and sophistication of RNA-Seq will require interdisciplinary approaches between brain barrier researchers and bioinformaticians as successfully performed in BtRAIN. The present guidelines are built on the BtRAIN interdisciplinary experience and aim to facilitate collaboration of brain barriers researchers with bioinformaticians to advance RNA-Seq study design in the brain barriers community.

Abstract The choroid plexus (CP) is a key regulator of the central nervous system (CNS) homeostasis through its secretory, immunological and barrier properties. Accumulating evidence suggests that the CP plays a pivotal role in the pathogenesis of multiple sclerosis (MS), but the underlying mechanisms remain largely elusive. To get a comprehensive view on the role of the CP in MS, we studied transcriptomic alterations of the human CP in progressive MS and non-neurological disease controls using RNA sequencing. We identified 17 genes with significantly higher expression in progressive MS patients relative to that in controls. Among them is the newly described long non-coding RNA HIF1A-AS3. Next to that, we uncovered disease-affected pathways related to hypoxia, secretion and neuroprotection, while only subtle immunological and no barrier alterations were observed. In an ex vivo CP explant model, a subset of the upregulated genes responded in a similar way to hypoxic conditions. Our results suggest a deregulation of the Hypoxia-Inducible Factor (HIF)-1 pathway in progressive MS CP. Importantly, cerebrospinal fluid levels of the hypoxia-responsive secreted peptide PAI-1 were higher in MS patients with high disability relative to those with low disability. These findings provide for the first time a complete overview of the CP transcriptome in health and disease, and suggest that the CP environment becomes hypoxic in progressive MS patients, highlighting the altered secretory and neuroprotective properties of the CP under neuropathological conditions. Together, these findings provide novel insights to target the CP and promote the secretion of neuroprotective factors into the CNS of progressive MS patients.

Abstract The choroid plexus (CP) is strategically located between the peripheral blood and the cerebrospinal fluid, and is involved in the regulation of central nervous system (CNS) homeostasis. In multiple sclerosis (MS), demyelination and inflammation occur in the CNS. While experimental animal models of MS pointed to the CP as a key route for immune cell invasion of the CNS, little is known about the distribution of immune cells in the human CP during progressive phases of MS. Here, we use immunohistochemistry and confocal microscopy to explore the main immune cell populations in the CP of progressive MS patients and non-neuroinflammatory controls, in terms of abundance and location within the distinct CP compartments. We show for the first time that the CP stromal density of granulocytes and CD8+ T cells is higher in progressive MS patients compared to controls. In line with previous studies, the CP of both controls and progressive MS patients contains relatively high numbers of macrophages and dendritic cells. Moreover, we found virtually no B cells or plasma cells in the CP. MHCII+ antigen-presenting cells were often found in close proximity to T cells, suggesting constitutive CNS immune monitoring functions of the CP. Together, our data highlights the role of the CP in immune homeostasis and indicates the occurrence of mild inflammatory processes in the CP of progressive MS patients. However, our findings suggest that the CP is only marginally involved in immune cell migration into the CNS in chronic MS.

El uso de microorganismos benéficos en conjunto con bioestimulantes vegetales puede ser una alternativa eficiente para mejorar la productividad del fríjol. El objetivo de este estudio fue determinar el efecto de la aplicación individual y combinada entre los bioestimulantes ME-50® y FitoMas-E® en el incremento agroproductivo del fríjol en época de siembra tardía. La investigación, se desarrolló en la Cooperativa de Créditos y Servicios “Mártires de Taguasco”, Sancti Spíritus, Cuba. Se realizó un experimento en condiciones de campo con el cultivar ʻVelazco largoʼ. Los tratamientos, se distribuyeron en bloques al azar, en esquema factorial 2×2, con cinco réplicas, dos niveles ausencia y presencia del consorcio ME-50® y su combinación con la no aplicación y aplicación de FitoMas-E. Los efectos de los bioestimulantes se observaron en los parámetros de i) crecimiento: hojas por planta, área foliar y la masa seca y ii) productivos: número de vainas por planta, granos por vaina, masa de 100 granos y el rendimiento. Los resultados revelaron que la aplicación conjunta de ambos bioestimulantes fue más eficiente en el aumento del crecimiento y la productividad, que la aplicación individual y la no aplicación de bioestimulantes, al incrementar el rendimiento en 10 y 71 %, respectivamente. Los hallazgos de este estudio sugieren que la combinación entre el ME-50® y el FitoMas-E® constituye una alternativa eficiente, económica y viable, para aumentar la productividad del fríjol en época de siembra tardía.

Seed morphology is an important source of information for plant taxonomy. Nevertheless, the characters under study are diverse, and a simple, unified method is lacking in the literature. A new method for the classification of seeds of the genus Silene based on optical images and image analysis has recently been described on the basis of morphological measurements of the lateral seed views. According to the outline of their silhouettes, seeds from 52 species (49 of Silene and three related species) were classified in three groups: smooth, rugose and echinate, revealing remarkable differences between these groups. This methodology has been applied here to 51 new species, making a total of 100 species of Silene analyzed so far. According to our data, a new group was described, termed papillose. The results showed morphological differences between the four mentioned seed groups, with reduced values of circularity for dorsal and lateral seed views in the papillose and echinate groups and reduced values of solidity in the papillose seeds. The method was applied to the analysis of individual as well as to average seed silhouettes and some of the differences between groups were maintained in both cases.

El objetivo de estudio fue analizar el efecto de la edad relativa (RAE) en todas las categorías formativas de un club de fútbol profesional, e identificar si este afecta al tiempo de participación de los jugadores en competición y a sus posibilidades de debutar en el fútbol profesional. Se analizó la distribución de las fechas de nacimiento de 334 futbolistas de élite del Real Club Deportivo de la Coruña: 195 jugadores en edades de formación (GCI) divididos en 11 subgrupos correspondientes a sus categorías de edad (U9-U23), 110 jugadores profesionales (GPE) y 29 jugadores que debutaron en partido oficial con el primer equipo del club desde de las categorías inferiores (GE). Se calculó la suma de todos los minutos disputados por un futbolista en competición oficial durante una temporada. Los resultados del test ji-cuadrado demostraron la existencia de RAE en los 3 grupos de jugadores analizados y en todos los subgrupos de edad de los jugadores del GCI. El RAE fue significativamente menor en el GPE en comparación con los grupos GCI y GE (Mann–Whitney U-test, p

Historically, little attention has been paid to the resemblance between seed silhouettes to geometric figures. Cardioid and derivatives, ellipses, heart curves, lemniscates, lenses, lunes, ovals, superellipses, waterdrops, and other figures can be used to describe seed shape, as well as models for quantification. Algebraic expressions representing the average silhouettes for a group of seeds are available, and their shape can be described and quantified by comparison with geometric models. Bidimensional closed-plane figures resulting from the representation of Fourier equations can be used as models for shape analysis. Elliptic Fourier Transform equations reproduce the seed silhouettes for any closed-plane curve corresponding to the contour of the image of a seed. We review the geometric properties of the silhouettes from seed images and discuss them in the context of seed development, plant taxonomy, and environmental adaptation. Silene is proposed as a model for the study of seed morphology. Three groups have been recently defined among Silene species based on the structure of their seed silhouettes, and their geometric properties are discussed. Using models based on Fourier Transform equations is useful in Silene species where the seeds are homogenous in shape but don’t adjust to described figures.

Multiple sclerosis (MS) is an inflammatory disease of the central nervous system (CNS) known for the manifestation of demyelinated lesions throughout the CNS, leading to neurodegeneration. To date, not all pathological mechanisms that drive disease progression are known, but the clinical benefits of anti-CD20 therapies have put B cells in the spotlight of MS research. Besides their pathological effects in the periphery in MS, B cells gain access to the CNS where they can contribute to disease pathogenesis. Specifically, B cells accumulate in perivascular infiltrates in the brain parenchyma and the subarachnoid spaces of the meninges, but are virtually absent from the choroid plexus. Hence, the possible migration of B cells over the blood–brain-, blood–meningeal-, and blood–cerebrospinal fluid (CSF) barriers appears to be a crucial step to understanding B cell-mediated pathology. To gain more insight into the molecular mechanisms that regulate B cell trafficking into the brain, we here provide a comprehensive overview of the different CNS barriers in health and in MS and how they translate into different routes for B cell migration. In addition, we review the mechanisms of action of diverse therapies that deplete peripheral B cells and/or block B cell migration into the CNS. Importantly, this review shows that studying the different routes of how B cells enter the inflamed CNS should be the next step to understanding this disease.

Alzheimer’s disease (AD) is the leading cause of dementia worldwide giving rise to devastating forms of cognitive decline, which impacts patients’ lives and that of their proxies. Pathologically, AD is characterized by extracellular amyloid deposition, neurofibrillary tangles and chronic neuroinflammation. To date, there is no cure that prevents progression of AD. In this review, we elaborate on how bioactive lipids, including sphingolipids (SL) and specialized pro-resolving lipid mediators (SPM), affect ongoing neuroinflammatory processes during AD and how we may exploit them for the development of new biomarker panels and/or therapies. In particular, we here describe how SPM and SL metabolism, ranging from ω-3/6 polyunsaturated fatty acids and their metabolites to ceramides and sphingosine-1-phosphate, initiates pro- and anti-inflammatory signaling cascades in the central nervous system (CNS) and what changes occur therein during AD pathology. Finally, we discuss novel therapeutic approaches to resolve chronic neuroinflammation in AD by modulating the SPM and SL pathways.

The description of shape in Silene seeds is based on adjectives coined by naturalists in the 19th century. The expressions reniform, dorso plana, and dorso canaliculata were applied in reference to lateral or dorsal views of seeds, but the characters described can be submitted now to an analytical description by quantitative methods, allowing shape quantification and the comparison between species or populations. A quantitative morphological analysis is based on the comparison with geometric models that adjust to the shape of seeds. Morphological analysis of the dorsal view of Silene seeds based on geometric models is applied here to 26 seed populations belonging to 12 species. According to their dorsal views, the seeds are classified as convex and non-convex. New geometric models are presented for both types, including figures such as super-ellipses and modified ellipses. The values of J index (percent of similarity of a seed image with the model) are obtained in representative seed samples from diverse populations and species. The quantitative description of seed shape based on the comparison with geometric models allows the study of variation in shape between species and in populations, as well as the identification of seeds in Silene species. The method is of application to other plant species.

Abstract Background S. latifolia is a model organism for the study of sex chromosome evolution in plants. Its sex chromosomes include large regions in which recombination became gradually suppressed. The regions tend to expand over time resulting in the formation of evolutionary strata. Non-recombination and later accumulation of repetitive sequences is a putative cause of the size increase in the Y chromosome. Gene decay and accumulation of repetitive DNA are identified as key evolutionary events. Transposons in the X and Y chromosomes are distributed differently and there is a regulation of transposon insertion by DNA methylation of the target sequences, this points to an important role of DNA methylation during sex chromosome evolution in Silene latifolia. The aim of this study was to elucidate whether the reduced expression of the Y allele in S. latifolia is caused by genetic degeneration or if the cause is methylation triggered by transposons and repetitive sequences. Results Gene expression analysis in S. latifolia males has shown expression bias in both X and Y alleles. To determine whether these differences are caused by genetic degeneration or methylation spread by transposons and repetitive sequences, we selected several sex-linked genes with varying degrees of degeneration and from different evolutionary strata. Immunoprecipitation of methylated DNA (MeDIP) from promoter, exon and intron regions was used and validated through bisulfite sequencing. We found DNA methylation in males, and only in the promoter of genes of stratum I (older). The Y alleles in genes of stratum I were methylation enriched compared to X alleles. There was also abundant and high percentage methylation in the CHH context in most sequences, indicating de novo methylation through the RdDM pathway. Conclusions We speculate that TE accumulation and not gene decay is the cause of DNA methylation in the S. latifolia Y sex chromosome with influence on the process of heterochromatinization.