RNA-Seq expression profile of genes related to neurodegenerative disorders affecting the human retina

Human neurodegenerative diseases, such as Parkinson’s disease (PD) and the neuromuscular disorders called dystroglycanopathies (DGPs), cause retinal impairments. We have used RNA-Seq technology to catalog all known genes linked to PD and DGPs expressed in the human retina and quantitate their mRNA levels in terms of FPKM. We have also characterized their expression profiles in the retina by determining their exonic, intronic and exon-intron junction expression levels, as well as the alternative splicing pattern of particular genes. We believe these data could pave the way toward understanding the molecular bases of sight deficiencies associated with neurodegenerative disorders.

Alterations in energy metabolism, neuroprotection and visual signal transduction in the retina of parkinsonian, MPTP-treated monkeys

Parkinson disease is mainly characterized by the degeneration of dopaminergic neurons in the central nervous system, including the retina. Different interrelated molecular mechanisms underlying Parkinson disease-associated neuronal death have been put forward in the brain, including oxidative stress and mitochondrial dysfunction. Systemic injection of the proneurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) to monkeys elicits the appearance of a parkinsonian syndrome, including morphological and functional impairments in the retina. However, the intracellular events leading to derangement of dopaminergic and other retinal neurons in MPTP-treated animal models have not been so far investigated. Here we have used a comparative proteomics approach to identify proteins differentially expressed in the retina of MPTP-treated monkeys. Proteins were solubilized from the neural retinas of control and MPTP-treated animals, labelled separately with two different cyanine fluorophores and run pairwise on 2D DIGE gels. Out of >700 protein spots resolved and quantified, 36 were found to exhibit statistically significant differences in their expression levels, of at least ±1.4-fold, in the parkinsonian monkey retina compared with controls. Most of these spots were excised from preparative 2D gels, trypsinized and subjected to MALDI-TOF MS and LC-MS/MS analyses. Data obtained were used for protein sequence database interrogation, and 15 different proteins were successfully identified, of which 13 were underexpressed and 2 overexpressed. These proteins were involved in key cellular functional pathways such as glycolysis and mitochondrial electron transport, neuronal protection against stress and survival, and phototransduction processes. These functional categories underscore that alterations in energy metabolism, neuroprotective mechanisms and signal transduction are involved in MPTPinduced neuronal degeneration in the retina, in similarity to mechanisms thought to underlie neuronal death in the Parkinson’s diseased brain and neurodegenerative diseases of the retina proper.

Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia

Pochonia chlamydosporia is a worldwide-distributed soil fungus with a great capacity to infect and destroy the eggs and kill females of plant-parasitic nematodes. Additionally, it has the ability to colonize endophytically roots of economically-important crop plants, thereby promoting their growth and eliciting plant defenses. This multitrophic behavior makes P. chlamydosporia a potentially useful tool for sustainable agriculture approaches. We sequenced and assembled ∼41 Mb of P. chlamydosporia genomic DNA and predicted 12,122 gene models, of which many were homologous to genes of fungal pathogens of invertebrates and fungal plant pathogens. Predicted genes (65%) were functionally annotated according to Gene Ontology, and 16% of them found to share homology with genes in the Pathogen Host Interactions (PHI) database. The genome of this fungus is highly enriched in genes encoding hydrolytic enzymes, such as proteases, glycoside hydrolases and carbohydrate esterases. We used RNA-Seq technology in order to identify the genes expressed during endophytic behavior of P. chlamydosporia when colonizing barley roots. Functional annotation of these genes showed that hydrolytic enzymes and transporters are expressed during endophytism. This structural and functional analysis of the P. chlamydosporia genome provides a starting point for understanding the molecular mechanisms involved in the multitrophic lifestyle of this fungus. The genomic information provided here should also prove useful for enhancing the capabilities of this fungus as a biocontrol agent of plant-parasitic nematodes and as a plant growth-promoting organism.

Cómo acceder a las BDd suscritas por la Universidad de Alicante, desde fuera del Campus: SCOPUS

El fichero es un autoejecutable realizado con la aplicación PowerPoint2010

Cómo acceder a las BDd suscritas por la Universidad de Alicante, desde fuera del Campus: FSTA

El fichero es un autoejecutable realizado con la aplicación PowerPoint2010

Platelet-activating factor downregulates the expression of liver X receptor-α and its target genes in human neutrophils

Liver X receptors (LXRs) are ligand-activated members of the nuclear receptor superfamily that regulate the expression of genes involved in lipid metabolism and inflammation, although their role in inflammation and immunity is less well known. It has been reported that oxysterols/LXRs may act as anti-inflammatory molecules, although opposite actions have also been reported. In this study, we investigated the effect of platelet-activating factor (PAF), a proinflammatory molecule, on LXRα signalling in human neutrophils. We found that PAF exerted an inhibitory effect on mRNA expression of TO901317-induced LXRα, ATP-binding cassette transporter A1, ATP-binding cassette transporter G1, and sterol response element binding protein 1c. This negative action was mediated by the PAF receptor, and was dependent on the release of reactive oxygen species elicited by PAF, as it was enhanced by pro-oxidant treatment and reversed by antioxidants. Current data also support the idea that PAF induces phosphorylation of the LXRα molecule in an extracellular signal-regulated kinase 1/2-mediated fashion. These results suggest that a possible mechanism by which PAF exerts its proinflammatory effect is through the downregulation of LXRα and its related genes, which supports the notion that LXRα ligands exert a modulatory role in the neutrophil-mediated inflammatory response.

Uso de material audiovisual como apoyo en las clases teóricas

La disponibilidad de nuevas herramientas multimedia favorece la generación de material docente auxiliar para la enseñanza de las diversas materias y puede suponer un aliciente añadido para el estudiante. Así, además de fomentar su interés por la materia, se puede potenciar su aprendizaje autónomo. Con el objetivo de evaluar las ventajas de la visualización de vídeos como apoyo a las explicaciones teóricas se planteó la siguiente experiencia: con alumnos de la asignatura "Farmacología", del Grado en Óptica y Optometría, se analizó y comparó la comprensión de la materia con y sin la visualización de vídeos como material de apoyo. El análisis mediante cuestionarios mostró que la visualización ayudó a fijar los conocimientos previamente adquiridos. El 79% de los estudiantes consideró que los vídeos les ayudaron a conseguir una mejor comprensión de la materia. El 95% de los alumnos consideró más útil escuchar primero la explicación del docente. El profesorado implicado manifiesta la dificultad de la selección de material óptimo debido su escasez, por lo que resulta conveniente la elaboración de material específico. Podemos concluir que el material audiovisual supone una buena herramienta complementaria para las clases teóricas, si bien debe integrarse de forma adecuada en el desarrollo de la clase.

Oleic acid modulates mRNA expression of liver X receptor (LXR) and its target genes ABCA1 and SREBP1c in human neutrophils

Purpose: Regulation of liver X receptors (LXRs) is essential for cholesterol homeostasis and inflammation. The present study was conducted to determine whether oleic acid (OA) could regulate mRNA expression of LXRα and LXRα-regulated genes and to assess the potential promotion of oxidative stress by OA in neutrophils. Methods: Human neutrophils were treated with OA at different doses and LXR target gene expression, oxidative stress production, lipid efflux and inflammation state were analyzed. Results: We describe that mRNA synthesis of both LXRα and ABCA1 (a reverse cholesterol transporter) was induced by OA in human neutrophils. This fatty acid enhanced the effects of LXR ligands on ABCA1 and LXR expression, but it decreased the mRNA levels of sterol regulatory element-binding protein 1c (a transcription factor that regulates the synthesis of triglycerides). Although OA elicited a slight oxidative stress in the short term (15–30 min) in neutrophils, it is unlikely that this is relevant for the modulation of transcription in our experimental conditions, which involve longer incubation time (i.e., 6 h). Of physiological importance is our finding that OA depresses intracellular lipid levels and that markers of inflammation, such as ERK1/2 and p38 mitogen-activated protein kinase phosphorylation, were decreased by OA treatment. In addition, 200 μM OA reduced the migration of human neutrophils, another marker of the inflammatory state. However, OA did not affect lipid peroxidation induced by pro-oxidant agents. Conclusions: This work presents for the first time evidence that human neutrophils are highly sensitive to OA and provides novel data in support of a protective role of this monounsaturated acid against the activation of neutrophils during inflammation.

Cellular responses following retinal injuries and therapeutic approaches for neurodegenerative diseases

Retinal neurodegenerative diseases like age-related macular degeneration, glaucoma, diabetic retinopathy and retinitis pigmentosa each have a different etiology and pathogenesis. However, at the cellular and molecular level, the response to retinal injury is similar in all of them, and results in morphological and functional impairment of retinal cells. This retinal degeneration may be triggered by gene defects, increased intraocular pressure, high levels of blood glucose, other types of stress or aging, but they all frequently induce a set of cell signals that lead to well-established and similar morphological and functional changes, including controlled cell death and retinal remodeling. Interestingly, an inflammatory response, oxidative stress and activation of apoptotic pathways are common features in all these diseases. Furthermore, it is important to note the relevant role of glial cells, including astrocytes, Müller cells and microglia, because their response to injury is decisive for maintaining the health of the retina or its degeneration. Several therapeutic approaches have been developed to preserve retinal function or restore eyesight in pathological conditions. In this context, neuroprotective compounds, gene therapy, cell transplantation or artificial devices should be applied at the appropriate stage of retinal degeneration to obtain successful results. This review provides an overview of the common and distinctive features of retinal neurodegenerative diseases, including the molecular, anatomical and functional changes caused by the cellular response to damage, in order to establish appropriate treatments for these pathologies.

Terapia génica de la enfermedad de Stargardt

El gen humano ABCA4 (=ABCR) se caracterizó en 1997 como el principal causante de la enfermedad de Stargardt, una distrofia macular hereditaria generalmente autosómica recesiva. Poco tiempo después se encontraron otras enfermedades asociadas a mutaciones en este gen, como son distrofia de conos y bastones, determinados casos de retinosis pigmentaria y un aumento de la susceptibilidad a la degeneración macular asociada a la edad. No existen tratamientos curativos para ninguna de estas distrofias. No obstante, dado que están causadas por un solo gen, cuya función es bien conocida, su curación se hace abordable mediante estrategias de terapia génica. En este artículo se resume el estado actual de las opciones de tratamientos basados en terapia génica de las enfermedades asociadas al gen ABCA4, las cuales implican el desarrollo de nuevos vectores derivados de virus adeno-asociados (AAV), lentivirus, y nanopartículas de ADN compactadas. Aunque este gen ha demostrado ser una diana de investigación difícil, los notables progresos realizados en los estudios genéticos, funcionales y traslacionales han permitido importantes avances en las aplicaciones terapéuticas de estas patologías, las cuales se espera que estén disponibles para los afectados en un futuro próximo. Resulta esperanzador, en este sentido, que ya están en marcha dos ensayos clínicos en fase I/II para tratar pacientes con la enfermedad de Stargardt.

Whole-exome sequencing reveals ZNF408 as a new gene associated with autosomal recessive retinitis pigmentosa with vitreal alterations

Retinitis pigmentosa (RP) is a group of progressive inherited retinal dystrophies that cause visual impairment as a result of photoreceptor cell death. RP is heterogeneous, both clinically and genetically making difficult to establish precise genotype–phenotype correlations. In a Spanish family with autosomal recessive RP (arRP), homozygosity mapping and whole-exome sequencing led to the identification of a homozygous mutation (c.358_359delGT; p.Ala122Leufs*2) in the ZNF408 gene. A screening performed in 217 additional unrelated families revealed another homozygous mutation (c.1621C>T; p.Arg541Cys) in an isolated RP case. ZNF408 encodes a transcription factor that harbors 10 predicted C2H2-type fingers thought to be implicated in DNA binding. To elucidate the ZNF408 role in the retina and the pathogenesis of these mutations we have performed different functional studies. By immunohistochemical analysis in healthy human retina, we identified that ZNF408 is expressed in both cone and rod photoreceptors, in a specific type of amacrine and ganglion cells, and in retinal blood vessels. ZNF408 revealed a cytoplasmic localization and a nuclear distribution in areas corresponding with the euchromatin fraction. Immunolocalization studies showed a partial mislocalization of the p.Arg541Cys mutant protein retaining part of the WT protein in the cytoplasm. Our study demonstrates that ZNF408, previously associated with Familial Exudative Vitreoretinopathy (FEVR), is a new gene causing arRP with vitreous condensations supporting the evidence that this protein plays additional functions into the human retina.

Ensayo de evaluación a distancia frente a evaluación presencial

El sistema de evaluación debe valorar las competencias adquiridas por el estudiante según los conocimientos, habilidades y aptitudes que ha desarrollado a lo largo del proceso de enseñanza-aprendizaje. Este proceso debe ser válido, además de confiable y práctico. Es necesario estudiar los diversos métodos de evaluación disponibles y su idoneidad para las distintas actividades de los grados. El hecho de disponer de herramientas que permiten realizar una evaluación a distancia nos hizo plantearnos la idoneidad de este sistema. Así pues, con el objeto de evaluar la fiabilidad de la evaluación a distancia, se realizó una experiencia en la que se compararon las calificaciones obtenidas en actividades prácticas y seminarios, empleando ambas modalidades de evaluación: presencial y a distancia, mediante las herramientas del campus virtual. Como pudimos comprobar, no hubo diferencias significativas según la modalidad de evaluación, por lo que, con los datos de los que disponemos, podemos aceptar ambos sistemas como igualmente efectivos. Estudiamos también el efecto de la realización de una prueba previa de autoevaluación. En este caso sí encontramos como consecuencia un ligero incremento en la nota, por lo que recomendamos esta actividad para la mejora del rendimiento académico.

Material docente electrónico como complemento a los recursos del aula

En el escenario actual, la disponibilidad de nuevas herramientas multimedia favorece la generación de materiales docentes con características diferenciales respecto a los tradicionalmente dispuestos. Las nuevas tecnologías y las redes sociales permiten la difusión de los contenidos, siendo mayor la aceptación por parte del alumnado cuanto más atractiva sea su presentación. Este fenómeno, bien diseñado y planteado puede resultar una herramienta útil como recurso de enseñanza-aprendizaje. El diseño de material docente que utilice estos recursos multimedia puede suponer, si se utiliza bien, un aliciente añadido para el alumno, de forma que, además de fomentar su interés por la materia, se puede potenciar su aprendizaje. En este contexto resulta de especial interés el diseño de herramientas a utilizar como material en formato de audio, vídeo u otros recursos electrónicos que estimulen el trabajo autónomo del estudiante. Pese a la buena planificación y diseño, la disponibilidad y/o elaboración de material docente de buena calidad, especialmente en el mundo audiovisual e interactivo en el que nos encontramos, supone una barrera a solventar.

The activating role of phospho-(Tyr)-calmodulin on the epidermal growth factor receptor

The activity of calmodulin (CaM) is modulated not only by oscillations in the cytosolic concentration of free Ca2+, but also by its phosphorylation status. In the present study, the role of tyrosine-phosphorylated CaM [P-(Tyr)-CaM] on the regulation of the epidermal growth factor receptor (EGFR) has been examined using in vitro assay systems. We show that phosphorylation of CaM by rat liver solubilized EGFR leads to a dramatic increase in the subsequent phosphorylation of poly-L-(Glu:Tyr) (PGT) by the receptor in the presence of ligand, both in the absence and in the presence of Ca2+. This occurred in contrast with assays where P-(Tyr)-CaM accumulation was prevented by the presence of Ca2+, absence of a basic cofactor required for CaM phosphorylation and/or absence of CaM itself. Moreover, an antibody against CaM, which inhibits its phosphorylation, prevented the extra ligand-dependent EGFR activation. Addition of purified P-(Tyr)-CaM, phosphorylated by recombinant c-Src (cellular sarcoma kinase) and free of non-phosphorylated CaM, obtained by affinity-chromatography using an immobilized anti-phospho-(Tyr)-antibody, also increased the ligand-dependent tyrosine kinase activity of the isolated EGFR toward PGT. Also a CaM(Y99D/Y138D) mutant mimicked the effect of P-(Tyr)-CaM on ligand-dependent EGFR activation. Finally, we demonstrate that P-(Tyr)-CaM binds to the same site (645R-R-R-H-I-V-R-K-R-T-L-R-R-L-L-Q660) as non-phosphorylated CaM, located at the cytosolic juxtamembrane region of the EGFR. These results show that P-(Tyr)-CaM is an activator of the EGFR and suggest that it could contribute to the CaM-mediated ligand-dependent activation of the receptor that we previously reported in living cells.

Endophytic colonization of barley (Hordeum vulgare) roots by the nematophagous fungus Pochonia chlamydosporia reveals plant growth promotion and a general defense and stress transcriptomic response

Plant crop yields are negatively conditioned by a large set of biotic and abiotic factors. An alternative to mitigate these adverse effects is the use of fungal biological control agents and endophytes. The egg-parasitic fungus Pochonia chlamydosporia has been traditionally studied because of its potential as a biological control agent of plant-parasitic nematodes. This fungus can also act as an endophyte in monocot and dicot plants, and has been shown to promote plant growth in different agronomic crops. An Affymetrix 22K Barley GeneChip was used in this work to analyze the barley root transcriptomic response to P. chlamydosporia root colonization. Functional gene ontology (GO) and gene set enrichment analyses showed that genes involved in stress response were enriched in the barley transcriptome under endophytism. An 87.5 % of the probesets identified within the abiotic stress response group encoded heat shock proteins. Additionally, we found in our transcriptomic analysis an up-regulation of genes implicated in the biosynthesis of plant hormones, such as auxin, ethylene and jasmonic acid. Along with these, we detected induction of brassinosteroid insensitive 1-associated receptor kinase 1 (BR1) and other genes related to effector-triggered immunity (ETI) and pattern-triggered immunity (PTI). Our study supports at the molecular level the growth-promoting effect observed in plants endophytically colonized by P. chlamydosporia, which opens the door to further studies addressing the capacity of this fungus to mitigate the negative effects of biotic and abiotic factors on plant crops.