Rootstock modify the productive response of ‘Verna’ lemon under regulated deficit irrigation

[SPA] El objetivo principal de este trabajo fue evaluar la respuesta agronómica del limonero ‘Verna’ injertado sobre dos patrones con diferente vigor en condiciones de riego deficitario controlado (RDC). El ensayo se llevó a cabo durante tres años en una parcela experimental del IMIDA en árboles de 8 años de la variedad de limonero ‘Verna’ injertados sobre Citrus macrophylla Wester (CM) y naranjo amargo (Citrus aurantium L.) (SO). Se aplicaron dos tratamientos de riego, un tratamiento control (100 % ETc) y un tratamiento de RDC, regado al 100% ETc durante todo el año menos durante dos fases de desarrollo del fruto, F-I (fase I) y F-III (fase III), en las que la dosis de riego se redujo al 25% ETc. En condiciones óptimas de riego, los árboles injertados sobre CM mostraron un mejor estado hídrico, un mayor crecimiento vegetativo y fueron más productivos. Sin embargo, el portainjerto menos vigoroso (SO) presentó un mejor comportamiento en condiciones de RDC, manteniendo la producción y el crecimiento vegetativo similares al tratamiento Control además de aumentar la productividad del agua, por lo que podría ser recomendado cuando la disponibilidad de agua no esté asegurada. [ENG] The aim of this study was to evaluate the agronomic response of ‘Verna’ lemon trees grafted on two different vigour rootstocks on regulated deficit irrigation (RDC) conditions. The experiment was carried out during 3 consecutive years in the IMIDA experimental orchard, using 8-years-old trees of the variety ‘Verna’ lemon, grafted on Citrus macrophylla Wester (CM) and on sour orange (Citrus aurantium L.) (SO). There were two irrigation treatments: Control (100% ETc) and a RDC treatment, where trees were full irrigated (100% ETc) along the season unless in two fruit growth periods, F-I (phase I) and F-III (phase III) that irrigation was 25% ETc. The ‘Verna’ lemon trees grafted on CM showed better plant water status, greater vegetative growth and were more productive on full irrigation conditions. However, the less vigorous rootstock SO showed a better performance under RDC conditions, increasing water productivity and maintaining production and vegetative growth similar to Control treatment, so that SO could be recommended when water availability is not assured.Los autores agradecen a M.I. García-Oller, J.M. Frutos, J.L. Lozano, E.M. Arques y V. Quinto por su ayuda tanto en el campo como en el laboratorio. Este trabajo fue financiado parcialmente por el proyecto POI07-12 y el contrato post-doctoral FIT a través de fondos FEDER-80%, con la colaboración del proyecto INIA RTA2012-00102-00-00

Comparison of potential irrigation strategies to confront water restriction period of yield and fruit quality in lemon tree

[SPA] El presente estudio comparó la respuesta agronómica de dos estrategias de riego (riego salino controlado (RSC) y riego deficitario controlado (RDC)) durante dos campañas. Se utilizaron árboles de limonero ‘Fino 49’ (Citrus limon (L.) (Burm. fil.) de 15 años injertados sobre Citrus macrophylla Wester. Se aplicaron tres tratamientos de riego: Control (100% ETc, de agua no salina); RDC (25% ETc, de agua no salina) y el RSC (145% ETc, agua salina 40 mM NaCl). Los tratamientos RDC y RSC se mantuvieron durante todo el ciclo de cultivo, excepto durante el período de alta evapotranspiración (ETo) (fase II de crecimiento del fruto) aplicando el 100% ETc con agua no salina. El tratamiento RDC no tuvo impacto en la distribución de recursos, pero en el RSC, la acumulación de Cl- en hoja, afectó mucho más a la producción que al crecimiento vegetativo. La producción total se vio afectada de manera similar, pero la reducción fue mayor en el RSC en el segundo año. El RDC no mejoró la EUA y el RSC la redujo al aplicar una dosis de lavado. El RSC no afectó a la calidad del fruto, mientras que el RDC retrasó la maduración del fruto. [ENG] This study compared the agronomic response of two irrigation strategies (regulated saline irrigation (RSC) and regulated deficit irrigation (RDC)) for two seasons. Lemon trees 'Fino 49' (Citrus limon (L.) (Burm. fil.) of 15 years old grafted on Citrus macrophylla Wester were used. Three irrigation treatments were applied: Control (100% ETc, non-saline water); RDC (25% ETc, non-saline water) and RSC (145% ETc, saline - 40 mM NaCl). The RDC and RSC treatments were maintained throughout the growing season, except during the period of high evapotranspiration (ETo) (phase II of fruit growth) using 100% ETc with non-saline water. The RDC treatment had no impact on the resources distribution, but in RSC, the accumulation of Cl- in the leave, affected much more production than vegetative growth. The total production was affected similarly, but the reduction was greater in the RSC in the second year. The RDC did not improve the EUA and the RSC reduced it by applying a leaching fraction. The RSC does not affect the quality of the fruit, while the RDC delayed fruit ripening.Este trabajo fue parcialmente financiado por el proyecto POI07-12 y el contrato FIT a través del programa FEDER-80% y por el proyecto INIA (RTA2012-00102-00-00

Respuesta del limonero ‘Fino 49’ al riego deficitario. Efectos sobre el crecimiento, la producción y la calidad del fruto

El limonero es uno de los cultivos más representativos en la Región de Murcia. Sin embargo, la escasez de recursos hídricos provoca que sea necesario utilizar otras técnicas de cultivo, como la aplicación de estrategias de riego deficitario para intentar optimizar los recursos hídricos disponibles. El ensayo se llevó a cabo durante dos años en una parcela experimental del IMIDA en Torre Pacheco (Murcia) en árboles de 13 años de la variedad de limonero Fino 49 injertados sobre Citrus macrophylla Wester. Se aplicaron dos tratamientos de riego, un tratamiento control (100 % ETc) y un tratamiento de riego deficitario (RD) al que se le suprimió el riego en dos periodos de desarrollo del fruto, P‐I (fase I de división celular e inicio de fase II de desarrollo del fruto) y P‐II (final desarrollo del fruto hasta la cosecha) y resto del año se mantuvo como el control. Durante los dos años de ensayo, la estrategia de riego provocó, en los periodos en los que se suprimió el riego, un déficit hídrico en el cultivo, causando una reducción de la tasa de crecimiento del tronco media de un 51 %. La cosecha disminuyó un 22 % debido a un menor peso medio del fruto (22 % menos). Respecto a la calidad del fruto, el tratamiento RD presentó frutos de menor calibre pero mayor acidez total y sólidos solubles totales en el zumo. En general, la estrategia de RD provoca un retraso del momento de recolección y una reducción de la cosecha.Este trabajo ha sido financiado por CICYT (AGL2006‐11319‐C04‐04 y AGL2007‐6537‐C04‐ 04) y por la beca predoctoral FPI concedida por el Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario (IMIDA) a J.M. Robles

Frontotemporal dementia: insights into the biological underpinnings of disease through gene co-expression network analysis

BACKGROUND: In frontotemporal dementia (FTD) there is a critical lack in the understanding of biological and molecular mechanisms involved in disease pathogenesis. The heterogeneous genetic features associated with FTD suggest that multiple disease-mechanisms are likely to contribute to the development of this neurodegenerative condition. We here present a systems biology approach with the scope of i) shedding light on the biological processes potentially implicated in the pathogenesis of FTD and ii) identifying novel potential risk factors for FTD. We performed a gene co-expression network analysis of microarray expression data from 101 individuals without neurodegenerative diseases to explore regional-specific co-expression patterns in the frontal and temporal cortices for 12 genes (MAPT, GRN, CHMP2B, CTSC, HLA-DRA, TMEM106B, C9orf72, VCP, UBQLN2, OPTN, TARDBP and FUS) associated with FTD and we then carried out gene set enrichment and pathway analyses, and investigated known protein-protein interactors (PPIs) of FTD-genes products. RESULTS: Gene co-expression networks revealed that several FTD-genes (such as MAPT and GRN, CTSC and HLA-DRA, TMEM106B, and C9orf72, VCP, UBQLN2 and OPTN) were clustering in modules of relevance in the frontal and temporal cortices. Functional annotation and pathway analyses of such modules indicated enrichment for: i) DNA metabolism, i.e. transcription regulation, DNA protection and chromatin remodelling (MAPT and GRN modules); ii) immune and lysosomal processes (CTSC and HLA-DRA modules), and; iii) protein meta/catabolism (C9orf72, VCP, UBQLN2 and OPTN, and TMEM106B modules). PPI analysis supported the results of the functional annotation and pathway analyses. CONCLUSIONS: This work further characterizes known FTD-genes and elaborates on their biological relevance to disease: not only do we indicate likely impacted regional-specific biological processes driven by FTD-genes containing modules, but also do we suggest novel potential risk factors among the FTD-genes interactors as targets for further mechanistic characterization in hypothesis driven cell biology work

An additional k-means clustering step improves the biological features of WGCNA gene co-expression networks

Background: Weighted Gene Co-expression Network Analysis (WGCNA) is a widely used R software package for the generation of gene co-expression networks (GCN). WGCNA generates both a GCN and a derived partitioning of clusters of genes (modules). We propose k-means clustering as an additional processing step to conventional WGCNA, which we have implemented in the R package km2gcn (k-means to gene co-expression network, https://github.com/juanbot/km2gcn). Results: We assessed our method on networks created from UKBEC data (10 different human brain tissues), on networks created from GTEx data (42 human tissues, including 13 brain tissues), and on simulated networks derived from GTEx data. We observed substantially improved module properties, including: (1) few or zero misplaced genes; (2) increased counts of replicable clusters in alternate tissues (x3.1 on average); (3) improved enrichment of Gene Ontology terms (seen in 48/52 GCNs) (4) improved cell type enrichment signals (seen in 21/23 brain GCNs); and (5) more accurate partitions in simulated data according to a range of similarity indices. Conclusions: The results obtained from our investigations indicate that our k-means method, applied as an adjunct to standard WGCNA, results in better network partitions. These improved partitions enable more fruitful downstream analyses, as gene modules are more biologically meaningful

Gene co-expression networks shed light into diseases of brain iron accumulation

Aberrant brain iron deposition is observed in both common and rare neurodegenerative disorders, including those categorized as Neurodegeneration with Brain Iron Accumulation (NBIA), which are characterized by focal iron accumulation in the basal ganglia. Two NBIA genes are directly involved in iron metabolism, but whether other NBIA-related genes also regulate iron homeostasis in the human brain, and whether aberrant iron deposition contributes to neurodegenerative processes remains largely unknown. This study aims to expand our understanding of these iron overload diseases and identify relationships between known NBIA genes and their main interacting partners by using a systems biology approach. We used whole-transcriptome gene expression data from human brain samples originating from 101 neuropathologically normal individuals (10 brain regions) to generate weighted gene co-expression networks and cluster the 10 known NBIA genes in an unsupervised manner. We investigated NBIA-enriched networks for relevant cell types and pathways, and whether they are disrupted by iron loading in NBIA diseased tissue and in an in vivo mouse model. We identified two basal ganglia gene co-expression modules significantly enriched for NBIA genes, which resemble neuronal and oligodendrocytic signatures. These NBIA gene networks are enriched for iron-related genes, and implicate synapse and lipid metabolism related pathways. Our data also indicates that these networks are disrupted by excessive brain iron loading. We identified multiple cell types in the origin of NBIA disorders. We also found unforeseen links between NBIA networks and iron-related processes, and demonstrate convergent pathways connecting NBIAs and phenotypically overlapping diseases. Our results are of further relevance for these diseases by providing candidates for new causative genes and possible points for therapeutic intervention

Ideales igualitarios y planes tradicionales: análisis de parejas primerizas en España

Esta investigación analiza los planes de cuidado del primer hijo en parejas, indagando en cómo influyen los ideales de maternidad/ paternidad, las actitudes de género y las limitaciones institucionales en el proyecto de cuidado del bebé. El estudio se basa en una muestra de 68 parejas de doble ingreso que esperaban su primer hijo en el año 2011. El análisis revela que gran parte de las parejas aspira a que ambos cónyuges continúen trabajando después del parto. Sin embargo, en el caso de prever dificultades de conciliación, siguen siendo las mujeres quienes manifiestan una mayor predisposición a adaptar su vida laboral a las necesidades del menor, desarrollando en gran medida preferencias adaptativas

Paired plasma lipidomics and proteomics analysis in the conversion from mild cognitive impairment to Alzheimer's disease.

Alzheimer's disease (AD) is a neurodegenerative condition for which there is currently no available medication that can stop its progression. Previous studies suggest that mild cognitive impairment (MCI) is a phase that precedes the disease. Therefore, a better understanding of the molecular mechanisms behind MCI conversion to AD is needed. Here, we propose a machine learning-based approach to detect the key metabolites and proteins involved in MCI progression to AD using data from the European Medical Information Framework for Alzheimer's Disease Multimodal Biomarker Discovery Study. Proteins and metabolites were evaluated separately in multiclass models (controls, MCI and AD) and together in MCI conversion models (MCI stable vs converter). Only features selected as relevant by 3/4 algorithms proposed were kept for downstream analysis. Multiclass models of metabolites highlighted nine features further validated in an independent cohort (0.726 mean balanced accuracy). Among these features, one metabolite, oleamide, was selected by all the algorithms. Further in-vitro experiments in rodents showed that disease-associated microglia excreted oleamide in vesicles. Multiclass models of proteins stood out with nine features, validated in an independent cohort (0.720 mean balanced accuracy). However, none of the proteins was selected by all the algorithms. Besides, to distinguish between MCI stable and converters, 14 key features were selected (0.872 AUC), including tTau, alpha-synuclein (SNCA), junctophilin-3 (JPH3), properdin (CFP) and peptidase inhibitor 15 (PI15) among others. This omics integration approach highlighted a set of molecules associated with MCI conversion important in neuronal and glia inflammation pathways

Regulatory sites for splicing in human basal ganglia are enriched for disease-relevant information

Genome-wide association studies have generated an increasing number of common genetic variants associated with neurological and psychiatric disease risk. An improved understanding of the genetic control of gene expression in human brain is vital considering this is the likely modus operandum for many causal variants. However, human brain sampling complexities limit the explanatory power of brain-related expression quantitative trait loci (eQTL) and allele-specific expression (ASE) signals. We address this, using paired genomic and transcriptomic data from putamen and substantia nigra from 117 human brains, interrogating regulation at different RNA processing stages and uncovering novel transcripts. We identify disease-relevant regulatory loci, find that splicing eQTLs are enriched for regulatory information of neuron-specific genes, that ASEs provide cell-specific regulatory information with evidence for cellular specificity, and that incomplete annotation of the brain transcriptome limits interpretation of risk loci for neuropsychiatric disease. This resource of regulatory data is accessible through our web server, http://braineacv2.inf.um.es/

Identification of Candidate Parkinson Disease Genes by Integrating Genome-Wide Association Study, Expression, and Epigenetic Data Sets

Importance Substantial genome-wide association study (GWAS) work in Parkinson disease (PD) has led to the discovery of an increasing number of loci shown reliably to be associated with increased risk of disease. Improved understanding of the underlying genes and mechanisms at these loci will be key to understanding the pathogenesis of PD. / Objective To investigate what genes and genomic processes underlie the risk of sporadic PD. / Design and Setting This genetic association study used the bioinformatic tools Coloc and transcriptome-wide association study (TWAS) to integrate PD case-control GWAS data published in 2017 with expression data (from Braineac, the Genotype-Tissue Expression [GTEx], and CommonMind) and methylation data (derived from UK Parkinson brain samples) to uncover putative gene expression and splicing mechanisms associated with PD GWAS signals. Candidate genes were further characterized using cell-type specificity, weighted gene coexpression networks, and weighted protein-protein interaction networks. / Main Outcomes and Measures It was hypothesized a priori that some genes underlying PD loci would alter PD risk through changes to expression, splicing, or methylation. Candidate genes are presented whose change in expression, splicing, or methylation are associated with risk of PD as well as the functional pathways and cell types in which these genes have an important role. / Results Gene-level analysis of expression revealed 5 genes (WDR6 [OMIM 606031], CD38 [OMIM 107270], GPNMB [OMIM 604368], RAB29 [OMIM 603949], and TMEM163 [OMIM 618978]) that replicated using both Coloc and TWAS analyses in both the GTEx and Braineac expression data sets. A further 6 genes (ZRANB3 [OMIM 615655], PCGF3 [OMIM 617543], NEK1 [OMIM 604588], NUPL2 [NCBI 11097], GALC [OMIM 606890], and CTSB [OMIM 116810]) showed evidence of disease-associated splicing effects. Cell-type specificity analysis revealed that gene expression was overall more prevalent in glial cell types compared with neurons. The weighted gene coexpression performed on the GTEx data set showed that NUPL2 is a key gene in 3 modules implicated in catabolic processes associated with protein ubiquitination and in the ubiquitin-dependent protein catabolic process in the nucleus accumbens, caudate, and putamen. TMEM163 and ZRANB3 were both important in modules in the frontal cortex and caudate, respectively, indicating regulation of signaling and cell communication. Protein interactor analysis and simulations using random networks demonstrated that the candidate genes interact significantly more with known mendelian PD and parkinsonism proteins than would be expected by chance. / Conclusions and Relevance Together, these results suggest that several candidate genes and pathways are associated with the findings observed in PD GWAS studies