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Valledor L.,University of Oviedo | Valledor L.,University of Aveiro | Pascual J.,University of Oviedo | Meijon M.,Regional Institute for Research and Agro Food Development SERIDA | And 2 more authors.
PLoS ONE | Year: 2015

Needle maturation is a complex process that involves cell growth, differentiation and tissue remodelling towards the acquisition of full physiological competence. Leaf induction mechanisms are well known; however, those underlying the acquisition of physiological competence are still poorly understood, especially in conifers. We studied the specific epigenetic regulation of genes defining organ function (PrRBCS and PrRBCA) and competence and stress response (PrCSDP2 and PrSHMT4) during three stages of needle development and one de-differentiated control. Gene-specific changes in DNA methylation and histone were analysed by bisulfite sequencing and chromatin immunoprecipitation (ChIP). The expression of PrRBCA and PrRBCS increased during needle maturation and was associated with the progressive loss of H3K9me3, H3K27me3 and the increase in AcH4. The maturation-related silencing of PrSHMT4 was correlated with increased H3K9me3 levels, and the repression of PrCSDP2, to the interplay between AcH4, H3K27me3, H3K9me3 and specific DNA methylation. The employ of HAT and HDAC inhibitors led to a further determination of the role of histone acetylation in the regulation of our target genes. The integration of these results with high-throughput analyses in Arabidopsis thaliana and Populus trichocarpa suggests that the specific epigenetic mechanisms that regulate photosynthetic genes are conserved between the analysed species. © 2015 Valledor et al.

Meijon M.,Gregor Mendel Institute of Molecular Plant Biology | Meijon M.,Regional Institute for Research and Agro Food Development SERIDA | Satbhai S.B.,Gregor Mendel Institute of Molecular Plant Biology | Tsuchimatsu T.,Gregor Mendel Institute of Molecular Plant Biology | Busch W.,Gregor Mendel Institute of Molecular Plant Biology
Nature Genetics | Year: 2014

With the increased availability of high-resolution sequence information, genome-wide association (GWA) studies have become feasible in a number of species. The vast majority of these studies are conducted in human populations, where it is difficult to provide strong evidence for the functional involvement of unknown genes that are identified using GWA. Here we used the model organism Arabidopsis thaliana to combine high-throughput confocal microscopy imaging of traits at the cellular level, GWA and expression analyses to identify genomic regions that are associated with developmental cell-type traits. We identify and characterize a new F-box gene, KUK, that regulates meristem and cell length. We further show that polymorphisms in the coding sequence are the major causes of KUK allele-dependent natural variation in root development. This work demonstrates the feasibility of GWA using cellular traits to identify causal genes for basic biological processes such as development. © 2014 Nature America, Inc.

Valledor L.,University of Aveiro | Valledor L.,Academy of Sciences of the Czech Republic | Escandon M.,University of Oviedo | Meijon M.,Regional Institute for Research and Agro Food Development SERIDA | And 3 more authors.
Plant Journal | Year: 2014

Here, we describe a method for the combined metabolomic, proteomic, transcriptomic and genomic analysis from one single sample as a major step for multilevel data integration strategies in systems biology. While extracting proteins and DNA, this protocol also allows the separation of metabolites into polar and lipid fractions, as well as RNA fractionation into long and small RNAs, thus allowing a broad range of transcriptional studies. The isolated biomolecules are suitable for analysis with different methods that range from electrophoresis and blotting to state-of-the-art procedures based on mass spectrometry (accurate metabolite profiling, shot-gun proteomics) or massive sequencing technologies (transcript analysis). The low amount of starting tissue, its cost-efficiency compared with the utilization of commercial kits, and its performance over a wide range of plant, microbial, and algal species such as Chlamydomonas, Arabidopsis, Populus, or Pinus, makes this method a universal alternative for multiple molecular isolation from plant tissues. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

Fernandez Pierna J.A.,Walloon Agricultural Research Center | Boix Sanfeliu A.,Institute for Reference Materials and Measurements | Slowikowski B.,Institute for Reference Materials and Measurements | van Hoist C.,Institute for Reference Materials and Measurements | And 8 more authors.
Biotechnology, Agronomy and Society and Environment | Year: 2013

The near-infrared microscope (NIRM) is an instrument that has demonstrated its great ability to detect contaminants not by analyzing a single spectrum but rather by analyzing hundreds or thousands of spectra from individual particles, while at the same time being a non-destructive and easy-to-use technique. It has been used for the detection of meat-and-bone meal (MBM) in compound feeds within the context of the European bovine spongiform encephalopathy (BSE; commonly known as "mad cow disease") crisis. This study describes, for the first time, an application of NIRM instrument standardization using a measurement cell in an inter-laboratory study conducted within the framework of a qualitative determination of animal proteins in compound feeds, based on spectra obtained with eight instruments. The standardization cell was assessed for its ability to produce good optical matching of the instruments and/or to evaluate instrument performance.

Soldado A.,Regional Institute for Research and Agro Food Development SERIDA | Quevedo J.R.,University of Oviedo | Bahamonde A.,University of Oviedo | Modrono S.,Regional Institute for Research and Agro Food Development SERIDA | And 6 more authors.
Spanish Journal of Agricultural Research | Year: 2011

For developing qualitative or quantitative applications with spectroscopic data, such as near infrared spectroscopy (NIRS), different methodologies have been proposed in the mathematical statistical and computer science literature. Useful chemometrical alternatives have emerged, such as support vector machines (SVM), widely used for modeling multivariate and non-linear systems. These methods are usually compared using the classification performance and the success of results. The aim of the present work was to develop and validate a robust, accurate and fast discriminant methodology based on NIRS data to detect presence of animal meals in feedstuffs. A linear method, modified partial least square (PLS) analysis and one non-linear method (SVM) were studied. Results showed that modified PLS model allows obtaining coefficients of determination for cross validation around 0.97. Applying SVM strategy no false negatives were detected during training step. With both strategies the lowest percentage of misclassified samples on external validation was achieved with SVM, 0% with certified standard samples containing from 0.05% to 4% of animal meals. These results show SVM strategy as a robust method of classification for detecting animal meals in feedstuffs using NIRS methodology.

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