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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.


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.


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.


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.


De La Roza-Delgado B.,Regional Institute for Research and Agro Food Development SERIDA | Modrono S.,Regional Institute for Research and Agro Food Development SERIDA | Vicente F.,Regional Institute for Research and Agro Food Development SERIDA | Martinez-Fernandez A.,Regional Institute for Research and Agro Food Development SERIDA | Soldado A.,Regional Institute for Research and Agro Food Development SERIDA
Spanish Journal of Agricultural Research | Year: 2015

A total of 220 faecal pig and poultry samples, collected from different experimental trials were employed with the aim to demonstrate the suitability of Near Infrared Reflectance Spectroscopy (NIRS) technology for estimation of gross calorific value on faeces as output products in energy balances studies. NIR spectra from dried and grounded faeces samples were analyzed using a Foss NIRSystem 6500 instrument, scanning over the wavelength range 400-2500 nm. Validation studies for quantitative analytical models were carried out to estimate the relevance of method performance associated to reference values to obtain an appropriate, accuracy and precision. The results for prediction of gross calorific value (GCV) of NIRS calibrations obtained for individual species showed high correlation coefficients comparing chemical analysis and NIRS predictions, ranged from 0.92 to 0.97 for poultry and pig. For external validation, the ratio between the standard error of cross validation (SECV) and the standard error of prediction (SEP) varied between 0.73 and 0.86 for poultry and pig respectively, indicating a sufficiently precision of calibrations. In addition a global model to estimate GCV in both species was developed and externally validated. It showed correlation coefficients of 0.99 for calibration, 0.98 for cross-validation and 0.97 for external validation. Finally, relative uncertainty was calculated for NIRS developed prediction models with the final value when applying individual NIRS species model of 1.3% and 1.5% for NIRS global prediction. This study suggests that NIRS is a suitable and accurate method for the determination of GCV in faeces, decreasing cost, timeless and for convenient handling of unpleasant samples. © 2015 INIA.


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.


Gonzalez-Arrojo A.,Regional Institute for Research and Agro Food Development SERIDA | Soldado A.,Regional Institute for Research and Agro Food Development SERIDA | Vicente F.,Regional Institute for Research and Agro Food Development SERIDA | de la Roza-Delgado B.,Regional Institute for Research and Agro Food Development SERIDA
Food Analytical Methods | Year: 2015

Fatty acids (FAs) play many essential roles in biological systems, and they are the aim of different research studies due to their benefits on human health. Milk and dairy products contribute significantly to the consumption of FAs in the human diet. In consequence, manipulation of FA composition of cows’ milk via nutritional strategies has been an important target for the dairy industry and a challenge from an analytical point of view. Milk FA composition is complex, and their analysis involves multiple steps (extraction procedure, methylation, FA methyl ester extraction and gas chromatography (GC) determination) that turn it into a tedious and time-consuming procedure. In recent years, some efforts have been made to develop an analytical approach with simultaneous extraction and derivatization of FAs. In this sense, microwave (MW)-assisted digestion and extraction methods have been used for many years and today can be considered standard operating procedures in many laboratories. It is a powerful tool for different analytical methodology development. This study is focused on one-step extraction/transmethylation MW-assisted methodology feasibility for FA analysis in milk compared to a reference method. © 2015, Springer Science+Business Media New York.


PubMed | Regional Institute for Research and Agro Food Development SERIDA
Type: | Journal: Talanta | Year: 2016

Significant advances achieved in different sensor technologies and computer processing data have made possible to respond the needs of livestock sector, providing precise and rapid information on feed composition, being an alternative to real time quality control on compound feed the use of handheld NIRS sensors. This work aimed to evaluate two hand-held portable NIR spectrophotometers for on-site and real time analysis of nutritive parameters in raw compound feed: Phazir 1624 Polychromix Inc (PhIR) and MicroNIR

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