<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors></contributors><titles><title><style face="normal" font="default" size="100%">Analysis of the expression of putative heat-stress related genes in relation to thermotolerance of cork oak</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Plant Physiology</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2014</style></year></dates><volume><style face="normal" font="default" size="100%">171</style></volume><pages><style face="normal" font="default" size="100%">399-406</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Cork oak (Quercus suber L.) is a research priority in the Mediterranean area and because of cork oaks’ dis- tribution these stands are experiencing daily stress. Based on projections of intensifying climate change and considering the key role of exploring the recovery abilities, cork oak seedlings were subjected to a cumulative temperature increase from 25◦C to 55◦C and subsequent recovery. CO2 assimilation rate, chlorophyll fluorescence, anthocyanins, proline and lipid peroxidation were used to evaluate plant per- formance, while the relative abundance of seven genes encoding for proteins of cork oak with a putative role in thermal/stress regulation (POX1, POX2, HSP10.4, HSP17a.22, CHS, MTL and RBC) was analyzed by qPCR (quantitative Polymerase Chain Reaction). A temperature change to 35◦C showed abundance alterations in the tested genes; at 45◦C, the molecular changes were associated with an antioxidant response, possibly modulated by anthocyanins. At 55◦C, HSP17a.22, MTL and proline accumulation were evident. After recovery, physiological balance was restored, whereas POX1, HSP10.4 and MTL abundances were suggested to be involved in increased thermotolerance. The data presented here are expected to pinpoint some pathways changes occurring during such stress and further recovery in this particular Mediterranean species. ©</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>7</ref-type><contributors></contributors><titles><title><style face="normal" font="default" size="100%">Back to Osborne. Sequential Protein Extraction and LC-MS Analysis for the Characterization of the Holm Oak Seed Proteome</style></title><secondary-title><style face="normal" font="default" size="100%">Plant Proteomics SE - 27</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2014</style></year></dates><publisher><style face="normal" font="default" size="100%">Humana Press</style></publisher><volume><style face="normal" font="default" size="100%">1072</style></volume><pages><style face="normal" font="default" size="100%">379-389</style></pages><isbn><style face="normal" font="default" size="100%">978-1-62703-630-6</style></isbn><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">It is impossible to capture in just one experiment all or most of the total set of protein species that constitute the cell’s proteome. Thus, according to our results, and even considering that they depend on the experimental system carried out (plant, yeast, fungi, or bacteria), the best protein extraction protocol yielded less than 20 % of the total amount of proteins, as determined by the Kjeldahl method. For this reason, protein cataloguing and the whole proteome characterization require the use of firstly, fractionation techniques at the cellular, subcellular, protein, or peptide level, and secondly, the use of complementary approaches. Within our current research on Holm oak (Quercus ilex subsp. ballota), we aim to characterize its seed proteome. For that we have optimized an experimental workflow in which the Osborne sequential protein extraction (Osborne, Science 28:417–427, 1908) is combined with downstream electrophoretic protein separation or shotgun MS analysis. In general, it can be used to study any plant seed, as well as to investigate on seed maturation and germination, genotype characterization, allergens identification, food traceability, and substantial equivalence, among others.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors></contributors><titles><title><style face="normal" font="default" size="100%">Improving the quality of protein identification in non-model species. Characterization of Quercus ilex seed and Pinus radiata needle proteomes by using SEQUEST and custom databases</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Proteomics</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2014</style></year></dates><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Nowadays the most used pipeline for protein identification consists in the comparison of the MS/MS spectra to reference databases. Search algorithms compare obtained spectra to an in silico digestion of a sequence database to find exact matches. In this context, the database has a paramount importance and will determine in a great deal the number of identifications and its quality, being this especially relevant for non-model plant species. Using a single Viridiplantae database (NCBI, UniProt, TAIR) is not the best choice for non-model species since they are underrepresented in databases resulting in poor identification rates. We demonstrate how it is possible to improve the rate and quality of identifications in two orphan species, Quercus ilex and Pinus radiata, by using SEQUEST and a combination of public (Viridiplantae NCBI, UniProt) and a custom-built specific database which contained 593,294 and 455,096 peptide sequences (Quercus and Pinus, respectively). These databases were built after gathering and processing (trimming, contiging, 6-frame translation) publicly available RNA sequences, mostly ESTs and NGS reads. A total of 149 and 1533 proteins were identified from Quercus seeds and Pinus needles, representing a 3.1- or 1.5-fold increase in the number of protein identifications and scores compared to the use of a single database. Since this approach greatly improves the identification rate, and is not significantly more complicated or time consuming than other approaches, we recommend its routine use when working with non-model species. BIOLOGICAL SIGNIFICANCE In this work we demonstrate how the construction of a custom database (DB) gathering all available RNA sequences and its use in combination with Viridiplantae public DBs (NCBI, UniProt) significantly improve protein identification when working with non-model species. Protein identification rate and quality is higher to those obtained in routine procedures based on using only one database (commonly Viridiplantae from NCBI), as we demonstrated analyzing Quercus seeds and Pine needles. The proposed approach based on the building of a custom database is not difficult or time consuming, so we recommend its routine use when working with non-model species. This article is part of a Special Issue entitled: Proteomics of non-model organisms.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors></contributors><titles><title><style face="normal" font="default" size="100%">Proteotyping of Holm Oak (Quercus ilex subsp. ballota) Provenances Through Proteomic Analysis of Acorn Flour</style></title><secondary-title><style face="normal" font="default" size="100%">Methods in Molecular Biology Plant Proteomics SE - 49</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2014</style></year></dates><publisher><style face="normal" font="default" size="100%">Humana Press</style></publisher><volume><style face="normal" font="default" size="100%">1072</style></volume><pages><style face="normal" font="default" size="100%">709-723</style></pages><isbn><style face="normal" font="default" size="100%">978-1-62703-630-6</style></isbn><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Proteomics has become a powerful tool to characterize biodiversity and natural variability in plant species, as well as to catalogue and establish phylogenetic relationships and distances among populations, provenances or ecotypes. In this chapter, we describe the standard proteomics workflow that we currently use in cataloguing Holm oak (Quercus ilex subsp. ballota [Desf.] Samp.) populations. Proteins are extracted from acorn flour or pollen by TCA/acetone or TCA/acetone-phenol methods, resolved by one- or two-dimensional gel electrophoresis, and gel images are captured and analyzed by appropriate software and statistical packages. Quantitative or qualitative variable bands or spots are subjected to MS analysis in order to identify them and correlate differences in the protein profile with the phenotypes or environmental conditions.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Correia, Barbara</style></author><author><style face="normal" font="default" size="100%">Valledor, Luis</style></author><author><style face="normal" font="default" size="100%">Meijón, Mónica</style></author><author><style face="normal" font="default" size="100%">Rodriguez, José Luis</style></author><author><style face="normal" font="default" size="100%">Dias, Maria Celeste</style></author><author><style face="normal" font="default" size="100%">Santos, Conceição</style></author><author><style face="normal" font="default" size="100%">Cañal, Maria Jesus</style></author><author><style face="normal" font="default" size="100%">Rodriguez, Roberto</style></author><author><style face="normal" font="default" size="100%">Pinto, Glória</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Is the Interplay between Epigenetic Markers Related to the Acclimation of Cork Oak Plants to High Temperatures?</style></title><secondary-title><style face="normal" font="default" size="100%">PLoS ONE</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acclimatization</style></keyword><keyword><style  face="normal" font="default" size="100%">Acclimatization: genetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Acetylation</style></keyword><keyword><style  face="normal" font="default" size="100%">Blotting</style></keyword><keyword><style  face="normal" font="default" size="100%">CHROMATIN</style></keyword><keyword><style  face="normal" font="default" size="100%">CORK oak (citation</style></keyword><keyword><style  face="normal" font="default" size="100%">Deoxycytidine</style></keyword><keyword><style  face="normal" font="default" size="100%">Deoxycytidine: analogs &amp; derivatives</style></keyword><keyword><style  face="normal" font="default" size="100%">Deoxycytidine: metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA methylation</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrolytes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrolytes: metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Epigenesis</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene expression</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic Markers</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome</style></keyword><keyword><style  face="normal" font="default" size="100%">Heat-Shock Response</style></keyword><keyword><style  face="normal" font="default" size="100%">Heat-Shock Response: genetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Histones</style></keyword><keyword><style  face="normal" font="default" size="100%">Histones: metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Physiological</style></keyword><keyword><style  face="normal" font="default" size="100%">Physiological: genetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Leaves</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Leaves: metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant: genetics</style></keyword><keyword><style  face="normal" font="default" size="100%">POST-translational modification</style></keyword><keyword><style  face="normal" font="default" size="100%">Quercus</style></keyword><keyword><style  face="normal" font="default" size="100%">Quercus: genetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Quercus: physiology</style></keyword><keyword><style  face="normal" font="default" size="100%">Random Amplified Polymorphic DNA Technique</style></keyword><keyword><style  face="normal" font="default" size="100%">Stress</style></keyword><keyword><style  face="normal" font="default" size="100%">tags)</style></keyword><keyword><style  face="normal" font="default" size="100%">Temperature</style></keyword><keyword><style  face="normal" font="default" size="100%">TREES -- Research</style></keyword><keyword><style  face="normal" font="default" size="100%">Western</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013///</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3543447&amp;tool=pmcentrez&amp;rendertype=abstracthttp://dx.doi.org/10.1371/journal.pone.0053543</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">8</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Trees necessarily experience changes in temperature, requiring efficient short-term strategies that become crucial in environmental change adaptability. DNA methylation and histone posttranslational modifications have been shown to play a key role in both epigenetic control and plant functional status under stress by controlling the functional state of chromatin and gene expression. Cork oak (Quercus suber L.) is a key stone of the Mediterranean region, growing at temperatures of 45°C. This species was subjected to a cumulative temperature increase from 25°C to 55°C under laboratory conditions in order to test the hypothesis that epigenetic code is related to heat stress tolerance. Electrolyte leakage increased after 35°C, but all plants survived to 55°C. DNA methylation and acetylated histone H3 (AcH3) levels were monitored by HPCE (high performance capillary electrophoresis), MS-RAPD (methylation-sensitive random-amplified polymorphic DNA) and Protein Gel Blot analysis and the spatial distribution of the modifications was assessed using a confocal microscope. DNA methylation analysed by HPCE revealed an increase at 55°C, while MS-RAPD results pointed to dynamic methylation-demethylation patterns over stress. Protein Gel Blot showed the abundance index of AcH3 decreasing from 25°C to 45°C. The immunohistochemical detection of 5-mC (5-methyl-2′-deoxycytidine) and AcH3 came upon the previous results. These results indicate that epigenetic mechanisms such as DNA methylation and histone H3 acetylation have opposite and particular dynamics that can be crucial for the stepwise establishment of this species into such high stress (55°C), allowing its acclimation and survival. This is the first report that assesses epigenetic regulation in order to investigate heat tolerance in forest trees.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><notes><style face="normal" font="default" size="100%">The following values have no corresponding Zotero field:&lt;br/&gt;publisher: Public Library of Science&lt;br/&gt;accession-num: 23326451</style></notes></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors></contributors><titles><title><style face="normal" font="default" size="100%">Proteomic analysis of Holm oak (Quercus ilex subsp. ballota [Desf.] Samp.) pollen.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of proteomics</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year></dates><publisher><style face="normal" font="default" size="100%">Elsevier B.V.</style></publisher><volume><style face="normal" font="default" size="100%">75</style></volume><pages><style face="normal" font="default" size="100%">2736-44</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">This paper presents an analysis of Holm oak pollen proteome, together with an evaluation of the potentiality that a proteomic approach may have in the provenance variability assessment. Proteins were extracted from pollen of four Holm oak provenances, and they were analyzed by gel-based (1- and 2-DE in combination with MALDI-TOF/TOF) and gel-free (nLC-LTQ Orbitrap MS) approaches. A comparison of 1- and 2-DE protein profiles of the four provenances revealed significant differences, both qualitative and quantitative, in abundance (18 bands and 16 spots, respectively). Multivariate statistical analysis carried out on bands and spots clearly showed distinct associations between provenances, which highlight their geographical origins. A total of 100 spots selected from the 402 spots observed on 2-DE gels were identified by MALDI-TOF/TOF. Moreover, a complementary gel-free shotgun approach was performed by nLC-LTQ Orbitrap MS. The identified proteins were classified according to biological processes, and most proteins in both approaches were related to metabolism and defense/stress processes. The nLC-LTQ Orbitrap MS analysis allowed us the identification of proteins belonging to the cell wall and division, transport and translation categories. Besides providing the first reference map of Holm oak pollen, our results confirm previous studies based on morphological observations and acorn proteomic analysis. Moreover, our data support the valuable use of proteomic techniques as phylogenetic tool in plant studies.</style></abstract><accession-num><style face="normal" font="default" size="100%">22484522</style></accession-num></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Abril, Nieves</style></author><author><style face="normal" font="default" size="100%">Gion, Jean-Marc</style></author><author><style face="normal" font="default" size="100%">Kerner, René</style></author><author><style face="normal" font="default" size="100%">Müller-Starck, Gerhard</style></author><author><style face="normal" font="default" size="100%">Cerrillo, Rafael M. Navarro</style></author><author><style face="normal" font="default" size="100%">Plomion, Christophe</style></author><author><style face="normal" font="default" size="100%">Renaut, Jenny</style></author><author><style face="normal" font="default" size="100%">Valledor, Luis</style></author><author><style face="normal" font="default" size="100%">Jorrin-Novo, Jesús V.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Proteomics research on forest trees, the most recalcitrant and orphan plant species.</style></title><secondary-title><style face="normal" font="default" size="100%">Phytochemistry</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Forest tree proteomics</style></keyword><keyword><style  face="normal" font="default" size="100%">forest trees</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant proteomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Woody plants</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011///</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21353265</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">72</style></volume><pages><style face="normal" font="default" size="100%">1219 - 1242</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The contribution of proteomics to the knowledge of forest tree (the most recalcitrant and almost forgotten plant species) biology is being reviewed and discussed, based on the author's own research work and papers published up to November 2010. This review is organized in four introductory sections starting with the definition of forest trees (1), the description of the environmental and economic importance (2) and its derived current priorities and research lines for breeding and conservation (3) including forest tree genomics (4). These precede the main body of this review: a general overview to proteomics (5) for introducing the forest tree proteomics section (6). Proteomics, defined as scientific discipline or experimental approach, it will be discussed both from a conceptual and methodological point of view, commenting on realities, challenges and limitations. Proteomics research in woody plants is limited to a reduced number of genera, including Pinus, Picea, Populus, Eucalyptus, and Fagus, mainly using first-generation approaches, e.g., those based on two-dimensional electrophoresis coupled to mass spectrometry. This area joins the own limitations of the technique and the difficulty and recalcitrance of the plant species as an experimental system. Furthermore, it contributes to a deeper knowledge of some biological processes, namely growth, development, organogenesis, and responses to stresses, as it is also used in the characterization and cataloguing of natural populations and biodiversity (proteotyping) and in assisting breeding programmes.</style></abstract><issue><style face="normal" font="default" size="100%">10</style></issue><notes><style face="normal" font="default" size="100%">The following values have no corresponding Zotero field:&lt;br/&gt;publisher: Elsevier Ltd&lt;br/&gt;accession-num: 21353265</style></notes></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors></contributors><titles><title><style face="normal" font="default" size="100%">Studies of variability in Holm oak (Quercus ilex subsp. ballota [Desf.] Samp.) through acorn protein profile analysis.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of proteomics</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year></dates><publisher><style face="normal" font="default" size="100%">Elsevier B.V.</style></publisher><volume><style face="normal" font="default" size="100%">74</style></volume><pages><style face="normal" font="default" size="100%">1244-1255</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Studies of variability in Holm oak (Quercus ilex subsp. ballota [Desf.] Samp.), the dominant tree species in the typical Mediterranean forest, have been carried out by using electrophoresis-based proteomic analysis of acorns. Ten populations distributed throughout the Andalusia region have been surveyed. Acorns were sampled from individual trees and proteins extracted from seed flour by using the TCA-acetone precipitation protocol. Extracts were subjected to SDS-PAGE and 2-DE for protein separation, gel images captured, spot or bands quantified, and subjected to statistical analysis (ANOVA, SOM and clustering). Variable bands or spots among populations were subjected to MALDI-TOF/TOF and LC-MS/MS for identification. The protein yield of the used protocol varied among populations, and it was in the 2.92-5.92 mg/g dry weight range. A total of 23 bands were resolved by SDS-PAGE in the 3-35 kDa Mr range, with 8 and 12, out of the total, showing respectively qualitative and quantitative statistically significant differences among populations. Data allowed grouping populations, with groups being correlated according to geographical location and climate conditions, to northern and southern, as well as the discrimination of both mesic and xeric groups. Acorn flour extracts from the most distant populations were analyzed by 2-DE, and 56 differential spots were proposed as markers of variability. Identified proteins were classified into two principal categories; storage and stress/defense protein. Besides providing the first reference map of mature acorn seeds, the use of SDS-PAGE and proteomics in characterizing natural biodiversity in forest trees will be discussed.</style></abstract><accession-num><style face="normal" font="default" size="100%">21605712</style></accession-num></record></records></xml>