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Teixeira, RT, AM Fortes, C. Pinheiro, and H. Pereira. "Comparison of good- and bad-quality cork: application of high-throughput sequencing of phellogenic tissue." Journal of Experimental Botany (2014). Abstract
Guerra-Guimaraes, Leonor, Ana Vieira, Ines Chaves, Carla Pinheiro, Vagner Queiroz, Jenny Renaut, and Candido P. Ricardo. "Effect of greenhouse conditions on the leaf apoplastic proteome of Coffea arabica plants." Journal of proteomics. 104 (2014): 128-39. AbstractWebsite
Fonseca, Catia, Sebastien Planchon, Carla Pinheiro, Jenny Renaut, Candido Pinto Ricardo, Margarida M. Oliveira, and Rita Batista. "Maize IgE binding proteins: each plant a different profile?" Proteome science. 12 (2014): 17. AbstractWebsite
Pinheiro, Carla, Leonor Guerra-Guimaraes, Teresa S. David, and Ana Vieira. "Proteomics: State of the art to study Mediterranean woody species under stress." Environmental and Experimental Botany. 103 (2014): 117-127. AbstractWebsite
Pinheiro, C., K. Sergeant, C. M. Machado, J. Renaut, and C. P. Ricardo. "Two Traditional Maize Inbred Lines of Contrasting Technological Abilities Are Discriminated by the Seed Flour Proteome." Journal of Proteome Research. 12 (2013): 3152-3165. AbstractWebsite
Zarrouk, Olfa, Rita Francisco, Marta Pinto-Marijuan, Ricard Brossa, Raquen Raissa Santos, Carla Pinheiro, Joaquim Miguel Costa, Carlos Lopes, and Maria Manuela Chaves. "Impact of irrigation regime on berry development and flavonoids composition in Aragonez (Syn. Tempranillo) grapevine." Agricultural Water Management. 114 (2012). AbstractWebsite
Alves, M., S. Moes, P. Jenoe, C. Pinheiro, J. Passarinho, and C. P. Ricardo. "The analysis of Lupinus albus root proteome revealed cytoskeleton altered features due to long-term boron deficiency." Journal of Proteomics. 74 (2011): 1351-1363. AbstractWebsite
Pinheiro, Carla, Carla Antonio, Maria Fernanda Ortuno, Petre I. Dobrev, Wolfram Hartung, Jane Thomas-Oates, Candido Pinto Ricardo, Radomira Vankova, Manuela M. Chaves, and Julie C. Wilson. "Initial water deficit effects on Lupinus albus photosynthetic performance, carbon metabolism, and hormonal balance: metabolic reorganization prior to early stress responses." Journal of Experimental Botany. 62 (2011): 4965-4974. AbstractWebsite

The early (2-4 d) effects of slowly imposed soil water deficit on Lupinus albus photosynthetic performance, carbon metabolism, and hormonal balance in different organs (leaf blade, stem stele, stem cortex, and root) were evaluated on 23-d-old plants (growth chamber assay). Our work shows that several metabolic adjustments occurred prior to alteration of the plant water status, implying that water deficit is perceived before the change in plant water status. The slow, progressive decline in soil water content started to be visible 3 d after withholding water (3 DAW). The earliest plant changes were associated with organ-specific metabolic responses (particularly in the leaves) and with leaf conductance and only later with plant water status and photosynthetic rate (4 DAW) or photosynthetic capacity (according to the Farquhar model; 6 DAW). Principal component analysis (PCA) of the physiological parameters, the carbohydrate and the hormone levels and their relative values, as well as leaf water-soluble metabolites full scan data (LC-MS/MS), showed separation of the different sampling dates. At 6 DAW classically described stress responses are observed, with plant water status, ABA level, and root hormonal balance contributing to the separation of these samples. Discrimination of earlier stress stages (3 and 4 DAW) is only achieved when the relative levels of indole-3-acetic acid (IAA), cytokinins (Cks), and carbon metabolism (glucose, sucrose, raffinose, and starch levels) are taken into account. Our working hypothesis is that, in addition to single responses (e.g. ABA increase), the combined alterations in hormone and carbohydrate levels play an important role in the stress response mechanism. Response to more advanced stress appears to be associated with a combination of cumulative changes, occurring in several plant organs. The carbohydrate and hormonal balance in the leaf (IAA to bioactive-Cks; soluble sugars to IAA and starch to IAA; relative abundances of the different soluble sugars) flag the initial responses to the slight decrease in soil water availability (10-15% decrease). Further alterations in sucrose to ABA and in raffinose to ABA relative values (in all organs) indicate that soil water availability continues to decrease. Such alterations when associated with changes in the root hormone balance indicate that the stress response is initiated. It is concluded that metabolic balance (e.g. IAA/bioactive Cks, carbohydrates/IAA, sucrose/ABA, raffinose/ABA, ABA/IAA) is relevant in triggering adjustment mechanisms.

Alves, M., P. Chicau, H. Matias, J. Passarinho, C. Pinheiro, and C. P. Ricardo. "Metabolic analysis revealed altered amino acid profiles in Lupinus albus organs as a result of boron deficiency." Physiologia Plantarum. 142 (2011): 224-232. AbstractWebsite

We analysed the changes in the metabolites of Lupinus albus organs (leaf-blades, petioles, apexes, hypocotyls and roots) as a consequence of B deficiency. The deficiency did not affect malate concentration and induced only minor changes in the sugar content, suggesting that the carbohydrate metabolism is little affected by the deficiency. Contrarily, marked changes in the content of free amino acids were observed, with some specific variations associated with the different organs. These changes indicate that various aspects of metabolism implicated in the amino acid accumulation were affected by B deficiency. Most of the detected changes appear to have implications with some stress responses or signalling processes. Asparagine and proline that increase in many stresses also accumulated in petioles, apexes and hypocotyls. Accumulation of gamma-aminobutyric acid shunt amino acids, indicative of production of reactive oxygen species, occurs in the same three organs and also the roots. The increase in the branched-chain amino acids, observed in all organs, suggests the involvement of B with the cytoskeleton, whereas glycine decrease in leaf-blades and active growing organs (apexes and roots) could be associated with the proposed role of this amino acids in plant signalling in processes that might be associated with the decreased growth rates observed in B deficiency. Despite the admitted importance of free amino acids in plant metabolism, the available information on this matter is scarce. So our results bring new information concerning the effects of B deficiency in the metabolism of the several L. albus organs.

Pinheiro, C., and M. M. Chaves. "Photosynthesis and drought: can we make metabolic connections from available data?" Journal of Experimental Botany. 62 (2011): 869-882. AbstractWebsite

Photosynthesis is one of the key processes to be affected by water deficits, via decreased CO2 diffusion to the chloroplast and metabolic constraints. The relative impact of those limitations varies with the intensity of the stress, the occurrence (or not) of superimposed stresses, and the species we are dealing with. Total plant carbon uptake is further reduced due to the concomitant or even earlier inhibition of growth. Leaf carbohydrate status, altered directly by water deficits or indirectly (via decreased growth), acts as a metabolic signal although its role is not totally clear. Other relevant signals acting under water deficits comprise: abscisic acid (ABA), with an impact on stomatal aperture and the regulation at the transcription level of a large number of genes related to plant stress response; other hormones that act either concurrently (brassinosteroids, jasmonates, and salycilic acid) or antagonistically (auxin, cytokinin, or ethylene) with ABA; and redox control of the energy balance of photosynthetic cells deprived of CO2 by stomatal closure. In an attempt to systematize current knowledge on the complex network of interactions and regulation of photosynthesis in plants subjected to water deficits, a meta-analysis has been performed covering > 450 papers published in the last 15 years. This analysis shows the interplay of sugars, reactive oxygen species (ROS), and hormones with photosynthetic responses to drought, involving many metabolic events. However, more significantly it highlights (i) how fragmented and often non-comparable the results are and (ii) how hard it is to relate molecular events to plant physiological status, namely photosynthetic activity, and to stress intensity. Indeed, the same data set usually does not integrate these different levels of analysis. Considering these limitations, it was hard to find a general trend, particularly concerning molecular responses to drought, with the exception of the genes ABI1 and ABI3. These genes, irrespective of the stress type (acute versus chronic) and intensity, show a similar response to water shortage in the two plant systems analysed (Arabidopsis and barley). Both are associated with ABA-mediated metabolic responses to stress and the regulation of stomatal aperture. Under drought, ABI1 transcription is up-regulated while ABI3 is usually down-regulated. Recently ABI3 has been hypothesized to be essential for successful drought recovery.

Ricardo, Candido P. P., Isabel Martins, Rita Francisco, Kjell Sergeant, Carla Pinheiro, Alexandre Campos, Jenny Renaut, and Pedro Fevereiro. "Proteins associated with cork formation in Quercus suber L. stem tissues." Journal of Proteomics. 74 (2011): 1266-1278. AbstractWebsite
Pinheiro, C., J. P. Baeta, A. M. Pereira, H. Domingues, and C. P. Ricardo. "Diversity of seed mineral composition of Phaseolus vulgaris L. germplasm." Journal of Food Composition and Analysis. 23 (2010): 319-325. AbstractWebsite

A collection of 155 accessions of ancient Portuguese common beans (Phaseolus vulgaris L) was evaluated in relation to the content of 8 minerals (Zn, Cu, Fe, Mn, Ca, Mg, P and K) important for human nutrition. A high degree of variability for P. Fe, Zn, Cu, Mn and Ca was observed in the collection. Total correlation matrix analysis revealed the existence of two important sets of strong positive correlations (P <= 0.0001), one involving P, Fe, Zn, Cu and protein, and the other Ca and Mn. The principal component analysis showed that Zn, Fe and Cu are highly correlated to the first component (27% of variability) and Mn and Ca to the second component (22% of the variability). The high mineral variability observed in the seeds of this common bean collection could be useful for the selection of cultivars with higher nutrition value and for the improvement of seed nutrition quality traits. (C) 2010 Elsevier Inc. All rights reserved.

Felisberto-Rodrigues, C., IC Ribeiro, M. Veloso, C. P. Ricardo, and C. Pinheiro. "Germination under aseptic conditions of different ecotypes of wild beet (Beta vulgaris L. ssp maritima)." Seed Science and Technology. 38 (2010): 517-521. Abstract
Chaves, M. M., J. Flexas, and C. Pinheiro. "Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell." Annals of Botany. 103 (2009): 551-560. AbstractWebsite

Plants are often subjected to periods of soil and atmospheric water deficits during their life cycle as well as, in many areas of the globe, to high soil salinity. Understanding how plants respond to drought, salt and co-occurring stresses can play a major role in stabilizing crop performance under drought and saline conditions and in the protection of natural vegetation. Photosynthesis, together with cell growth, is among the primary processes to be affected by water or salt stress. The effects of drought and salt stresses on photosynthesis are either direct (as the diffusion limitations through the stomata and the mesophyll and the alterations in photosynthetic metabolism) or secondary, such as the oxidative stress arising from the superimposition of multiple stresses. The carbon balance of a plant during a period of salt/water stress and recovery may depend as much on the velocity and degree of photosynthetic recovery, as it depends on the degree and velocity of photosynthesis decline during water depletion. Current knowledge about physiological limitations to photosynthetic recovery after different intensities of water and salt stress is still scarce. From the large amount of data available on transcript-profiling studies in plants subjected to drought and salt it is becoming apparent that plants perceive and respond to these stresses by quickly altering gene expression in parallel with physiological and biochemical alterations; this occurs even under mild to moderate stress conditions. From a recent comprehensive study that compared salt and drought stress it is apparent that both stresses led to down-regulation of some photosynthetic genes, with most of the changes being small (ratio threshold lower than 1) possibly reflecting the mild stress imposed. When compared with drought, salt stress affected more genes and more intensely, possibly reflecting the combined effects of dehydration and osmotic stress in salt-stressed plants.

Chaves, I., C. Pinheiro, JAP Paiva, S. Planchon, K. Sergeant, J. Renaut, JA Graca, G. Costa, AV Coelho, and CPP Ricardo. "Proteomic evaluation of wound-healing processes in potato (Solanum tuberosum L.) tuber tissue." PROTEOMICS. 9 (2009): 4154-4175. Abstract
Sergeant, K., C. Pinheiro, JF Hausman, and "Taking Advantage of Nonspecific Trypsin Cleavages for the Identification of Seed Storage Proteins in Cereals." JOURNAL OF PROTEOME RESEARCH. 8 (2009): 3182-3190. Abstract
Antonio, Carla, Carla Pinheiro, Maria Manuela Chaves, Candido Pinto Ricardo, Maria Fernanda Ortuno, and Jane Thomas-Oates. "Analysis of carbohydrates in Lupinus albus stems on imposition of water deficit, using porous graphitic carbon liquid chromatography-electrospray ionization mass spectrometry." Journal of Chromatography A. 1187 (2008): 111-118. AbstractWebsite
Pinheiro, C., MHC de Carvalho, D. Bartels, CP Ricarddo, and M. M. Chaves. "Dehydrins in Lupinus albus: pattern of protein accumulation in response to drought." FUNCTIONAL PLANT BIOLOGY. 35 (2008): 85-91. Abstract
Pinheiro, C., J. Kehr, and C. P. Ricardo. "Effect of water stress on lupin stem protein analysed by two-dimensional gel electrophoresis." Planta. 221 (2005): 716-728. AbstractWebsite
Pinheiro, C., A. P. Rodrigues, IS de Carvalho, M. M. Chaves, and C. P. Ricardo. "Sugar metabolism in developing lupin seeds is affected by a short-term water deficit." Journal of Experimental Botany. 56 (2005): 2705-2712. Abstract
Pinheiro, C., J. A. Passarinho, and C. P. Ricardo. "Effect of drought and rewatering on the metabolism of Lupinus albus organs." Journal of Plant Physiology. 161 (2004): 1203-1210. AbstractWebsite
Price, NJ, C. Pinheiro, C. M. Soares, DA Ashford, C. P. Ricardo, and PA Jackson. "A biochemical and molecular characterization of LEP1, an extensin peroxidase from lupin." Journal of Biological Chemistry. 278 (2003): 41389-41399. Abstract