Characterization of vineyard's canopy through fuzzy clustering and svm over color images

In this work we propose an image acquisition and processing methodology (framework) developed for performance in-field grapes and leaves detection and quantification, based on a six step methodology: 1) image segmentation through Fuzzy C-Means with Gustafson Kessel (FCM-GK) clustering; 2) obtaining of FCM-GK outputs (centroids) for acting as seeding for K-Means clustering; 3) Identification of the clusters generated by K-Means using a Support Vector Machine (SVM) classifier. 4) Performance of morphological operations over the grapes and leaves clusters in order to fill holes and to eliminate small pixels clusters; 5)Creation of a mosaic image by Scale-Invariant Feature Transform (SIFT) in order to avoid overlapping between images; 6) Calculation of the areas of leaves and grapes and finding of the centroids in the grape bunches. Image data are collected using a colour camera fixed to a mobile platform. This platform was developed to give a stabilized surface to guarantee that the images were acquired parallel to de vineyard rows. In this way, the platform avoids the distortion of the images that lead to poor estimation of the areas. Our preliminary results are promissory, although they still have shown that it is necessary to implement a camera stabilization system to avoid undesired camera movements, and also a parallel processing procedure in order to speed up the mosaicking process.

Canopy fruit location can affect olive oil quality in Arbequina hedgerow orchards

The effect of location of fruit in canopies of hedgerow olive trees (Olea europaea L., cv. ���Arbequina���) on quality of virgin oil was tested by analyzing oils extracted from different height layers and faces of 9 olive hedgerows (6 North-South oriented and 3 East-West). Although sensory attributes were not different other oil quality parameters may be significantly modified by fruit position. In some hedgerows, oils extracted from fruits harvested from higher layers exhibited significantly higher stability against oxidation, along with higher palmitic acid, linoleic acid and phenol contents, but lower oleic acid content. Oils extracted from fruits harvested from East and North facing hedgerows oriented North-South and East-West, respectively, exhibited higher oleic contents and lower saturated and polyunsaturated fatty acid contents. The mean phenol content of oils extracted from fruits from a North-South oriented hedgerow was significantly greater from one of the East-West oriented hedgerows. These findings may be relevant for the design of future olive hedgerows destined for olive oil production.

A bacterial cysteine protease effector protein interferes with photosynthesis to suppress plant innate immune responses

The bacterial pathogen Pseudomonas syringae pv tomato DC3000 suppresses plant innate immunity with effector proteins injected by a type III secretion system (T3SS). The cysteine protease effector HopN1, which reduces the ability of DC3000 to elicit programmed cell death in non-host tobacco, was found to also suppress the production of defence-associated reactive oxygen species (ROS) and callose when delivered by Pseudomonas fluorescens heterologously expressing a P. syringae T3SS. Purified His 6 -tagged HopN1 was used to identify tomato PsbQ, a member of the oxygen evolving complex of photosystem II (PSII), as an interacting protein. HopN1 localized to chloroplasts and both degraded PsbQ and inhibited PSII activity in chloroplast preparations, whereas a HopN1 D299A non-catalytic mutant lost these abilities. Gene silencing of NtPsbQ in tobacco compromised ROS production and programmed cell death.

Canopy fruit location can affect olive oil quality in Arbequina hedgerow orchards.

En este trabajo se recogieron muestras de aceituna procedente de distintas alturas de setos cultivados en diferentes condiciones para evaluar el efecto en la calidad del aceite.

Canopy fruit location can affect olive oil quality in Arbequina hedgerow orchards.

The effect of location of fruit in canopies of hedgerow olive trees (Olea europaea L., cv. ���Arbequina���) on quality of virgin oil was tested by analyzing oils extracted from different height layers and faces of nine olive hedgerows (6 North���South oriented and 3 East��� West). Although sensory attributes were not different, other oil quality parameters may be significantly modified by fruit position. Oils extracted from fruits harvested from higher layers exhibited significantly higher stability against oxidation, along with higher palmitic acid, linoleic acid and phenol contents, but lower oleic acid content. Oils extracted from fruits harvested from East and North facing hedgerows oriented North���South and East���West, respectively, exhibited higher oleic contents and lower saturated and polyunsaturated fatty acid contents. The mean phenol content of oils extracted from fruits from a North���South oriented hedgerow was significantly greater from one of the East���West oriented hedgerows. These findings may be relevant for the design of future olive hedgerows destined for olive oil production.

Assessment of watercore development in apples with MRI: Effect offruit location in the canopy

tWatercore distribution inside apple fruit (block or radial), and its incidence (% of tissue) were relatedto the effect of solar radiation inside the canopy as measured by a set of low-cost irradiation sensors.221 samples were harvested in two seasons from the top and the bottom of the canopy and submittedto the non-invasive and non-destructive technique of magnetic resonance imaging (MRI) in order toobtain 20 inner tomography slices from each fruit and analyze the damaged areas using an interactive3D segmentation method. The number of fruit corresponding to each type of damage and the relevantpercentage were calculated and it was found that apples from the top of the tree were mainly of the radialtype (84%) and had more watercore (approx. 5% more) than apples from the bottom (65% radial). From theimage segmentation, the Euler number, a morphometric parameter, was extracted from the segmentedimages and related to the type of watercore symptoms. Apples with block watercore were grouped inEuler numbers between ���400 and 400 with a small evolution. For apples with radial development, theEuler number was highly negative: up to ���1439. Significant differences were also found regarding sugarcomposition, with higher fructose and total sugar contents in apples from the upper canopy, compared tothose in the lower canopy location. In the seasons studied (2011 and 2012), significantly higher sorbitoland lower sucrose and fructose contents were found in watercore-affected tissue compared to the healthytissue of affected apples and also compared to healthy apples.

Conductancia del mes��filo en especies forestales: implicaciones en la respuesta fotosint��tica a la disponibilidad de agua y luz

La fotos��ntesis es el proceso biol��gico que permite la producci��n primaria y, por tanto, la vida en nuestro planeta. La tasa fotosint��tica viene determinada por la ���maquinaria��� bioqu��mica y las resistencias difusivas al paso del CO2 desde la atm��sfera hasta su fijaci��n en el interior de los cloroplastos. Hist��ricamente la mayor resistencia difusiva se ha atribuido al cierre estom��tico, sin embargo ahora sabemos, debido a las mejoras en las t��cnicas experimentales, que existe tambi��n una resistencia grande que se opone a la difusi��n del CO2 desde los espacios intercelulares a los lugares de carboxilaci��n. Esta resistencia, llamada normalmente por su inversa: la conductancia del mes��filo (gm), puede ser igual o incluso superior a la resistencia debida por el cierre estom��tico. En la presente tesis doctoral he caracterizado la limitaci��n que ejerce la resistencia del mes��filo a la fijaci��n de CO2 en diversas especies forestales y en distintos momentos de su ciclo biol��gico. En la fase de regenerado, hemos estudiado tres situaciones ambientales relevantes en el mayor ��xito de su supervivencia, que son: el d��ficit h��drico, su interacci��n con la irradiancia y el paso del crecimiento en la sombra a mayor irradiancia, como puede suceder tras la apertura de un hueco en el dosel forestal. En la fase de arbolado adulto se ha caracterizado el estado h��drico y el intercambio gaseoso en hojas desarrolladas a distinta irradiancia dentro del dosel vegetal durante tres a��os contrastados en pluviometr��a. Para cada tipo de estudio se han empleado las t��cnicas ecofisiol��gicas m��s pertinentes para evaluar el estado h��drico y el intercambio gaseoso. Por su complejidad y la falta de un m��todo que permita su cuantificaci��n directa, la gm ha sido evaluada por los m��todos m��s usados, que son: la discriminaci��n isot��pica del carbono 13, el m��todo de la J variable, el m��todo de la J constante y el m��todo de la curvatura. Los resultados m��s significativos permiten concluir que la limitaci��n relativa a la fotos��ntesis por la conductancia estom��tica, del mes��filo y bioqu��mica es dependiente de la localizaci��n de la hoja en el dosel forestal. Por primera vez se ha documentado que bajo estr��s h��drico las hojas desarrolladas a la sombra estuvieron m��s limitadas por una reducci��n en la gm, mientras que las hojas desarrolladas a pleno sol estuvieron m��s limitadas por reducci��n mayor de la conductancia estom��tica (gsw). Encontramos buena conexi��n entre el aparato fotosint��tico foliar y el sistema h��drico debido al alto grado de correlaci��n entre la conductancia hidr��ulica foliar aparente y la concentraci��n de CO2 en los cloroplastos en distintas especies forestales. Adem��s, hemos mostrado diferentes pautas de regulaci��n del intercambio gaseoso seg��n las particularidades ecol��gicas de las especies estudiadas. Tanto en brinzales crecidos de forma natural y en el arbolado adulto como en pl��ntulas cultivadas en el invernadero la ontogenia afect�� a las limitaciones de la fotos��ntesis producidas por estr��s h��drico, resultando que las limitaciones estom��ticas fueron dominantes en hojas m��s j��venes mientras que las no estom��ticas en hojas m��s maduras. La puesta en luz supuso un gran descenso en la gm durante los d��as siguientes a la transferencia, siendo este efecto mayor seg��n el grado de sombreo previo en el que se han desarrollado las hojas. La aclimataci��n de las hojas a la alta irradiancia estuvo ligada a las modificaciones anat��micas foliares y al estado de desarrollo de la hoja. El ratio entre la gm/gsw determin�� la mayor eficiencia en el uso del agua y un menor estado oxidativo durante la fase de estr��s h��drico y su posterior rehidrataci��n, lo cual sugiere el uso de este ratio en los programas de mejora gen��tica frente al estr��s h��drico. Debido a que la mayor��a de modelos de estimaci��n de la producci��n primaria bruta (GPP) de un ecosistema no incluye la gm, los mismos est��n incurriendo en una sobreestimaci��n del GPP particularmente bajo condiciones de estr��s h��drico, porque m��s de la mitad de la reducci��n en fotos��ntesis en hojas desarrolladas a la sombra se debe a la reducci��n en gm. Finalmente se presenta un an��lisis de la importancia en las estimas de la gm bajo estr��s h��drico de la refijaci��n del CO2 emitido en la mitocondria a consecuencia de la fotorrespiraci��n y la respiraci��n mitocondrial en luz. ABSTRACT Photosynthesis is the biological process that supports primary production and, therefore, life on our planet. Rates of photosynthesis are determined by biochemical ���machinery��� and the diffusive resistance to the transfer of CO2 from the atmosphere to the place of fixation within the chloroplasts. Historically the largest diffusive resistance was attributed to the stomata, although we now know via improvements in experimental techniques that there is also a large resistance from sub-stomatal cavities to sites of carboxylation. This resistance, commonly quantified as mesophyll conductance (gm), can be as large or even larger than that due to stomatal resistance. In the present PhD I have characterized the limitation exerted by the mesophyll resistance to CO2 fixation in different forest species at different stages of their life cycle. In seedlings, we studied three environmental conditions that affect plant fitness, namely, water deficit, the interaction of water deficit with irradiance, and the transfer of plants grown in the shade to higher irradiance as can occur when a gap opens in the forest canopy. At the stage of mature trees we characterized water status and gas exchange in leaves developed at different irradiance within the canopy over the course of three years that had contrasting rainfall. For each study we used the most relevant ecophysiological techniques to quantify water relations and gas exchange. Due to its complexity and the lack of a method that allows direct quantification, gm was estimated by the most commonly used methods which are: carbon isotope discrimination, the J-variable, constant J and the curvature method The most significant results suggest that the relative limitation of photosynthesis by stomata, mesophyll and biochemistry depending on the position of the leaf within the canopy. For the first time it was documented that under water stress shaded leaves were more limited by a reduction in gm, while the sun-adapted leaves were more limited by stomatal conductance (gsw). The connection between leaf photosynthetic apparatus and the hydraulic system was shown by the good correlations found between the apparent leaf hydraulic conductance and the CO2 concentration in the chloroplasts in shade- and sun-adapted leaves of several tree species. In addition, we have revealed different patterns of gas exchange regulation according to the functional ecology of the species studied. In field grown trees and greenhouse-grown seedlings ontogeny affected limitations of photosynthesis due to water stress with stomatal limitations dominating in young leaves and nonstomatal limitations in older leaves. The transfer to high light resulted in major decrease of gm during the days following the transfer and this effect was greater as higher was the shade which leaves were developed. Acclimation to high light was linked to the leaf anatomical changes and the state of leaf development. The ratio between the gm/gsw determined the greater efficiency in water use and reduced the oxidative stress during the water stress and subsequent rehydration, suggesting the use of this ratio in breeding programs aiming to increase avoidance of water stress. Because most models to estimate gross primary production (GPP) of an ecosystem do not include gm, they are incurring an overestimation of GPP particularly under conditions of water stress because more than half of An decrease in shade-developed leaves may be due to reduction in gm. Finally, we present an analysis of the importance of how estimates of gm under water stress are affected by the refixation of CO2 that is emitted from mitochondria via photorespiration and mitochondrial respiration in light.