Ana Cabral
Instituto Superior de Agronomia
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Publication
Featured researches published by Ana Cabral.
Mycological Progress | 2012
Ana Cabral; Johannes Z. Groenewald; Cecília Rego; Helena Oliveira; Pedro W. Crous
Ilyonectria radicicola and its Cylindrocarpon-like anamorph represent a species complex that is commonly associated with root rot disease symptoms on a range of hosts. During the course of this study, several species could be distinguished from I. radicicola sensu stricto based on morphological and culture characteristics. DNA sequence analysis of the partial β-tubulin, histone H3, translation elongation factor 1-α and nuclear ribosomal RNA-Internal Transcribed Spacer (nrRNA-ITS) genes were employed to provide further support for the morphological species resolved among 68 isolates associated with root rot disease symptoms. Of the various loci screened, nrRNA-ITS sequences were the least informative, while histone H3 sequences were the most informative, resolving the same number of species as the combined dataset across the four genes. Within the Ilyonectria radicicola species complex, 12 new taxa are delineated occurring on a diverse range of hosts, the most common being Cyclamen, Lilium, Panax, Pseudotsuga, Quercus and Vitis.
Fungal Biology | 2012
Ana Cabral; Cec ılia Rego; Teresa Nascimento; Helena Oliveira; Johannes Z. Groenewald; Pedro W. Crous
Black foot is an important disease of grapevines, which has in recent years been recorded with increased incidence and severity throughout the world, affecting grapevines both in nurseries and young vineyards. In the past the disease has been associated with infections by Ilyonectria macrodidyma, Ilyonectria liriodendri, Campylocarpon fasciculare, and Campylocarpon pseudofasciculare. Based on published data, a high level of genetic diversity was detected among isolates of I. macrodidyma. To resolve this issue, we employed a multigene analysis strategy (based on the β-tubulin, histone H3, translation elongation factor 1-α, and the internal transcribed spacers on both sides of the 5.8S nuclear ribosomal RNA gene) along with morphological characterisation to study a collection of 81 I. macrodidyma-like isolates from grapevine and other hosts. Morphological characters (particularly conidial size) and molecular data (highest resolution achieved with histone H3 nucleotide sequence) enabled the distinction of six monophyletic species within the I. macrodidyma complex, four of which (Ilyonectria alcacerensis, Ilyonectria estremocensis, Ilyonectria novozelandica, and Ilyonectria torresensis) are described here. This work forms part of an effort by the International Council on Grapevine Trunk Diseases to resolve the species associated with black foot disease, which we believe will clarify their taxonomy, and therefore help researchers to devise control strategies to reduce the devastating impact of this disease.
Phytopathologia Mediterranea | 2006
Cecília Rego; Lídia Farropas; Helena Oliveira; Ana Cabral; Teresa Nascimento
Black foot disease of grapevine is caused by Cylindrocarpon spp., with C. destructans being the main pathogen isolated from vine cuttings and young vineyards in Portugal. Few recommendations for black foot disease control are presently available, and they are not easy to implement within commercial nurseries. In this study, 14 fungicides were evaluated for their effect on the mycelial growth and conidium germination of four field isolates of C. destructans. Mycelial growth of the pathogen was inhibited by DMI fungicides, prochloraz (EC50 values <0.09 mg l-1) and to a lesser extent by difenoconazole (EC50 values <2.25 mg l-1), by the benzimidazole fungicide benomyl (EC50 values <0.35 mg l-1), and by the mixtures cyprodinil + fludioxonil and carbendazim + flusilazole, which gave EC50 values <0.75 mg l-1. Among these, only cyprodinil + fludioxonil (EC50 values <0.15 mg l-1), the strobilurin fungicides, azoxystrobin and trifloxystrobin (EC50 values <2.27 mg l-1) and the phenylsulphamide fungicide tolylfluanid (EC50 < 0.54 mg l-1) were effective in reducing conidium germination. Results from in vivo studies, carried out on potted grapevine plants (cultivar Castelao) showed that benomyl, tebuconazole and the mixtures carbendazim + flusilazole and cyprodinil + fludioxonil significantly (α=0.05) improved plant growth (plant height and number of roots) and decreased disease incidence compared with non-treated plants.
european conference on applications of evolutionary computation | 2013
Mauro Castelli; Sara Silva; Leonardo Vanneschi; Ana Cabral; Maria J. Vasconcelos; Luís Catarino; João M. B. Carreiras
Multiclass classification is a common requirement of many land cover/land use applications, one of the pillars of land science studies. Even though genetic programming has been applied with success to a large number of applications, it is not particularly suited for multiclass classification, thus limiting its use on such studies. In this paper we take a step forward towards filling this gap, investigating the performance of recently defined geometric semantic operators on two land cover/land use multiclass classification problems and also on a benchmark problem. Our results clearly indicate that genetic programming using the new geometric semantic operators outperforms standard genetic programming for all the studied problems, both on training and test data.
International Journal of Remote Sensing | 2006
Ana Cabral; Maria J. Vasconcelos; José M. C. Pereira; E. Martins; É. Bartholomé
The main purpose of this study is to derive a method suitable for producing a land cover map of southern hemisphere Africa at a spatial resolution of 1 km. Daily SPOT‐Vegetation images from the year 2000 were used to build a dataset of monthly composite images. The composites were used in the development of two different classifiers obtained through the induction of classification trees. The selection of image data for training the classifiers and for accuracy assessment was supported by maps at several different scales, expert knowledge, Landsat Thematic Mapper (TM) imagery, and a preliminary unsupervised classification of the monthly image composites. One classification is based on the construction and application of a single tree classifier, and a second classification relies on the construction and application of an ensemble of tree classifiers using bootstrap aggregation (bagging). Classification accuracy was assessed using a validation dataset. The ensemble of trees produced better results than the single tree classifier. The advantages and limitations of the methods used are discussed, and suggestions for future work presented.
European Journal of Plant Pathology | 2016
Carlos Agustí-Brisach; Ana Cabral; Elisa González-Domínguez; A. Pérez-Sierra; M. León; P. Abad-Campos; J. García-Jiménez; Helena Oliveira; J. Armengol
Thirty-one loquat orchards (Eriobotrya japonica ‘Algerie’) with plants exhibiting decline symptoms were surveyed between 2004 and 2007 in the province of Alicante, Spain. Twenty-eight representative isolates with Cylindrocarpon-like asexual morphs recovered from affected roots were included in this study, with the objective to characterize them by means of phenotypical characterization, DNA analysis and pathogenicity tests. Dactylonectria alcacerensis, D. torresensis and Ilyonectria robusta were identified based on morphological and cultural characteristics as well as DNA sequence data for part of histone H3, with D. torresensis the most frequent species. All of them are reported for the first time on loquat, and I. robusta is reported for the first time in Spain. In addition, one species is newly described, Cylindrodendrum alicantinum. Pathogenicity tests with representative isolates showed that these species were able to induce typical root rot disease symptoms, affecting plant development or even leading to plant death. This research demonstrates the association of species belonging to the genera Cylindrodendrum, Dactylonectria and Ilyonectria with root rot of loquat and loquat decline in the province of Alicante (eastern Spain). This information should be considered for the improvement of the current management strategies against these soil-borne pathogens when establishing new loquat plantations or introducing new susceptible fruit crops in the region.
PLOS ONE | 2016
Ana Rita Vieira; Ana Cabral; Joana Fino; Helena Gil Azinheira; Andreia Loureiro; Pedro Talhinhas; Ana Sofia Pires; Vítor Várzea; Pilar Moncada; Helena Oliveira; Maria do Céu Silva; Octávio S. Paulo; Dora Batista
Colletotrichum kahawae is an emergent fungal pathogen causing severe epidemics of Coffee Berry Disease on Arabica coffee crops in Africa. Currently, the molecular mechanisms underlying the Coffea arabica—C. kahawae interaction are still poorly understood, as well as the differences in pathogen aggressiveness, which makes the development of functional studies for this pathosystem a crucial step. Quantitative real time PCR (qPCR) has been one of the most promising approaches to perform gene expression analyses. However, proper data normalization with suitable reference genes is an absolute requirement. In this study, a set of 8 candidate reference genes were selected based on two different approaches (literature and Illumina RNA-seq datasets) to assess the best normalization factor for qPCR expression analysis of C. kahawae samples. The gene expression stability of candidate reference genes was evaluated for four isolates of C. kahawae bearing different aggressiveness patterns (Ang29, Ang67, Zim12 and Que2), at different stages of fungal development and key time points of the plant-fungus interaction process. Gene expression stability was assessed using the pairwise method incorporated in geNorm and the model-based method used by NormFinder software. For C. arabica—C. kahawae interaction samples, the best normalization factor included the combination of PP1, Act and ck34620 genes, while for C. kahawae samples the combination of PP1, Act and ck20430 revealed to be the most appropriate choice. These results suggest that RNA-seq analyses can provide alternative sources of reference genes in addition to classical reference genes. The analysis of expression profiles of bifunctional catalase-peroxidase (cat2) and trihydroxynaphthalene reductase (thr1) genes further enabled the validation of the selected reference genes. This study provides, for the first time, the tools required to conduct accurate qPCR studies in C. kahawae considering its aggressiveness pattern, developmental stage and host interaction.
Swarm and evolutionary computation | 2017
Sara Silva; Leonardo Vanneschi; Ana Cabral; Maria João M. Vasconcelos
Abstract Data gathered in the real world normally contains noise, either stemming from inaccurate experimental measurements or introduced by human errors. Our work deals with classification data where the attribute values were accurately measured, but the categories may have been mislabeled by the human in several sample points, resulting in unreliable training data. Genetic Programming (GP) compares favorably with the Classification and Regression Trees (CART) method, but it is still highly affected by these errors. Despite consistently achieving high accuracy in both training and test sets, many classification errors are found in a later validation phase, revealing a previously hidden overfitting to the erroneous data. Furthermore, the evolved models frequently output raw values that are far from the expected range. To improve the behavior of the evolved models, we extend the original training set with additional sample points where the class label is unknown, and devise a simple way for GP to use this additional information and learn in a semi-supervised manner. The results are surprisingly good. In the presence of the exact same mislabeling errors, the additional unlabeled data allowed GP to evolve models that achieved high accuracy also in the validation phase. This is a brand new approach to semi-supervised learning that opens an array of possibilities for making the most of the abundance of unlabeled data available today, in a simple and inexpensive way.
Frontiers in Plant Science | 2017
Dora Batista; Diogo N. Silva; Ana Rita Vieira; Ana Cabral; Ana Sofia Pires; Andreia Loureiro; Leonor Guerra-Guimarães; Ana Paula Pereira; Helena Gil Azinheira; Pedro Talhinhas; Maria do Céu Silva; Vítor Várzea
Colletotrichum kahawae Waller and Bridge is a highly aggressive and specialized fungal pathogen of coffee, causing the devastating Coffee Berry Disease (CBD), particularly at high altitudes. The disease arises from the unique ability of the pathogen to infect green developing coffee berries. This pathogen is currently confined to the African continent in all countries that grow Arabica coffee (Coffea arabica L.), leading to up to 80% yield losses, if no control measures are applied (Silva et al., 2006; Vossen and Walyaro, 2009; Hindorf and Omondi, 2011). For such huge economic impact, it is ranked as a quarantine pathogen and even as a biological weapon (Australia Group, 2014). Consequently, the pathogens potential dispersal to other Arabica coffee cultivation regions is greatly feared, particularly to those at high altitude also found in Latin America and Asia. Recently, this recognized species was brought down to a subspecific level (C. kahawae subsp. kahawae) based on molecular data (Weir et al., 2012), clustering together with a generalist and cosmopolitan group of Colletotrichum isolates unable to cause CBD (C. kahawae subsp. ciggaro). Since then a growing number of studies have reported the identification of C. kahawae in various hosts and regions of the world (Liu et al., 2013; Afanador-Kafuri et al., 2014; Mosca et al., 2014; Schena et al., 2014; Ismail et al., 2015; Garibaldi et al., 2016a,b; Perrone et al., 2016). Although these reports are referring to C. kahawae subsp. ciggaro, some of them could not distinguish the pathogen at the subspecific level, and this is leading to a wave of confusion of whether the long accepted species C. kahawae, the CBD pathogen, has escaped from Africa and extended its host range. Given the extreme impact that this situation may trigger and the subsequent biosecurity implications, there is a practical need to completely distinguish these pathogens taxonomically as to avoid the risk of misidentification, and caution should be taken on assigning/reassigning taxonomic ranking and nomenclature. Here we consider the evidences sustaining and contradicting the classification proposed by Weir et al. (2012), and discuss the risks and practical implications of changing the CBD pathogens species status in a plant pathology context.
Journal of Geophysical Research | 2003
João M. N. Silva; José M. C. Pereira; Ana Cabral; Ana C. L. Sá; Maria J. Vasconcelos; Bernardo Mota; Jean-Marie Grégoire