Browsing by Author "Ferrada, E."

Now showing 1 - 7 of 7
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    Diaporthe species identified from postharvest rot on kiwifruits during long term storage
    (American Phytopathological Soc, 2014) Díaz, G. A.; Latorre Guzmán, Bernardo; Jara, S.; Ferrada, E.; Naranjo, P.; Zoffoli Guerra, Juan Pablo
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    Effective knowledge-based potentials
    (2009) Ferrada, E.; Melo Ledermann, Francisco Javier
    Empirical or knowledge-based potentials have many applications in structural biology such as the prediction of protein structure, protein–protein, and protein–ligand interactions and in the evaluation of stability for mutant proteins, the assessment of errors in experimentally solved structures, and the design of new proteins. Here, we describe a simple procedure to derive and use pairwise distance-dependent potentials that rely on the definition of effective atomic interactions, which attempt to capture interactions that are more likely to be physically relevant. Based on a difficult benchmark test composed of proteins with different secondary structure composition and representing many different folds, we show that the use of effective atomic interactions significantly improves the performance of potentials at discriminating between native and near-native conformations. We also found that, in agreement with previous reports, the potentials derived from the observed effective atomic interactions in native protein structures contain a larger amount of mutual information. A detailed analysis of the effective energy functions shows that atom connectivity effects, which mostly arise when deriving the potential by the incorporation of those indirect atomic interactions occurring beyond the first atomic shell, are clearly filtered out. The shape of the energy functions for direct atomic interactions representing hydrogen bonding and disulfide and salt bridges formation is almost unaffected when effective interactions are taken into account. On the contrary, the shape of the energy functions for indirect atom interactions (i.e., those describing the interaction between two atoms bound to a direct interacting pair) is clearly different when effective interactions are considered. Effective energy functions for indirect interacting atom pairs are not influenced by the shape or the energy minimum observed for the corresponding direct interacting atom pair. Our results suggest that the dependency between the signals in different energy functions is a key aspect that need to be addressed when empirical energy functions are derived and used, and also highlight the importance of additivity assumptions in the use of potential energy functions.
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    First report of diaporthe novem causing postharvest rot of kiwifruit during controlled atmosphere storage in Chile
    (The American Phytopathological Society, 2014) Díaz, G. A.; Latorre Guzmán, Bernardo; Jara, S.; Ferrada, E.; Naranjo, P.; Rodríguez, J.; Zoffoli Guerra, Juan Pablo
    Chile is considered the third major exporter of kiwifruits (Actinidia deliciosa (A. Chev.) C. F. Liang & A. R. Ferguson) worldwide after Italy and New Zealand (1). The genus Diaporthe Nitschke (anamorph: genus Phomopsis) has been reported as causing postharvest rot in kiwifruit (4). During the current study, 1,400 fruits arbitrarily collected from seven controlled atmosphere (CA) rooms after 90 days of storage conditions (2% O2, 5% CO2) determined that 21.5% of the fruit were affected by decay and 0.86% developed symptoms different than those caused by Botrytis cinerea, the main postharvest pathogen associated to kiwifruit. Symptoms were soft rot with brown skin that started at the stem-end and in severe cases affected the entire fruit. Internally, affected fruit showed browning and watery tissues. Twelve affected fruits were surface disinfested (75% ethanol) and small pieces of internal rotten tissues were placed on acidified potato dextrose agar (APDA) for 7 days at 20°C. Twelve isolates were obtained, and four of them were identified morphologically and molecularly as Diaporthe ambigua, a species that has been previously described causing rot in stored kiwifruits in Chile (2). However, eight other flat, white to grayish colonies with sparse dirty-white aerial mycelium at the edge of the dish were obtained (3). Black pycnidia contained unicellular, hyaline, biguttulate, oval to cylindrical alpha conidia, with obtuse ends of (7.9) 6.7 (5.3) × (2.9) 2.5 (2.1) μm (n = 30). These isolates were tentatively identified as a Diaporthe sp. The species identification was determined by sequencing comparison of the internal transcribed spacer (ITS1-5.8S-ITS2) region of the rDNA (GenBank Accession Nos. KJ210020 to 24, KJ210027, and KJ210033) and a portion of beta-tubulin (BT) (KJ210034 to 38, KJ210041, and KJ210047) using primers ITS4-ITS5 and Bt2a-Bt2b, respectively. BLAST analyses showed 99 to 100% identity with D. novem J.M. Santos, Vrandecic & A.J.L Phillips reference ex-type (KC343156 and KC344124 for ITS and BT, respectively) (3). Eighteen mature kiwifruits cv. Hayward were inoculated using a sterile cork borer on the surface of the fruit and placing 5-mm agar plugs with mycelial of D. novem (DN-1-KF). An equal number of fruits treated with sterile agar plugs were used as negative controls. After 30 days at 0°C under CA, all inoculated fruit showed rot symptoms with lesions 7.8 to 16.4 mm in diameter. The same D. novem isolate was inoculated with 30 μl of a conidial suspension (106 conidia/ml) on the surface of 18 ripe kiwifruits that were previously wounded and non-wounded as described above. An equal number of wounded and non-wounded fruits, treated with 30 μl sterile water, were used as negative controls. All inoculated wounded fruits developed rot symptoms with necrotic lesions of 14.1 to 20.2 mm of diameter after 14 days at 25°C. Inoculated non-wounded and negative control fruits remained symptomless. Koch's postulates were fulfilled by re-isolating D. novem only from the symptomatic fruits. To our knowledge, this is the first report of rot caused by D. novem on kiwifruit during cold storage in Chile and worldwide. Therefore, both Diaporthe species appears to be associated to Diaporthe rot of kiwifruit in Chile.
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    Identification and Characterization of Diaporthe ambigua, D-australafricana, D-novem, and D-rudis Causing a Postharvest Fruit Rot in Kiwifruit
    (2017) Diaz, G.; Latorre G., Bernardo; Lolas, M.; Ferrada, E.; Naranjo Gatica, María Paulina; Zoffoli, Juan Pablo
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    Nonbonded terms extrapolated from nonlocal knowledge-based energy functions improve error detection in near-native protein structure models
    (2007) Ferrada, E.; Melo Ledermann, Francisco Javier
    The accurate assessment of structural errors plays a key role in protein structure prediction, constitutes the first step of protein structure refinement, and has a major impact on subsequent functional inference from structural data. In this study, we assess and compare the ability of different full atom knowledge-based potentials to detect small and localized errors in comparative protein structure models of known accuracy. We have evaluated the effect of incorporating close nonbonded pairwise atom terms on the task of classifying residue modeling accuracy. Since the direct and unbiased derivation of close nonbonded terms from current experimental data is not possible, we extrapolated those terms from the corresponding pseudo-energy functions of a nonlocal knowledge-based potential. It is shown that this methodology clearly improves the detection of errors in protein models, suggesting that a proper description of close nonbonded terms is important to achieve a more complete and accurate description of native protein conformations. The use of close nonbonded terms directly derived from experimental data exhibited a poor performance, demonstrating that these terms cannot be accurately obtained by using the current data and methodology. Some external knowledge-based energy functions that are widely used in model assessment also performed poorly, which suggests that the benchmark of models and the specific error detection task tested in this study constituted a difficult challenge. The methodology presented here could be useful to detect localized structural errors not only in high-quality protein models, but also in experimental protein structures.
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    StAR: a simple tool for the statistical comparison of ROC curves
    (2008) Vergara, I. A.; Norambuena, T.; Ferrada, E.; Slater, A. W.; Melo Ledermann, Francisco Javier
    Background As in many different areas of science and technology, most important problems in bioinformatics rely on the proper development and assessment of binary classifiers. A generalized assessment of the performance of binary classifiers is typically carried out through the analysis of their receiver operating characteristic (ROC) curves. The area under the ROC curve (AUC) constitutes a popular indicator of the performance of a binary classifier. However, the assessment of the statistical significance of the difference between any two classifiers based on this measure is not a straightforward task, since not many freely available tools exist. Most existing software is either not free, difficult to use or not easy to automate when a comparative assessment of the performance of many binary classifiers is intended. This constitutes the typical scenario for the optimization of parameters when developing new classifiers and also for their performance validation through the comparison to previous art. Results In this work we describe and release new software to assess the statistical significance of the observed difference between the AUCs of any two classifiers for a common task estimated from paired data or unpaired balanced data. The software is able to perform a pairwise comparison of many classifiers in a single run, without requiring any expert or advanced knowledge to use it. The software relies on a non-parametric test for the difference of the AUCs that accounts for the correlation of the ROC curves. The results are displayed graphically and can be easily customized by the user. A human-readable report is generated and the complete data resulting from the analysis are also available for download, which can be used for further analysis with other software. The software is released as a web server that can be used in any client platform and also as a standalone application for the Linux operating system. Conclusion A new software for the statistical comparison of ROC curves is released here as a web server and also as standalone software for the LINUX operating system.