scholarly journals CitrusKB: A Comprehensive Knowledge Base for Transcriptome and Interactome of Citrus spp. Infected by Xanthomonas citri subsp. citri at Different Infection Stages

2020 ◽  
Author(s):  
Adriano Ferrasa ◽  
Mayara M. Murata ◽  
Teresa D. C. G. Cofre ◽  
Juliana S. Cavallini ◽  
Gustavo Peron ◽  
...  
Keyword(s):  
Knowledge Base ◽  
Citrus Canker ◽  
Limited Information ◽  
Xanthomonas Citri ◽  
Comprehensive Knowledge ◽  
Genetic Mechanisms ◽  
Serious Disease ◽  
Canker Development ◽  
User Friendly

AbstractCitrus canker type A is a serious disease caused by Xanthomonas citri subsp. citri (X. citri), which is responsible for severe losses to growers and to the citrus industry worldwide. To date, no canker-resistant citrus genotypes are available, and there is limited information regarding the molecular and genetic mechanisms involved in the early stages of the citrus canker development. Here, we present the knowledge base for transcriptome of in vivo citrus interactome, the CitrusKB. This is the first in vivo interactome database for different citrus cultivars, and it was produced to provide a valuable source of information on citrus and their interaction with the citrus canker bacterium X. citri. The database provides tools for a user-friendly web interface to search and analyze a large amount of information regarding eight citrus cultivars with distinct levels of susceptibility to the disease and their interaction, at different stages of infection, with the citrus canker bacterium X. citri. Currently, CitrusKB comprises a reference citrus genome and its transcriptome, expressed transcripts, pseudogenes and predicted genomic variations (SNPs and SSRs). The updating process will continue by incorporating annotations and analysis tools. We expect that CitrusKB may substantially contribute to the area of citrus genomics. CitrusKB is accessible at http://bioinfo.deinfo.uepg.br/citrus. Users can download all the generated raw sequences and generated datasets by this study from the CitrusKB website.

scholarly journals CitrusKB: a comprehensive knowledge base for transcriptome and interactome of Citrus spp. infected by Xanthomonas citri subsp. citri at different infection stages

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Adriano Ferrasa ◽  
Mayara M Murata ◽  
Teresa D C G Cofre ◽  
Juliana S Cavallini ◽  
Gustavo Peron ◽  
...  
Keyword(s):  
Knowledge Base ◽  
Citrus Canker ◽  
Limited Information ◽  
Xanthomonas Citri ◽  
Comprehensive Knowledge ◽  
Genetic Mechanisms ◽  
Serious Disease ◽  
Canker Development ◽  
User Friendly

Abstract Citrus canker type A is a serious disease caused by Xanthomonas citri subsp. citri (X. citri), which is responsible for severe losses to growers and to the citrus industry worldwide. To date, no canker-resistant citrus genotypes are available, and there is limited information regarding the molecular and genetic mechanisms involved in the early stages of the citrus canker development. Here, we present the CitrusKB knowledge base. This is the first in vivo interactome database for different citrus cultivars, and it was produced to provide a valuable resource of information on citrus and their interaction with the citrus canker bacterium X. citri. CitrusKB provides tools for a user-friendly web interface to let users search and analyse a large amount of information regarding eight citrus cultivars with distinct levels of susceptibility to the disease, with controls and infected plants at different stages of infection by the citrus canker bacterium X. citri. Currently, CitrusKB comprises a reference citrus genome and its transcriptome, expressed transcripts, pseudogenes and predicted genomic variations (SNPs and SSRs). The updating process will continue over time by the incorporation of novel annotations and analysis tools. We expect that CitrusKB may substantially contribute to the field of citrus genomics. CitrusKB is accessible at http://bioinfo.deinfo.uepg.br/citrus. Users can download all the generated raw sequences and generated datasets by this study from the CitrusKB website.

scholarly journals Bismerthiazol Inhibits Xanthomonas citri subsp. citri Growth and Induces Differential Expression of Citrus Defense-Related Genes

2016 ◽  
Vol 106 (7) ◽  
pp. 693-701 ◽  
Author(s):  
Xiaoyue Yu ◽  
Cheryl M. Armstrong ◽  
Mingguo Zhou ◽  
Yongping Duan
Keyword(s):  
Defense Response ◽  
Citrus Canker ◽  
Economic Losses ◽  
Marker Genes ◽  
Flavonoid Pathway ◽  
Xanthomonas Citri ◽  
Pr Genes ◽  
Rice Bacterial Blight ◽  
Host Defense Response ◽  
Serious Disease

Citrus canker, caused by Xanthomonas citri ssp. citri, is a serious disease that causes substantial economic losses to the citrus industry worldwide. The bactericide bismerthiazol has been used to control rice bacterial blight (X. oryzae pv. oryzae). In this paper, we demonstrate that bismerthiazol can effectively control citrus canker by both inhibiting the growth of X. citri ssp. citri and triggering the plant’s host defense response through the expression of several pathogenesis-related genes (PR1, PR2, CHI, and RpRd1) and the nonexpresser of PR genes (NPR1, NPR2, and NPR3) in ‘Duncan’ grapefruit, especially at early treatment times. In addition, we found that bismerthiazol induced the expression of the marker genes CitCHS and CitCHI in the flavonoid pathway and the PAL1 (phenylalanine ammonia lyase 1) gene in the salicylic acid (SA) biosynthesis pathway at different time points. Moreover, bismerthiazol also induced the expression of the priming defense-associated gene AZI1. Taken together, these results indicate that the induction of the defense response in ‘Duncan’ grapefruit by bismerthiazol may involve the SA signaling pathway and the priming defense and that bismerthiazol may serve as an alternative to copper bactericides for the control of citrus canker.

scholarly journals In Vitro and In Vivo Antibacterial Activity of Some Organic and Inorganic Salts Against Asiatic Citrus Canker Agent Xanthomonas Citri Subsp. Citri

2014 ◽  
Vol 2 (6) ◽  
pp. 296
Author(s):  
Vahideh Hasabi ◽  
Hossein Askari ◽  
Seyed Mehdi Alavi ◽  
Masood Soltani Najafabadi
Keyword(s):  
Antibacterial Activity ◽  
Citrus Canker ◽  
Inhibitory Effect ◽  
Inorganic Salts ◽  
Xanthomonas Citri ◽  
Canker Disease ◽  
Growth Inhibitory ◽  
Iron And Zinc

Asiatic citrus canker caused by Xanthomonas citri subsp. citri is becoming a disease of high economic impact, affecting all types of important citrus crops. In this study, the potential antibacterial activity of ten organic and inorganic salts on X. citri subsp. citri and on citrus canker disease development was evaluated. Among the salt compounds, copper, iron and zinc inorganic salts particularly zinc (with the highest diameter of inhibition, the lowest MIC and MBC values and the highest bacterial growth inhibitory effect) had direct antibacterial activity and strongly reduced the development of canker disease and bacterial population of lime plants.

scholarly journals Citrus MAF1, a Repressor of RNA Polymerase III, Binds the Xanthomonas citri Canker Elicitor PthA4 and Suppresses Citrus Canker Development

2013 ◽  
Vol 163 (1) ◽  
pp. 232-242 ◽  
Author(s):  
Adriana Santos Soprano ◽  
Valeria Yukari Abe ◽  
Juliana Helena Costa Smetana ◽  
Celso Eduardo Benedetti
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Iii ◽  
Citrus Canker ◽  
Xanthomonas Citri ◽  
Polymerase Iii ◽  
Canker Development

scholarly journals Hippocampome.org: a knowledge base of neuron types in the rodent hippocampus

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Diek W Wheeler ◽  
Charise M White ◽  
Christopher L Rees ◽  
Alexander O Komendantov ◽  
David J Hamilton ◽  
...  
Keyword(s):  
Knowledge Base ◽  
Hippocampal Formation ◽  
Literature Mining ◽  
Extensive Literature ◽  
Systematic Analysis ◽  
Synaptic Specificity ◽  
Formidable Challenge ◽  
Comprehensive Knowledge ◽  
User Friendly ◽  
Machine Readable

Hippocampome.org is a comprehensive knowledge base of neuron types in the rodent hippocampal formation (dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex). Although the hippocampal literature is remarkably information-rich, neuron properties are often reported with incompletely defined and notoriously inconsistent terminology, creating a formidable challenge for data integration. Our extensive literature mining and data reconciliation identified 122 neuron types based on neurotransmitter, axonal and dendritic patterns, synaptic specificity, electrophysiology, and molecular biomarkers. All ∼3700 annotated properties are individually supported by specific evidence (∼14,000 pieces) in peer-reviewed publications. Systematic analysis of this unprecedented amount of machine-readable information reveals novel correlations among neuron types and properties, the potential connectivity of the full hippocampal circuitry, and outstanding knowledge gaps. User-friendly browsing and online querying of Hippocampome.org may aid design and interpretation of both experiments and simulations. This powerful, simple, and extensible neuron classification endeavor is unique in its detail, utility, and completeness.

Personalized cloud service review analysis based on modularized ontology

2020 ◽  
Vol 44 (5) ◽  
pp. 953-975
Author(s):  
Emna Ben-Abdallah ◽  
Khouloud Boukadi ◽  
Mohamed Hammami ◽  
Mohamed Hedi Karray
Keyword(s):  
Knowledge Base ◽  
Positive Impact ◽  
Cloud Service ◽  
Service Evaluation ◽  
End Users ◽  
Cloud Services ◽  
Limited Information ◽  
Content Type ◽  
Ontology Language ◽  
Modular Ontology

PurposeThe purpose of this paper is to analyze cloud reviews according to the end-user context and requirements.Design/methodology/approachpropose a comprehensive knowledge base composed of interconnected Web Ontology Language, namely, modular ontology for cloud service opinion analysis (SOPA). The SOPA knowledge base will be the basis of context-aware cloud service analysis using consumers' reviews. Moreover, the authors provide a framework to evaluate cloud services based on consumers' reviews opinions.FindingsThe findings show that there is a positive impact of personalizing the cloud service analysis by considering the reviewers' contexts in the performance of the framework. The authors also proved that the SOPA-based framework outperforms the available cloud review sites in term of precision, recall and F-measure.Research limitations/implicationsLimited information has been provided in the semantic web literature about the relationships between the different domains and the details on how that can be used to evaluate cloud service through consumer reviews and latent opinions. Furthermore, existing approaches are lacking lightweight and modular mechanisms which can be utilized to effectively exploit information existing in social media.Practical implicationsThe SOPA-based framework facilitates the opinion based service evaluation through a large number of consumer's reviews and assists the end-users in analyzing services as per their requirements and their own context.Originality/valueThe SOPA ontology is capable of representing the content of a product/service as well as its related opinions, which are extracted from the customer's reviews written in a specific context. Furthermore, the SOPA-based framework facilitates the opinion based service evaluation through a large number of consumer's reviews and assists the end-users in analyzing services as per their requirements and their own context.

scholarly journals The pharmacokinetics of [18F]UCB-H revisited in the healthy non-human primate brain

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sébastien Goutal ◽  
Martine Guillermier ◽  
Guillaume Becker ◽  
Mylène Gaudin ◽  
Yann Bramoullé ◽  
...  
Keyword(s):  
Slow Component ◽  
Specific Binding ◽  
Compartment Model ◽  
Brain Regions ◽  
Volume Of Distribution ◽  
Pharmacokinetic Data ◽  
Limited Information ◽  
Positron Emission ◽  
Human Primate

Abstract Background Positron Emission Tomography (PET) imaging of the Synaptic Vesicle glycoprotein (SV) 2A is a new tool to quantify synaptic density. [18F]UCB-H was one of the first promising SV2A-ligands to be labelled and used in vivo in rodent and human, while limited information on its pharmacokinetic properties is available in the non-human primate. Here, we evaluate the reliability of the three most commonly used modelling approaches for [18F]UCB-H in the non-human cynomolgus primate, adding the coupled fit of the non-displaceable distribution volume (VND) as an alternative approach to improve unstable fit. The results are discussed in the light of the current state of SV2A PET ligands. Results [18F]UCB-H pharmacokinetic data was optimally fitted with a two-compartment model (2TCM), although the model did not always converge (large total volume of distribution (VT) or large uncertainty of the estimate). 2TCM with coupled fit K1/k2 across brain regions stabilized the quantification, and confirmed a lower specific signal of [18F]UCB-H compared to the newest SV2A-ligands. However, the measures of VND and the influx parameter (K1) are similar to what has been reported for other SV2A ligands. These data were reinforced by displacement studies using [19F]UCB-H, demonstrating only 50% displacement of the total [18F]UCB-H signal at maximal occupancy of SV2A. As previously demonstrated in clinical studies, the graphical method of Logan provided a more robust estimate of VT with only a small bias compared to 2TCM. Conclusions Modeling issues with a 2TCM due to a slow component have previously been reported for other SV2A ligands with low specific binding, or after blocking of specific binding. As all SV2A ligands share chemical structural similarities, we hypothesize that this slow binding component is common for all SV2A ligands, but only hampers quantification when specific binding is low.

scholarly journals Mechanistic physiology-based pharmacokinetic modeling to elucidate vincristine-induced peripheral neuropathy following treatment with novel kinase inhibitors

2021 ◽  
Author(s):  
Venkatesh Pilla Reddy ◽  
Adrian J. Fretland ◽  
Diansong Zhou ◽  
Shringi Sharma ◽  
Buyun Chen ◽  
...  
Keyword(s):  
Peripheral Neuropathy ◽  
Kinase Inhibitors ◽  
Pbpk Model ◽  
Model Development ◽  
Limited Information ◽  
Time Curve ◽  
Btk Inhibitor ◽  
Chop Therapy

Abstract Purpose Limited information is available regarding the drug–drug interaction (DDI) potential of molecular targeted agents and rituximab plus cyclophosphamide, doxorubicin (hydroxydaunorubicin), vincristine (Oncovin), and prednisone (R-CHOP) therapy. The addition of the Bruton tyrosine kinase (BTK) inhibitor ibrutinib to R-CHOP therapy results in increased toxicity versus R-CHOP alone, including higher incidence of peripheral neuropathy. Vincristine is a substrate of P-glycoprotein (P-gp, ABCB1); drugs that inhibit P-gp could potentially cause increased toxicity when co-administered with vincristine through DDI. While the combination of the BTK inhibitor acalabrutinib and R-CHOP is being explored clinically, the DDI potential between these therapies is unknown. Methods A human mechanistic physiology-based pharmacokinetic (PBPK) model of vincristine following intravenous dosing was developed to predict potential DDI interactions with combination therapy. In vitro absorption, distribution, metabolism, and excretion and in vivo clinical PK parameters informed PBPK model development, which was verified by comparing simulated vincristine concentrations with observed clinical data. Results While simulations suggested no DDI between vincristine and ibrutinib or acalabrutinib in plasma, simulated vincristine exposure in muscle tissue was increased in the presence of ibrutinib but not acalabrutinib. Extrapolation of the vincristine mechanistic PBPK model to other P-gp substrates further suggested DDI risk when ibrutinib (area under the concentration–time curve [AUC] ratio: 1.8), but not acalabrutinib (AUC ratio: 0.92), was given orally with venetoclax or digoxin. Conclusion Overall, these data suggest low DDI risk between acalabrutinib and P-gp substrates with negligible increase in the potential risk of vincristine-induced peripheral neuropathy when acalabrutinib is added to R-CHOP therapy.

Chlorine dioxide, peroxyacetic acid, and calcium oxychloride for post-harvest decontamination of citrus fruit against Xanthomonas citri subsp. citri, causal agent of citrus canker

2021 ◽  
Vol 146 ◽  
pp. 105679
Author(s):  
Franklin Behlau ◽  
Alexandre Paloschi ◽  
Tamiris G.S. Marin ◽  
Talita A. Santos ◽  
Henrique Ferreira ◽  
...  
Keyword(s):  
Chlorine Dioxide ◽  
Citrus Fruit ◽  
Citrus Canker ◽  
Causal Agent ◽  
Peroxyacetic Acid ◽  
Xanthomonas Citri ◽  
Post Harvest

scholarly journals Modified Monosaccharides Content of Xanthan Gum Impairs Citrus Canker Disease by Affecting the Epiphytic Lifestyle of Xanthomonas citri subsp. citri

2021 ◽  
Vol 9 (6) ◽  
pp. 1176
Author(s):  
Simone Cristina Picchi ◽  
Laís Moreira Granato ◽  
Maria Júlia Festa Franzini ◽  
Maxuel Oliveira Andrade ◽  
Marco Aurélio Takita ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Xanthan Gum ◽  
Wild Type Strain ◽  
Natural Infection ◽  
Citrus Canker ◽  
Wild Type ◽  
Xanthomonas Citri ◽  
Canker Disease ◽  
Key Enzyme ◽  
Citrus Canker Disease

Xanthomonas citri subsp. citri (X. citri) is a plant pathogenic bacterium causing citrus canker disease. The xanA gene encodes a phosphoglucomutase/phosphomannomutase protein that is a key enzyme required for the synthesis of lipopolysaccharides and exopolysaccharides in Xanthomonads. In this work, firstly we isolated a xanA transposon mutant (xanA::Tn5) and analyzed its phenotypes as biofilm formation, xanthan gum production, and pathogenesis on the sweet orange host. Moreover, to confirm the xanA role in the impaired phenotypes we further produced a non-polar deletion mutant (ΔxanA) and performed the complementation of both xanA mutants. In addition, we analyzed the percentages of the xanthan gum monosaccharides produced by X. citri wild-type and xanA mutant. The mutant strain had higher ratios of mannose, galactose, and xylose and lower ratios of rhamnose, glucuronic acid, and glucose than the wild-type strain. Such changes in the saccharide composition led to the reduction of xanthan yield in the xanA deficient strain, affecting also other important features in X. citri, such as biofilm formation and sliding motility. Moreover, we showed that xanA::Tn5 caused no symptoms on host leaves after spraying, a method that mimetics the natural infection condition. These results suggest that xanA plays an important role in the epiphytical stage on the leaves that is essential for the successful interaction with the host, including adaptive advantage for bacterial X. citri survival and host invasion, which culminates in pathogenicity.

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