Effector Biology in Focus: A Primer for Computational Prediction and Functional Characterization.

Plant-pathogen interactions are controlled by a multilayered immune system, which is activated by pathogen recognition in the host. Pathogens secrete effector molecules to interfere with the immune recognition or signaling network and reprogram cell structure or metabolism. Understanding the effector repertoires of diverse pathogens will contribute to unraveling the molecular mechanism of virulence and developing sustainable disease-control strategies for crops and natural ecosystems. Effector functionality has been investigated extensively in only a small number of pathogen species. However, many more pathogen genomes are becoming available, and much can be learned from a broader view of effector biology in diverse pathosystems. The purpose of this review is to summarize methodology for computational prediction of protein effectors, functional characterization of effector proteins and their targets, and the use of effectors as probes to screen for new sources of host resistance. Although these techniques were generally developed in model pathosystems, many of the approaches are directly applicable for exploration and exploitation of effector biology in pathosystems that are less well studied. We hope to facilitate such exploration, which will broaden understanding of the mechanisms that underpin the biological diversity of plant-pathogen interactions, and maximize the impact of new approaches that leverage effector biology for disease control.

Deep Sequencing Analysis of RNAs from Citrus Plants Grown in a Citrus Sudden Death-Affected Area Reveals Diverse Known and Putative Novel Viruses.

Citrus sudden death (CSD) has caused the death of approximately four million orange trees in a very important citrus region in Brazil. Although its etiology is still not completely clear, symptoms and distribution of affected plants indicate a viral disease. In a search for viruses associated with CSD, we have performed a comparative high-throughput sequencing analysis of the transcriptome and small RNAs from CSD-symptomatic and -asymptomatic plants using the Illumina platform. The data revealed mixed infections that included Citrus tristeza virus (CTV) as the most predominant virus, followed by the Citrus sudden death-associated virus (CSDaV), Citrus endogenous pararetrovirus (CitPRV) and two putative novel viruses tentatively named Citrus jingmen-like virus (CJLV), and Citrus virga-like virus (CVLV). The deep sequencing analyses were sensitive enough to differentiate two genotypes of both viruses previously associated with CSD-affected plants: CTV and CSDaV. Our data also showed a putative association of the CSD-symptomatic plants with a specific CSDaV genotype and a likely association with CitPRV as well, whereas the two putative novel viruses showed to be more associated with CSD-asymptomatic plants. This is the first high-throughput sequencing-based study of the viral sequences present in CSD-affected citrus plants, and generated valuable information for further CSD studies.

PAMPs, PRRs, effectors and R-genes associated with citrus-pathogen interactions.

BACKGROUND: Recent application of molecular-based technologies has considerably advanced our understanding of complex processes in plant-pathogen interactions and their key components such as PAMPs, PRRs, effectors and R-genes. To develop novel control strategies for disease prevention in citrus, it is essential to expand and consolidate our knowledge of the molecular interaction of citrus plants with their pathogens. SCOPE: This review provides an overview of our understanding of citrus plant immunity, focusing on the molecular mechanisms involved in the interactions with viruses, bacteria, fungi, oomycetes and vectors related to the following diseases: tristeza, psorosis, citrus variegated chlorosis, citrus canker, huanglongbing, brown spot, post-bloom, anthracnose, gummosis and citrus root rot.

Characterization of Pharmaceuticals and Personal Care products in hospital effluent and waste water influent/effluent by direct-injection LC-MS-MS.

Two USEPA Regional Laboratories developed direct-injection LC/MS/MS methods to measure Pharmaceuticals and Personal Care Products (PPCPs) in water matrices. Combined, the laboratories were prepared to analyze 185 PPCPs (with 74 overlapping) belonging to more than 20 therapeutical categories with reporting limits at low part-per-trillion. In partnership with Suffolk County in NY, the laboratories conducted PPCP analysis on 72 samples belonging to 4 Water Systems (WS). Samples were collected at different stages of the WS (hospital effluents, WWTP influents/effluents) to assess PPCP relevance in hospital discharges, impact on WWTP performance and potential ecological risk posed by analytes not eliminated during treatment. Major findings include: a) acceptable accuracy between the two laboratories for most overlapping PPCPs with better agreement for higher concentrations; b) the measurement of PPCPs throughout all investigated WS with total PPCP concentrations ranging between 324 and 965 µg L(-1) for hospital effluent, 259 and 573 µg L(-1) for WWTP influent and 19 and 118 µg L(-1) for WWTP effluent; c) the variable contribution of hospital effluents to the PPCP loads into the WWTP influents (contribution ranging between 1% (WS-2) and 59% (WS-3); d) the PPCP load reduction after treatment for all WS reaching more than 95% for WS using activated sludge processes (WS-2 and WS-4), with inflow above 6500 m(3) d(-1), and having a lower percentage of hospital effluent in the WWTP influent; e) the relevance of four therapeutical categories for the PPCP load in WWTP effluents (analgesics, antidiabetics, antiepileptics and psychoanaleptics); and f) the risk quotients calculated using screening-level Predicted Non Effect Concentration indicate that WWTP effluents contain 33 PPCPs with potential medium to high ecological risk. To our knowledge no other monitoring investigation published in the scientific literature uses direct-injection methods to cover as many PPCPs and therapeutical categories in different types of WS.