Sequential delivery of host-induced virulence effectors by appressoria and intracellular hyphae of the phytopathogen Colletotrichum higginsianum.

Phytopathogens secrete effector proteins to manipulate their hosts for effective colonization. Hemibiotrophic fungi must maintain host viability during initial biotrophic growth and elicit host death for subsequent necrotrophic growth. To identify effectors mediating these opposing processes, we deeply sequenced the transcriptome of Colletotrichum higginsianum infecting Arabidopsis. Most effector genes are host-induced and expressed in consecutive waves associated with pathogenic transitions, indicating distinct effector suites are deployed at each stage. Using fluorescent protein tagging and transmission electron microscopy-immunogold labelling, we found effectors localised to stage-specific compartments at the host-pathogen interface. In particular, we show effectors are focally secreted from appressorial penetration pores before host invasion, revealing new levels of functional complexity for this fungal organ. Furthermore, we demonstrate that antagonistic effectors either induce or suppress plant cell death. Based on these results we conclude that hemibiotrophy in Colletotrichum is orchestrated through the coordinated expression of antagonistic effectors supporting either cell viability or cell death.

Reduced order constrained optimization (ROCO): clinical application to lung IMRT.

PURPOSE: The authors use reduced-order constrained optimization (ROCO) to create clinically acceptable IMRT plans quickly and automatically for advanced lung cancer patients. Their new ROCO implementation works with the treatment planning system and full dose calculation used at Memorial Sloan-Kettering Cancer Center (MSKCC). The authors have implemented mean dose hard constraints, along with the point-dose and dose-volume constraints that the authors used for our previous work on the prostate. METHODS: ROCO consists of three major steps. First, the space of treatment plans is sampled by solving a series of optimization problems using penalty-based quadratic objective functions. Next, an efficient basis for this space is found via principal component analysis (PCA); this reduces the dimensionality of the problem. Finally, a constrained optimization problem is solved over this basis to find a clinically acceptable IMRT plan. Dimensionality reduction makes constrained optimization computationally efficient. RESULTS: The authors apply ROCO to 12 stage III non-small-cell lung cancer (NSCLC) cases, generating IMRT plans that meet all clinical constraints and are clinically acceptable, and demonstrate that they are competitive with the clinical treatment plans. The authors also test how many samples and PCA modes are necessary to achieve an adequate lung plan, demonstrate the importance of long-range dose calculation for ROCO, and evaluate the performance of nonspecific normal tissue ("rind") constraints in ROCO treatment planning for the lung. Finally, authors show that ROCO can save time for planners, and they estimate that in the clinic, planning using their approach would save a median of 105 min for the patients in the study. CONCLUSIONS: New challenges arise when applying ROCO to the lung site, which include the lack of a class solution, a larger treatment site, an increased number of parameters and beamlets, a variable number of beams and beam arrangement, and the customary use of rinds in clinical plans to avoid high-dose areas outside the PTV. In the authors previous work, use of an approximate dose calculation in the hard constraint optimization sometimes meant that clinical constraints were not met when evaluated with the full dose calculation. This difficulty has been removed in the current work by using the full dose calculation in the hard constraint optimization. The authors have demonstrated that ROCO offers a fast and automatic way to create IMRT plans for advanced NSCLC, which extends their previous application of ROCO to prostate cancer IMRT planning.

Characterization of the full length mRNA coding for Lucina pectinata HbIII revealed an alternative polyadenylation site.

Lucina pectinata is a bivalve mollusk that lives in the Southwestern coast of Puerto Rico and houses intracellular symbiotic bacteria. This peculiar organism contains three types of hemoglobin, each characterized by distinct physico-chemical properties. Hemoglobin I (HbI) is a sulfide-reactive protein that reacts with H(2)S to form ferric hemoglobin sulfide. In contrast, hemoglobin II and III are oxygen-reactive proteins that remain oxygenated in the presence of hydrogen sulfide. The partial coding region contained in the cDNA sequences we have cloned confirmed the L. pectinata HbIII amino sequence reported in the NCBI protein database) with a single amino acid difference (Asn72Asp; AsnE12Asp). The characterization of the full length mRNA coding for L. pectinata HbIII revealed an alternative polyadenylation site and an alternate transcription start site. The open reading frame (ORF) of the HbIII cDNA is composed of 459nts containing 153 codons. The initiation codon is preceded by 62 nts of untranslated region (5'UTR), whereas two 3'UTR regions of 640 nt and 455 nt long were identified, revealing the presence of alternative polyadenylation sites. Isoforms of the 3'UTR of HbIII only differed in the length of their sequences. It has been hypothesized that alternative polyadenylation acts through shortening of mRNA to regulate RNA localization, translation and stability. Interestingly, the HbIII mRNA is the only one of all the hemoglobin mRNAs from L. pectinata characterized so far with more than one 3'UTR. Primer extension products suggest two closely located start sites of HbIII mRNA transcription. We suggest that the L. pectinata hemoglobin genes may be under different cellular controls that direct them to exert their particular functions. These hypotheses need to be tested by functional studies and analysis of the regulatory elements of the cognate genes for L. pectinata hemoglobins.

Diagrammatic scales for the estimation of black node disease severity in common bean / Escalas diagramáticas para a estimativa da gravidade da doença do nó negro no feijão comum

ABSTRACT: The objective of this study was to design two diagrammatic scales for the evaluation of black node disease (Stagonosporopsis hortensis and Boeremia spp.) in common bean (Phaseolus vulgaris L.). The developed scales corresponded to logarithmic intervals (SADL) of seven levels and equal intervals (SADE) of nine levels. These scales were compared to the scale developed by the International Center for Tropical Agriculture (CIAT), which corresponds to a descriptive scale (NoSAD). In the scale validation the accuracy, precision, and concordance of repeatability were determined using Lin's concordance correlation coefficient, whereas inter-rater reproducibility was determined by the overall concordance correlation coefficient (OCCC). It was observed that with the use of the proposed scales, reproducibility and repeatability were significantly improved for inexperienced raters, and reproducibility was improved in the case of experienced raters. Thus, the designed standard area diagrams with equal and logarithmic intervals are a useful tool for estimating severity under field and experimental conditions as part of the study of this patho-system.

RESUMO: O objetivo deste estudo foi delinear duas escalas diagramáticas para avaliação da doença do nó preto (Stagonosporopsis hortensis e Boeremia spp.) em feijoeiro (Phaseolus vulgaris L.). As escalas desenvolvidas corresponderam a intervalos logarítmicos (SADL) de sete níveis e intervalos iguais (SADE) de nove níveis. Essas escalas foram comparadas com a escala desenvolvida pelo Centro Internacional de Agricultura Tropical (CIAT), que corresponde a uma escala descritiva (NoSAD). Na validação da escala, a exatidão, precisão e concordância da repetibilidade foram determinadas usando o coeficiente de correlação de concordância de Lin, enquanto a reprodutibilidade entre avaliadores foi determinada pelo coeficiente de correlação de concordância geral (OCCC). Observou-se que, com o uso das escalas propostas, a reprodutibilidade e a repetibilidade foram significativamente melhoradas para os avaliadores inexperientes, e a reprodutibilidade foi melhorada no caso dos avaliadores experientes. Assim, as escalas diagramáticas projetadas são uma ferramenta útil para estimar a severidade em condições experimentais e de campo como parte do estudo desse sistema patológico.

Characterization and Expression of the Lucina pectinata Oxygen and Sulfide Binding Hemoglobin Genes.

The clam Lucina pectinata lives in sulfide-rich muds and houses intracellular symbiotic bacteria that need to be supplied with hydrogen sulfide and oxygen. This clam possesses three hemoglobins: hemoglobin I (HbI), a sulfide-reactive protein, and hemoglobin II (HbII) and III (HbIII), which are oxygen-reactive. We characterized the complete gene sequence and promoter regions for the oxygen reactive hemoglobins and the partial structure and promoters of the HbI gene from Lucina pectinata. We show that HbI has two mRNA variants, where the 5'end had either a sequence of 96 bp (long variant) or 37 bp (short variant). The gene structure of the oxygen reactive Hbs is defined by having 4-exons/3-introns with conservation of intron location at B12.2 and G7.0 and the presence of pre-coding introns, while the partial gene structure of HbI has the same intron conservation but appears to have a 5-exon/ 4-intron structure. A search for putative transcription factor binding sites (TFBSs) was done with the promoters for HbII, HbIII, HbI short and HbI long. The HbII, HbIII and HbI long promoters showed similar predicted TFBSs. We also characterized MITE-like elements in the HbI and HbII gene promoters and intronic regions that are similar to sequences found in other mollusk genomes. The gene expression levels of the clam Hbs, from sulfide-rich and sulfide-poor environments showed a significant decrease of expression in the symbiont-containing tissue for those clams in a sulfide-poor environment, suggesting that the sulfide concentration may be involved in the regulation of these proteins. Gene expression evaluation of the two HbI mRNA variants indicated that the longer variant is expressed at higher levels than the shorter variant in both environments.

Macrophage derived cystatin B/cathepsin B in HIV replication and neuropathogenesis.

Mononuclear phagocytes including monocytes and macrophages, are important defense components of innate immunity, but can be detrimental in HIV-1 infection by serving as the principal reservoirs of virus in brain and triggering a strong immune response. These viral reservoirs represent a challenge to HIV-1 eradication since they continue producing virus in tissue despite antiretroviral therapy. HIV-1 associated neurocognitive disorders (HAND) involve alterations to the blood-brain barrier and migration of activated HIV-1 infected monocytes to the brain with subsequent induced immune activation response. Our group recently showed that HIV replication in monocyte-derived macrophages is associated with increased cystatin B. This cysteine protease inhibitor also inhibits the interferon-induced antiviral response by decreasing levels of tyrosine phosphorylated STAT-1. These recent discoveries reveal novel mechanisms of HIV persistence that could be targeted by new therapeutic approaches to eliminate HIV in macrophage reservoirs. However, cystatin B has been also associated with neuroprotection. Cystatin B is an inhibitor of the cysteine protease cathepsin B, a potent neurotoxin. During HIV-1 infection cystatin B and cathepsin B are upregulated in macrophages. Reduction in cystatin/cathepsin interactions in infected macrophages leads to increased cathepsin B secretion and activity which contributes to neuronal apoptosis. Increased intracellular expression of both proteins was recently found in monocytes from Hispanic women with HAND. These findings provide new evidence for the role of cathepsin /cystatin system in the neuropathogenesis induced by HIV-infected macrophages. We summarize recent research on cystatin B and one of its substrates, cathepsin B, in HIV replication in macrophages and neuropathogenesis.

Reduced-order constrained optimization (ROCO): clinical application to head-and-neck IMRT.

PURPOSE: The authors present the application of the reduced order constrained optimization (ROCO) method, previously successfully applied to the prostate and lung sites, to the head-and-neck (H&N) site, demonstrating that it can quickly and automatically generate clinically competitive IMRT plans. We provide guidelines for applying ROCO to larynx, oropharynx, and nasopharynx cases, and report the results of a live experiment that demonstrates how an expert planner can save several hours of trial-and-error interaction using the proposed approach. METHODS: The ROCO method used for H&N IMRT planning consists of three major steps. First, the intensity space of treatment plans is sampled by solving a series of unconstrained optimization problems with a parameter range based on previously treated patient data. Second, the dominant modes in the intensity space are estimated by dimensionality reduction using principal component analysis (PCA). Third, a constrained optimization problem over this basis is quickly solved to find an IMRT plan that meets organ-at-risk (OAR) and target coverage constraints. The quality of the plan is assessed using evaluation tools within Memorial Sloan-Kettering Cancer Center (MSKCC)'s treatment planning system (TPS). RESULTS: The authors generated ten H&N IMRT plans for previously treated patients using the ROCO method and processed them for deliverability by a dynamic multileaf collimator (DMLC). The authors quantitatively compared the ROCO plans to the previously achieved clinical plans using the TPS tools used at MSKCC, including DVH and isodose contour analysis, and concluded that the ROCO plans would be clinically acceptable. In our current implementation, ROCO H&N plans can be generated using about 1.6 h of offline computation followed by 5-15 min of semiautomatic planning time. Additionally, the authors conducted a live session for a plan designated by MSKCC performed together with an expert H&N planner. A technical assistant set up the first two steps, which were performed without further human interaction, and then collaborated in a virtual meeting with the expert planner to perform the third (constrained optimization) step. The expert planner performed in-depth analysis of the resulting ROCO plan and deemed it to be clinically acceptable and in some aspects superior to the clinical plan. This entire process took 135 min including two constrained optimization runs, in comparison to the estimated 4 h that would have been required using traditional clinical planning tools. CONCLUSIONS: The H&N site is very challenging for IMRT planning, due to several levels of prescription and a large, variable number (6-20) of OARs that depend on the location of the tumor. ROCO for H&N shows promise in generating clinically acceptable plans both more quickly and with substantially less human interaction.

Proteomic analysis of HIV-infected macrophages.

Mononuclear phagocytes (monocytes, macrophages, and microglia) play an important role in innate immunity against pathogens including HIV. These cells are also important viral reservoirs in the central nervous system and secrete inflammatory mediators and toxins that affect the tissue environment and function of surrounding cells. In the era of antiretroviral therapy, there are fewer of these inflammatory mediators. Proteomic approaches including surface enhancement laser desorption ionization, one- and two-dimensional difference in gel electrophoresis, and liquid chromatography tandem mass spectrometry have been used to uncover the proteins produced by in vitro HIV-infected monocytes, macrophages, and microglia. These approaches have advanced the understanding of novel mechanisms for HIV replication and neuronal damage. They have also been used in tissue macrophages that restrict HIV replication to understand the mechanisms of restriction for future therapies. In this review, we summarize the proteomic studies on HIV-infected mononuclear phagocytes and discuss other recent proteomic approaches that are starting to be applied to this field. As proteomic instruments and methods evolve to become more sensitive and quantitative, future studies are likely to identify more proteins that can be targeted for diagnosis or therapy and to uncover novel disease mechanisms.