Phi Based Research Articles

Chitosan modulates Pochonia chlamydosporia gene expression during nematode egg parasitism.

SummaryClimate change makes plant‐parasitic nematodes (PPN) an increasing threat to commercial crops. PPN can be managed sustainably by the biocontrol fungus Pochonia chlamydosporia (Pc). Chitosan generated from chitin deacetylation enhances PPN parasitism by Pc. In this work, we investigate the molecular mechanisms of Pc for chitosan resistance and root‐knot nematode (RKN) parasitism, using transcriptomics. Chitosan and RKN modify the expression of Pc genes, mainly those involved in oxidation–reduction processes. Both agents significantly modify the expression of genes associated to 113 GO terms and 180 Pc genes. Genes encoding putative glycoproteins (Pc adhesives) to nematode eggshell, as well as genes involved in redox, carbohydrate and lipid metabolism trigger the response to chitosan. We identify genes expressed in both the parasitic and endophytic phases of the Pc lifecycle; these include proteases, chitosanases and transcription factors. Using the Pathogen—Host Interaction database (PHI‐base), our previous RNA‐seq data and RT‐PCR of Pc colonizing banana we have investigated genes expressed both in the parasitic and endophytic phases of Pc lifecycle.

Abstract 14040: Hospitalizations for Respiratory Syncytial Virus and Vaccine Preventable Infections Following Pediatric Heart Transplantation: A PHIS Database Analysis

Introduction: Despite improvements in pediatric heart transplant outcomes, respiratory syncytial virus (RSV) and vaccine preventable infections (R/VPI) are a major cause of morbidity and hospital resource use. The frequency and risk factors for hospitalizations due to R/VPI in heart transplant recipients are unknown. Methods: Patients ≤18 years who underwent heart transplantation at hospitals contributing to the Pediatric Health Information System database from 9/2003 to 12/2018 were identified. The transplant hospitalization and subsequent hospitalizations for R/VPI through 12/2018 were analyzed. Risk factors for R/VPI hospitalizations were evaluated using negative regression binomial models adjusted for potential demographic and clinical confounders. Total hospital costs were determined adjusted for 2018 US $. Results: Of 3,815 transplant recipients, 681 (17.9%) had a R/VPI hospitalization during 23,746 available person-years of follow-up after transplant. There were 984 R/VPIs diagnosed during 951 hospitalizations, and 440 (44.7%) occurred in the first year after transplant (Figure). The most common causes were RSV (n=380; 38.6%), influenza (n=265; 26.9%), and pneumococcus (n=105; 10.7%). In adjusted analyses, there was an increased risk of R/VPI hospitalization in patients requiring mechanical circulatory support prior to transplant, those who received induction with ≥ 2 immunosuppressive agents, and patients <2 years old. The median length of stay for a R/VPI hospitalization was 4 days (interquartile range [IQR]: 2-8 days) with a median total cost of $11,081 (IQR: $6,215 - $24,322). Conclusions: Hospitalization for R/VPIs occurred frequently following pediatric heart transplantation and were associated with significant cost. Potential strategies to minimize R/VPI could include expanding vaccine use through accelerated immunization schedules in younger patients and routine monitoring of immunogenicity after vaccination.

Complete genome analysis of a virulent Vibrio scophthalmi strain VSc190401 isolated from diseased marine fish half-smooth tongue sole, Cynoglossus semilaevis

BackgroundVibrio scophthalmi is an opportunistic bacterial pathogen, which is widely distributed in the marine environment. Earlier studies have suggested that it is a normal microorganism in the turbot gut. However, recent studies have confirmed that this bacterial strain can cause diseases in many different marine animals. Therefore, it is necessary to investigate its whole genome for better understanding its physiological and pathogenic mechanisms.ResultsIn the present study, we obtained a pathogenic strain of V. scophthalmi from diseased half-smooth tongue sole (Cynoglossus semilaevis) and sequenced its whole genome. Its genome contained two circular chromosomes and two plasmids with a total size of 3,541,838 bp, which harbored 3185 coding genes. Among these genes, 2648, 2298, and 1915 genes could be found through annotation information in COG, Blast2GO, and KEGG databases, respectively. Moreover, 10 genomic islands were predicted to exist in the chromosome I through IslandViewer online system. Comparison analysis in VFDB and PHI databases showed that this strain had 334 potential virulence-related genes and 518 pathogen-host interaction-related genes. Although it contained genes related to four secretion systems of T1SS, T2SS, T4SS, and T6SS, there was only one complete T2SS secretion system. Based on CARD database blast results, 180 drug resistance genes belonging to 27 antibiotic resistance categories were found in the whole genome of such strain. However, there were many differences between the phenotype and genotype of drug resistance.ConclusionsBased on the whole genome analysis, the pathogenic V. scophthalmi strain contained many types of genes related to pathogenicity and drug resistance. Moreover, it showed inconsistency between phenotype and genotype on drug resistance. These results suggested that the physiological mechanism seemed to be complex.

Genome-scale analyses and characteristics of putative pathogenicity genes of Stagonosporopsis cucurbitacearum, a pumpkin gummy stem blight fungus

Outbreaks of gummy stem blight (GSB), an emerging seed pumpkin disease, have increased in number and have become more widespread in recent years. Previously we reported that Stagonosporopsis cucurbitacearum (Sc.) is the dominant fungal cause of pumpkin seedling GSB in Northeast China, where it has greatly reduced crop yields in that region. Here, high-throughput whole-genome sequencing and assembly of the Sc. genome were conducted toward revealing pathogenic molecular regulatory mechanisms involved in fungal growth and development. Zq-1 as representative Sc. strain, DNA of Zq-1was prepared for genomic sequencing, we obtained 5.24 Gb of high-quality genomic sequence data via PacBio RS II sequencing. After sequence data was processed to filter out low quality reads, a hierarchical genome-assembly process was employed that generated a genome sequence of 35.28 Mb in size. A total of 9844 genes were predicted, including 237 non-coding RNAs, 1024 genes encoding proteins with signal peptides, 2066 transmembrane proteins and 756 secretory proteins.Transcriptional identification revealed 54 differentially expressed secretory proteins. Concurrently, 605, 130 and 2869 proteins were matched in the proprietary databases Carbohydrate-Active EnZymes database (CAZyme), Transporter Classification Database (TCDB) and Pathogen–Host Interactions database (PHI), respectively. And 96 and 36 DEGs were identified form PHI database and CAZyme database, respectively. In addition, contig00011.93 was an up-regulated DEG involving ATP-binding cassette metabolism in the procession of infection. In order to test relevance of gene predictions to GSB, DEGs with potential pathogenic relevance were revealed through transcriptome data analysis of Sc. strains pre- and post-infection of pumpkin. Interestingly, Sc. and Leptosphaeria maculans (Lm.) exhibited relatively similar with genome lengths, numbers of protein-coding genes and other characteristics. This work provides a foundation for future exploration of additional Sc. gene functions toward the development of more effective GSB control strategies.

Multiple transcriptomic analyses and characterization of pathogen-related core effectors and LysM family members reveal their differential roles in fungal growth and pathogenicity in Penicillium expansum

Penicillium expansum is a destructive phytopathogen causing postharvest decay on many stored fruits. To develop effective and safe management strategies, it is important to investigate its pathogenicity-related mechanisms. In this study, a bioinformatic pipeline was constructed and 50 core effector genes were identified in P. expansum using multiple RNA-seq data sets and their putative functions were implicated by comparatively homologous analyses using pathogen-host interaction database. To functionally characterize P. expansum LysM domain proteins during infection, null mutants for the 15 uncharacterized putative LysM effectors were constructed and the fungal growth rate on either PDA or Cazpek medium or lesion expansion rate on the infected apple fruits was evaluated. The results showed the growth rate of knockout mutants from PeLysM5, PeLysM12 and PeLysM15 was retarded on PDA medium. No significant difference in growth rate was observed between wild type and all mutants on solid Cazpek medium. Nevertheless, the hypha of wild type displayed deeper yellow on the back of Cazpek medium than those of knockout mutants. On the infecting apples fruits, the knockout mutants from PeLysM5, PeLysM7, PeLysM8, PeLysM9, PeLysM10, PeLysM11, PeLysM14, PeLysM15, PeLysM16, PeLysM18 and PeLysM19 showed enhanced fungal virulence, with faster decaying on infected fruits than those from wild type. By contrast, the knockout mutation at PeLysM12 locus led to reduced lesion expansion rate on the infected apple fruits. In addition, P. expansum-apple interaction RNA-seq experiment was performed using apple fruit tissues infected by the wild type and knockout mutant ΔPeLysM15, respectively. Transcriptome analyses indicated that deletion of PeLysM15 could activate expression of several core effector genes, such as PEX2_055830, PEX2_036960 and PEX2_108150, and a chitin-binding protein, PEX2_064520. These results suggest PeLysM15 may play pivotal roles in fungal growth and development and involve pathogen-host interaction by modulating other effector genes' expression. Our results could provide solid data reference and good candidates for further pathogen-related studies in P. expansum.

Identification and expression analysis of pathogenicity-related genes in Tilletia indica inciting Karnal bunt of wheat

Wheat (Triticum aestivum L.) is a major cereal crop cultivated all over the world. Karnal bunt disease is an internationally quarantined disease caused by Tilletia indica. In modern resistance breeding, effectors have been efficiently used to identify, functionally characterize and deploy resistance genes. The present study was carried out to identify the genes related to pathogenicity in T. indica by mining whole genome sequence and transcriptome data. The secretory proteins were identified using bioinformatics tools. In total, 1337 unique proteins having secretory signatures were predicted in T. indica genome. Out of 192 genes related to host-pathogen interaction (PHI database), 7 pathogenicity-related genes were selected for relative expression analysis at different time points under in vitro and in planta conditions using qPCR. Under in vitro, maximum expression of genes was up to 3 fold on amendment with spike tissue extract from susceptible host. Under in planta, three genes (Ti2035, Ti2347 and Ti3774) showed the maximum expression at 3 days post inoculation (dpi). Further two genes (Ti57 and Ti198) showed the maximum up-regulation at 3 dpi followed by 10 dpi and 15 dpi. Two genes (Ti10340 and Ti12741) were up regulated at later stages at 10 dpi and 15 dpi only in susceptible genotype. Ti2035, Ti2347 and Ti3774 genes might have role in penetration, Ti57 and Ti198 genes may be related to penetration & infection, Ti10340 and Ti12741 genes may have role in sporulation when co-related with earlier reported histo-pathological studies. This study could be utilized to understand the mechanism(s) of pathogenesis through functional genomics for developing strategies for management of Karnal bunt of wheat.

Distinctive Gene Expression Profiles and Effectors Consistent With Host Specificity in Two Formae Speciales of Marssonina brunnea.

The knowledge on the host specificity of a pathogen underlying an interaction is becoming an urgent necessity for global warming. In this study, the gene expression profiles and the roles of effectors in host specificity were integrally characterized with two formae speciales, multigermtubi and monogermtubi, of a hemibiotrophic pathogen Marssonina brunnea when they were infecting respective susceptible poplar hosts. With a functional genome comparison referring to a de novo transcriptome of M. brunnea and Pathogen–Host Interaction database functional annotations, the multigermtubi strain showed abundant and significant differentially expressed unigenes (DEGs) (more than 40%) in colonizing the initial invasion stage and in the necrotrophic stage. The monogermtubi strain induced less than 10% of DEGs in the initial invasion stage but which abruptly increased to more than 80% DEGs in the necrotrophic stage. Both strains induced the least DEGs in the biotrophic stage compared to the initial invasion and necrotrophic stages. The orthologs of the effector genes Ecp6, PemG1, XEG1, ACE1, and Mg3LysM were exclusively induced by one of the two formae speciales depending on the infection stages. Some unigenes homologous to carbohydrate lytic enzyme genes, especially pectate lyases, were notably induced with multigermtubi forma specialis infection but not expressed in the monogermtubi forma specialis at an earlier infection stage. The extraordinary differences in the functional genome level between the two formae speciales of M. brunnea could be fundamental to exploring their host specificity determinant and evolution. This study also firstly provided the fungal transcriptome of the monogermtubi forma specialis for M. brunnea.

Sequencing and Functional Annotation of the Whole Genome of Shiraia bambusicola.

Shiraia bambusicola is a rare medicinal fungus found in China that causes bamboo plants to decay and die with severe infection. Hypocrellin, its main active ingredient, is widely used in several fields, such as medicine, agriculture, and food industry. In this study, to clarify the genomic components, taxonomic status, pathogenic genes, secondary metabolite synthesis pathways, and regulatory mechanisms of S. bambusicola, whole-genome sequencing, assembly, and functional annotation were performed using high-throughput sequencing and bioinformatics approaches. It was observed that S. bambusicola has 33 Mb genome size, 48.89% GC content, 333 scaffolds, 2590 contigs, 10,703 genes, 82 tRNAs, and 21 rRNAs. The total length of the repeat sequence is 2,151,640 bp. The annotation of 5945 proteins was obtained from InterProScan hits based on the Gene Ontology database. Phylogenetic analysis showed that S. bambusicola belongs to Shiraiaceae, a new family of Pleosporales. It was speculated that there are more than two species or genus in Shiraiaceae. According to the annotation, 777 secreted proteins were associated with virulence or detoxification, including 777 predicted by the PHI database, 776 by the CAZY and Fungal CytochromeP450 database, and 441 by the Proteases database. The 252 genes associated with the secondary metabolism of S. bambusicola were screened and enriched into 28 pathways, among which the terpenoids, staurosporine, aflatoxin, and folate synthesis pathways have not been reported in S. bambusicola. The T1PKS was the main gene cluster among the 28 secondary metabolite synthesis gene clusters in S. bambusicola. The analysis of the T3PKS gene cluster related to the synthesis of hypocrellin showed that there was some similarity between S. bambusicola and 10 other species of fungi; however, the similarity was very low wherein the highest similarity was 17%. The genomic information of S. bambusicola obtained in this study was valuable to understand its genetic function and pathogenicity. The genomic information revealed that several enzyme genes and secreted proteins might be related to their host interactions and pathogenicity. The annotation and analysis of its secondary metabolite synthesis genes and gene clusters will be an important reference for future studies on the biosynthesis and regulation mechanism of the secondary metabolites, contributing to the discovery of new metabolites and accelerating drug development and application.

Transcriptome analysis of the fungal pathogen Rosellinia necatrix during infection of a susceptible avocado rootstock identifies potential mechanisms of pathogenesis.

BackgroundWhite root rot disease caused by Rosellinia necatrix is one of the most important threats affecting avocado productivity in tropical and subtropical climates. Control of this disease is complex and nowadays, lies in the use of physical and chemical methods, although none have proven to be fully effective. Detailed understanding of the molecular mechanisms underlying white root rot disease has the potential of aiding future developments in disease resistance and management. In this regard, this study used RNA-Seq technology to compare the transcriptomic profiles of R. necatrix during infection of susceptible avocado ‘Dusa’ roots with that obtained from the fungus cultured in rich medium.ResultsThe transcriptomes from three biological replicates of R. necatrix colonizing avocado roots (RGA) and R. necatrix growing on potato dextrose agar media (RGPDA) were analyzed using Illumina sequencing. A total of 12,104 transcripts were obtained, among which 1937 were differentially expressed genes (DEG), 137 exclusively expressed in RGA and 160 in RGPDA. During the root infection process, genes involved in the production of fungal toxins, detoxification and transport of toxic compounds, hormone biosynthesis, gene silencing and plant cell wall degradation were overexpressed. Interestingly, 24 out of the 137 contigs expressed only during R. necatrix growth on avocado roots, were predicted as candidate effector proteins (CEP) with a probability above 60%. The PHI (Pathogen Host Interaction) database revealed that three of the R. necatrix CEP showed homology with previously annotated effectors, already proven experimentally via pathogen-host interaction.ConclusionsThe analysis of the full-length transcriptome of R. necatrix during the infection process is suggesting that the success of this fungus to infect roots of diverse crops might be attributed to the production of different compounds which, singly or in combination, interfere with defense or signaling mechanisms shared among distinct plant families. The transcriptome analysis of R. necatrix during the infection process provides useful information and facilitates further research to a more in -depth understanding of the biology and virulence of this emergent pathogen. In turn, this will make possible to evolve novel strategies for white root rot management in avocado.

PHI-base: the pathogen-host interactions database.

The pathogen–host interactions database (PHI-base) is available at www.phi-base.org. PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen–host interactions reported in peer reviewed research articles. PHI-base also curates literature describing specific gene alterations that did not affect the disease interaction phenotype, in order to provide complete datasets for comparative purposes. Viruses are not included, due to their extensive coverage in other databases. In this article, we describe the increased data content of PHI-base, plus new database features and further integration with complementary databases. The release of PHI-base version 4.8 (September 2019) contains 3454 manually curated references, and provides information on 6780 genes from 268 pathogens, tested on 210 hosts in 13,801 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species consist of approximately 60% plants (split 50:50 between cereal and non-cereal plants), and 40% other species of medical and/or environmental importance. The information available on pathogen effectors has risen by more than a third, and the entries for pathogens that infect crop species of global importance has dramatically increased in this release. We also briefly describe the future direction of the PHI-base project, and some existing problems with the PHI-base curation process.

Increasing Burden of Lyme Carditis in United States Children's Hospitals.

We sought to characterize the shifting epidemiology and resource utilization of Lyme disease and associated carditis in US children's hospitals. We hypothesized that the Lyme carditis burden has increased and that hospitalizations for Lyme carditis are costlier than those for Lyme disease without carditis. The PHIS database was queried for Lyme disease encounters between January 1, 2007 and December 31, 2013. Additional diagnostic codes consistent with carditis identified Lyme carditis cases. Demographic, clinical, and resource utilization data were analyzed. All costs were adjusted to 2014 US dollars. Lyme disease was identified in 3620 encounters with 189 (5%) associated with carditis. Lyme disease (360 cases in 2007 vs. 672 in 2013, p = 0.01) and Lyme carditis (17 cases in 2007 vs. 40 in 2013, p = 0.03) both significantly increased in frequency. This is primarily accounted for by their increase within the Midwest region. Carditis frequency among cases of Lyme disease was stable (p = 0.15). Encounters for Lyme carditis are dramatically costlier than those for Lyme disease without carditis [median $9104 (3741-19,003) vs. 922 (238-4987), p < 0.001] The increase in Lyme carditis cases in US children's hospitals is associated with an increased Lyme disease incidence, suggesting that there has not been a change in its virulence or cardiac tropism. The increasing number of serious cardiac events and costs associated with Lyme disease emphasize the need for prevention and early detection of disease and control of its spread.

Overnight inpatient admission and revisit rates after pediatric adenotonsillectomy.

Objective: Overnight admission may be necessary following adenotonsillectomy (T&A) in pediatric patients. This practice may reduce unplanned revisits following hospital discharge.Study design: Retrospective cohort study.Subjects: Children from the PHIS database.Methods: T&A performed in children during the years 2007–2015 were identified in the Pediatric Health Information System. The primary outcome was 7-day, all-cause readmission or emergency department (ED) revisit. Secondary analysis examined specific revisit types and 30-day revisits. The primary exposure was each institution’s annual rate of overnight stay after T&A.Results: The analysis included 411,876 procedures at 48 hospitals. Hospitals’ annual rates of overnight stay following T&A ranged from 3% to 100%, and 7-day revisit rates varied from 0% to 15%. The percentage or rate of 7-day revisits did not differ based on the use of overnight stay following T&A. At hospitals with higher overnight admission rates after T&A, 7-day revisits were more likely to take the form of inpatient admission rather than an ED visit.Conclusions: The current study confirms that pediatric hospitals vary widely in inpatient admission practices following T&A. This variation is not associated with differences in revisit rates at 7 and 30 days related to any cause. Although no mortality was noted in the current study, caution is suggested when deciding on the disposition of patients with comorbid conditions as risks related to various patients, anesthetic, and surgical-related issues exist. Risk stratification with appropriate identification of patients requiring overnight stay may be the most important for preventing acute care revisits after T&A.

PHI-base: Capturing phenotypes for inclusion in a multi-species interaction database

PHI-base: Capturing phenotypes for inclusion in a multi-species interaction database

Transcriptome analysis of a powdery mildew pathogen (Podosphaera pannosa) infecting Eucalyptus urophylla: De novo assembly, expression profiling and secretome prediction

AbstractPodosphaera pannosa is the causal agent of powdery mildew on eucalypt in Brazil. This powdery mildew disease is important in nurseries causing leaf and shoot distortion, shoot discoloration and reduction in growth, which decreases mini‐cutting production. Improved RNA sequencing (RNA‐Seq) technologies have allowed increased information about the transcriptome of several pathogens and hosts, enabling a better understanding of their interaction at the gene level. For this study, we analysed the transcriptome of P. pannosa during leaf infection of Eucalyptus urophylla leaves using RNA‐Seq and de novo transcriptome assembly. The transcriptome was Illumina sequenced and assembled de novo, generating over 178 million RNA‐Seq reads assembled onto 200,473 contigs. After filtering steps, the resulting 12,106 (6%) transcripts were identified as the P. pannosa transcriptome data set. The 10 most abundant transcripts included genes encoding enzymes likely involved in fungal establishment and growth, such as dihydrofolate reductase, putative methyltransferases, acyl‐desaturase, glycoside hydrolase and dehydrogenases. In addition, genes putatively encoding an aquaporin and an orthologue to the effector protein, GoEC2 of Golovinomyces orontii were identified. The predicted secretome consisted of 1,899 translated transcripts, of which 310 exhibited homology to proteins described in the PHI database, 144 of these showing homology to fungal PHI accessions that affected pathogenicity or that are described as effectors. In addition, 81 transcripts encoded secreted proteins homologous to effectors described in the Erysiphales. These results provide a basis for continued studies to better understand the P. pannosa‐eucalypt (Eucalyptus spp.) pathosystem and could parallel studies of the eucalypt transcriptome to help determine host resistance mechanisms.

Expanding analytic possibilities in pediatric solid organ transplantation through linkage of administrative and clinical registry databases.

Database linkage is a common strategy to expand analytic possibilities. Our group recently completed a linkage between the SRTR and PHIS databases for pediatric heart transplant recipients. The aim of this project was to expand the linkage between SRTR and PHIS to include liver, kidney, lung, heart-lung, and small bowel transplants. All patients (<21years) who underwent liver, kidney, lung, heart-lung, or small bowel transplant were identified from the PHIS database using APR-DRG codes (2002-2018). Linkage was performed in a stepwise approach using indirect identifiers. Hospital costs were estimated based on hospital charges and cost-to-charge ratios, inflated to 2018 dollars and described by transplant type. A total of 14061 patients overlapped between databases. Of these, 13388 (95.2%) were uniquely linked. Linkage success ranged from 92.6% to 97.8% by organ system. A total of 12940 (92%) patients had complete cost data. Hospitalization costs were greatest for patients undergoing small bowel transplantation with a median cost of $734454 (IQR $336174 - $1504167), followed by heart $565386 (IQR $352813 - $999216), heart-lung $471573 (IQR $328523 - 992438), lung $303536 (IQR $215383 - $612749), liver $200448 (IQR $130880 - $357897), and kidney transplant $94796 (IQR $73157 -$131040). We report a robust linkage between the SRTR and PHIS databases, providing an invaluable tool to assess resource utilization in solid organ transplant recipients. Our analysis provides contemporary cost data for pediatric solid organ transplantation from the largest US sample reported to date. It also provides a platform for expanded analyses in the pediatric transplant population.

Health Care Utilization and Financial Impact of Acute Graft-Versus-Host Disease (aGVHD) Among Children Undergoing Allogeneic Hematopoietic Cell Transplantation (alloHCT)

Introduction Steroids are the only effective treatment for acute GVHD and optimal salvage regimen for steroid refractory (SR) GVHD remains elusive. Impact of steroid sensitive (SS) and SR-AGVHD on healthcare utilization and cost is not well described. Methods In this is a single center study, we analyzed data on of 97/240 (40%) consecutive pediatric patients who developed grade I-IV AGVHD. Among patients with AGVHD, we analyzed cost, healthcare utilization and patient outcomes for the first year post-alloHCT. Costs were estimated from charges recorded in the PHIS database and hospital accounting. SR-AGVHD was defined as failure to respond to steroid treatment. Failure to respond was defined as any Grade II-IV AGVHD that showed progression within 3 days or had no improvement within 7 consecutive days of treatment with 2 mg/kg/day methylprednisolone or equivalent. Results The median age of children with SS-AGVHD vs. SR-AGVHD was 9.44 years (0.26-21.0) vs. 12.2 years (0.42-21.0), p=0.204. The incidence of SR-AGVHD was 27%. Median time to onset of AGVHD was 28 days (6-232). AGVHD was grade III at diagnosis in 71% patients with SR-AGVHD vs. 29% patients with SS-AGVHD, P In multivariable analysis, patients with aGVHD had an average of 45.4 days (p 1-year OS for SR-AGVHD compared to SS-AGVHD was 50% (SE=9.81%) vs. 69.0% (SE=5.49%), p=0.046. Conclusion SR-AGVHD is associated with prolonged hospitalization, higher cost and inferior survival among children. Better AGVHD prevention strategies are desperately needed. Despite significant advances, lack of effective salvage regimens for SR-AGVHD remains a major concern.

Prediction of pathogenesis-related secreted proteins from Stemphylium lycopersici

BackgroundGray leaf spot is a devastating disease caused by Stemphylium lycopersici that threatens tomato-growing areas worldwide. Typically, many pathogenesis-related and unrelated secreted proteins can be predicted in genomes using bioinformatics and computer-based prediction algorithms, which help to elucidate the molecular mechanisms of pathogen-plant interactions.ResultsS. lycopersici-secreted proteins were predicted from 8997 proteins using a set of internet-based programs, including SignalP v4.1 TMHMM v2.0, big-PI Fungal Predictor, ProtComp V9.0 and TargetP v1.1. Analysis showed that 511 proteins are predicted to be secreted. These proteins vary from 51 to 600 residues in length, with signal peptides ranging from 14 to 30 residues in length. Functional analysis of differentially expressed proteins was performed using Blast2GO. Gene ontology analysis of 305 proteins classified them into 8 groups in biological process (BP), 6 groups in molecular function (MF), and 10 groups in cellular component (CC). Pathogen-host interaction (PHI) partners were predicted by performing BLASTp analysis of the predicted secreted proteins against the PHI database. In total, 159 secreted proteins in S. lycopersici might be involved in pathogenicity and virulence pathways. Scanning S. lycopersici-secreted proteins for the presence of carbohydrate-active enzyme (CAZyme)-coding gene homologs resulted in the prediction of 259 proteins. In addition, 12 of the 511 proteins predicted to be secreted are small cysteine-rich proteins (SCRPs).ConclusionsS. lycopersici secretory proteins have not yet been studied. The study of S. lycopersici genes predicted to encode secreted proteins is highly significant for research aimed at understanding the hypothesized roles of these proteins in host penetration, tissue necrosis, immune subversion and the identification of new targets for fungicides.

Comprehensive analysis of Verticillium nonalfalfae in silico secretome uncovers putative effector proteins expressed during hop invasion.

The vascular plant pathogen Verticillium nonalfalfae causes Verticillium wilt in several important crops. VnaSSP4.2 was recently discovered as a V. nonalfalfae virulence effector protein in the xylem sap of infected hop. Here, we expanded our search for candidate secreted effector proteins (CSEPs) in the V. nonalfalfae predicted secretome using a bioinformatic pipeline built on V. nonalfalfae genome data, RNA-Seq and proteomic studies of the interaction with hop. The secretome, rich in carbohydrate active enzymes, proteases, redox proteins and proteins involved in secondary metabolism, cellular processing and signaling, includes 263 CSEPs. Several homologs of known fungal effectors (LysM, NLPs, Hce2, Cerato-platanins, Cyanovirin-N lectins, hydrophobins and CFEM domain containing proteins) and avirulence determinants in the PHI database (Avr-Pita1 and MgSM1) were found. The majority of CSEPs were non-annotated and were narrowed down to 44 top priority candidates based on their likelihood of being effectors. These were examined by spatio-temporal gene expression profiling of infected hop. Among the highest in planta expressed CSEPs, five deletion mutants were tested in pathogenicity assays. A deletion mutant of VnaUn.279, a lethal pathotype specific gene with sequence similarity to SAM-dependent methyltransferase (LaeA), had lower infectivity and showed highly reduced virulence, but no changes in morphology, fungal growth or conidiation were observed. Several putative secreted effector proteins that probably contribute to V. nonalfalfae colonization of hop were identified in this study. Among them, LaeA gene homolog was found to act as a potential novel virulence effector of V. nonalfalfae. The combined results will serve for future characterization of V. nonalfalfae effectors, which will advance our understanding of Verticillium wilt disease.

Retained foreign bodies and associated risk factors and outcomes in pediatric surgical patients

BackgroundRetained foreign bodies discovered after surgery are documented as Agency for Health Care Quality and Research Patient Safety Indicators. Our goal was to identify pediatric patient and procedure risk factors and outcomes associated with RFB based on AHRQ Definitions. MethodsWe performed a retrospective case–control study of children with RFB using the PHIS database. Patients were defined as having RFB based on the AHRQ PSI definition. Controls were matched in a 5:1 ratio on age, procedure date, and hospital. Our primary outcome was the presence of RFB. Secondary outcomes included hospital length of stay and mortality. ResultsPatients with RFB often underwent emergent procedures, experienced one or more chronic conditions, and required ICU admission or mechanical ventilation. Musculoskeletal procedures contribute the largest numbers of RFB (30.4%), but interventional radiology procedures had higher odds of having RFB (AOR 7.88, p < 0.0001). After multivariate adjustment, children with RFB required 4 more days of hospitalization (p < .001), but there was no difference in mortality (p = .579). ConclusionsThe implications of our study include identifying which administrative flags can be used to identify children at higher risks for RFB. Early identification of at-risk patients and prevention are key towards addressing the primary problem and corresponding sequela of RFB. Levels of EvidencePrognostic Study Level III.

The Interactomic Analysis Reveals Pathogenic Protein Networks in Phomopsis longicolla Underlying Seed Decay of Soybean.

Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla) is the primary cause of Phomopsis seed decay (PSD) in soybean, Glycine max (L.) Merrill. This disease results in poor seed quality and is one of the most economically important seed diseases in soybean. The objectives of this study were to infer protein–protein interactions (PPI) and to identify conserved global networks and pathogenicity subnetworks in P. longicolla including orthologous pathways for cell signaling and pathogenesis. The interlog method used in the study identified 215,255 unique PPIs among 3,868 proteins. There were 1,414 pathogenicity related genes in P. longicolla identified using the pathogen host interaction (PHI) database. Additionally, 149 plant cell wall degrading enzymes (PCWDE) were detected. The network captured five different classes of carbohydrate degrading enzymes, including the auxiliary activities, carbohydrate esterases, glycoside hydrolases, glycosyl transferases, and carbohydrate binding molecules. From the PPI analysis, novel interacting partners were determined for each of the PCWDE classes. The most predominant class of PCWDE was a group of 60 glycoside hydrolases proteins. The glycoside hydrolase subnetwork was found to be interacting with 1,442 proteins within the network and was among the largest clusters. The orthologous proteins FUS3, HOG, CYP1, SGE1, and the g5566t.1 gene identified in this study could play an important role in pathogenicity. Therefore, the P. longicolla protein interactome (PiPhom) generated in this study can lead to a better understanding of PPIs in soybean pathogens. Furthermore, the PPI may aid in targeting of genes and proteins for further studies of the pathogenicity mechanisms.