Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans

The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task. Haemonchus contortus is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism Caenorhabditis elegans, making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the H. contortus genome and undertook detailed annotation and comparative analysis with C. elegans. The adult H. contortus transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in C. elegans of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in H. contortus than in C. elegans, with annotated H. contortus genes being an average of two-to-three times larger than their putative C. elegans orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent. C. elegans operons appear to be partially conserved in H. contortus. Our findings suggest that a combination of RNA-seq and comparative analysis with C. elegans is a powerful approach for the annotation and analysis of strongylid nematode genomes

Electron ionization mass spectral fragmentation study of sulfation derivatives of polychlorinated biphenyls

<p>Abstract</p> <p>Background</p> <p>Polychlorinated biphenyls are persistent organic pollutants that can be metabolized via hydroxylated PCBs to PCB sulfate metabolites. The sensitive and selective analysis of PCB sulfate monoesters by gas chromatography-mass spectrometry (GC-MS) requires their derivatization, for example, as PCB 2,2,2-trichloroethyl (TCE) sulfate monoesters. To aid in the identification of unknown PCB sulfate metabolites isolated from biological samples, the electron impact MS fragmentation pathways of selected PCB TCE sulfate diesters were analyzed and compared to the fragmentation pathways of the corresponding methoxylated PCBs.</p> <p>Results</p> <p>The most abundant and characteristic fragment ions of PCB TCE sulfate diesters were formed by releasing CHCCl₃, SO₃, HCl₂and/or CCl₃from the TCE sulfate moiety and Cl₂, HCl, ethyne and chloroethyne from an intermediate phenylcyclopentadienyl cation. The fragmentation pattern depended on the degree of chlorination and the position of the TCE sulfate moiety (i.e., <it>ortho </it>vs. <it>meta/para </it>to the second phenyl ring), but were independent of the chlorine substitution pattern. These fragmentation pathways are similar to the fragmentation pathways of structurally related methoxylated PCBs.</p> <p>Conclusion</p> <p>Knowledge of the fragmentation patterns of PCB TCE sulfate diesters will greatly aid in determining the position of sulfate moiety (<it>ortho </it>vs. <it>meta/para</it>) of unknown PCB sulfate metabolites isolated from environmental or laboratory samples.</p

Barriers to participation in mental health research: are there specific gender, ethnicity and age related barriers?

<p>Abstract</p> <p>Background</p> <p>It is well established that the incidence, prevalence and presentation of mental disorders differ by gender, ethnicity and age, and there is evidence that there is also differential representation in mental health research by these characteristics. The aim of this paper is to a) review the current literature on the nature of barriers to participation in mental health research, with particular reference to gender, age and ethnicity; b) review the evidence on the effectiveness of strategies used to overcome these barriers.</p> <p>Method</p> <p>Studies published up to December 2008 were identified using MEDLINE, PsycINFO and EMBASE using relevant mesh headings and keywords.</p> <p>Results</p> <p>Forty-nine papers were identified. There was evidence of a wide range of barriers including transportation difficulties, distrust and suspicion of researchers, and the stigma attached to mental illness. Strategies to overcome these barriers included the use of bilingual staff, assistance with travel, avoiding the use of stigmatising language in marketing material and a focus on education about the disorder under investigation. There were very few evaluations of such strategies, but there was evidence that ethnically matching recruiters to potential participants did not improve recruitment rates. Educational strategies were helpful and increased recruitment.</p> <p>Conclusion</p> <p>Mental health researchers should consider including caregivers in recruitment procedures where possible, provide clear descriptions of study aims and describe the representativeness of their sample when reporting study results. Studies that systematically investigate strategies to overcome barriers to recruitment are needed.</p

Chemokines cooperate with TNF to provide protective anti-viral immunity and to enhance inflammation

The role of cytokines and chemokines in anti-viral defense has been demonstrated, but their relative contribution to protective anti-viral responses in vivo is not fully understood. Cytokine response modifier D (CrmD) is a secreted receptor for TNF and lymphotoxin containing the smallpox virus-encoded chemokine receptor (SECRET) domain and is expressed by ectromelia virus, the causative agent of the smallpox-like disease mousepox. Here we show that CrmD is an essential virulence factor that controls natural killer cell activation and allows progression of fatal mousepox, and demonstrate that both SECRET and TNF binding domains are required for full CrmD activity. Vaccination with recombinant CrmD protects animals from lethal mousepox. These results indicate that a specific set of chemokines enhance the inflammatory and protective anti-viral responses mediated by TNF and lymphotoxin, and illustrate how viruses optimize anti-TNF strategies with the addition of a chemokine binding domain as soluble decoy receptors.We thank Javier Salguero for help with animal experimentation and immunohistochemistry, Rocío Martín and Carolina Sánchez for technical assistance and Daniel Rubio for discussions on the project. This work was funded by Grants from the Spanish Ministry of Economy and Competitiviness and European Union (European Regional Development’s Funds, FEDER) (grant SAF2015-67485-R), and the Wellcome Trust (grant 051087/Z97/Z). M.B.R.-A. and A. Alejo were recipients of a Ramón y Cajal Contract from the Spanish Ministry of Science and Innovation

A922 Sequential measurement of 1 hour creatinine clearance (1-CRCL) in critically ill patients at risk of acute kidney injury (AKI)

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Attitudes of patients with schizophrenia and depression to psychiatric research: a study in seven European countries

Background: Relatively few studies have examined how patients with schizophrenia and depression view psychiatric research and what influences their readiness to participate.Methods: A total of 763 patients (48% schizophrenia, 52% depression) from 7 European countries were examined using a specifically designed self-report questionnare ["Hamburg Attitudes to Psychiatric Research Questionnaire" (HAPRQ)].Results: Most patients (98%) approved of psychiatric research, in general, at least "a little". There was a tendency to approve psychosocial rather than biological research topics (e.g. research on the role of the family by 91% of patients compare to 79% in genetics). Reasons to participate were mainly altruistic. Only a minority (28%) considered monetary incentives important. Patients wanted extensive background information and a feedbak of the results; both were significantly more expressed by schizophrenia as compared to depressive patients, although these findings need to be interpreted with care because of age and gender differences between the diagnostic groups.Conclusion: While patients expressed discerning views of psychiatric reserch, only few differences were apparent between the two diagnostic groups. Patients' research priorities are not the same as those of many professionals and funding bodies. Their demonstrated critical appraisal should inform future research ensuring an increased patient role in the research process.</p

Methylomic profiling implicates cortical deregulation of ANK1 in Alzheimer's disease

Alzheimer's disease (AD) is a chronic neurodegenerative disorder that is characterized by progressive neuropathology and cognitive decline. We performed a cross-tissue analysis of methylomic variation in AD using samples from four independent human post-mortem brain cohorts. We identified a differentially methylated region in the ankyrin 1 (ANK1) gene that was associated with neuropathology in the entorhinal cortex, a primary site of AD manifestation. This region was confirmed as being substantially hypermethylated in two other cortical regions (superior temporal gyrus and prefrontal cortex), but not in the cerebellum, a region largely protected from neurodegeneration in AD, or whole blood obtained pre-mortem from the same individuals. Neuropathology-associated ANK1 hypermethylation was subsequently confirmed in cortical samples from three independent brain cohorts. This study represents, to the best of our knowledge, the first epigenome-wide association study of AD employing a sequential replication design across multiple tissues and highlights the power of this approach for identifying methylomic variation associated with complex disease.US National Institutes of HealthAlzheimer's Research UKDepartment of Veterans Affair

Cardiopulmonary performance in allogeneic hematopoietic cell transplantation recipients—evaluation of pre-transplant risk assessments

Cardiopulmonary performance reflects how well different organ systems interact. It is inter alia influenced by body composition, determines patients' quality of life and can also predict mortality. However, it is not yet used for risk prediction prior to allogeneic hematopoietic cell transplantations (alloHCT). Thus, we aimed to examine the predictive power of peak oxygen consumption (VO2peak) as a representative of cardiopulmonary performance and that of body composition before alloHCT to determine overall survival (OS) and non-relapse mortality (NRM) 2 years after transplantation. We also compared it with the predictive power of four commonly-used risk scores: revised Pretransplant Assessment of Mortality (rPAM), Hematopoietic Cell Transplantation-specific Comorbidity Index (HCT-CI), revised Disease Risk Index (rDRI), European Society for Blood and Marrow Transplantation (EBMT). Fifty-nine patients performed a cardiopulmonary exercise test and body composition assessments before alloHCT and were observed for 2 years. Sixteen patients died. VO2peak and most risk scores assessed pre-transplant revealed no association with OS or NRM. Body composition parameters only within univariable analyses. But higher rDRI and the male sex, were associated with shorter OS and higher NRM. We thus propose that the current risk assessments be reconsidered. The predictive value of VO2peak and body composition need further clarification, however