关键词： Interferons   Pattern recognition receptors   Viral infection  

摘要： The stress-granule protein G3BP1 forms a high-molecular-weight protein complex with the sensor cGAS and enhances its detection of cytoplasmic DNA.

关键词： gene expression patterns   heterosis   chicken   RNA-Seq  

摘要： The superior performance of hybrids to parents, termed heterosis, has been widely utilized in animal and plant breeding programs, but the molecular mechanism underlying heterosis remains an enigma. RNA-Seq provides a novel way to investigate heterosis at the transcriptome-wide level, because gene expression functions as an intermediate phenotype that contributes to observable traits. Here we compared embryonic gene expression between chicken hybrids and their inbred parental lines to identify inheritance patterns of gene expression. Inbred Fayoumi and Leghorn were crossed reciprocally to obtain F1 fertile eggs. RNA-Seq was carried out using 24 brain and liver samples taken from day 12 embryos, and the differentially expressed (DE) genes were identified by pairwise comparison among the hybrids, parental lines, and mid-parent expression values. Our results indicated the expression levels of the majority of the genes in the F1 cross are not significantly different from the mid-parental values, suggesting additivity as the predominant gene expression pattern in the F1. The second and third prevalent gene expression patterns are dominance and over-dominance. Additionally, we found only 7-20% of the DE genes exhibit allele-specific expression in the F1, suggesting that trans regulation is the main driver for differential gene expression and thus contributes to heterosis effect in the F1 crosses.

关键词： Atherosclerosis   Monocytes subsets   Heat shock protein 60   Intermediate monocytes  

摘要： Background and aims: Macrophages derived from monocytes play an important role in atherosclerosis progression. Subpopulations of circulating classical, intermediate, and non-classical monocytes possess distinct functions and phenotypes, and participate in the pathogenesis of disease. The aim of this study was to compare the quantity and phenotypes of circulating monocyte subpopulations in patients with established atherosclerosis and healthy control individuals. Additionally, the study aimed to provide insight into the functional activity of monocytes against a heat shock protein (HSP60). Methods: Chemokine and pattern recognition receptors in monocyte subsets obtained from peripheral blood of acute and chronic coronary artery disease patients and controls were quantified by flow cytometry. Furthermore, monocytes from healthy controls were stimulated in vitro with HSP60, and the cytokines produced by them were evaluated by flow cytometry. Results: Eighteen controls (C), 34 individuals with risk factors for cardiovascular disease (RF), 32 patients with stable angina (SA), and 16 patients with unstable angina (UA) were enrolled in the study. The absolute count of intermediate monocytes was found to be increased in patients of the UA group;high frequencies of the chemokine receptors CCR2, CCR5, and CX3CR1 were also observed in this subpopulation. Moreover, the pattern recognition receptors TLR2 and TLR4 were more frequent in intermediate monocytes from the UA group. Furthermore, the intermediate monocytes from healthy individuals produced IL-12p70 after stimulation with HSP60. Conclusions: Our results show that intermediate monocytes of UA patients exhibited an enhanced expression of the receptors involved in the recognition of damage-associated molecular patterns (DAMPs) and enhancement of the migratory function. Hence, they might contribute to the propagation and progression of inflammation observed in atherosclerosis, especially in the acute setting.

关键词： Data evolution   Cellular automata   CALP   Handwritten pattern recognition   Data generation   Dynamic generation of pool of ensembles   Ensembles  

摘要： Recently a cellular automata learning and prediction (CALP) model was proposed that used evolution to generate handwritten data for pattern recognition. However, the proposed method by CALP was mechanical and not intuitive, as it did not consider the degree of image deformation that takes place during evolution. The problem with this approach is that it evolved handwritten shapes to a completely different form. We propose a new data generation through evolution method called m-CALP, that evolves handwritten shapes using an objective function that also considers the degree of image deformation as it evolves. We replicated the exact same experimental setup of CALP - with the same 5 handwritten data sets, and classifiers with the exact same settings, and then used it to record the performance of our evolved data. We show that data evolved using our method maintains the interesting properties of a pattern. CALP was shown to have performed better than the state-of-theart synthetic over sampling methods such as SMOTE and BORDERLINE-SMOTE, and m CALP performs better than CALP in most cases, in the same environment. Data generation using evolution is a promising field, as it allows researchers to develop trainers and classifier for even small-sized training data. Therefore, we also show that evolving small-sized training data to generate more data using m-CALP performs better than both CALP and larger sized training data.

关键词： Crassostrea gigas   C1q domain containing proteins   Pattern recognition receptors   Gram-negative bacteria recognition  

摘要： The globular C1q domain containing (C1qDC) proteins are a family of versatile pattern recognition receptors (PRRs) to bind various ligands by their globular C1q (gC1q) domain. In the present study, a novel globular C1qDC (CgC1qDC-7) was characterized from Pacific oyster Crassostrea gigas. The open reading frame of CgC1qDC-7 was of 555 bp, encoding a polypeptide of 185 amino acids. Phylogenetic analysis indicated that CgC1qDC-7 shared high homology with C1qDCs from Crassostrea virginica, Mytilus galloprovincialis, and Mizuhopecten yessoensis. The mRNA transcripts of CgC1qDC-7 were widely expressed in all the tested tissues including mantle, gonad, gills, adductor muscle, hemocytes, hepatopancreas and labial palps, with the highest expression level in hemocytes and gills. The recombinant protein of CgC1qDC-7 (rCgC1qDC-7) exhibited binding activity towards Gram-negative bacteria (Vibrio splendidus, V. anguillarum, Escherichia coli, V. alginolyticus, and Aeromonas hydrophila), Gram-positive bacteria (Micrococcus luteus and Staphylococcus aureus) and fungi (Pichia pastoris and Yarrowia lipolytica), and displayed strongest binding affinity towards Gram-negative bacteria V. splendidus and V. anguillarwn. It also exhibited affinity to vital pathogen-associated molecular patterns (PAMPs), such as lipopolysaccharide (LPS), peptidoglycan (PGN), mannan (MAN) and Poly (I:C) with high affinity towards LPS and PGN, and low affinity to MAN and Poly (I:C). These results collectively indicated that CgC1qDC-7 was a novel PRR in C. gigas with high binding affinity towards LPS and PGN as well as Gram-negative bacteria.

关键词： Ca2+ dependent   Lipopolysaccharide and beta-1,3-glucan-binding protein (LGBP)   LPS   Recognition   Scylla paramamosain   Vibro parahaemolyticus  

摘要： The early developmental stages of the mud crab Scylla paramamosain suffer from high mortality caused by pathogen infections;however, few immune associated factors are known. Lipopolysaccharide and beta-1,3-glucanbinding protein (LGBP) functions as a typical pathogen recognition receptor and plays an important role in the innate immune system of invertebrates. In this study we characterized a LGBP gene (SpLGBP) which was highly expressed in the late embryonic, zoea I larval stage and hepatopancreas of S. paramamosain. It encodes 364 amino acids, composed of several conserved domains like the bacterial glucanase motif. The recombinant SpLGBP protein (rSpLGBP) was obtained through the *** expression system, in which two 6 lozenge His-tags were added to both C and N terminals during vector construction for the improvement of purification efficiency. In vivo the study showed that the SpLGBP mRNA was significantly up -regulated under Vibrio parahaemolyticus and a lipopolysaccharide (LPS) challenge in the hemocytes and hepatopancreas. The ELISA binding assay in vitro indicated that the rSpLGBP was capable of binding to LPSs and peptidoglycan (PGN). The rSpLGBP could agglutinate both G+ and G- bacteria in the presence of Ca2+. Our results suggest that SpLGBP may play an immunological role against pathogenic infection in the early developmental stages of S. paramamosain.

关键词： Buried Pb-Zn mineralisation   Soil geochemistry   Singular value decomposition   Semi-discrete decomposition   Non-negative matrix factorisation   Irankuh  

摘要： This study compares the use of joint singular value decomposition and semi-discrete decomposition (JSS) and non-negative matrix factorisation with univariate analysis of raw data, to detect multi-element patterns in soils related to geochemical dispersion from Mississippi Valley-Type Pb-Zn deposits in the Irankuh area of central Iran. Joint singular value decomposition and semi-discrete decomposition clustering of the data identified a suite of mineralisation-related variables and corresponding sample clusters that are spatially associated with mineralisation or variations in parent lithology. Non-negative matrix factorisation generated three main factors and sample clusters that relate to the main zones of sulphide mineralisation, variations in clay mineralogy and the composition of unaltered host rocks. These two matrix decomposition techniques deliver similar results, though JSS delivers a significantly higher sample classification accuracy. Both methods result in delineation of a contiguous cluster of samples above an extensive zone of blind mineralisation at the Tappe Sorkh Pb-Zn deposit and define new potentially mineralised targets between this deposit and the Gushfil Pb-Zn deposit. More conventional univariate methods to detect anomalous populations of Pb and Zn in the soil geochemical data, such as number-size fractal analysis, were less effective at defining these targets. Joint application of practical matrix decomposition techniques, utilising noise removal and modelling of the underlying geochemical patterns associated with ore-forming processes, has led to more reliable prospectivity mapping of the Pb-Zn deposits in Irankuh.

关键词： Child maltreatment   Latent class analysis  

摘要： Maltreatment experiences are complex, and it is difficult to characterize the heterogeneity in types of maltreatment. Subtypes, such as emotional maltreatment, sexual abuse, physical abuse, and neglect commonly co-occur and may persist across development. Therefore, treating individual maltreatment subtypes as independently occurring is not representative of the nature of maltreatment as it occurs in children's lives. Latent class analysis (LCA) is employed herein to identify subgroups of maltreated children based on commonalities in maltreatment subtype and chronicity. In a sample of 674 low-income urban children, 51.6% of whom experienced officially documented maltreatment, our analyses identified four classes of children, with three distinct classes based on maltreatment subtypes and chronicity, and one group of children who did not experience maltreatment. The largest class of maltreated children identified was the chronic, multi-subtype maltreatment class (57% of maltreated children);a second class was characterized by only neglect in a single developmental period (31% of maltreated children), and the smallest class was characterized by a single subtype of maltreatment (emotional maltreatment, physical, or sexual abuse) occurring in a single developmental period (12% of maltreated children). Characterization of these groups confirms the overlapping nature of maltreatment subtypes. There were notable differences between latent classes on child behavioral and socio-emotional outcomes measured by child self-report and camp counselors report during a one-week summer camp. The largest differences were between the non-maltreated class and the chronic maltreatment class. Children who experienced chronic, multi-subtype maltreatment showed higher levels of externalizing behavior, emotion dysregulation, depression, and anxiety.

关键词： Asthma exacerbation   rhinovirus infection   type I interferon   pattern recognition receptors  

摘要： Background: The innate immune system senses viral infection through pattern recognition receptors (PRRs), leading to type I interferon production. The role of type I interferon and PPRs in rhinovirus-induced asthma exacerbations in vivo are uncertain. Objectives: We sought to compare bronchial mucosal type I interferon and PRR expression at baseline and after rhinovirus infection in atopic asthmatic patients and control subjects. Methods: Immunohistochemistry was used to detect expression of IFN-alpha, IFN-beta, and the PRRs: Toll-like receptor 3, melanoma differentiation-associated gene 5, and retinoic acid-inducible protein I in bronchial biopsy specimens from 10 atopic asthmatic patients and 15 nonasthmatic nonatopic control subjects at baseline and on day 4 and 6 weeks after rhinovirus infection. Results: We observed IFN-alpha/beta deficiency in the bronchial epithelium at 3 time points in asthmatic patients in vivo. Lower epithelial IFN-alpha/beta expression was related to greater viral load, worse airway symptoms, airway hyperresponsiveness, and reductions in lung function during rhinovirus infection. We found lower frequencies of bronchial subepithelial monocytes/macrophages expressing IFN-alpha/beta in asthmatic patients during infection. Interferon deficiency at baseline was not accompanied by deficient PRR expression in asthmatic patients. Both epithelial and subepithelial PRR expression were induced during rhinovirus infection. Rhinovirus infection-increased numbers of subepithelial interferon/PRR-expressing inflammatory cells were related to greater viral load, airway hyperresponsiveness, and reductions in lung function. Conclusions: Bronchial epithelial IFN-alpha/beta expression and numbers of subepithelial IFN-alpha/beta-expressing monocytes/macrophages during infection were both deficient in asthmatic patients. Lower epithelial IFN-alpha/beta expression was associated with adverse clinical outcomes after rhinovirus infection in vivo. Increases in numb