The Turkey Ig-like receptor family: identification, expression and function.

The chicken leukocyte receptor complex located on microchromosome 31 encodes the chicken Ig-like receptors (CHIR), a vastly expanded gene family which can be further divided into three subgroups: activating CHIR-A, bifunctional CHIR-AB and inhibitory CHIR-B. Here, we investigated the presence of CHIR homologues in other bird species. The available genome databases of turkey, duck and zebra finch were screened with different strategies including BLAST searches employing various CHIR sequences, and keyword searches. We could not identify CHIR homologues in the distantly related zebra finch and duck, however, several partial and complete sequences of CHIR homologues were identified on chromosome 3 of the turkey genome. They were designated as turkey Ig-like receptors (TILR). Using cDNA derived from turkey blood and spleen RNA, six full length TILR could be amplified and further divided according to the typical sequence features into one activating TILR-A, one inhibitory TILR-B and four bifunctional TILR-AB. Since the TILR-AB sequences all displayed the critical residues shown to be involved in binding to IgY, we next confirmed the IgY binding using a soluble TILR-AB1-huIg fusion protein. This fusion protein reacted with IgY derived from various gallinaceous birds, but not with IgY from other bird species. Finally, we tested various mab directed against CHIR for their crossreactivity with either turkey or duck leukocytes. Whereas no staining was detectable with duck cells, the CHIR-AB1 specific mab 8D12 and the CHIR-A2 specific mab 13E2 both reacted with a leukocyte subpopulation that was further identified as thrombocytes by double immunofluorescence employing B-cell, T-cell and thrombocyte specific reagents. In summary, although the turkey harbors similar LRC genes as the chicken, their distribution seems to be distinct with predominance on thrombocytes rather than lymphocytes

Comprehensive investigation and regulatory function of lncRNAs engaged in western honey bee larval immune response to Ascosphaera apis invasion

Ascosphaera apis is a fungal pathogen that exclusively infects bee larvae, causing chalkbrood disease, which results in severe damage for beekeeping industry. Long non-coding RNAs (lncRNAs) are versatile regulators in various biological processes such as immune defense and host-pathogen interaction. However, expression pattern and regulatory role of lncRNAs involved in immune response of bee host to A. apis invasion is still very limited. Here, the gut tissues of Apis mellifera ligustica 4-, 5-, and 6-day-old larvae inoculated by A. apis spores (AmT1, AmT2, and AmT3 groups) and corresponding un-inoculated larval guts (AmCK1, AmCK2, and AmCK3 groups) were prepared and subjected to deep sequencing, followed by identification of lncRNAs, analysis of differentially expressed lncRNAs (DElncRNAs), and investigation of competing endogenous RNA (ceRNA) network. In total, 3,746 A. m. ligustica lncRNAs were identified, including 78 sense lncRNAs, 891 antisense lncRNAs, 1,893 intergenic lncRNAs, 346 bidirectional lncRNAs, and 210 intronic lncRNAs. In the 4-, 5-, and 6- comparison groups, 357, 236, and 505 DElncRNAs were discovered. Additionally, 217, 129, and 272 DElncRNAs were respectively predicted to regulate neighboring genes via cis-acting manner, and these targets were associated with a series of GO terms and KEGG pathways of great importance, such as response to stimulus and Jak-STAT signaling pathway. Moreover, 197, 95, and 356 DElncRNAs were observed to target 10, eight, and 21 DEmiRNAs and further target 147, 79, and 315 DEmRNAs, forming complex regulatory networks. Further investigation suggested that these targets were engaged in several key cellular and humoral immune pathways, such as phagosome and MAPK signaling pathway. Ultimately, the expression trends of nine randomly selected DElncRNAs were verified by RT-qPCR, confirming the authenticity and reliability of our transcriptome data. Findings in this current work not only provide candidate DElncRNAs for functional study, but also lay a foundation for unclosing the mechanism underlying DElncRNA-regulated larval immune responses to A. apis invasion

Pemphigus is associated withKIR3DL2expression levels and provides evidence that KIR3DL2 may bind HLA-A3 and A11 in vivo

Although HLA‐A3 and A11 have been reported to be ligands for KIR3DL2, evidence for any in vivo relevance of this interaction is still missing. To explore the functional importance of KIR3DL2 allelic variation, we analyzed the autoimmune disease pemphigus foliaceus, previously associated (lower risk) with activating KIR genes. KIR3DL2*001 was increased in patients (odds ratio (OR) = 2.04; p = 0.007). The risk was higher for the presence of both KIR3DL2*001 and HLA‐A3 or A11 (OR = 3.76, p = 0.013), providing the first evidence that HLA‐A3 and A11 may interact with KIR3DL2 in vivo. The nonsynonymous single nucleotide polymorphism 1190T (rs3745902) was associated with protection (OR = 0.52, p = 0.018). This SNP results in a threonine‐to‐methionine substitution. Individuals who have methionine in this position exhibit a lower percentage of KIR3DL2‐positive natural killer (NK) cells and also lower intensity of KIR3DL2 on expressing natural killer cells; additionally, we show that the expression of KIR3DL2 is independent of other killer cell immunoglobulin‐like receptors. Pemphigus foliaceus is a very unique complex disease strongly associated with immune‐related genes. It is the only autoimmune disease known to be endemic, showing a strong correlation with environmental factors. Our data demonstrate that this relatively unknown autoimmune disease may facilitate understanding of the molecular mechanisms of KIR3DL2 ligand recognition

Genomic organisation analysis of novel immunoglobulin-like transcripts in Atlantic salmon (Salmo salar) reveals a tightly clustered and multigene family

Copyright 2011 Elsevier B.V., All rights reserved.Peer reviewedPublisher PD

Securing Context-Aware Applications Using Environment Roles

In the future, a largely invisible and ubiquitous computing infrastructure will assist people with a variety of activities in the home and at work. The applications that will be deployed in such systems will create and manipulate private information and will provide access to a variety of other resources. Securing such applications is challenging for a number of reasons. Unlike traditional systems where access control has been explored, access decisions may depend on the context in which requests are made. We show how the well-developed notion of roles can be used to capture security-relevant context of the environment in which access requests are made. By introducing environment roles, we create a uniform access control framework that can be used to secure context-aware applications. We also present a security architecture that supports security policies that make use of environment roles to control access to resources

Abstract Securing Context-Aware Applications Using Environment Roles

In the future, a largely invisible and ubiquitous computing infrastructure will assist people with a variety of activities in the home and at work. The applications that will be deployed in such systems will create and manipulate private information and will provide access to a variety of other resources. Securing such applications is challenging for a number of reasons. Unlike traditional systems where access control has been explored, access decisions may depend on the context in which requests are made. We show how the well-developed notion of roles can be used to capture security-relevant context of the environment in which access requests are made. By introducing environment roles, we create a uniform access control framework that can be used to secure context-aware applications. We also present a security architecture that supports security policies that make use of environment roles to control access to resources.

Autonomous atomic Hamiltonian construction and active sampling of X-ray absorption spectroscopy by adversarial Bayesian optimization

Abstract X-ray absorption spectroscopy (XAS) is a well-established method for in-depth characterization of electronic structure. In practice hundreds of energy-points should be sampled during the measurements, and most of them are redundant. Additionally, it is also tedious to estimate reasonable parameters in the atomic Hamiltonians for mechanistic understanding. We implement an Adversarial Bayesian optimization (ABO) algorithm comprising two coupled BOs to automatically fit the many-body model Hamiltonians and to sample effectively based on active learning (AL). Taking NiO as an example, we find that less than 30 sampling points are sufficient to recover the complete XAS with the corresponding crystal field and charge transfer models, which can be selected based on intuitive hypothesis learning. Further applications on the experimental XAS spectra reveal that less than 80 sampling points give reasonable XAS and reliable atomic model parameters. Our ABO algorithm has a great potential for future applications on automated physics-driven XAS analysis and AL sampling

Systems pharmacology dissection of the anti-stroke mechanism for the Chinese traditional medicine Xing-Nao-Jing

Xing-Nao-Jing (XNJ) is a well-known injection that has been extensively applied in clinical treatment of stroke in China. However, the underlying mechanism of clinical administration of XNJ in stroke remains unclear. In this study, a systems pharmacology strategy based on pharmacokinetic and pharmacodynamics data was applied to analyze the pharmacological effect of XNJ on stroke. Sixteen active compounds were filtered from XNJ through Drug-likeness (DL) and Brain-blood-barrier (BBB) evaluations. Ninety-four potential targets of these active components were identified by SysDT and SEA. Biological process and pathway enrichment analyses of these targets demonstrated that XNJ exerted anti-stroke effects by biological processes and pathways, such as the response to oxidative stress, regulation of blood pressure, calcium signaling pathway, and apoptosis. Integrating the compound-target network and stroke-related PPI network, we found that Akt1, HIF-1α and ITGB2 may play key roles in the treatment of stroke. The experiments demonstrated that oxycurcumenol may prevent PC12 cells from oxidative stress-induced cell damage. Our study indicates that XNJ has an effect on stroke by protecting neuro cells from oxidative stress-induced cell damage via HIF1α, and the research strategy at the systems pharmacology level is feasible to reveal the mechanisms of novel lead compounds from natural products

SOFT X-RAY LASER CAVITIES

We report progress in the development of multilayer components for use in multiple pass soft x-ray laser cavities operating in the 100Å-300Å spectral range. Our work includes fabrication and characterization of multilayer components ; simple resonant cavity design ; damage threshold assessment for multilayers in the x-ray laser environment ; and multipass cavity experiments for efficiency enhancement and transverse mode selection

SOFT X-RAY LASER CAVITIES

We report progress in the development of multilayer components for use in multiple pass soft x-ray laser cavities operating in the 100Å-300Å spectral range. Our work includes fabrication and characterization of multilayer components ; simple resonant cavity design ; damage threshold assessment for multilayers in the x-ray laser environment ; and multipass cavity experiments for efficiency enhancement and transverse mode selection