Diverse Spatial, Temporal, and Sexual Expression of Recently Duplicated Androgen-Binding Protein Genes in \u3ci\u3eMus musculus\u3c/i\u3e

Background The genes for salivary androgen-binding protein (ABP) subunits have been evolving rapidly in ancestors of the house mouse Mus musculus, as evidenced both by recent and extensive gene duplication and by high ratios of nonsynonymous to synonymous nucleotide substitution rates. This makes ABP an appropriate model system with which to investigate how recent adaptive evolution of paralogous genes results in functional innovation (neofunctionalization). Results It was our goal to find evidence for the expression of as many of the Abp paralogues in the mouse genome as possible. We observed expression of six Abpa paralogues and five Abpbg paralogues in ten glands and other organs located predominantly in the head and neck (olfactory lobe of the brain, three salivary glands, lacrimal gland, Harderian gland, vomeronasal organ, and major olfactory epithelium). These Abp paralogues differed dramatically in their specific expression in these different glands and in their sexual dimorphism of expression. We also studied the appearance of expression in both late-stage embryos and postnatal animals prior to puberty and found significantly different timing of the onset of expression among the various paralogues. Conclusion The multiple changes in the spatial expression profile of these genes resulting in various combinations of expression in glands and other organs in the head and face of the mouse strongly suggest that neofunctionalization of these genes, driven by adaptive evolution, has occurred following duplication. The extensive diversification in expression of this family of proteins provides two lines of evidence for a pheromonal role for ABP: 1) different patterns of Abpa/Abpbg expression in different glands; and 2) sexual dimorphism in the expression of the paralogues in a subset of those glands. These expression patterns differ dramatically among various glands that are located almost exclusively in the head and neck, where the sensory organs are located. Since mice are nocturnal, it is expected that they will make extensive use of olfactory as opposed to visual cues. The glands expressing Abp paralogues produce secretions (lacrimal and salivary) or detect odors (MOE and VNO) and thus it appears highly likely that ABP proteins play a role in olfactory communication

Integral length scales in a low-roughness atmospheric boundary layer

This paper discusses the integral length scales in a low-roughness atmospheric boundary layer (ABL), based on the high-fidelity measurements of wind velocity. Results from the analysis shows that longitudinal integral length scales follow a linear relationship with height in a low-roughness ABL that deviates significantly from semi-empirical Engineering Sciences Data Unit (ESDU) 85020 model derived for open country and urban terrains with larger surface roughness heights. Although the model accurately predicts the integral length scales non-dimensionalised relative to the boundary layer thickness for the majority of the profile, they are over-predicted by more than double in the lowest 10% of the ABL, corresponding to the atmospheric surface layer (ASL). The analysis shows that the largest eddies at lower heights in the ASL over a very low roughness desert terrain have length scales similar to the characteristic lengths of physical structures positioned on the ground, which corresponds to the maximum wind loads for buildings. Hence, it is recommended that the integral length scales in the ASL are characterised over an estimated range at each of the four terrain categories in AS/NZS 1170.2 to ensure that buildings and other large physical structures can be optimised in terms of their size and location.M.J. Emes, M. Arjomandi, R.M. Kelso and F. Ghanad

\tau\to \mu \bar{\nu_i} \nu_i decay in the general two Higgs doublet model

We study \tau\to \mu \bar{\nu_i} \nu_i, i=e,\mu,\tau decay in the model III version of the two Higgs doublet model. We calculated the BR at the order of the magnitude of 10^{-6}-10^{-4} for the intermediate values of the Yukawa couplings. Furthermore, we predict the upper limit of the coupling for the \tau-h^0 (A^0)-\tau transition as \sim 0.3 in the case that the BR is \sim 10^{-6}. We observe that the experimental result of the process under consideration can give comprehensive information about the physics beyond the standard model and the free parameters existing.Comment: 9 pages, 5 figure

Genome-wide profiling in treatment-naive early rheumatoid arthritis reveals DNA methylome changes in T and B lymphocytes

AIM: Although aberrant DNA methylation has been described in rheumatoid arthritis (RA), no studies have interrogated this epigenetic modification in early disease. Following recent investigations of T- and B-lymphocytes in established disease, we now characterize in these cell populations genome-wide DNA methylation in treatment-naive patients with early RA. PATIENTS & METHODS: HumanMethylation450 BeadChips were used to examine genome-wide DNA methylation in lymphocyte populations from 23 early RA patients and 11 healthy individuals. RESULTS: Approximately 2000 CpGs in each cell type were differentially methylated in early RA. Clustering analysis identified a novel methylation signature in each cell type (150 sites in T-lymphocytes, 113 sites in B-lymphocytes) that clustered all patients separately from controls. A subset of sites differentially methylated in early RA displayed similar changes in established disease. CONCLUSION: Treatment-naive early RA patients display novel disease-specific DNA methylation aberrations, supporting a potential role for these changes in the development of RA

Epigenome-wide profiling identifies significant differences in DNA methylation between matched-pairs of T- and B-lymphocytes from healthy individuals

Multiple reports now describe changes to the DNA methylome in rheumatoid arthritis and in many cases have analyzed methylation in mixed cell populations from whole blood. However, these approaches may preclude the identification of cell type-specific methylation, which may subsequently bias identification of disease-specific changes. To address this possibility, we conducted genome-wide DNA methylation profiling using HumanMethylation450 BeadChips to identify differences within matched pairs of T-lymphocytes and B-lymphocytes isolated from the peripheral blood of 10 healthy females. Array data were processed and differential methylation identified using NIMBL software. Validation of array data was performed by bisulfite Pyrosequencing. Genome-wide DNA methylation was initially determined by analysis of LINE-1 sequences and was higher in B-lymphocytes than matched T-lymphocytes (69.8 vs. 65.2%, p ≤ 0.01). Pairwise analysis identified 679 CpGs, representing 250 genes, which were differentially methylated between T-lymphocytes and B-lymphocytes. The majority of sites (76.6%) were hypermethylated in B-lymphocytes. Pyrosequencing of selected candidates confirmed the array data in all cases. Hierarchical clustering revealed perfect segregation of samples into two distinct clusters based on cell type. Differentially methylated genes showed enrichment for biological functions/pathways associated with leukocytes and T-lymphocytes. Our work for the first time shows that T-lymphocytes and B-lymphocytes possess intrinsic differences in DNA methylation within a restricted set of functionally-related genes. These data provide a foundation for investigating DNA methylation in diseases in which these cell types play important and distinct roles

Adaptive evolution of Toll-like receptor 5 in domesticated mammals

<p>Abstract</p> <p>Background</p> <p>Previous studies have proposed that mammalian toll like receptors (TLRs) have evolved under diversifying selection due to their role in pathogen detection. To determine if this is the case, we examined the extent of adaptive evolution in the TLR5 gene in both individual species and defined clades of the mammalia.</p> <p>Results</p> <p>In support of previous studies, we find evidence of adaptive evolution of mammalian TLR5. However, we also show that TLR5 genes of domestic livestock have a concentration of single nucleotide polymorphisms suggesting a specific signature of adaptation. Using codon models of evolution we have identified a concentration of rapidly evolving codons within the TLR5 extracellular domain a site of interaction between host and the bacterial surface protein flagellin.</p> <p>Conclusions</p> <p>The results suggest that interactions between pathogen and host may be driving adaptive change in TLR5 by competition between species. In support of this, we have identified single nucleotide polymorphisms (SNP) in sheep and cattle TLR5 genes that are co-localised and co-incident with the predicted adaptive codons suggesting that adaptation in this region of the TLR5 gene is on-going in domestic species.</p

Identifying the cellular targets of drug action in the central nervous system following corticosteroid therapy

This document is the Accepted Manuscript version of a Published Work that appeared in final form in ACS Chemical Neuroscience, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/cn400167nCorticosteroid (CS) therapy is used widely in the treatment of a range of pathologies, but can delay production of myelin, the insulating sheath around central nervous system nerve fibers. The cellular targets of CS action are not fully understood, that is, "direct" action on cells involved in myelin genesis [oligodendrocytes and their progenitors the oligodendrocyte precursor cells (OPCs)] versus "indirect" action on other neural cells. We evaluated the effects of the widely used CS dexamethasone (DEX) on purified OPCs and oligodendrocytes, employing complementary histological and transcriptional analyses. Histological assessments showed no DEX effects on OPC proliferation or oligodendrocyte genesis/maturation (key processes underpinning myelin genesis). Immunostaining and RT-PCR analyses show that both cell types express glucocorticoid receptor (GR; the target for DEX action), ruling out receptor expression as a causal factor in the lack of DEX-responsiveness. GRs function as ligand-activated transcription factors, so we simultaneously analyzed DEX-induced transcriptional responses using microarray analyses; these substantiated the histological findings, with limited gene expression changes in DEX-treated OPCs and oligodendrocytes. With identical treatment, microglial cells showed profound and global changes post-DEX addition; an unexpected finding was the identification of the transcription factor Olig1, a master regulator of myelination, as a DEX responsive gene in microglia. Our data indicate that CS-induced myelination delays are unlikely to be due to direct drug action on OPCs or oligodendrocytes, and may occur secondary to alterations in other neural cells, such as the immune component. To the best of our knowledge, this is the first comparative molecular and cellular analysis of CS effects in glial cells, to investigate the targets of this major class of anti-inflammatory drugs as a basis for myelination deficits.British Neuro-pathological Society, North Staffordshire Medical Institute, and The University of Nottingham

Development and User Satisfaction of “Plan-It Commander,” a Serious Game for Children with ADHD

The need for engaging treatment approaches within mental health care has led to the application of gaming approaches to existing behavioral training programs (i.e., gamification). Because children with attention deficit/hyperactivity disorder (ADHD) tend to have fewer problems with concentration and engagement when playing digital games, applying game technologies and design approaches to complement treatment may be a useful means to engage this population in their treatment. Unfortunately, gamified training programs currently available for ADHD have been limited in their ability to demonstrate in-game behavior skills that generalize to daily life situations. Therefore, we developed a new serious game (called “Plan-It Commander”) that was specifically designed to promote behavioral learning and promotes strategy use in domains of daily life functioning such as time management, planning/organizing, and prosocial skills that are known to be problematic for children with ADHD. An interdisciplinary team contributed to the development of the game. The game's content and approach are based on psychological principles from the Self-Regulation Model, Social Cognitive Theory, and Learning Theory. In this article, game development and the scientific background of the behavioral approach are described, as well as results of a survey (n = 42) to gather user feedback on the first prototype of the game. The findings suggest that participants were satisfied with this game and provided the basis for further development and research to the game. Implications for developing serious games and applying user feedback in game development are discussed

New Results from the Cryogenic Dark Matter Search Experiment

Using improved Ge and Si detectors, better neutron shielding, and increased counting time, the Cryogenic Dark Matter Search (CDMS) experiment has obtained stricter limits on the cross section of weakly interacting massive particles (WIMPs) elastically scattering from nuclei. Increased discrimination against electromagnetic backgrounds and reduction of neutron flux confirm WIMP-candidate events previously detected by CDMS were consistent with neutrons and give limits on spin-independent WIMP interactions which are >2X lower than previous CDMS results for high WIMP mass, and which exclude new parameter space for WIMPs with mass between 8-20 GeV/c^2.Comment: 4 pages, 4 figure

Phenotypic microarrays suggest Escherichia coli ST131 is not a metabolically distinct lineage of extra-intestinal pathogenic E. coli

Extraintestinal pathogenic E. coli (ExPEC) are the major aetiological agent of urinary tract infections (UTIs) in humans. The emergence of the CTX-M producing clone E. coli ST131 represents a major challenge to public health worldwide. A recent study on the metabolic potential of E. coli isolates demonstrated an association between the E. coli ST131 clone and enhanced utilisation of a panel of metabolic substrates. The studies presented here investigated the metabolic potential of ST131 and other major ExPEC ST isolates using 120 API test reagents and found that ST131 isolates demonstrated a lower metabolic activity for 5 of 120 biochemical tests in comparison to non-ST131 ExPEC isolates. Furthermore, comparative phenotypic microarray analysis showed a lack of specific metabolic profile for ST131 isolates countering the suggestion that these bacteria are metabolically fitter and therefore more successful human pathogens