Comparative analysis of homology models of the Ah receptor ligand binding domain: Verification of structure-function predictions by site-directed mutagenesis of a nonfunctional receptor

The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that mediates the biological and toxic effects of a wide variety of structurally diverse chemicals, including the toxic environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). While significant interspecies differences in AHR ligand binding specificity, selectivity, and response have been observed, the structural determinants responsible for those differences have not been determined, and homology models of the AHR ligand-binding domain (LBD) are available for only a few species. Here we describe the development and comparative analysis of homology models of the LBD of 16 AHRs from 12 mammalian and nonmammalian species and identify the specific residues contained within their ligand binding cavities. The ligand-binding cavity of the fish AHR exhibits differences from those of mammalian and avian AHRs, suggesting a slightly different TCDD binding mode. Comparison of the internal cavity in the LBD model of zebrafish (zf) AHR2, which binds TCDD with high affinity, to that of zfAHR1a, which does not bind TCDD, revealed that the latter has a dramatically shortened binding cavity due to the side chains of three residues (Tyr296, Thr386, and His388) that reduce the amount of internal space available to TCDD. Mutagenesis of two of these residues in zfAHR1a to those present in zfAHR2 (Y296H and T386A) restored the ability of zfAHR1a to bind TCDD and to exhibit TCDD-dependent binding to DNA. These results demonstrate the importance of these two amino acids and highlight the predictive potential of comparative analysis of homology models from diverse species. The availability of these AHR LBD homology models will facilitate in-depth comparative studies of AHR ligand binding and ligand-dependent AHR activation and provide a novel avenue for examining species-specific differences in AHR responsiveness. © 2013 American Chemical Society

The dermal skeleton of the jawless vertebrate Tremataspis mammilata (Osteostraci, stem-Gnathostomata)

Osteostracans are the closest jawless relatives of jawed vertebrates, informing the gradual assembly of the vertebrate mineralised skeleton. Conflicting interpretations of their dermal skeletal histology arise from failure to account for topological variation, obscuring their significance in elucidating vertebrate skeletal evolution. To resolve this, we characterize the cranial and trunk dermal skeleton of a single individual of Tremataspis mammilata (Osteostraci, Thyestiida) at submicron resolution using synchrotron tomography. Our results show that the architecture of the Tremataspis dermal skeleton is, for the most part, conserved over the skeleton and is broadly consistent with previous histological hypotheses based on 2-dimensional thin section study. We resolve debate over the homology of the basal layer, identifying it as osteogenic acellular isopedin rather than odontogenic elasmodine or metaplastic ossification of the stratum compactum of the dermis. We find topological variation between all dermal skeletal elements studied, and particularly between the cranial and postcranial dermal skeleton. This variation can be largely explained by reduction in differentiation due to geometric constraints imposed within smaller skeletal elements, such as scales. Our description of the dermal skeleton of Tremataspis mammilata provides a foundation for interpreting data from cursory topological samples of dermal skeletal diversity obtained in other osteostracans. This reveals general aspects of histological structure that must be primitive for osteostracans and, likely, ancestral jawed vertebrates. Finally, we draw the distinction between hypotheses and descriptions in palaeohistology

The pseudo‐brookite spin‐glass system studied by means of muon spin relaxation

Zero-field muon spin relaxation (µSR) experiments have been performed on the spin glass Fe1.75Ti1.25O5. Above the spin-glass temperature of 44 K a distinct exponential µSR rate (¿) is observed, while below Tg a square-root exponential decay occurs, indicating fast spin fluctuations. Near 8 K, a maximum in ¿ is indicative of transverse spin ordering. The low ¿ values and the sharp ¿ peak at Tg are very promising for the study of spin freezing models like the Vogel–Fulcher law or the power law

Reverse genetics with a full-length infectious cDNA of severe acute respiratory syndrome coronavirus

A previously undescribed coronavirus (CoV) is the etiologic agent responsible for severe acute respiratory syndrome (SARS). Using a panel of contiguous cDNAs that span the entire genome, we have assembled a full-length cDNA of the SARS-CoV Urbani strain, and have rescued molecularly cloned SARS viruses (infectious clone SARS-CoV) that contained the expected marker mutations inserted into the component clones. Recombinant viruses replicated as efficiently as WT virus and both were inhibited by treatment with the cysteine proteinase inhibitor (2S,3S)-transepoxysuccinyl-l-leucylamido-3-methylbutane ethyl ester. In addition, subgenomic transcripts were initiated from the consensus sequence ACGAAC in both the WT and infectious clone SARS-CoV. Availability of a SARS-CoV full-length cDNA provides a template for manipulation of the viral genome, allowing for the rapid and rational development and testing of candidate vaccines and therapeutics against this important human pathogen

Leadership and decision-making practices in public versus private universities in Pakistan

The goal of this study is to examine differences in leadership and decision-making practices in public and private universities in Pakistan, with a focus on transformational leadership (TL) and participative decision-making (PDM). We conducted semi-structured interviews with 46 deans and heads of department from two public and two private universities in Pakistan. Our findings indicate that leadership and decision-making practices are different in public and private universities. While differences were observed in all six types of TL-behaviour, the following three approaches emerged to be crucial in both public and private universities: (1) articulating a vision, (2) fostering the acceptance of group goals, and (3) high-performance expectations. In terms of PDM, deans and heads of department in public and private universities adopt a collaborative approach. However, on a practical level this approach is limited to teacher- and student-related matters. Overall, our findings suggest that the leadership and decision-making practices in Pakistani public and private universities are transformational and participative in nature

'Working out’ identity: distance runners and the management of disrupted identity

This article contributes fresh perspectives to the empirical literature on the sociology of the body, and of leisure and identity, by analysing the impact of long-term injury on the identities of two amateur but serious middle/long-distance runners. Employing a symbolic interactionist framework,and utilising data derived from a collaborative autoethnographic project, it explores the role of ‘identity work’ in providing continuity of identity during the liminality of long-term injury and rehabilitation, which poses a fundamental challenge to athletic identity. Specifically, the analysis applies Snow and Anderson’s (1995) and Perinbanayagam’s (2000) theoretical conceptualisations in order to examine the various forms of identity work undertaken by the injured participants, along the dimensions of materialistic, associative and vocabularic identifications. Such identity work was found to be crucial in sustaining a credible sporting identity in the face of disruption to the running self, and in generating momentum towards the goal of restitution to full running fitness and reengagement with a cherished form of leisure. KEYWORDS: identity work, symbolic interactionism, distance running, disrupted identit

Multiple-gap spark gap switch

A triggered multiple-gap spark gap switch has been developed and tested under atmosphere. By means of an LCR trigger circuit, the multiple-gap switch can be used very reliably. For the same switching voltage (35.5 kV), with increasing the number of gaps from 2 to 6, the switching current rise time is reduced from 13.5 to 6 ns, and the energy efficiency is increased from 87% to 92%. An eight-gap switch was also tested, and the switching current rise time is much smaller than the usable rise time of the current probe (3.5 ns). One interesting application of the multiple-gap switch is to improve the switching performance in the multiple-switch and transmission lines based pulsed power circuit. To verify this application, a six-gap switch was tested. In contrast to a single-gap switch, the output current rise time was improved from 21 to 11 ns by the six-gap switch

Bayesian Inference in Processing Experimental Data: Principles and Basic Applications

This report introduces general ideas and some basic methods of the Bayesian probability theory applied to physics measurements. Our aim is to make the reader familiar, through examples rather than rigorous formalism, with concepts such as: model comparison (including the automatic Ockham's Razor filter provided by the Bayesian approach); parametric inference; quantification of the uncertainty about the value of physical quantities, also taking into account systematic effects; role of marginalization; posterior characterization; predictive distributions; hierarchical modelling and hyperparameters; Gaussian approximation of the posterior and recovery of conventional methods, especially maximum likelihood and chi-square fits under well defined conditions; conjugate priors, transformation invariance and maximum entropy motivated priors; Monte Carlo estimates of expectation, including a short introduction to Markov Chain Monte Carlo methods.Comment: 40 pages, 2 figures, invited paper for Reports on Progress in Physic

\u27I need time to start antiretroviral therapy\u27: Understanding reasons for delayed ART initiation among people diagnosed with HIV in Lusaka, Zambia

INTRODUCTION: Rapid antiretroviral therapy (ART) initiation can improve patient outcomes such as viral suppression and prevent new infections. However, not everyone who can start ART does so immediately. METHODS: We conducted a qualitative study to inform interventions supporting rapid initiation in the \u27Test and Start\u27 era. We purposively sampled 20 adult patients living with HIV and a previous gap in care from ten health facilities in Lusaka, Zambia for interviews. We inductively analysed transcripts using a thematic, narrative approach. In their narratives, seven participants discussed delaying ART initiation. RESULTS: Drawing on messages gleaned from facility-based counselling and community information, many cited greater fear of rapid sickness or death due to imperfect adherence or treatment side effects than negative health consequences due to delayed initiation. Participants described needing time to \u27prepare\u27 their minds for a lifetime treatment commitment. Concerns about inadvertent HIV status disclosure during drug collection discouraged immediate initiation, as did feeling healthy, and worries about the impact of ART initiation on relationship dynamics. CONCLUSION: Findings suggest that counselling messages should accurately communicate treatment risks, without perpetuating fear-based narratives about HIV. Identifying and managing patient-specific concerns and reasons for the \u27need for time\u27 may be important for supporting individuals to rapidly accept lifelong treatment.Key messagesFear-based adherence messaging in health facilities about the dangers of missing a treatment dose or changing the time when ART is taken contributes to Zambian patients\u27 refusals of immediate ART initiationResponsive health systems that balance a stated need for time to accept one\u27s diagnosis and prepare to embark on a lifelong treatment plan with interventions to identify and manage patient-specific treatment related fears and concerns may support more rapid ART initiationPerceived social stigma around HIV continues to be a significant challenge for treatment initiation