Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20.

UnlabelledThe genomes of sulfate-reducing bacteria remain poorly characterized, largely due to a paucity of experimental data and genetic tools. To meet this challenge, we generated an archived library of 15,477 mapped transposon insertion mutants in the sulfate-reducing bacterium Desulfovibrio alaskensis G20. To demonstrate the utility of the individual mutants, we profiled gene expression in mutants of six regulatory genes and used these data, together with 1,313 high-confidence transcription start sites identified by tiling microarrays and transcriptome sequencing (5' RNA-Seq), to update the regulons of Fur and Rex and to confirm the predicted regulons of LysX, PhnF, PerR, and Dde_3000, a histidine kinase. In addition to enabling single mutant investigations, the D. alaskensis G20 transposon mutants also contain DNA bar codes, which enables the pooling and analysis of mutant fitness for thousands of strains simultaneously. Using two pools of mutants that represent insertions in 2,369 unique protein-coding genes, we demonstrate that the hypothetical gene Dde_3007 is required for methionine biosynthesis. Using comparative genomics, we propose that Dde_3007 performs a missing step in methionine biosynthesis by transferring a sulfur group to O-phosphohomoserine to form homocysteine. Additionally, we show that the entire choline utilization cluster is important for fitness in choline sulfate medium, which confirms that a functional microcompartment is required for choline oxidation. Finally, we demonstrate that Dde_3291, a MerR-like transcription factor, is a choline-dependent activator of the choline utilization cluster. Taken together, our data set and genetic resources provide a foundation for systems-level investigation of a poorly studied group of bacteria of environmental and industrial importance.ImportanceSulfate-reducing bacteria contribute to global nutrient cycles and are a nuisance for the petroleum industry. Despite their environmental and industrial significance, the genomes of sulfate-reducing bacteria remain poorly characterized. Here, we describe a genetic approach to fill gaps in our knowledge of sulfate-reducing bacteria. We generated a large collection of archived, transposon mutants in Desulfovibrio alaskensis G20 and used the phenotypes of these mutant strains to infer the function of genes involved in gene regulation, methionine biosynthesis, and choline utilization. Our findings and mutant resources will enable systematic investigations into gene function, energy generation, stress response, and metabolism for this important group of bacteria

Attitudes of Religious Leaders Toward Integrating Psychology and Church Ministry

Although psychology and religion deal with overlapping subject matter, the relationship between psychology and the church has a tumultuous history. The current study examined religious leaders’ attitudes toward integrating psychological science into church ministry. Religious leaders (N = 394) completed measures of (a) congregants’ mental health and social concerns, (b) attitudes toward psychological science (i.e., perceived barriers of integration, compatibility with church ministry), and (c) hypothesized predictors of attitudes toward the integration of psychology and church ministry (i.e., political conservatism, intratextual fundamentalism, religious intellectual humility, emotional intelligence). Overall, religious leaders expressed both positive and negative attitudes toward psychology. Conservative political orientation and intratextual fundamentalism were associated with negative attitudes toward integration, whereas religious intellectual humility and emotional intelligence were associated with positive attitudes. We conclude by discussing limitations, suggestions for future research, and practical applications for psychologists and church leaders

Compensatory responses to insulin resistance in obese A frican‐ A merican and L atina girls

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/101770/1/ijpo184.pd

Strong lensing constraints on the velocity dispersion and density profile of elliptical galaxies

We use the statistics of strong gravitational lensing from the CLASS survey to impose constraints on the velocity dispersion and density profile of elliptical galaxies. This approach differs from much recent work, where the luminosity function, velocity dispersion and density profile were typically {\it assumed} in order to constrain cosmological parameters. It is indeed remarkable that observational cosmology has reached the point where we can consider using cosmology to constrain astrophysics, rather than vice versa. We use two different observables to obtain our constraints (total optical depth and angular distributions of lensing events). In spite of the relatively poor statistics and the uncertain identification of lenses in the survey, we obtain interesting constraints on the velocity dispersion and density profiles of elliptical galaxies. For example, assuming the SIS density profile and marginalizing over other relevant parameters, we find 168 km/s < sigma_* < 200 km/s (68% CL), and 158 km/s < sigma_* < 220 km/s (95% CL). Furthermore, if we instead assume a generalized NFW density profile and marginalize over other parameters, the slope of the profile is constrained to be 1.50 < beta < 2.00 (95% CL). We also constrain the concentration parameter as a function of the density profile slope in these models. These results are essentially independent of the exact knowledge of cosmology. We briefly discuss the possible impact on these constraints of allowing the galaxy luminosity function to evolve with redshift, and also possible useful future directions for exploration.Comment: Uses the final JVAS/CLASS sample, more careful choice of ellipticals, added discussion of possible biases. Final results essentially unchanged. Matches the MNRAS versio

Experiencing Grace: A Review of the Empirical Literature

Positive psychologists have used science to understand many virtues but have only just started to study grace, recently defined as ‘ . . . the gift of acceptance given unconditionally and voluntarily to an undeserving person by an unobligated giver’. The purpose of the current article is to provide a systematic review of all empirical studies (published and unpublished) on grace. Broadly, the empirical study of grace has focused on what people believe and how people experience both divine and human grace. Additionally, empirical attention has shifted to explore outcomes of grace-based interventions (e.g., congregation-wide interventions, marital interventions). In general, beliefs and experiences of grace were associated with (a) positive mental health outcomes, (b) religiosity, (c) virtue development, and (d) interpersonal functioning. Human grace has not been extensively explored and divine grace has been studied mostly among Christians; future studies should address these limitations and explore causal relationships

Profiling a decade of information systems frontiers’ research

This article analyses the first ten years of research published in the Information Systems Frontiers (ISF) from 1999 to 2008. The analysis of the published material includes examining variables such as most productive authors, citation analysis, universities associated with the most publications, geographic diversity, authors’ backgrounds and research methods. The keyword analysis suggests that ISF research has evolved from establishing concepts and domain of information systems (IS), technology and management to contemporary issues such as outsourcing, web services and security. The analysis presented in this paper has identified intellectually significant studies that have contributed to the development and accumulation of intellectual wealth of ISF. The analysis has also identified authors published in other journals whose work largely shaped and guided the researchers published in ISF. This research has implications for researchers, journal editors, and research institutions

Brain function distinguishes female carriers and non-carriers of familial risk for autism

BACKGROUND: Autism spectrum disorder (ASD) is characterized by high population-level heritability and a three-to-one male-to-female ratio that occurs independent of sex linkage. Prior research in a mixed-sex pediatric sample identified neural signatures of familial risk elicited by passive viewing of point light motion displays, suggesting the possibility that both resilience and risk of autism might be associated with brain responses to biological motion. To confirm a relationship between these signatures and inherited risk of autism, we tested them in families enriched for genetic loading through undiagnosed ( carrier ) females. METHODS: Using functional magnetic resonance imaging, we examined brain responses to passive viewing of point light displays-depicting biological versus non-biological motion-in a sample of undiagnosed adult females enriched for inherited susceptibility to ASD on the basis of affectation in their respective family pedigrees. Brain responses in carrier females were compared to responses in age-, SRS-, and IQ-matched non-carrier-females-i.e., females unrelated to individuals with ASD. We conducted a hypothesis-driven analysis focused on previously published regions of interest as well as exploratory, brain-wide analyses designed to characterize more fully the rich responses to this paradigm. RESULTS: We observed robust responses to biological motion. Notwithstanding, the 12 regions implicated by prior research did not exhibit the hypothesized interaction between group (carriers vs. controls) and point light displays (biological vs. non-biological motion). Exploratory, brain-wide analyses identified this interaction in three novel regions. Post hoc analyses additionally revealed significant variations in the time course of brain activation in 20 regions spanning occipital and temporal cortex, indicating group differences in response to point light displays (irrespective of the nature of motion) for exploration in future studies. LIMITATIONS: We were unable to successfully eye-track all participants, which prevented us from being able to control for potential differences in eye gaze position. CONCLUSIONS: These methods confirmed pronounced neural signatures that differentiate brain responses to biological and scrambled motion. Our sample of undiagnosed females enriched for family genetic loading enabled discovery of numerous contrasts between carriers and non-carriers of risk of ASD that may index variations in visual attention and motion processing related to genetic susceptibility and inform our understanding of mechanisms incurred by inherited liability for ASD

The TropD software package (v1): standardized methods for calculating tropical-width diagnostics

Observational and modeling studies suggest that Earth's tropical belt has widened over the late 20th century and will continue to widen throughout the 21st century. Yet, estimates of tropical-width variations differ significantly across studies. This uncertainty, to an unknown degree, is partly due to the large variety of methods used in studies of the tropical width. Here, methods for eight commonly used metrics of the tropical width are implemented in the Tropical-width Diagnostics (TropD) code package in the MATLAB programming language. To consolidate the various methods, the operations used in each of the implemented methods are reduced to two basic calculations: finding the latitude of a zero crossing and finding the latitude of a maximum. A detailed description of the methods implemented in the code and of the code syntax is provided, followed by a method sensitivity analysis for each of the metrics. The analysis provides information on how to reduce the methodological component of the uncertainty associated with fundamental aspects of the calculations, such as monthly vs. seasonal averaging biases, grid dependence, sensitivity to noise, and sensitivity to threshold criteria.</p

Transcript-indexed ATAC-seq for precision immune profiling.

T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide-major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples. In peripheral blood CD4+ T cells from healthy individuals, we identified cis and trans regulators of naive and memory T cell states and found substantial heterogeneity in surface-marker-defined T cell populations. In patients with a leukemic form of&nbsp;cutaneous T cell lymphoma, T-ATAC-seq enabled identification of leukemic and nonleukemic regulatory pathways in T cells from the same individual by allowing separation of the signals that arose from the malignant clone from the background T cell noise. Thus, T-ATAC-seq is a new tool that enables analysis of epigenomic landscapes in clonal T cells and should be valuable for studies of T cell malignancy, immunity and immunotherapy