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Search Results: 1 - 10 of 306276 matches for " Stephen J. Callister "
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An Empirical Strategy for Characterizing Bacterial Proteomes across Species in the Absence of Genomic Sequences
Joshua E. Turse,Matthew J. Marshall,James K. Fredrickson,Mary S. Lipton,Stephen J. Callister
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0013968
Abstract: Global protein identification through current proteomics methods typically depends on the availability of sequenced genomes. In spite of increasingly high throughput sequencing technologies, this information is not available for every microorganism and rarely available for entire microbial communities. Nevertheless, the protein-level homology that exists between related bacteria makes it possible to extract biological information from the proteome of an organism or microbial community by using the genomic sequences of a near neighbor organism. Here, we demonstrate a trans-organism search strategy for determining the extent to which near-neighbor genome sequences can be applied to identify proteins in unsequenced environmental isolates. In proof of concept testing, we found that within a CLUSTAL W distance of 0.089, near-neighbor genomes successfully identified a high percentage of proteins within an organism. Application of this strategy to characterize environmental bacterial isolates lacking sequenced genomes, but having 16S rDNA sequence similarity to Shewanella resulted in the identification of 300–500 proteins in each strain. The majority of identified pathways mapped to core processes, as well as to processes unique to the Shewanellae, in particular to the presence of c-type cytochromes. Examples of core functional categories include energy metabolism, protein and nucleotide synthesis and cofactor biosynthesis, allowing classification of bacteria by observation of conserved processes. Additionally, within these core functionalities, we observed proteins involved in the alternative lactate utilization pathway, recently described in Shewanella.
Relating perturbation magnitude to temporal gene expression in biological systems
Stephen J Callister, J Jacob Parnell, Michael E Pfrender, Syed A Hashsham
BMC Research Notes , 2009, DOI: 10.1186/1756-0500-2-43
Abstract: Patterns of gene expression were measured in response to increasing sodium chloride concentrations (0, 0.5, 0.7, 1.0, and 1.2 M) for sixty genes impacted by osmotic shock. Expression of these genes was quantified over five time points using reverse transcriptase real-time polymerase chain reaction. Magnitudes of cumulative response for specific pathways, and the set of all genes, were obtained by combining the temporal response envelopes for genes exhibiting significant changes in expression with time. A linear relationship between perturbation magnitude and response was observed for the range of concentrations studied.This study develops a quantitative approach to describe the stability of gene response and pathways to environmental perturbation and illustrates the utility of this approach. The approach should be applicable to quantitatively evaluate the response of organisms via the magnitude of response and stability of the transcriptome to environmental change.The cause and effect relationship between perturbation and response is routinely used to study and characterize ecosystems in terms of stability. To extend this concept, we investigated the relationship between the affect of different perturbation magnitudes on the dynamic level of transcriptional response. The establishment of a quantitative relationship between stress and response has implications for predictive capabilities related to the behavior of organisms in natural and engineered systems and can be established on many levels including community, population, proteome, and transcriptome.Transcription is often compared by measuring the fold-change in relative expression [1,2]; however, a simple fold-change approach only accounts for one aspect of the response. Adjusting to perturbation spans a continuum of short-term stress responses, long-term acclimation, and genetic adaptation. Improved analytical tools for understanding the transcriptional mechanisms underlying variation in environmental toleranc
Comparative Bacterial Proteomics: Analysis of the Core Genome Concept
Stephen J. Callister, Lee Ann McCue, Joshua E. Turse, Matthew E. Monroe, Kenneth J. Auberry, Richard D. Smith, Joshua N. Adkins, Mary S. Lipton
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0001542
Abstract: While comparative bacterial genomic studies commonly predict a set of genes indicative of common ancestry, experimental validation of the existence of this core genome requires extensive measurement and is typically not undertaken. Enabled by an extensive proteome database developed over six years, we have experimentally verified the expression of proteins predicted from genomic ortholog comparisons among 17 environmental and pathogenic bacteria. More exclusive relationships were observed among the expressed protein content of phenotypically related bacteria, which is indicative of the specific lifestyles associated with these organisms. Although genomic studies can establish relative orthologous relationships among a set of bacteria and propose a set of ancestral genes, our proteomics study establishes expressed lifestyle differences among conserved genes and proposes a set of expressed ancestral traits.
Neural Responses to Visual Food Cues According to Weight Status: A Systematic Review of Functional Magnetic Resonance Imaging Studies
Kirrilly Pursey,Robert J. Callister
Frontiers in Nutrition , 2014, DOI: 10.3389/fnut.2014.00007
Abstract: Emerging evidence from recent neuroimaging studies suggests specific food related behaviours contribute to the development of obesity. The aim of this review was to report the neural responses to visual food cues, as assessed by functional magnetic resonance imaging (fMRI), in humans of differing weight status. Published studies to 2014 were retrieved and included if they: used visual food cues, studied humans >18 years old, reported weight status, and included fMRI outcomes. Sixty studies were identified that investigated the neural responses of healthy weight participants (n=26), healthy weight compared to obese participants (n=17), and weight loss interventions (n=12). High calorie food images were used in the majority of studies (n=36), however, image selection justification was only provided in 19 studies. Obese individuals had increased activation of reward-related brain areas including the insula and orbitofrontal cortex in response to visual food cues compared to healthy weight individuals, and this was particularly evident in response to energy dense cues. Additionally, obese individuals were more responsive to food images when satiated. Meta-analysis of changes in neural activation post- weight loss revealed small areas of convergence of activation across studies in brain areas related to emotion, memory and learning such as the cingulate gyrus, lentiform nucleus and precuneus. Differential activation patterns to visual food cues were observed between obese, healthy weight and weight loss populations. Future studies require standardisation of dietetic variables and fMRI outcomes to enable more direct comparisons between studies.
Increasing Positive Perceptions of Diversity for Religious Conservative Students  [PDF]
Alison Cook, Ronda Roberts Callister
Creative Education (CE) , 2010, DOI: 10.4236/ce.2010.12014
Abstract: Evidence suggests that positive perceptions toward diversity enhance the potential group and organizational benefits resulting from diversity. Given the make-up of today’s organizations, encountering diversity has become the norm ra-ther than the exception. As such, it is becoming increasingly important to address diversity issues, and take steps to increase positive perceptions of diversity within the business classroom in order to carry that advantage into the workplace. Religious conservative students present a unique challenge to diversity education in that they likely hold value- laden attitudes that lack alignment with diversity principles. This study prescribes a scaffolding approach to increase positive perceptions of diversity within a classroom comprised predominantly of religious conservative students
Patriotic duty or resented imposition? Public reactions to military conscription in white South Africa, 1952-1972
Graeme Callister
Scientia Militaria: South African Journal of Military Studies , 2007,
Abstract:
PATRIOTIC DUTY OR RESENTED IMPOSITION? PUBLIC REACTIONS TO MILITARY CONSCRIPTION IN WHITE SOUTH AFRICA, 1952-1972
Graeme Callister
Scientia Militaria : South African Journal of Military Studies , 2011, DOI: 10.5787/35-1-29
Abstract: It is widely known that from the introduction of the Defence Amendment Act of 1967 (Act no. 85 of 1967) until the fall of apartheid in 1994, South Africa had a system of universal national service for white males, and that the men conscripted into the South African Defence Force (SADF) under this system were engaged in conflicts in Namibia, Angola, and later in the townships of South Africa itself. What is widely ignored however, both in academia and in wider society, is that the South African military relied on conscripts, selected through a ballot system, to fill its ranks for some fifteen years before the introduction of universal service. This article intends to redress this scholastic imbalance.
Reply to “Critical Comments on the Paper ‘On the Logical Inconsistency of the Special Theory of Relativity’”  [PDF]
Stephen J. Crothers
Journal of Applied Mathematics and Physics (JAMP) , 2018, DOI: 10.4236/jamp.2018.66103
Abstract: It has been critically argued by V. A. Leus (Sobolev Institute of Mathematics, Novosibirsk, Russia) that in my proof that Einstein’s Special Theory of Relativity is logically inconsistent and therefore false, I violated the basic tenets of Special Relativity and foisted an alternative theory upon Einstein’s. A careful study of the critical analysis reveals however a failure to address the key arguments I adduced to prove Special Relativity logically inconsistent, and a concomitant invocation of Einstein’s theory to try to argue that my analysis is incorrect because it does not concur with Einstein. There is therefore no proof advanced of any alleged error in my analysis. In my paper I did not introduce an alternative theory. The aforementioned critical paper affords opportunity in rebuttal to amplify the invalidity of A. Einstein’s tacit assumption, in constructing the Special Theory of Relativity, that systems of clock-synchronised stationary observers consistent with Lorentz Transformation can be mathematically constructed. Since such systems of observers have in fact no mathematical existence the Special Theory of Relativity is logically inconsistent. It is therefore invalid. The consequences for physics, astronomy, and cosmology, are significant.
What does my patient's coronary artery calcium score mean? Combining information from the coronary artery calcium score with information from conventional risk factors to estimate coronary heart disease risk
Mark J Pletcher, Jeffrey A Tice, Michael Pignone, Charles McCulloch, Tracy Q Callister, Warren S Browner
BMC Medicine , 2004, DOI: 10.1186/1741-7015-2-31
Abstract: We measured the independent cross-sectional associations between conventional cardiac risk factors and the CAC score among asymptomatic persons referred for non-contrast electron beam computed tomography. Using the resulting multivariable models and published CAC score-specific relative risk estimates, we estimated post-test coronary heart disease risk in a number of different scenarios.Among 9341 asymptomatic study participants (age 35–88 years, 40% female), we found that conventional coronary heart disease risk factors including age, male sex, self-reported hypertension, diabetes and high cholesterol were independent predictors of the CAC score, and we used the resulting multivariable models for predicting post-test risk in a variety of scenarios. Our models predicted, for example, that a 60-year-old non-smoking non-diabetic women with hypertension and high cholesterol would have a 47% chance of having a CAC score of zero, reducing her 10-year risk estimate from 15% (per Framingham) to 6–9%; if her score were over 100, however (a 17% chance), her risk estimate would be markedly higher (25–51% in 10 years). In low risk scenarios, the CAC score is very likely to be zero or low, and unlikely to change management.Combining information from the CAC score with information from conventional risk factors can change assessment of coronary heart disease risk to an extent that may be clinically important, especially when the pre-test 10-year risk estimate is intermediate. The attached spreadsheet makes these calculations easy.Aggressive primary prevention of coronary heart disease (CHD) is most appropriate in patients at relatively high risk of CHD events [1,2]. The coronary artery calcium (CAC) score is an independent predictor of coronary heart disease risk [3-7], and therefore may help in deciding how aggressively to pursue cholesterol-lowering, anti-platelet therapy and other primary prevention strategies. To use a given CAC score result, however, one must know how that
Exploring the mechanisms of weight loss in the SHED-IT intervention for overweight men: a mediation analysis
David R Lubans, Philip J Morgan, Clare E Collins, Janet M Warren, Robin Callister
International Journal of Behavioral Nutrition and Physical Activity , 2009, DOI: 10.1186/1479-5868-6-76
Abstract: The Self-Help, Exercise and Diet using Information Technology (SHED-IT) program was a 3-month randomized controlled trial (Internet-based intervention group vs information only control group) that was implemented in 2007 with baseline and 6-month follow-up assessment of weight, physical activity and dietary behaviors. Intention-to-treat and per-protocol mediation analyses were conducted using a product-of-coefficients test.Participants (N = 65) were overweight and obese male academic (n = 10) and non-academic (n = 27) staff and students (n = 28) from the University of Newcastle, Australia. Mean (SD) age = 35.9 (11.1) years and mean (SD) BMI = 30.6 (2.8). In the intention-to-treat analysis, both groups lost weight, but relative to the control group, the intervention did not have a statistically significant 'total effect' on weight, τ = -.507, p = .716 (95% CI = -3.277 to 2.263). In the per-protocol analysis, the intervention had a statistically significant 'total effect' on weight, τ = -4.487, p < .05 (95% CI = -8.208 to -.765). The intervention did not have a statistically significant effect on any of the hypothesized mediators and none of the behavioral variables mediated weight loss in the SHED-IT program. Although participants in the intervention group reduced their fat intake over the study period, the changes did not satisfy the criteria for mediation.Few studies have examined the mediators of weight loss in obesity treatment interventions. While none of the hypothesized mediators satisfied the criteria for mediation in the current study, there was some evidence to suggest that overweight men in the SHED-IT intervention reduced their fat intake over the study period. Future obesity treatment and prevention programs should explore behavioral mediators of weight loss using appropriate statistical methods.Australian New Zealand Clinical Trials Registry No: ANZCTRN12607000481471.Obesity is a major cause of preventable death and is associated with substantial direct
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