Evaluating the potential of IP-10 and MCP-2 as biomarkers for the diagnosis of tuberculosis

The aim of the present study was to evaluate the potential of diagnostic tests based on interferon-gamma inducible protein (IP)-10 and monocyte chemotactic protein (MCP)-2, and compare the performance with the QuantiFERON TB Gold In-Tube (QFT-IT; Cellestis, Carnagie, Australia) test. IP-10 and MCP-2 were determined in supernatants from whole blood stimulated with Mycobacterium tuberculosis-specific antigens. Samples were obtained from 80 patients with culture- and/or PCR-proven tuberculosis (TB), and 124 unexposed healthy controls: 86 high school students and 38 high school staff. IP-10 and MCP-2 test cut-offs were established based on receiver operating characteristic curve analysis. TB patients produced significantly higher levels (median) of IP-10 (2158 pg x mL(-1)) and MCP-2 (379 pg x mL(-1)) compared with interferon (IFN)-gamma (215 pg x mL(-1)). The QFT-IT, IP-10 and MCP-2 tests detected 81, 83 and 71% of the TB patients; 0, 3 and 0% of the high school students and 0, 16 and 3% of the staff, respectively. Agreement between tests was high (>89%). By combining IP-10 and IFN-gamma tests, the detection rate increased among TB patients to 90% without a significant increase in positive responders among the students. In conclusion, interferon-gamma inducible protein-10 and monocyte chemotactic protein-2 responses to Mycobacterium tuberculosis-specific antigens could be used to diagnose infection. Combining interferon-gamma inducible protein-10 and interferon-gamma may be a simple approach to increase the detection rate of the Mycobacterium tuberculosis-specific in vitro tests.

Evolution of the leukotoxin promoter in genus Mannheimia

BACKGROUND: The Mannheimia species encompass a wide variety of bacterial lifestyles, including opportunistic pathogens and commensals of the ruminant respiratory tract, commensals of the ovine rumen, and pathogens of the ruminant integument. Here we present a scenario for the evolution of the leukotoxin promoter among representatives of the five species within genus Mannheimia. We also consider how the evolution of the leukotoxin operon fits with the evolution and maintenance of virulence. RESULTS: The alignment of the intergenic regions upstream of the leukotoxin genes showed significant sequence and positional conservation over a 225-bp stretch immediately proximal to the transcriptional start site of the lktC gene among all Mannheimia strains. However, in the course of the Mannheimia genome evolution, the acquisition of individual noncoding regions upstream of the conserved promoter region has occurred. The rate of evolution estimated branch by branch suggests that the conserved promoter may be affected to different extents by the types of natural selection that potentially operate in regulatory regions. Tandem repeats upstream of the core promoter were confined to M. haemolytica with a strong association between the sequence of the repeat units, the number of repeat units per promoter, and the phylogenetic history of this species. CONCLUSION: The mode of evolution of the intergenic regions upstream of the leukotoxin genes appears to be highly dependent on the lifestyle of the bacterium. Transition from avirulence to virulence has occurred at least once in M. haemolytica with some evolutionary success of bovine serotype A1/A6 strains. Our analysis suggests that changes in cis-regulatory systems have contributed to the derived virulence phenotype by allowing phase-variable expression of the leukotoxin protein. We propose models for how phase shifting and the associated virulence could facilitate transmission to the nasopharynx of new hosts.

Emended description of porcine [Pasteurella] aerogenes, [Pasteurella] mairii and [Actinobacillus] rossii

The aim of this study was to improve the definition and identification of a group of veterinarily important bacteria referred to as the [Pasteurella] aerogenes-[Pasteurella] mairii-[Actinobacillus] rossii complex. These organisms have mainly been isolated from the reproductive and intestinal tracts of pigs and in most cases have been considered as opportunistic pathogens. A collection of 87 strains were characterized by phenotypic analysis from which 41 strains were selected for 16S rRNA gene sequence comparison, out of which 23 have been sequenced in the present study. One group of 21 strains phenotyped as biovars 1, 3-5, 9-11, 19 and 25-27, including the type strain of [P.] aerogenes, showed 16S rRNA gene sequence similarities of 99.6 % or higher; another group of 18 strains including biovars 2, 6-8, 12-15, 21, 23, 24 and 26A and the type strain of [A.] rossii showed 97.8 % or higher 16S rRNA gene sequence similarity. Between the two groups, 93.8-95.7 % 16S rRNA gene sequence similarity was observed. Strains of [P.] mairii showed 99.5 % similarity, with 95.5-97.2 and 93.8-95.5 % similarity to strains of [P.] aerogenes and [A.] rossii, respectively. Four strains could not be classified with any of these groups and belonged to other members of Pasteurellaceae. Comparisons were also made to DNA-DNA hybridization data. Biovars 1, 9, 10, 11 and 19, including the type strain of [P.] aerogenes, linked at 70 % DNA reassociation, whereas strains identified as biovars 2, 6, 7, 8, 12, 15 and 21 of [P.] aerogenes linked at 81 %. The latter group most likely represents [A.] rossii based on the 16S rRNA gene sequence comparisons. DNA reassociation between the [P.] aerogenes and [A.] rossii groups was at most 37 %, whereas 47 % was the highest DNA reassociation found between [P.] aerogenes and [P.] mairii. The study showed that [P.] aerogenes, [P.] mairii and [A.] rossii can not be easily separated and may consequently be misidentified based on current knowledge of their phenotypic characteristics. In addition, these taxa are difficult to separate from other taxa of the Pasteurellaceae. A revised scheme for separation based upon phenotypic characters is suggested for the three species [P.] aerogenes emend., [P.] mairii emend. and [A.] rossii emend., with the respective type strains ATCC 27883T, NCTC 10699T and ATCC 27072T.

Comparative phylogenies of the housekeeping genes atpD, infB and rpoB and the 16S rRNA gene within the Pasteurellaceae

Phylogenies of housekeeping gene and 16S rRNA gene sequences were compared to improve the classification of the bacterial family Pasteurellaceae and knowledge of the evolutionary relationships of its members. Deduced partial protein sequences of the housekeeping genes atpD, infB and rpoB were compared in 28, 36 and 28 representative taxa of the Pasteurellaceae, respectively. The monophyly of representatives of the genus Gallibacterium was recognized by analysis of all housekeeping genes, while members of Mannheimia, Actinobacillus sensu stricto and the core group of Pasteurella sensu stricto formed monophyletic groups with two out of three housekeeping genes. Representatives of Mannheimia, Actinobacillus sensu stricto, [Haemophilus] ducreyi and [Pasteurella] trehalosi formed a monophyletic unit by analysis of all three housekeeping genes, which was in contrast to the 16S rRNA gene-derived phylogeny, where these taxa occurred at separate positions in the phylogenetic tree. Representatives of the Rodent, Avian and Aphrophilus-Haemophilus 16S rRNA gene groups were weakly supported by phylogenetic analysis of housekeeping genes. Phylogenies derived by comparison of the housekeeping genes diverged significantly from the 16S rRNA gene-derived phylogeny as evaluated by the likelihood ratio test. A low degree of congruence was also observed between the individual housekeeping gene-derived phylogenies. Estimates on speciation derived from 16S rRNA and housekeeping gene sequence comparisons resulted in quite different evolutionary scenarios for members of the Pasteurellaceae. The phylogeny based on the housekeeping genes supported observed host associations between Mannheimia, Actinobacillus sensu stricto and [Pasteurella] trehalosi and animals with paired hooves.

Is characterization of a single isolate sufficient for valid publication of a new genus or species? Proposal to modify recommendation 30b of the Bacteriological Code (1990 Revision)

From 1990 to 2000, the number of published named taxa based upon new isolates at species and genus levels in International Journal of Systematic and Evolutionary Microbiology, formerly International Journal of Systematic Bacteriology, have increased by approximately four- and sevenfold, respectively. New taxa based upon characterization of only a single isolate remained at around 40% for both categories. The Bacteriological Code (1990 Revision) has no recommendations on the number of strains required for definition of new taxa. For a few groups, a minimum number of 5-10 strains has been suggested in minimal standards. Since an exponential increase in new taxa can be expected in the future, the authors discuss problems related to naming new species and genera based upon descriptions of a single isolate and suggest that this practice is re-evaluated. It is proposed that the following should be added to Recommendation 30b of the Bacteriological Code: 'Descriptions should be based on as many strains as possible (minimum five), representing different sources with respect to geography and ecology in order to be well characterized both phenotypically and genotypically, to establish the centre (from which the type strain could be chosen) and the extent of the cluster to be named. In addition, comparative studies should be performed, including reference strains that represent neighbouring species and/or genera, in order to give descriptions that are sufficiently detailed to allow differentiation from these neighbours.'

A universal description of ultraslow glass dynamics

The dynamics of glass is of importance in materials science but its nature has not yet been fully understood. Here we report that a verification of the temperature dependencies of the primary relaxation time or viscosity in the ultraslowing/ultraviscous domain of glass-forming systems can be carried out via the analysis of the inverse of the Dyre-Olsen temperature index. The subsequent analysis of experimental data indicates the possibility of the self-consistent description of glass-forming low-molecular-weight liquids, polymers, liquid crystals, orientationally disordered crystals and Ising spin-glass-like systems, as well as the prevalence of equations associated with the 'finite temperature divergence'. All these lead to a new formula for the configurational entropy in glass-forming systems. Furthermore, a link to the dominated local symmetry for a given glass former is identified here. Results obtained show a new relationship between the glass transition and critical phenomena.

Historical and idealized climate model experiments: an intercomparison of Earth system models of intermediate complexity

Both historical and idealized climate model experiments are performed with a variety of Earth system models of intermediate complexity (EMICs) as part of a community contribution to the Intergovernmental Panel on Climate Change Fifth Assessment Report. Historical simulations start at 850 CE and continue through to 2005. The standard simulations include changes in forcing from solar luminosity, Earth's orbital configuration, CO2, additional greenhouse gases, land use, and sulphate and volcanic aerosols. In spite of very different modelled pre-industrial global surface air temperatures, overall 20th century trends in surface air temperature and carbon uptake are reasonably well simulated when compared to observed trends. Land carbon fluxes show much more variation between models than ocean carbon fluxes, and recent land fluxes appear to be slightly underestimated. It is possible that recent modelled climate trends or climate–carbon feedbacks are overestimated resulting in too much land carbon loss or that carbon uptake due to CO2 and/or nitrogen fertilization is underestimated. Several one thousand year long, idealized, 2 × and 4 × CO2 experiments are used to quantify standard model characteristics, including transient and equilibrium climate sensitivities, and climate–carbon feedbacks. The values from EMICs generally fall within the range given by general circulation models. Seven additional historical simulations, each including a single specified forcing, are used to assess the contributions of different climate forcings to the overall climate and carbon cycle response. The response of surface air temperature is the linear sum of the individual forcings, while the carbon cycle response shows a non-linear interaction between land-use change and CO2 forcings for some models. Finally, the preindustrial portions of the last millennium simulations are used to assess historical model carbon-climate feedbacks. Given the specified forcing, there is a tendency for the EMICs to underestimate the drop in surface air temperature and CO2 between the Medieval Climate Anomaly and the Little Ice Age estimated from palaeoclimate reconstructions. This in turn could be a result of unforced variability within the climate system, uncertainty in the reconstructions of temperature and CO2, errors in the reconstructions of forcing used to drive the models, or the incomplete representation of certain processes within the models. Given the forcing datasets used in this study, the models calculate significant land-use emissions over the pre-industrial period. This implies that land-use emissions might need to be taken into account, when making estimates of climate–carbon feedbacks from palaeoclimate reconstructions.

Long-term climate change commitment and reversibility: An EMIC Intercomparison

This paper summarizes the results of an intercomparison project with Earth System Models of Intermediate Complexity (EMICs) undertaken in support of the Intergovernmental Panel on Climate Change (IPCC) Fifth Assessment Report (AR5). The focus is on long-term climate projections designed to 1) quantify the climate change commitment of different radiative forcing trajectories and 2) explore the extent to which climate change is reversible on human time scales. All commitment simulations follow the four representative concentration pathways (RCPs) and their extensions to year 2300. Most EMICs simulate substantial surface air temperature and thermosteric sea level rise commitment following stabilization of the atmospheric composition at year-2300 levels. The meridional overturning circulation (MOC) is weakened temporarily and recovers to near-preindustrial values in most models for RCPs 2.6-6.0. The MOC weakening is more persistent for RCP8.5. Elimination of anthropogenic CO2 emissions after 2300 results in slowly decreasing atmospheric CO2 concentrations. At year 3000 atmospheric CO2 is still at more than half its year-2300 level in all EMICs for RCPs 4.5-8.5. Surface air temperature remains constant or decreases slightly and thermosteric sea level rise continues for centuries after elimination of CO2 emissions in all EMICs. Restoration of atmospheric CO2 from RCP to preindustrial levels over 100-1000 years requires large artificial removal of CO2 from the atmosphere and does not result in the simultaneous return to preindustrial climate conditions, as surface air temperature and sea level response exhibit a substantial time lag relative to atmospheric CO2.

Transcriptional analysis of left-sided colitis, pancolitis, and ulcerative colitis-associated dysplasia.

BACKGROUND It is unknown why patients with extensive ulcerative colitis (UC) have a higher risk of colorectal cancer compared with patients with left-sided UC. This study characterizes the inflammatory processes in left-sided UC, pancolitis, and UC-associated dysplasia at the transcriptional level to identify potential biomarkers and transcripts of importance for the carcinogenic behavior of chronic inflammation. METHODS The Affymetrix GeneChip Human Genome U133 Plus 2.0 was applied on colonic biopsies from UC patients with left-sided UC, pancolitis, dysplasia, and controls. Reverse transcription polymerase chain reaction and immunohistochemistry were performed for validating selected transcripts in the initial cohort and in 2 independent cohorts of patients with UC. Microarray data were analyzed by principal component analysis, and reverse transcription polymerase chain reaction and immunohistochemistry data by the Wilcoxon's rank-sum test. RESULTS The principal component analysis results revealed separate clusters for left-sided UC, pancolitis, dysplasia, and controls. Close clustering of dysplastic and pancolitic samples indicated similarities in gene expression. Indeed, 101 and 656 parallel upregulated and downregulated transcripts, respectively, were identified in specimens from dysplasia and pancolitis. Validation of selected transcripts hereof identified insulin receptor alpha (INSRA) and MAP kinase interacting serine/threonine kinase 2 (MKNK2) with an enhanced expression in dysplasia compared with left-sided UC and controls, whereas laminin γ2 (LAMC2) was found with a lower expression in dysplasia compared with the remaining 3 groups. CONCLUSIONS This study demonstrates pancolitis and left-sided UC as distinct inflammatory processes at the transcriptional level, and identifies INSRA, MKNK2, and LAMC2 as potential critical transcripts in the inflammation-driven preneoplastic process of UC.

Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization

The QT interval, an electrocardiographic measure reflecting myocardial repolarization, is a heritable trait. QT prolongation is a risk factor for ventricular arrhythmias and sudden cardiac death (SCD) and could indicate the presence of the potentially lethal mendelian long-QT syndrome (LQTS). Using a genome-wide association and replication study in up to 100,000 individuals, we identified 35 common variant loci associated with QT interval that collectively explain ∼8-10% of QT-interval variation and highlight the importance of calcium regulation in myocardial repolarization. Rare variant analysis of 6 new QT interval-associated loci in 298 unrelated probands with LQTS identified coding variants not found in controls but of uncertain causality and therefore requiring validation. Several newly identified loci encode proteins that physically interact with other recognized repolarization proteins. Our integration of common variant association, expression and orthogonal protein-protein interaction screens provides new insights into cardiac electrophysiology and identifies new candidate genes for ventricular arrhythmias, LQTS and SCD.

Decision-Making Processes in Voluntary Football Clubs in Relation to External Counselling

Introduction Recruiting and retaining volunteers who are prepared to make a long-term commitment is a major problem for Swiss sports clubs. With the inclusion of external counselling for the change and systematisation of volunteer management, sports clubs have a possibility to develop and defuse problems in spite of existing barriers and gaps in knowledge. To what extent is external counselling for personnel problems effective? It is often observed that standardised counselling inputs lead to varying consequences for sports clubs. It can be assumed that external impulses are interpreted and transformed differently into the workings of the club. However, this cannot be solely attributed to the situational or structural conditions of the clubs. It is also important to consider the underlying decision-making processes of a club. According to Luhmann’s organisational sociological considerations (2000), organisations (sports clubs) have to be viewed as social systems consisting of (communicated) decisions. This means that organisations are continually reproduced by decision-making processes. All other (observable) factors such as an organisation’s goals, recruiting strategies, support schemes for volunteers etc., have to be seen as an outcome of the operation of prior organisational decisions. Therefore: How do decision-making processes in sports clubs work in the context of the implementation of external counselling? Theoretical Framework An examination of the actual situation in sports clubs shows that decisions frequently appear to be shaped by inconsistency, unexpected outcomes, and randomness (Amis & Slack, 2003). Therefore, it must be emphasised that these decisions cannot be analysed according to any rational decision-making model. Their specific structural characteristics only permit a limited degree of rationality – bounded rationality. Non-profit organisations in particular are shaped by a specific mode of decisionmaking that Cohen, March, and Olsen (1972) have called the “garbage can model”. As sport clubs can also be conceived as “organised anarchies”, this model seems to offer an appropriate approach to understanding their practices and analysing their decision-making processes. The key concept in the garbage can model is the assumption that decision-making processes in organisations consist of four “streams”: (a) problems, (b) actors, (c) decision-making opportunities, and (d) solutions. Method Before presenting the method of the analysis of the decision-making processes in sports clubs, the external counselling will be described. The basis of the counselling is generated by a sports clubs’ capability to change. Due to the specific structural characteristics and organisational principles, change processes in sports clubs often merge with barriers and restrictions. These need to be considered when developing counselling guidelines for a successful planning and realisation of change processes. Furthermore, important aspects of personnel management in sports clubs and especially volunteer management must be implied in order to elaborate key elements for the counselling to recruit new volunteers (e.g., approach, expectations). A counselling of four system-counselling workshops was conceptualised by considering these specific characteristics. The decision-making processes in the sports clubs were analysed during the counselling and the implementation process. A case study is designed with the appropriate methodological approach for such explorative research. The approach adopted for these single case analyses was oriented toward the research program of behavioural decision-making theory (garbage can model). This posits that in-depth insights into organisational decision-making processes can only be gained through relevant case studies of existing organisational situations (Skille, 2013). Before, during and after the intervention, questionnaires and guided interviews were conducted with the project teams of the twelve par-ticipating football clubs to assess the different components of the “streams” in the context of external counselling. These interviews have been analysed using content analysis following guidelines as for-mulated by Mayring (2010). Results The findings show that decision-making processes in football clubs occur differently in the context of external counselling. Different initial positions and problems are the triggers for these decision-making processes. Furthermore, the implementation of the solutions and the external counselling is highly dependent on the commitment of certain people as central players within the decision-mak-ing process. The importance of these relationships is confirmed by previous findings in regard to decision-making and change processes in sports clubs. The decision-making processes in sports clubs can be theoretically analysed using behavioural decision-making theory and the “garbage can model”. Bounded rationality characterises all “streams” of the decision-making processes. Moreo-ver, the decision-making process of the football clubs can be well illustrated in the framework, and the interplay of the different dimensions illustrates the different decision-making practices within the football clubs. References Amis, J., & Slack, T. (2003). Analysing sports organisations: Theory and practice. In B. Houlihan (Eds.), Sport & Society (pp. 201–217). London, England: Sage. Cohen, M.D., March, J.G., & Olsen, J.P. (1972). A garbage can model of organisational choice. Ad-ministrative Science Quarterly, 17, 1-25. Luhmann, N. (2000). Organisation und Entscheidung. Opladen: Westdeutscher Verlag. Mayring, P. (2010). Qualitative Inhaltsanalyse. Grundlagen und Techniken. Weinheim: Beltz. Skille, E. Å. (2013). Case study research in sport management: A reflection upon the theory of science and an empirical example. In S. Söderman & H. Dolles (Eds.), Handbook of research on sport and business (pp. 161–175). Cheltenham, England: Edward Elgar.

Childhood cancer survivor cohorts in Europe.

With the advent of multimodality therapy, the overall five-year survival rate from childhood cancer has improved considerably now exceeding 80% in developed European countries. This growing cohort of survivors, with many years of life ahead of them, has raised the necessity for knowledge concerning the risks of adverse long-term sequelae of the life-saving treatments in order to provide optimal screening and care and to identify and provide adequate interventions. Childhood cancer survivor cohorts in Europe. Considerable advantages exist to study late effects in individuals treated for childhood cancer in a European context, including the complementary advantages of large population-based cancer registries and the unrivalled opportunities to study lifetime risks, together with rich and detailed hospital-based cohorts which fill many of the gaps left by the large-scale population-based studies, such as sparse treatment information. Several large national cohorts have been established within Europe to study late effects in individuals treated for childhood cancer including the Nordic Adult Life after Childhood Cancer in Scandinavia study (ALiCCS), the British Childhood Cancer Survivor Study (BCCSS), the Dutch Childhood Oncology Group (DCOG) LATER study, and the Swiss Childhood Cancer Survivor Study (SCCSS). Furthermore, there are other large cohorts, which may eventually become national in scope including the French Childhood Cancer Survivor Study (FCCSS), the French Childhood Cancer Survivor Study for Leukaemia (LEA), and the Italian Study on off-therapy Childhood Cancer Survivors (OTR). In recent years significant steps have been taken to extend these national studies into a larger pan-European context through the establishment of two large consortia - PanCareSurFup and PanCareLIFE. The purpose of this paper is to present an overview of the current large, national and pan-European studies of late effects after childhood cancer. This overview will highlight the strong cooperation across Europe, in particular the EU-funded collaborative research projects PanCareSurFup and PanCareLIFE. Overall goal. The overall goal of these large cohort studies is to provide every European childhood cancer survivor with better care and better long-term health so that they reach their full potential, and to the degree possible, enjoy the same quality of life and opportunities as their peers.