A novel targeted/untargeted GC-Orbitrap metabolomics methodology applied to Candida albicans and Staphylococcus aureus biofilms

Introduction: Combined infections from Candida albicans and Staphylococcus aureus are a leading cause of death in the developed world. Evidence suggests that Candida enhances the virulence of Staphylococcus—hyphae penetrate through tissue barriers, while S. aureus tightly associates with the hyphae to obtain entry to the host organism. Indeed, in a biofilm state, C. albicans enhances the antimicrobial resistance characteristics of S. aureus. The association of these microorganisms is also associated with significantly increased morbidity and mortality. Due to this tight association we hypothesised that metabolic effects were also in evidence. Objectives: To explore the interaction, we used a novel GC-Orbitrap-based mass spectrometer, the Q Exactive GC, which combines the high peak capacity and chromatographic resolution of gas chromatography with the sub-ppm mass accuracy of an Orbitrap system. This allows the capability to leverage the widely available electron ionisation libraries for untargeted applications, along with expanding accurate mass libraries and targeted matches based around authentic standards. Methods: Optimised C. albicans and S. aureus mono- and co-cultured biofilms were analysed using the new instrument in addition to the fresh and spent bacterial growth media. Results: The targeted analysis experiment was based around 36 sugars and sugar phosphates, 22 amino acids and five organic acids. Untargeted analysis resulted in the detection of 465 features from fresh and spent medium and 405 from biofilm samples. Three significantly changing compounds that matched to high scoring library fragment patterns were chosen for validation. Conclusion: Evaluation of the results demonstrates that the Q Exactive GC is suitable for metabolomics analysis using a targeted/untargeted methodology. Many of the results were as expected: e.g. rapid consumption of glucose and fructose from the medium regardless of the cell type. Modulation of sugar-phosphate levels also suggest that the pentose phosphate pathway could be enhanced in the cells from co-cultured biofilms. Untargeted metabolomics results suggested significant production of cell-wall biosynthesis components and the consumption of non-proteinaceous amino-acids

Novel ecosystems: theoretical and management aspects of the new ecological world order

We explore the issues relevant to those types of ecosystems containing new combinations of species that arise through human action, environmental change, and the impacts of the deliberate and inadvertent introduction of species from other regions. Novel ecosystems (also termed 'emerging ecosystems') result when species occur in combinations and relative abundances that have not occurred previously within a given biome. Key characteristics are novelty, in the form of new species combinations and the potential for changes in ecosystem functioning, and human agency, in that these ecosystems are the result of deliberate or inadvertent human action. As more of the Earth becomes transformed by human actions, novel ecosystems increase in importance, but are relatively little studied. Either the degradation or invasion of native or 'wild' ecosystems or the abandonment of intensively managed systems can result in the formation of these novel systems. Important considerations are whether these new systems are persistent and what values they may have. It is likely that it may be very difficult or costly to return such systems to their previous state, and hence consideration needs to be given to developing appropriate management goals and approaches.Ctr Invas Bio

The role of protected areas in the avoidance of anthropogenic conversion in a high pressure region : a matching method analysis in the core region of the brazilian cerrado

Global efforts to avoid anthropogenic conversion of natural habitat rely heavily on the establishment of protected areas. Studies that evaluate the effectiveness of these areas with a focus on preserving the natural habitat define effectiveness as a measure of the influence of protected areas on total avoided conversion. Changes in the estimated effectiveness are related to local and regional differences, evaluation methods, restriction categories that include the protected areas, and other characteristics. The overall objective of this study was to evaluate the effectiveness of protected areas to prevent the advance of the conversion of natural areas in the core region of the Brazil’s Cerrado Biome, taking into account the influence of the restriction degree, governmental sphere, time since the establishment of the protected area units, and the size of the area on the performance of protected areas. The evaluation was conducted using matching methods and took into account the following two fundamental issues: control of statistical biases caused by the influence of covariates on the likelihood of anthropogenic conversion and the non-randomness of the allocation of protected areas throughout the territory (spatial correlation effect) and the control of statistical bias caused by the influence of auto-correlation and leakage effect. Using a sample design that is not based on ways to control these biases may result in outcomes that underestimate or overestimate the effectiveness of those units. The matching method accounted for a bias reduction in 94–99% of the estimation of the average effect of protected areas on anthropogenic conversion and allowed us to obtain results with a reduced influence of the auto-correlation and leakage effects. Most protected areas had a positive influence on the maintenance of natural habitats, although wide variation in this effectiveness was dependent on the type, restriction, governmental sphere, size and age group of the unit

High levels of genetic differentiation and selfing in the Brazilian cerrado fruit tree Dipteryx alata Vog. (Fabaceae)

Dipteryx alata is a native fruit tree species of the cerrado (Brazilian savanna) that has great economic potential because of its multiple uses. Knowledge of how the genetic variability of this species is organized within and among populations would be useful for genetic conservation and breeding programs. We used nine simple sequence repeat (SSR) primers developed for Dipteryx odorata to evaluate the genetic structure of three populations of D. alata located in central Brazil based on a leaf sample analysis from 101 adults. The outcrossing rate was evaluated using 300 open-pollinated offspring from 25 seed-trees. Pollen dispersal was measured by parentage analysis. We used spatial genetic structure (SGS) to test the minimal distance for harvesting seeds in conservation and breeding programs. Our data indicate that the populations studied had a high degree of genetic diversity and population structure, as suggested by the high level of divergence among populations . The estimated outcrossing rate suggested a mixed mating system, and the intrapopulation fixation index was influenced by SGS. We conclude that seed harvesting for genetic conservation and breeding programs requires a minimum distance between trees of 196 m to avoid collecting seeds from related seed-trees

The Four-Dimensional Symptom Questionnaire (4DSQ): a validation study of a multidimensional self-report questionnaire to assess distress, depression, anxiety and somatization

BACKGROUND: The Four-Dimensional Symptom Questionnaire (4DSQ) is a self-report questionnaire that has been developed in primary care to distinguish non-specific general distress from depression, anxiety and somatization. The purpose of this paper is to evaluate its criterion and construct validity. METHODS: Data from 10 different primary care studies have been used. Criterion validity was assessed by comparing the 4DSQ scores with clinical diagnoses, the GPs' diagnosis of any psychosocial problem for Distress, standardised psychiatric diagnoses for Depression and Anxiety, and GPs' suspicion of somatization for Somatization. ROC analyses and logistic regression analyses were used to examine the associations. Construct validity was evaluated by investigating the inter-correlations between the scales, the factorial structure, the associations with other symptom questionnaires, and the associations with stress, personality and social functioning. The factorial structure of the 4DSQ was assessed through confirmatory factor analysis (CFA). The associations with other questionnaires were assessed with Pearson correlations and regression analyses. RESULTS: Regarding criterion validity, the Distress scale was associated with any psychosocial diagnosis (area under the ROC curve [AUC] 0.79), the Depression scale was associated with major depression (AUC = 0.83), the Anxiety scale was associated with anxiety disorder (AUC = 0.66), and the Somatization scale was associated with the GPs' suspicion of somatization (AUC = 0.65). Regarding the construct validity, the 4DSQ scales appeared to have considerable inter-correlations (r = 0.35-0.71). However, 30–40% of the variance of each scale was unique for that scale. CFA confirmed the 4-factor structure with a comparative fit index (CFI) of 0.92. The 4DSQ scales correlated with most other questionnaires measuring corresponding constructs. However, the 4DSQ Distress scale appeared to correlate with some other depression scales more than the 4DSQ Depression scale. Measures of stress (i.e. life events, psychosocial problems, and work stress) were mainly associated with Distress, while Distress, in turn, was mainly associated with psychosocial dysfunctioning, including sick leave. CONCLUSION: The 4DSQ seems to be a valid self-report questionnaire to measure distress, depression, anxiety and somatization in primary care patients. The 4DSQ Distress scale appears to measure the most general, most common, expression of psychological problems

Gender and age differences in the recurrence of sickness absence due to common mental disorders: a longitudinal study

Background: Common mental disorders (CMDs) are an important cause of sickness absence and long-term work disability. Although CMDs are known to have high recurrence rates, little is known about the recurrence of sickness absence due to CMDs. The aim of this study was to investigate the recurrence of sickness absence due to CMDs, including distress, adjustment disorders, depressive disorders and anxiety disorders, according to age, in male and female employees in the Netherlands. Methods: Data on sickness absence episodes due to CMDs were obtained for 137,172 employees working in the Dutch Post and Telecommunication companies between 2001 and 2007. The incidence density (ID) and recurrence density (RD) of sickness absence due to CMDs was calculated per 1000 person-years in men and women in the age-groups of < 35 years, 35-44 years, 45-54 years, and >= 55 years. Results: The ID of one episode of CMDs sickness absence was 25.0 per 1000 person-years, and the RD was 76.7 per 1000 person-years. Sickness absence due to psychiatric disorders (anxiety and depression) does not have a higher recurrence density of sickness absence due to any CMDs as compared to stress-related disorders (distress and adjustment disorders): 81.6 versus 76.0 per 1000 person-years. The ID of sickness absence due to CMDs was higher in women than in men, but the RD was similar. Recurrences were more frequent in women < 35 years and in women between 35 and 44 years of age. We observed no differences between age groups in men. Recurrences among employees with recurrent episodes occurred within 3 years in 90% of cases and the median time-to-onset of recurrence was 11 (10-13) months in men and 10 (9-12) months in women. Conclusions: Employees who have been absent from work due to CMDs are at increased risk of recurrent sickness absence due to CMDs and should be monitored after they return to work. The RD was similar in men and in women. In women < 45 years the RD was higher than in women >= 45 years. In men no age differences were observed