Metabolites in Blood for Prediction of Bacteremic Sepsis in the Emergency Room

A metabolomics approach for prediction of bacteremic sepsis in patients in the emergency room (ER) was investigated. In a prospective study, whole blood samples from 65 patients with bacteremic sepsis and 49 ER controls were compared. The blood samples were analyzed using gas chromatography coupled to time-of-flight mass spectrometry. Multivariate and logistic regression modeling using metabolites identified by chromatography or using conventional laboratory parameters and clinical scores of infection were employed. A predictive model of bacteremic sepsis with 107 metabolites was developed and validated. The number of metabolites was reduced stepwise until identifying a set of 6 predictive metabolites. A 6-metabolite predictive logistic regression model showed a sensitivity of 0.91(95% CI 0.69–0.99) and a specificity 0.84 (95% CI 0.58–0.94) with an AUC of 0.93 (95% CI 0.89–1.01). Myristic acid was the single most predictive metabolite, with a sensitivity of 1.00 (95% CI 0.85–1.00) and specificity of 0.95 (95% CI 0.74–0.99), and performed better than various combinations of conventional laboratory and clinical parameters. We found that a metabolomics approach for analysis of acute blood samples was useful for identification of patients with bacteremic sepsis. Metabolomics should be further evaluated as a new tool for infection diagnostics.     

Environmentally induced morphological variation in the Barnacle Goose,Branta leucopsis

The environmental conditions to which juvenile barnacle geese (Branta leucopsis) were exposed during growth were found to affect their body size at fledging as well as their final adult body size. Small juveniles showed compensatory growth from the time of fledging up to one year of age, but this did not fully compensate the differences in body size that were established before fledging. The variation in protein content in plants eaten during growth could probably explain the observed body size differences, sometimes of more than 10%, between different categories of adult geese. Our results imply that one cannot infer selection on morphological characters from differences between samples of adult birds from different localities or from different cohorts within a population, without first showing that environmental conditions during growth do not affect the development of the characters under study.     

Nesting holes and food supply in relation to forest bird densities on islands and mainland

Summary Bird densities were estimated on 41 small islands and two mainland plots at a South Swedish lake both in 1976 and 1983. In the latter year, three additional plots were also censused. The ratio between combined densities of hole-nesting birds on the mainland and on islands was 3:1 both in plots without and with nest boxes. In plots with boxes combined densities of hole-nesting birds doubled compared with control plots. This increase was caused by a tenfold increase of pied flycatcher Ficedula hypoleuca. Territories of this species were on average established about a week later on the islands compared with the mainland. Furthermore, 50% of the males on the islands did not attract a female. Densities of great tit Parus major, marsh tit Parus palustris and nuthatch Sitta europaea were unaffected by increased nesthole availability. For P. major this result contrasts with those in other studies.The density of chaffinch Fringilla coelebs in habitats with similar height and vertical structure was two times higher on the islands compared to the mainland. On the islands the density was the same on islands with only one pair and on those with two or more pairs. In spring, there were no significant differences between islands and the mainland in the proportion of leaves with insect feeding traces. The proportion of Salix leaves with feeding traces increased with island size, but this was not so for Alnus and Betula leaves. In late summer, the proportion of leaves with feeding traces were halved inside a plot with nest boxes and hence increased bird densities compared to a nearby control plot. This result was the same along the lake shore and about 150 m away from the shore.The discussion centers on the effect of man on the food-and nest site-availability of hole-nesting birds, food limitation of insectivorous birds and density compensation on islands.     

RosettaDDGPrediction for high-throughput mutational scans: From stability to binding

Reliable prediction of free energy changes upon amino acid substitutions (ΔΔGs) is crucial to investigate their impact on protein stability and protein–protein interaction. Advances in experimental mutational scans allow high-throughput studies thanks to multiplex techniques. On the other hand, genomics initiatives provide a large amount of data on disease-related variants that can benefit from analyses with structure-based methods. Therefore, the computational field should keep the same pace and provide new tools for fast and accurate high-throughput ΔΔG calculations. In this context, the Rosetta modeling suite implements effective approaches to predict folding/unfolding ΔΔGs in a protein monomer upon amino acid substitutions and calculate the changes in binding free energy in protein complexes. However, their application can be challenging to users without extensive experience with Rosetta. Furthermore, Rosetta protocols for ΔΔG prediction are designed considering one variant at a time, making the setup of high-throughput screenings cumbersome. For these reasons, we devised RosettaDDGPrediction, a customizable Python wrapper designed to run free energy calculations on a set of amino acid substitutions using Rosetta protocols with little intervention from the user. Moreover, RosettaDDGPrediction assists with checking completed runs and aggregates raw data for multiple variants, as well as generates publication-ready graphics. We showed the potential of the tool in four case studies, including variants of uncertain significance in childhood cancer, proteins with known experimental unfolding ΔΔGs values, interactions between target proteins and disordered motifs, and phosphomimetics. RosettaDDGPrediction is available, free of charge and under GNU General Public License v3.0, at https://github.com/ELELAB/RosettaDDGPrediction .     

GENETIC AND SOCIAL INHERITANCE OF BODY AND EGG SIZE IN THE BARNACLE GOOSE (BRANTA LEUCOPSIS)

We present heritability estimates for final size of body traits and egg size as well as phenotypic and genetic correlations between body and egg traits in a recently established population of the barnacle goose (Branta leucopsis) in the Baltic area. Body traits as well as egg size were heritable and, hence, could respond evolutionarily to phenotypic selection. Genetic correlations between body size traits were significantly positive and of similar magnitude or higher than the corresponding phenotypic correlations. Heritability estimates for tarsus length obtained from full-sib analyses were higher than those obtained from midoffspring-midparent regressions, and this indicates common environment effects on siblings. Heritabilities for tarsus length obtained from midoffspring-mother regressions were significantly higher than estimates from midoffspring-father regressions. The results suggest that this discrepancy is not caused by maternal effects through egg size, nor by extra-pair fertilizations, but by a socially inherited foraging site fidelity in females.     

Cholinesterase Levels in Blood Plasma and Erythrocytes from Calves,Normal Delivering Cows and Cows Suffering from Parturient Paresis

Plasma cholinesterase (pChE) levels and erythrocyte acetylcholinesterase (eAChE) levels were studied in 6 cows before, during and after parturition (Group I), their calves (Group II), 38 cows suffering from parturient paresis (Group III) and 14 newly delivered non-paretic cows (Group IV). The mean of the pChE level in Group I was 1.5 μkat/1 ± 0.20 before parturition and decreased significantly (P ≦ 0.05) to 1.2 ukat/1 ± 0.16 after parturition. The eAChE level was before parturition ≅ 140 ukat/1 and decreased to ≅ 130 μkat/1 4–5 weeks after parturition. At birth the pChE level was 12.8 ukat/1 ± 5.9 in Group II. After 4 weeks the level had decreased to 2.3 ukat/1 ±0.3. In the bull calves the pChE level started to increase when they were 6 weeks old and reached a level of 5.7 μkat/1 ± 0.6 before slaughter at 6 months of age. The heifers did not show this increase. They had a level of around 2 μkat/1 throughout the investigation. The eAChE level at birth was 119 μkat/1 and increased slowly to a level of 145 μkat/1 at 6 months. No differences between the sexes were found. The cows suffering from parturient paresis had a pChE level of 1.80 μkat/1 ± 0.30 before treatment with calcium (Ca). The level decreased significantly (P ≦ 0.001) after Ca-infusion to a level of 1.67 ukat/1 ±0.29. Group IV had a pChE level of 1.65 μkat/1 ± 0.42 at parturition. Two to 4 months later the cows that had recovered from milk fever had a level of 1.61 μkat/1 ± 0.31 and the control cows 1.66 ukat/1 ± 0.48. No differences between the groups were found for the eAChE level. The findings show that parturition influences the pChE level in cows and that sex influences the pChE level in calves between 6 weeks to at least 6 months of age. Furthermore the elevated pChE level found in the cows suffering from parturient paresis before Ca infusion may be a further sign of a disturbance in the cholinergic system with a special preference to the neuromuscular junctions.     

Reconstitution of the Anti-Apoptotic Bcl-2 Protein into Lipid Membranes and Biophysical Evidence for Its Detergent-Driven Association with the Pro-Apoptotic Bax Protein

The anti-apoptotic B-cell CLL/lymphoma-2 (Bcl-2) protein and its counterpart, the pro-apoptotic Bcl-2-associated X protein (Bax), are key players in the regulation of the mitochondrial pathway of apoptosis. However, how they interact at the mitochondrial outer membrane (MOM) and there determine whether the cell will live or be sentenced to death remains unknown. Competing models have been presented that describe how Bcl-2 inhibits the cell-killing activity of Bax, which is common in treatment-resistant tumors where Bcl-2 is overexpressed. Some studies suggest that Bcl-2 binds directly to and sequesters Bax, while others suggest an indirect process whereby Bcl-2 blocks BH3-only proteins and prevents them from activating Bax. Here we present the results of a biophysical study in which we investigated the putative interaction of solubilized full-length human Bcl-2 with Bax and the scope for incorporating the former into a native-like lipid environment. Far-UV circular dichroism (CD) spectroscopy was used to detect direct Bcl-2-Bax-interactions in the presence of polyoxyethylene-(23)-lauryl-ether (Brij-35) detergent at a level below its critical micelle concentration (CMC). Additional surface plasmon resonance (SPR) measurements confirmed this observation and revealed a high affinity between the Bax and Bcl-2 proteins. Upon formation of this protein-protein complex, Bax also prevented the binding of antimycin A₂ (a known inhibitory ligand of Bcl-2) to the Bcl-2 protein, as fluorescence spectroscopy experiments showed. In addition, Bcl-2 was able to form mixed micelles with Triton X-100 solubilized neutral phospholipids in the presence of high concentrations of Brij-35 (above its CMC). Following detergent removal, the integral membrane protein was found to have been fully reconstituted into a native-like membrane environment, as confirmed by ultracentrifugation and subsequent SDS-PAGE experiments.     

Climate limitation at the cold edge: contrasting perspectives from species distribution modelling and a transplant experiment

The role of climate in determining range margins is often studied using species distribution models (SDMs), which are easily applied but have well-known limitations, e.g. due to their correlative nature and colonization and extinction time lags. Transplant experiments can give more direct information on environmental effects, but often cover small spatial and temporal scales. We simultaneously applied a SDM using high-resolution spatial predictors and an integral projection (demographic) model based on a transplant experiment at 58 sites to examine the effects of microclimate, light and soil conditions on the distribution and performance of a forest herb, Lathyrus vernus, at its cold range margin in central Sweden. In the SDM, occurrences were strongly associated with warmer climates. In contrast, only weak effects of climate were detected in the transplant experiment, whereas effects of soil conditions and light dominated. The higher contribution of climate in the SDM is likely a result from its correlation with soil quality, forest type and potentially historic land use, which were unaccounted for in the model. Predicted habitat suitability and population growth rate, yielded by the two approaches, were not correlated across the transplant sites. We argue that the ranking of site habitat suitability is probably more reliable in the transplant experiment than in the SDM because predictors in the former better describe understory conditions, but that ranking might vary among years, e.g. due to differences in climate. Our results suggest that L. vernus is limited by soil and light rather than directly by climate at its northern range edge, where conifers dominate forests and create suboptimal conditions of soil and canopy-penetrating light. A general implication of our study is that to better understand how climate change influences range dynamics, we should not only strive to improve existing approaches but also to use multiple approaches in concert.