A new approach to toxicity testing in Daphnia magna: application of high throughput FT-ICR mass spectrometry metabolomics

Currently there is a surge of interest in exploiting toxicogenomics to screen the toxicity of chemicals, enabling rapid and accurate categorisation into classes of defined mode-of-action (MOA), and prioritising chemicals for further testing. Direct infusion FT-ICR mass spectrometry-based metabolomics can provide a sensitive and unbiased analysis of metabolites in only 15 mins and therefore has considerable potential for chemical screening. The water flea, Daphnia magna, is an OECD test species and is utilised internationally for toxicity testing. However, no metabolomics studies of this species have been reported. Here we optimised and evaluated the effectiveness of FT-ICR mass spectrometry metabolomics for toxicity testing in D. magna. We confirmed that high-quality mass spectra can be recorded from as few as 30 neonates (<24 h old; 224 μg dry mass) or a single adult daphnid (301 μg dry mass). An OECD 24 h acute toxicity test was conducted with neonates at copper concentrations of 0, 5, 10, 25, 50 μg l⁻¹. A total of 5447 unique peaks were detected reproducibly, of which 4768 were assigned at least one empirical formula and 1017 were putatively identified based upon accurate mass measurements. Significant copper-induced changes to the daphnid metabolome, consistent with the documented MOA of copper, were detected thereby validating the approach. In addition, N-acetylspermidine was putatively identified as a novel biomarker of copper toxicity. Collectively, our results highlight the excellent sensitivity, reproducibility and mass accuracy of FT-ICR mass spectrometry, and provide strong evidence for its applicability to high-throughput screening of chemical toxicity in D. magna. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

How Many 3D Structures Do We Need to Train a Predictor？

It has been shown that the progress in the determination of membrane protein structure grows exponentially, with approximately the same growth rate as that of the water-soluble proteins. In order to investigate the effect of this, on the performance of prediction algorithms for both α-helical and β-barrel membrane proteins, we conducted a prospective study based on historical records. We trained separate hidden Markov models with different sized training sets and evaluated their performance on topology pred...     

Methodology of evaluation of morphology of the spine and the trunk in idiopathic scoliosis and other spinal deformities - 6th SOSORT consensus paper

Background

Comprehensive evaluation of the morphology of the spine and of the whole body is essential in order to correctly manage patients suffering from progressive idiopathic scoliosis. Although methodology of clinical and radiological examination is well described in manuals of orthopaedics, there is deficit of data which clinical and radiological parameters are considered in everyday practise. Recently, an increasing tendency to extend scoliosis examination beyond the measure of the Cobb angle can be observed, reflecting a more patient-oriented approach. Such evaluation often involves surface parameters, aesthetics, function and quality of life.

Aim of the study

To investigate current recommendations of experts on methodology of evaluation of the patient with spinal deformity, essentially idiopathic scoliosis.

Methods

Structured Delphi procedure for collecting and processing knowledge from a group of experts with a series of questionnaires and controlled opinion feedback was performed. Experience and opinions of the professionals - physicians and physiotherapists managing scoliosis patients - were studied. According to Delphi method a Meeting Questionnaire (MQ) has been developed, resulting from a preliminary Pre-Meeting Questionnaire (PMQ) which had been previously discussed and approved on line. The MQ was circulated among the SOSORT experts during Consensus Session on "Measurements" which took place at the Annual Meeting of the Society, totally 23 panellists being engaged. Clinical, radiological and surface topography parameters were checked for agreement.

Results

90% agreement or more was reached in 35 items and superior than 75% agreement was reached in further 25 items. An evaluation form was proposed to be used by clinicians and researchers.

Conclusion

The consensus was reached on evaluation of the morphology of the patient with idiopathic scoliosis, comprising clinical, radiological and, to less extend, surface topography assessment. Considering the variety of parameters indicated by the panellists, the Cobb angle, yet the gold standard, can be seen neither as the unique nor the only decisive parameter in the management of patients with idiopathic scoliosis.     

A methodological approach to assess and compare the sustainability level of agricultural plant production systems

A large number of indicators have been developed, in order to assess agricultural sustainability. However, there is no unified theoretical basis for the creation of a scientifically substantiated system of indicators and especially for data collection, analysis, scale and final goal. This paper proposes a methodological approach to assess and to compare the sustainability level of agricultural plant production systems on regional scale combining the three pillars of sustainability environment, economy and society. The combination of 21 individual indicators expressed a unique indicator was realized using the Multiattribute Value Theory (MAVT). The proposed methodology was testified on two geographical regions in Greece, through an empirical study, utilizing questionnaires completed during interviews with farm managers. The questionnaire was designed to gather data on current agricultural practices applied in each particular region and was separated into three broad groups of questions concerning (a) crop management practices, (b) economic performance and (c) social characteristics of each farm. The results of our study demonstrate the overall status of the studied regions, regarding their level of agricultural sustainability. Finally, findings related to the acceptability of the proposed methodological framework were discussed.     

Life History,Reproduction, Growth,Population Dynamics and Production of Gammarus aequicauda (Crustacea: Amphipoda) at Extremely Low Salinities in a Mediterranean Lagoon

Aspects of the biology of Gammarus aequicauda were studied at extremely low salinities (0.3–5.7 psu) in Monolimni Lagoon, N. Aegean Sea. Samples were collected monthly from February 1998 to February 1999. Breeding occurred continuously but peaked in late spring, late summer and autumn and three cohorts were produced. The spring and summer cohorts showed fast growth (0.15 mm d^–1), accelerated maturity and life span of about three and seven months respectively, while the overwintering cohort showed a life span of about nine months. The largest individual had a body length of 23.6 mm. Mean brood size was 54.5 early embryos, while the intramarsupial loss was 46%. Population density sharply increased in late spring, summer and autumn. Secondary production calculated by Hynes' method gave a mean annual density of 1077.4 ind. m^–2, a mean annual crop (B) of 2.93 g DW m^–2, an annual production (P) of 35.03 g DW m^–2 and a P: B ratio of 11.96. Gammarus aequicauda showed a life‐history pattern similar to those previously reported for this species at higher salinity environments with comparatively large final body length and high growth rate during summer, brood size and P: B ratio, but with high embryo loss as well. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

MAPKs and NF-κB differentially regulate cytokine expression in the diaphragm in response to resistive breathing: the role of oxidative stress

Inspiratory resistive breathing (IRB) induces cytokine expression in the diaphragm. The mechanism of this cytokine induction remains elusive. The roles of MAPKs and NF-κB and the impact of oxidative stress in IRB-induced cytokine upregulation in the diaphragm were studied. Wistar rats were subjected to IRB (50% of maximal inspiratory pressure) via a two-way nonrebreathing valve for 1, 3, or 6 h. Additional groups of rats subjected to IRB for 6 h were randomly assigned to receive either solvent or N-acetyl-cysteine (NAC) or inhibitors of NF-κB (BAY-11-7082), ERK1/2 (PD98059), and P38 MAPK (SB203580) to study the effect of oxidative stress, NF-κB, and MAPKs in IRB-induced cytokine upregulation in the diaphragm. Quietly breathing animals served as controls. IRB upregulated cytokine (IL-6, TNF-α, IL-10, IL-2, IL-1β) protein levels in the diaphragm and resulted in increased activation of MAPKs (P38, ERK1/2) and NF-κB. Inhibition of NF-κB and ERK1/2 blunted the upregulation of all cytokines except that of IL-6, which was further increased. P38 inhibition attenuated all cytokine (including IL-6) upregulation. Both P38 and ERK1/2 inhibition decreased NF-κB/p65 subunit phosphorylation. NAC pretreatment blunted IRB-induced cytokine upregulation in the diaphragm and resulted in decreased ERK1/2, P38, and NF-κB/p65 phosphorylation. In conclusion, IRB-induced cytokine upregulation in the diaphragm is under the regulatory control of MAPKs and NF-κB. IL-6 is regulated differently from all other cytokines through a P38-dependent and NF-κB independent pathway. Oxidative stress is a stimulus for IRB-induced cytokine upregulation in the diaphragm.     

Mutagenesis of surfactant protein D informed by evolution and x-ray crystallography enhances defenses against influenza A virus in vivo

The recognition of influenza A virus (IAV) by surfactant protein D (SP-D) is mediated by interactions between the SP-D carbohydrate recognition domains (CRD) and glycans displayed on envelope glycoproteins. Although native human SP-D shows potent antiviral and aggregating activity, trimeric recombinant neck+CRDs (NCRDs) show little or no capacity to influence IAV infection. A mutant trimeric NCRD, D325A/R343V, showed marked hemagglutination inhibition and viral neutralization, with viral aggregation and aggregation-dependent viral uptake by neutrophils. D325A/R343V exhibited glucose-sensitive binding to Phil82 hemagglutinin trimer (HA) by surface plasmon resonance. By contrast, there was very low binding to the HA trimer from another virus (PR8) that lacks glycans on the HA head. Mass spectrometry demonstrated the presence of high mannose glycans on the Phil82 HA at positions known to contribute to IAV binding. Molecular modeling predicted an enhanced capacity for bridging interactions between HA glycans and D325A/R343V. Finally, the trimeric D325A/R343V NCRD decreased morbidity and increased viral clearance in a murine model of IAV infection using a reassortant A/WSN/33 virus with a more heavily glycosylated HA. The combined data support a model in which altered binding by a truncated mutant SP-D to IAV HA glycans facilitates viral aggregation, leading to significant viral neutralization in vitro and in vivo. These studies demonstrate the potential utility of homology modeling and protein structure analysis for engineering effective collectin antivirals as in vivo therapeutics.     

Multivariate meta-analysis of the association of G-protein beta 3 gene (GNB3) haplotypes with cardiovascular phenotypes

The objective of the present study was to review previous investigations on the association of haplotypes in the G-protein β3 subunit (GNB3) gene with representative cardiovascular risk factors/phenotypes: hypertension, overweight, and variation in the systolic and diastolic blood pressures (SBP and DBP, respectively) and as well as body mass index (BMI). A comprehensive literature search was undertaken in Pubmed, Web of Science, EMBASE, Biological Abstracts, LILACS and Google Scholar to identify potentially relevant articles published up to April 2011. Six genetic association studies encompassing 16,068 participants were identified. Individual participant data were obtained for all studies. The three most investigated GNB3 polymorphisms (G-350A, C825T and C1429T) were considered. Expectation–maximization and generalized linear models were employed to estimate haplotypic effects from data with uncertain phase while adjusting for covariates. Study-specific results were combined through a random-effects multivariate meta-analysis. After carefully adjustments for relevant confounding factors, our analysis failed to support a role for GNB3 haplotypes in any of the investigated phenotypes. Sensitivity analyses excluding studies violating Hardy–Weinberg expectations, considering gender-specific effects or more extreme phenotypes (e.g. obesity only) as well as a fixed-effects “pooled” analysis also did not disclose a significant influence of GNB3 haplotypes on cardiovascular phenotypes. We conclude that the previous cumulative evidence does not support the proposal that haplotypes formed by common GNB3 polymorphisms might contribute either to the development of hypertension and obesity, or to the variation in the SBP, DBP and BMI.