Tissue proteomics by one-dimensional gel electrophoresis combined with label-free protein quantification

Label-free methods streamline quantitative proteomics of tissues by alleviating the need for metabolic labeling of proteins with stable isotopes. Here we detail and implement solutions to common problems in label-free data processing geared toward tissue proteomics by one-dimensional gel electrophoresis followed by liquid chromatography tandem mass spectrometry (geLC MS/MS). Our quantification pipeline showed high levels of performance in terms of duplicate reproducibility, linear dynamic range, and number of proteins identified and quantified. When applied to the liver of an adenomatous polyposis coli (APC) knockout mouse, we demonstrated an 8-fold increase in the number of statistically significant changing proteins compared to alternative approaches, including many more previously unidentified hydrophobic proteins. Better proteome coverage and quantification accuracy revealed molecular details of the perturbed energy metabolism.     

Novel regulatory mechanisms for generation of the soluble leptin receptor: implications for leptin action

Background

The adipokine leptin realizes signal transduction via four different membrane-anchored leptin receptor (Ob-R) isoforms in humans. However, the amount of functionally active Ob-R is affected by constitutive shedding of the extracellular domain via a so far unknown mechanism. The product of the cleavage process the so-called soluble leptin receptor (sOb-R) is the main binding protein for leptin in human blood and modulates its bioavailability. sOb-R levels are differentially regulated in metabolic disorders like type 1 diabetes mellitus or obesity and can, therefore, enhance or reduce leptin sensitivity.

Methodology/Principal Findings

To describe mechanisms of Ob-R cleavage and to investigate the functional significance of differential sOb-R levels we established a model of HEK293 cells transiently transfected with different human Ob-R isoforms. Using siRNA knockdown experiments we identified ADAM10 (A Disintegrin And Metalloproteinase 10) as a major protease for constitutive and activated Ob-R cleavage. Additionally, the induction of lipotoxicity and apoptosis led to enhanced shedding shown by increased levels of the soluble leptin receptor (sOb-R) in cell supernatants. Conversely, high leptin concentrations and ER stress reduced sOb-R levels. Decreased amounts of sOb-R due to ER stress were accompanied by impaired leptin signaling and reduced leptin binding.

Conclusions

Lipotoxicity and apoptosis increased Ob-R cleavage via ADAM10-dependent mechanisms. In contrast high leptin levels and ER stress led to reduced sOb-R levels. While increased sOb-R concentrations seem to directly block leptin action, reduced amounts of sOb-R may reflect decreased membrane expression of Ob-R. These findings could explain changes of leptin sensitivity which are associated with variations of serum sOb-R levels in metabolic diseases.     

Turning the 'mustard oil bomb' into a 'cyanide bomb': aromatic glucosinolate metabolism in a specialist insect herbivore

Plants have evolved a variety of mechanisms for dealing with insect herbivory among which chemical defense through secondary metabolites plays a prominent role. Physiological, behavioural and sensorical adaptations to these chemicals provide herbivores with selective advantages allowing them to diversify within the newly occupied ecological niche. In turn, this may influence the evolution of plant metabolism giving rise to e.g. new chemical defenses. The association of Pierid butterflies and plants of the Brassicales has been cited as an illustrative example of this adaptive process known as 'coevolutionary armsrace'. All plants of the Brassicales are defended by the glucosinolate-myrosinase system to which larvae of cabbage white butterflies and related species are biochemically adapted through a gut nitrile-specifier protein. Here, we provide evidence by metabolite profiling and enzyme assays that metabolism of benzylglucosinolate in Pieris rapae results in release of equimolar amounts of cyanide, a potent inhibitor of cellular respiration. We further demonstrate that P. rapae larvae develop on transgenic Arabidopsis plants with ectopic production of the cyanogenic glucoside dhurrin without ill effects. Metabolite analyses and fumigation experiments indicate that cyanide is detoxified by β-cyanoalanine synthase and rhodanese in the larvae. Based on these results as well as on the facts that benzylglucosinolate was one of the predominant glucosinolates in ancient Brassicales and that ancient Brassicales lack nitrilases involved in alternative pathways, we propose that the ability of Pierid species to safely handle cyanide contributed to the primary host shift from Fabales to Brassicales that occured about 75 million years ago and was followed by Pierid species diversification.     

Resurgence of HIV Infection among Men Who Have Sex with Men in Switzerland: Mathematical Modelling Study

Background

New HIV infections in men who have sex with men (MSM) have increased in Switzerland since 2000 despite combination antiretroviral therapy (cART). The objectives of this mathematical modelling study were: to describe the dynamics of the HIV epidemic in MSM in Switzerland using national data; to explore the effects of hypothetical prevention scenarios; and to conduct a multivariate sensitivity analysis.

Methodology/Principal Findings

The model describes HIV transmission, progression and the effects of cART using differential equations. The model was fitted to Swiss HIV and AIDS surveillance data and twelve unknown parameters were estimated. Predicted numbers of diagnosed HIV infections and AIDS cases fitted the observed data well. By the end of 2010, an estimated 13.5% (95% CI 12.5, 14.6%) of all HIV-infected MSM were undiagnosed and accounted for 81.8% (95% CI 81.1, 82.4%) of new HIV infections. The transmission rate was at its lowest from 1995–1999, with a nadir of 46 incident HIV infections in 1999, but increased from 2000. The estimated number of new infections continued to increase to more than 250 in 2010, although the reproduction number was still below the epidemic threshold. Prevention scenarios included temporary reductions in risk behaviour, annual test and treat, and reduction in risk behaviour to levels observed earlier in the epidemic. These led to predicted reductions in new infections from 2 to 26% by 2020. Parameters related to disease progression and relative infectiousness at different HIV stages had the greatest influence on estimates of the net transmission rate.

Conclusions/Significance

The model outputs suggest that the increase in HIV transmission amongst MSM in Switzerland is the result of continuing risky sexual behaviour, particularly by those unaware of their infection status. Long term reductions in the incidence of HIV infection in MSM in Switzerland will require increased and sustained uptake of effective interventions.     

Energy gain and energy gap in normal-weight children: longitudinal data of the KOPS

Population-based prevention of overweight needs evidence-based goals consistent with our present knowledge about energy gap (i.e., daily imbalance between energy intake and energy expenditure resulting in overweight). Longitudinal data of normal-weight children (1,029 girls and 1,028 boys; Kiel Obesity Prevention Study, KOPS) were used to calculate energy gain (i.e., increase in fat mass (FM) and fat-free mass (FFM)) in normal-weight children staying normal weight (persistent children) or becoming overweight (incident children). Taking into account weight gain in proportion to height gain (normal development) energy gap was calculated from increases in FM and FFM exceeding normal development. Children were divided into two groups and were followed from age 6 to 10 (group A) and 10 to 14 years (group B). FM and FFM were measured. Medians of 4-year BMI- (kg/m(2))/weight changes (kg) were +1.8/+13.2 (A) and +3.0/+18.7 (B) in girls, and +1.6/+12.8 (A) and +2.6/21.7 (B) in boys. Corresponding data for FM/FFM (kg) were +3.1/+10.2 (A) and +5.1/12.7 (B) in girls, and +2.3/10.8 (A) and +3.0/18.6 (B) in boys. The 4-year-incidence of overweight (%) were 9.4 (A) and 5.4 (B) in girls, and 11.0 (A) and 3.8 (B) in boys, respectively. Mean energy gains (kcal/day) were 26.8 (A) and 46.4 (B) in girls, and 22.1 (A) and 32.5 (B) in boys. The 90th percentile of energy gap (kcal/day) in incident children were 58.1 (A) and 72.0 (B) in girls and 46.0 (A) and 53.2 (B) in boys. To prevent overweight in children energy gap should not exceed 46-72 kcal/day.     

Spontaneous neurotransmitter release and Ca2+--how spontaneous is spontaneous neurotransmitter release?

Neurotransmitter release from neurons takes place at specialized structures called synapses. Action potential-evoked exocytosis requires Ca(2+) influx through voltage-gated Ca(2+) channels. Spontaneous vesicle fusion occurs both in the absence of action potentials and without any apparent stimulus and is hence thought to be Ca(2+)-independent. However, increasing evidence shows that this form of neurotransmitter discharge can be modulated by changes in intracellular Ca(2+) concentration, suggesting that it is not truly spontaneous. This idea is supported by the fact that spontaneous release can be modulated by interfering with proteins involved in the exocytotic process. Interestingly, modulation of spontaneous discharge at the level of the release machinery is not always accompanied by corresponding modulation of action potential-evoked release, suggesting that two independent processes may underlie spontaneous and action potential-evoked exocytosis, at least at some synapses. This provides an attractive model whereby cells can modulate the two forms of neurotransmitter liberation, which often serve different physiological roles, independently of each other.     

In situ mapping of nitrifiers and anammox bacteria in microbial aggregates by means of confocal resonance Raman microscopy

In the present work the exploration of microbial communities by confocal resonance Raman microscopy (CRRM) is reported. Using the resonance Raman effect of cytochrome c (Cyt c) we were able to record the microbial distribution of nitrifiers and anammox bacteria directly in their natural environment without the need of sample preparation. For this new non-invasive investigation a reference database of bacteria assumed to be found in microbial aggregates obtained from biological wastewater treatment was created. Reference spectra of enriched cultures of the interesting bacteria were taken by means of optical tweezers. Significant spectra were achieved in less than 1 s (excitation wavelength 532 nm, laser power 9 mW) due to the resonance Raman effect. In addition, the impact of different parameters on the reference spectra, such as integration time and culture conditions, was analysed. We successfully demonstrate the grouping of bacteria down to strain level based on the heterogeneity of the resonance Raman spectra of the heme protein Cyt c.