Application of different fragmentation techniques for the analysis of phosphopeptides using a hybrid linear ion trap-FTICR mass spectrometer

Electron capture dissociation (ECD) and infrared multiphoton dissociation (IRMPD) present complementary techniques for the fragmentation of peptides and proteins in Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) in addition to the commonly used collisionally activated dissociation (CAD). Both IRMPD and ECD have been shown to be applicable for an efficient sequencing of peptides and proteins, whereas ECD has proven especially valuable for mapping labile posttranslational modifications (PTMs), such as phosphorylations. In this work, we compare the different fragmentation techniques and MS detection in a linear ion trap and the ICR cell with respect to their abilities to efficiently identify and characterize phosphorylated peptides. For optimizing fragmentation parameters, sets of synthetic peptides with molecular weights ranging from approximately 1 to 4 kDa and different levels of phosphorylation were analyzed. The influence of spectrum averaging for obtaining high-quality spectra was investigated. Our results show that the fragmentation methods CAD and ECD allow for a facilitated analysis of phosphopeptides; however, their general applicability for analyzing phosphopeptides has to be evaluated in each specific case with respect to the given analytical task. The major advantage of complementary peptide cleavages by combining different fragmentation methods is the increased amount of information that is obtained during MS/MS analysis of modified peptides. On the basis of the obtained results, we are planning to design LC time-scale compatible, data-dependent MS/MS methods using the different fragmentation techniques in order to improve the identification and characterization of phosphopeptides.     

The effect of increased branched-chain amino acid transaminase activity in yeast on the production of higher alcohols and on the flavour profiles of wine and distillates

In Saccharomyces cerevisiae, branched-chain amino acid transaminases (BCAATases) are encoded by the BAT1 and BAT2 genes. BCAATases catalyse the transfer of amino groups between those amino acids and alpha-keto-acids. alpha-Keto-acids are precursors for the biosynthesis of higher alcohols, which significantly influence the aroma and flavour of yeast-derived fermentation products. The objective of this study was to investigate the influence of BAT-gene expression on general yeast physiology, on aroma and flavour compound formation and on the sensory characteristics of wines and distillates. For this purpose, the genes were overexpressed and deleted in a laboratory strain, BY4742, and overexpressed in an industrial wine yeast strain, VIN13. The data show that, with the exception of a slow growth phenotype observed for the BAT1 deletion strain, the fermentation behaviour of the strains was unaffected by the modifications. The chemical and sensory analysis of fermentation products revealed a strong correction between BAT gene expression and the formation of many aroma compounds. The data suggest that the adjustment of BAT gene expression could play an important role in assisting winemakers in their endeavour to produce wines with specific flavour profiles.     

Assessment of hair mineral analysis commercially offered in Germany.

To evaluate intra- and inter-laboratory agreement concerning hair mineral analysis and interpretation of results, hair samples from 2 volunteers were sent to seven laboratories, which commercially offer hair mineral analysis in Germany. 6 weeks later, another identical part from the hair sample of volunteer 1 was sent to all seven labs. Altogether, 50 elements were analyzed, 23 by all seven labs. For comparability, only the results for these 23 elements were assessed. The intra-laboratory reproducibility was evaluated by the 2 identical hair samples from volunteer 1. On the average, the reproducibility seems to be sufficient (median +/- 9.48% to +/- 20.59%), but for individual elements there were unacceptable out-rulers up to 100%. Only one lab classified all elements of the first and the second analysis of the identical hair sample in the same category (below, within, or above normal range). The others grouped 4 to 7 elements different. This is not tolerable. The inter-laboratory comparability was assessed by the results of the hair samples of both volunteers. For the sample of volunteer 1 at least the results of 6 (out of 23) elements were within an acceptable range of +/- 30% from the consensus value (= mean of all seven labs). For volunteer 2 this was only the case for 2 (!) elements. Differences of more than 100% were found for most other elements. Moreover, in the vast majority of the tested elements there was no comparability of the cLassification to the respective reference ranges of the different laboratories. For example, for volunteer 1 only 3 elements (our of 23!) were identically classified by all seven labs. As neither the analytical results nor the classification to the individual reference ranges by the laboratories correspond in tolerable borders, conclusions, drawn from these results, cannot be valid. Hair mineral analysis from these laboratories is unreliable. Therefore we must recommend to refrain from using such analysis to assess individual nutritional status or suspected environmental exposure.     

Orthogonal P-wave morphology is affected by intra-atrial pressures

Background

It has previously been shown that the morphology of the P-wave neither depends on atrial size in healthy subjects with physiologically enlarged atria nor on the physiological anatomical variation in transverse orientation of the left atrium. The present study aimed to investigate if different pressures in the left and right atrium are associated with different P-wave morphologies.

Methods

38 patients with isolated, increased left atrial pressure, 51 patients with isolated, increased right atrial pressure and 76 patients with biatrially increased pressure were studied. All had undergone right heart catheterization and had 12-lead electrocardiographic recordings, which were transformed into vectorcardiograms for detailed P-wave morphology analysis.

Results

Normal P-wave morphology (type 1) was more common in patients with isolated increased pressure in the right atrium while abnormal P-wave morphology (type 2) was more common in the groups with increased left atrial pressure (P = 0.032). Moreover, patients with increased left atrial pressure, either isolated or in conjunction with increased right atrial pressure, had significantly more often a P-wave morphology with a positive deflection in the sagittal plane (P = 0.004).

Conclusion

Isolated elevated right atrial pressure was associated with normal P-wave morphology while left-sided atrial pressure elevation, either isolated or in combination with right atrial pressure elevation, was associated with abnormal P-wave morphology.

     

Eosinophilic granulomatosis with polyangiitis: myocardial thickening reversed by corticosteroids

Background

In 1951 Churg and Strauss first described the clinical condition now known as eosinophilic granulomatosis with polyangiitis (EGPA), characterized by asthma, nasal polyposis, rhinosinusitis, hypereosinophilia with organ infiltration, and necrotizing vasculitis. It is classified as an antineutrophil cytoplasmic antibody (ANCA) associated vasculitis, but ANCA negativity is common and more frequently encountered in EGPA with myocardial involvement. Long-term survival has substantially improved with corticosteroid treatment but myocardial involvement is still the leading cause of death in EGPA.

Case presentation

A 53-year old man with a history of asthma and nasal polyposis presented with acute chest pain and elevated troponin; a percutaneous coronary intervention was performed. The left ventricle was described as hypertrophic. After 20 days the myocardium had markedly increased in thickness of both the right and left ventricle. Evaluation revealed hypereosinophilia in the blood and nasal mucosal tissue, which confirmed the diagnosis of EGPA. He presented with signs of active vasculitis including weight loss, tiredness, intracerebral hemorrhage, and increasing serum creatinine. After 6 days of corticosteroid treatment, the myocardium returned to its initial thickness.

Conclusion

Rapid and marked thickening of the myocardium is not frequently reported but may occur in EGPA. Myocardial thickening in EGPA can be quickly reversed by corticosteroids, and is most likely caused by edema.

     

Barley xyloglucan xyloglucosyl transferases bind xyloglucan-derived oligosaccharides in their acceptor-binding regions in multiple conformational states

Three barley xyloglucan endotransglycosylases (HvXETs), known as xyloglucan xyloglucosyl transferases (EC 2.4.1.207), were subjected to kinetic and computational docking studies. The k_cat·K_m⁻¹ values with the reduced [³H]-labelled XXXG, XXLG/XLXG and XLLG acceptor substrates were 0.02 × 10⁻², 0.1 × 10⁻² and 3.2 × 10⁻² s⁻¹ μM⁻¹, while the K_m constants were 10.6, 8.6 and 5.3 mM, obtained for HvXET3, HvXET4 and HvXET6, respectively. Docking of XLLG in acceptor-binding regions revealed that at least two conformational states were likely to participate in all isoforms. The assessments of kinetic and computational data indicated that the disposition of aromatic residues at the entrance to the active sites and the flexibility of proximal COOH-terminal loops could orient acceptors more or less favourably during binding, thus leading to tighter or weaker K_m constants. The data suggested that binding of acceptors in HvXETs is guided by contributions from the conserved residues in the active sites and by the of neighbouring loops.     

Structural basis for the recognition of histone H4 by the histone-chaperone RbAp46

RbAp46 and RbAp48 (pRB-associated proteins p46 and p48, also known as RBBP7 and RBBP4, respectively) are highly homologous histone chaperones that play key roles in establishing and maintaining chromatin structure. We report here the crystal structure of human RbAp46 bound to histone H4. RbAp46 folds into a seven-bladed beta propeller structure and binds histone H4 in a groove formed between an N-terminal alpha helix and an extended loop inserted into blade six. Surprisingly, histone H4 adopts a different conformation when interacting with RbAp46 than it does in either the nucleosome or in the complex with ASF1, another histone chaperone. Our structural and biochemical results suggest that when a histone H3/H4 dimer (or tetramer) binds to RbAp46 or RbAp48, helix 1 of histone H4 unfolds to interact with the histone chaperone. We discuss the implications of our findings for the assembly and function of RbAp46 and RbAp48 complexes.     

Cellular and extracellular miRNAs are blood‐compartment‐specific diagnostic targets in sepsis

Septic shock is a common medical condition with a mortality approaching 50% where early diagnosis and treatment are of particular importance for patient survival. Novel biomarkers that serve as prompt indicators of sepsis are urgently needed. High‐throughput technologies assessing circulating microRNAs represent an important tool for biomarker identification, but the blood‐compartment specificity of these miRNAs has not yet been investigated. We characterized miRNA profiles from serum exosomes, total serum and blood cells (leukocytes, erythrocytes, platelets) of sepsis patients by next‐generation sequencing and RT‐qPCR (n = 3 × 22) and established differences in miRNA expression between blood compartments. In silico analysis was used to identify compartment‐specific signalling functions of differentially regulated miRNAs in sepsis‐relevant pathways. In septic shock, a total of 77 and 103 miRNAs were down‐ and up‐regulated, respectively. A majority of these regulated miRNAs (14 in serum, 32 in exosomes and 73 in blood cells) had not been previously associated with sepsis. We found a distinctly compartment‐specific regulation of miRNAs between sepsis patients and healthy volunteers. Blood cellular miR‐199b‐5p was identified as a potential early indicator for sepsis and septic shock. miR‐125b‐5p and miR‐26b‐5p were uniquely regulated in exosomes and serum, respectively, while one miRNA (miR‐27b‐3p) was present in all three compartments. The expression of sepsis‐associated miRNAs is compartment‐specific. Exosome‐derived miRNAs contribute significant information regarding sepsis diagnosis and survival prediction and could serve as newly identified targets for the development of novel sepsis biomarkers.