Using statistical models to identify factors that have a role in defining the abundance of ions produced by tandem MS

A database of 5448 peptide tandem mass spectra acquired in a quadrupole time-of-flight mass spectrometer was generated for peptides derived from proteins digested with trypsin. Peptides were identified from their mass spectra by the Mascot algorithm. Statistical models were then used to investigate factors influencing the abundance of ions formed. Separate models were formulated for b and y ions as it was thought that different factors may influence the formation of each type of ion. Several factors were found to have a highly significant influence on the abundance of ions formed. These include the actual mass of the ion formed after fragmentation as well as the location of the cleavage. The composition of the fragmenting peptide was also found to be important, and amino acids either side of the fragmentation site influenced the abundance of ions produced. To increase understanding of fragmentation mechanisms, the effect of several physicochemical properties of these residues was also investigated in a separate model. In conclusion, the models formulated for b and y ions provide useful characterization of the abundance of ions formed, and this information could be used to develop improved algorithms for peptide identification.     

Influence of hydrogen on the deformation morphology of vanadium (1 0 0) micropillars in the α-phase of the vanadium–hydrogen system

1. Download : Download high-res image (67KB)
2. Download : Download full-size image

     

Co-Stimulation of Oxytocin and Arginine-Vasopressin Receptors Affect Hypothalamic Neurospheroid Size

Oxytocin (OXT) is a neuropeptide involved in a plethora of behavioral and physiological processes. However, there is a prominent lack of 3D cell culture models that investigate the effects of OXT on a cellular/molecular level. In this study, we established a hypothalamic neuronal spheroid model to investigate the cellular response in a more realistic 3D setting. Our data indicate that the formation of spheroids itself does not alter the basic characteristics of the cell line and that markers of cellular morphology and connectivity are stably expressed. We found that both OXT and arginine vasopressin (AVP) treatment increase spheroid size (surface area and volume), as well as individual nucleus size, which serves as an indicator for cellular proliferation. The cellular response to both OXT and AVP seems mainly to be mediated by the AVP receptor 1a (V1aR); however, the OXT receptor (OXTR) contributes significantly to the observed proliferative effect. When we blocked the OXTR pharmacologically or knocked down the OXTR by siRNA, the OXT- or AVP-induced cellular proliferation decreased. In summary, we established a 3D cell culture model of the neuronal response to OXT and AVP and found that spheroids react to the treatment via their respective receptors but also via cross-talk between the two receptor types.     

Modulation of the Cardiac Myocyte Action Potential by the Magnesium-Sensitive TRPM6 and TRPM7-like Current

The cardiac Mg²⁺-sensitive, TRPM6, and TRPM7-like channels remain undefined, especially with the uncertainty regarding TRPM6 expression in cardiomyocytes. Additionally, their contribution to the cardiac action potential (AP) profile is unclear. Immunofluorescence assays showed the expression of the TRPM6 and TRPM7 proteins in isolated pig atrial and ventricular cardiomyocytes, of which the expression was modulated by incubation in extracellular divalent cation-free conditions. In patch clamp studies of cells dialyzed with solutions containing zero intracellular Mg²⁺ concentration ([Mg²⁺]_i) to activate the Mg²⁺-sensitive channels, raising extracellular [Mg²⁺] ([Mg²⁺]_o) from the 0.9-mM baseline to 7.2 mM prolonged the AP duration (APD). In contrast, no such effect was observed in cells dialyzed with physiological [Mg²⁺]_i. Under voltage clamp, in cells dialyzed with zero [Mg²⁺]_i, depolarizing ramps induced an outward-rectifying current, which was suppressed by raising [Mg²⁺]_o and was absent in cells dialyzed with physiological [Mg²⁺]_i. In cells dialyzed with physiological [Mg²⁺]_i, raising [Mg²⁺]_o decreased the L-type Ca²⁺ current and the total delayed-rectifier current but had no effect on the APD. These results suggest a co-expression of the TRPM6 and TRPM7 proteins in cardiomyocytes, which are therefore the molecular candidates for the native cardiac Mg²⁺-sensitive channels, and also suggest that the cardiac Mg²⁺-sensitive current shortens the APD, with potential implications in arrhythmogenesis.     

Lactobacilli isolated from the Armenian fermented milk product matsoun: Growth properties,antibacterial and proteolytic activity and their dependence on pH

Growth, antibacterial and proteolytic activities of two new lactobacilli strains isolated from matsoun (Armenian traditional dairy product) and their pH dependence were studied. The results demonstrated the antibacterial activity of lactobacilli against Gram‐positive and Gram‐negative test strains. This activity was stable when pH of cell culture medium was adjusted to the value of 6.5. At pH 8, the antibacterial activity of only one strain was stable. Both strains were able to hydrolyse casein in pH range of 5.5–8 with maximal activity at pH 5.5. Controlled pH conditions were suitable for biomass yield, while noncontrolled pH was better for expression of antibacterial activity.     

Changes in the Profiles of Metabolites Originating from Protein Degradation During Ripening of Dry Cured Ham

Ripening of dry cured ham involves a high number of complex enzymatic and chemical reactions. Due to long processing time, there is a need for analytical methods that can be applied to monitor the ripening in optimization of process conditions and development of new products. In this study, nontargeted metabolite analysis by mass spectrometry (MS) was employed to determine the ripening rates at different water activities in small-scale laboratory experiments and to follow the progress of the ripening of hams from a dry cured ham production facility. Approximately 1000 metabolites were detected. Of these, 90–95% had molecular masses below 800 Da, and more than 60% below 500 Da. In the order of 150 metabolites were putatively annotated. In addition to free amino acids and muscle metabolites, the nontargeted analysis revealed the time profiles of di- and tripeptides, as well as a high number of compounds generated by further conversion of amino acids, muscle metabolites and probably lipids. Statistical processing of the data sets showed that the metabolite profiles changed with the storage time, and that ripening of fresh and unsalted, dried meat, generated other profiles than salted samples. In conclusion, our approach represents a simple and efficient tool for comparison of process conditions and to follow the time course of the ripening, useful in product development and process optimization.     

Mapping the polarization pattern of plasmon modes reveals nanoparticle symmetry

We study the wavelength and polarization dependent plasmon resonances of single silver and gold nanorods, triangles, cubes, and dimers with a novel single particle spectroscopy method (RotPOL). In RotPOL, a rotating wedge-shaped polarizer encodes the full polarization information of each particle within one image. This reveals the symmetry of the particles and their plasmon modes, allows analyzing inhomogeneous samples and the monitoring of particle shape changes during growth in situ.     

Complex Diagnostics of Non-Specific Intellectual Developmental Disorder

Intellectual development disorder (IDD) is characterized by a general deficit in intellectual and adaptive functioning. In recent years, there has been a growing interest in studying the genetic structure of IDD. Of particular difficulty are patients with non-specific IDD, for whom it is impossible to establish a clinical diagnosis without complex genetic diagnostics. We examined 198 patients with non-specific IDD from 171 families using whole-exome sequencing and chromosome microarray analysis. Hereditary forms of IDD account for at least 35.7% of non-specific IDD, of which 26.9% are monogenic forms. Variants in the genes associated with the BAF (SWI/SNF) complex were the most frequently identified. We were unable to identify phenotypic features that would allow differential diagnosis of monogenic and microstructural chromosomal rearrangements in non-specific IDD at the stage of clinical examination, but due to its higher efficiency, exome sequencing should be the diagnostic method of the highest priority study after the standard examination of patients with NIDD in Russia.     

Stabilization of immiscible polymer blends using structure directing metal organic frameworks (MOFs)

We have developed a novel approach for compatibilizing immiscible polymer blends using metal organic frameworks (MOFs). For the first time we demonstrated that the droplet diameter of the dispersed phase in a 1:1 immiscible polymer blend composed of 6FDA-DAM:DABA [copolymer of 4,4-hexafluoroisopropylidene diphthalic anhydride (6FDA), 2,4,6-trimethyl-1,3-phenylenediamine and 3,5-diaminobenzoic acid (DABA)], and polybenzimidazole (PBI), is dramatically reduced obtaining a uniform microstructure with the incorporation of as low as 5% (w/w) of the zeolitic imidazolate framework-8 (ZIF-8). This indicates a large improvement in the compatibility of the immiscible polymers with the inclusion of ZIF-8. As the ZIF-8 loading was further increased to 10% (w/w), the droplet diameter further decreased resulting in even higher compatibility. The compatibilizing effect can be attributed to a reduction in the interfacial energy of the immiscible polymers due to the interfacial localization of ZIF-8. This MOF based compatibilization of immiscible polymer blends can open up opportunities for the combination of different properties of polymers in membrane-based separations and in more applications.