MS/MS library facilitated MRM quantification of native peptides prepared by denaturing ultrafiltration

ABSTRACT: Naturally occurring native peptides provide important information about physiological states of an organism and its changes in disease conditions but protocols and methods for assessing their abundance are not well-developed. In this paper, we describe a simple procedure for the quantification of non-tryptic peptides in body fluids. The workflow includes an enrichment step followed by two-dimensional fractionation of native peptides and MS/MS data management facilitating the design and validation of LC- MRM MS assays. The added value of the workflow is demonstrated in the development of a triplex LC-MRM MS assay used for quantification of peptides potentially associated with the progression of liver disease to hepatocellular carcinoma.     

Demographic, temporal and environmental effects on the frequency of cribra orbitalia in three Early Medieval populations from western Slovakia

The frequency of cribra orbitalia was examined in Early Medieval skeletal samples from Devín and Borovce (Slovakia). The effects of environmental and socio-economic factors on the distribution of orbital lesions are explored and discussed. The frequency of cribra orbitalia was lowest in Devín-Hrad (11th-12th c. A.D.), followed by Devín-Za kostolom (9th c. A.D.) and Borovce (8th-beginning of 12th c. A.D.). The increased frequency of cribra orbitalia at Borovce can be attributed to inadequate sanitation and increased pathogen load at this rural site compared to urban Devín. Borovce (BO) sub-adults displayed orbital lesions significantly more frequently than BO adults and sub-adults in the Devín-Za kostolom (FR) and Devín-Hrad (DH) samples. Although the total mortality of sub-adults did not differ between the sites, BO sub-adults with cribra orbitalia showed a considerably higher mortality. Their counterparts from FR and DH showed similar mortality patterns irrespective of the presence of orbital lesions. As in most reference samples, no significant sex differences in the frequency of cribra orbitalia were observed in BO, DH and FR. However, a considerably increased mortality was observed in young males from Devín-Hrad irrespective of the presence of orbital lesions. This finding can be attributed to their involvement in violent conflicts. Reference data from Medieval Central European skeletal samples suggest that an increased occurrence of cribra orbitalia was associated with crop failures, migration and interpersonal conflicts. These factors favour the spread of and vulnerability to infectious diseases, which are considered to be the major cause of iron deficiency anaemia.     

Thermotropism and hydration properties of POPE and POPE-cholesterol systems as revealed by solid state2H and31P-NMR

The partial phase diagram and the hydration properties of the 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE)-water system, in the absence and presence of 30 mol% cholesterol, have been investigated by solid state phosphorus NMR of the lipid and deuterium NMR of heavy water. The POPE-D₂O phase diagram resembles other phosphatidylethanolamine (PE)-water systems: below water-to-lipid molar ratios (R_i) of 3 the lamellar gel (L or L_c)-to-hexagonal type II (H_II) phase sequence is observed on increasing the temperature. For R_i3 the thermotropic sequence (L or L_c)-L-H_II is detected. On increasing hydration from R_i=3, the H_II phase is detected from 40°C to 85°C whereas the gel phase is observed from 40°C to 30°C. The limiting hydrations of the gel, L and H_II phases are R_i 3, 17 and 20, respectively. The number of bound water molecules per lipid is ca. 8 in both the La and HII phases. The presence of cholesterol stabilizes the hexagonal phase 20°C below temperatures at which it is observed in its absence and reduces the limiting hydration of the fluid and hexagonal phases to Ri 9 and 14, respectively. The structure and/or dynamics of the water bound to the interface are markedly modified on going from the L to the H_II phase.Abbreviations NMR Nuclear magnetic resonance - DDPE 1,2-Didodecyl-rac-glycerol-3-phosphoethanol-amine - DHPE 1,2-Dihexadecyl-sn-glycerol-3-phosphoethanol-amine - DOPE 1,2-Dioleoyl-sn-glycerol-3-phosphoethanol-amine - POPE 1-Palmitoyl-2-oleoyl-sn-glycerol-3-phosphoetha-nolamine - DAPE 1,2-Diarachinoyl-sn-glycerol-3-phosphoethanol-amine - DMPC 1,2-Dimyristol-sn-glycerol-3-phosphocholine - DPPC 1,2-Dipalmitoyl-sn-glycerol-3-phosphocholine - T_c lamellar gel-to-lamellar fluid transition temperature - T_h lamellar fluid-to-hexagonal transition temperature     

Neuronal Spike Timing Adaptation Described with a Fractional Leaky Integrate-and-Fire Model

The voltage trace of neuronal activities can follow multiple timescale dynamics that arise from correlated membrane conductances. Such processes can result in power-law behavior in which the membrane voltage cannot be characterized with a single time constant. The emergent effect of these membrane correlations is a non-Markovian process that can be modeled with a fractional derivative. A fractional derivative is a non-local process in which the value of the variable is determined by integrating a temporal weighted voltage trace, also called the memory trace. Here we developed and analyzed a fractional leaky integrate-and-fire model in which the exponent of the fractional derivative can vary from 0 to 1, with 1 representing the normal derivative. As the exponent of the fractional derivative decreases, the weights of the voltage trace increase. Thus, the value of the voltage is increasingly correlated with the trajectory of the voltage in the past. By varying only the fractional exponent, our model can reproduce upward and downward spike adaptations found experimentally in neocortical pyramidal cells and tectal neurons in vitro. The model also produces spikes with longer first-spike latency and high inter-spike variability with power-law distribution. We further analyze spike adaptation and the responses to noisy and oscillatory input. The fractional model generates reliable spike patterns in response to noisy input. Overall, the spiking activity of the fractional leaky integrate-and-fire model deviates from the spiking activity of the Markovian model and reflects the temporal accumulated intrinsic membrane dynamics that affect the response of the neuron to external stimulation.     

Simultaneous subchronic exposure to selenium and diazinon as possible risk factor for osteoporosis in adult male rats

Background

Osteoporosis and its main health outcome, fragility fractures, are large and escalating health problems. Skeletal damage may be the critical result of low-level prolonged exposure to several xenobiotics in the general population, but the mechanisms of their adverse effects are not clearly understood. The current study was aimed to investigate the possible ability of simultaneous subchronic peroral administration of selenium (Se) and diazinon (DZN) to induce changes in bone of adult male rats.In our study, twenty 1-month-old male Wistar rats were randomly divided into two experimental groups. In the first group, young males were exposed to 5 mg Na₂SeO₃/L and 40 mg of DZN/L in drinking water, for 90 days. Ten 1-month-old males without Se and DZN intoxication served as a control group. At the end of the experiment, macroscopic and microscopic structures of the femurs were analysed using analytical scales, sliding instrument, and polarized light microscopy.

Results

The body weight, femoral length and cortical bone thickness were significantly decreased in rats simultaneously exposed to Se and DZN (P?<?0.05). These rats also displayed different microstructure in the middle part of the compact bone where vascular canals expanded into central area of substantia compacta. The canals occurred only near endosteal surfaces in rats from the control group. Additionally, a smaller number of primary and secondary osteons, as well as a few resorption lacunae were observed near endosteal surfaces in rats simultaneously administered to Se and DZN. The resorption lacunae as typical structures of bone resorption manifestation are connected with an early stage of osteoporosis. Histomorphometric analysis revealed that area, perimeter, maximum and minimum diameters of primary osteons’ vascular canals were significantly increased (P?<?0.05) in the Se-DZN-exposed rats. On the other hand, all measured variables of Haversian canals and secondary osteons were considerable reduced (P?<?0.05) in these rats.

Conclusions

Simultaneous subchronic peroral exposure to Se and DZN induces changes in macroscopic and microscopic structures of the femurs in adult male rats, and also it can be considered as possible risk factor for osteoporosis. The current study contributes to the knowledge on damaging impact of several xenobiotics on the bone.

     

Temperature-stress tolerance of the fungal strain Aspergillus niger 26: physiological and ultrastructural changes

The study focuses on the morphological and physiological cell responses to oxidative stress induced by high temperature treatment in the industrially relevant fungus Aspergillus niger 26. Temperatures above 30 °C lead to growth suppression and changes in morphological characteristics: decrease in the size of hyphal elements and increase in “active length” by switching from slightly branched long filaments to a multitude of branched forms containing active cytoplasm. Transmission electron microscopy of fungal cultures heated at 40 °C demonstrated abnormal wavy septation with reduced amount of chitin (as shown by WGA-gold labelling), intrahyphal hyphae development, disintegration of mitochondria and extensive autolysis. Temperature-dependent decrease in the total intracellular protein content and a sharp increase (six to tenfold) in oxidatively damaged proteins were also demonstrated. Elevated temperatures caused a two and threefold increase in catalase and superoxide dismutase activities, respectively.     

A simplified immunoprecipitation method for quantitatively measuring antibody responses in clinical sera samples by using mammalian-produced <Emphasis Type="Italic">Renilla</Emphasis>luciferase-antigen fusion proteins

Background  

Assays detecting human antigen-specific antibodies are medically useful. However, the usefulness of existing simple immunoassay formats is limited by technical considerations such as sera antibodies to contaminants in insufficiently pure antigen, a problem likely exacerbated when antigen panels are screened to obtain clinically useful data.     

Functional distinctions between the mitochondrial ATP-dependent K+ channel (mitoKATP) and its inward rectifier subunit (mitoKIR)

The ATP-sensitive potassium channel from the inner mitochondrial membrane (mitoK(ATP)) is a highly selective conductor of K(+) ions. When isolated in the presence of nonionic detergent and reconstituted in liposomes, mitoK(ATP) is inhibited with high affinity by ATP (K((1/2)) = 20-30 microM). We have suggested that holo-mitoK(ATP) is a heteromultimer consisting of an inwardly rectifying K(+) channel (mitoKIR) and a sulfonylurea receptor (Grover, G. J., and Garlid, K. D. (2000) J. Mol. Cell. Cardiol. 32, 677-695). Here, we show that a 55-kDa protein isolated by ethanol extraction and reconstituted in bilayer lipid membranes and liposomes is the mitoKIR. This protein, which lacks the sulfonylurea receptor subunit, is inhibited with low affinity by ATP, with K(1/2) approximately 550 microM. ATP inhibition of both mitoKIR and holo-mitoK(ATP) is reversed by UDP (K((1/2))1/2 = 10-15 microM). Holo-mitoK(ATP) is and diazoxide, and the opened by cromakalim flux through the open channel is inhibited by glibenclamide and 5-hydroxydecanoate. None of these agents has any effect upon mitoKIR. We have identified two compounds that act specifically on mitoKIR. p-diethylaminoethylbenzoate reverses inhibition of mitoKIR by ATP and ADP at micromolar concentrations and also opens mitoK(ATP) in isolated mitochondria. Tetraphenylphosphonium inhibits K(+) flux through both mitoKIR and mitoK(ATP) with the same apparent affinity. These findings support the hypothesis that the 55-kDa mitoKIR is the channel component of mitoK(ATP).