Orbitrap mass analyzer--overview and applications in proteomics

The orbitrap mass analyzer is proving itself as a useful addition to a proteomics tool box. The key attributes of this analyzer are accurate mass and high resolution similar to those achievable with FT ICR instrumentation. The basic principles underlying these capabilities, and how they translate into benefits in real-life proteomics experiments are discussed. The focus is on reviewing examples of protein identification with bottom-up and top-down approaches, and detection of post-translational modifications.     

Consumption of redox energy by glutathione metabolism contributes to hypoxia/ reoxygenation-induced injury in astrocytes

The assumption of oxidative stress as a mechanism in oxalate induced renal damage suggests that antioxidants might play a beneficial role against oxalate toxicity. An in vivo model was used to investigate the effect of C-phycocyanin (from aquatic micro algae; Spirulina spp.), a known antioxidant, against calcium oxalate urolithiasis. Hyperoxaluria was induced in two of the 4 groups of Wistar albino rats (n = 6 in each) by intraperitoneally injecting sodium oxalate (70,mg/kg body weight). A pretreatment of phycocyanin (100,mg/kg body weight) as a single oral dosage was given, one hour prior to oxalate challenge. An untreated control and drug control (phycocyanin alone) were employed. Phycocyanin administration resulted in a significant improvement (p < 0.001) in the thiol content of renal tissue and RBC lysate via increasing glutathione and reducing malondialdehyde levels in the plasma of oxalate induced rats (p < 0.001), indicating phycocyanin’s antioxidant effect on oxalate mediated oxidative stress. Administering phycocyanin after oxalate treatment significantly increased catalase and glucose-6-phosphate dehydrogenase activity (p < 0.001) in RBC lysate suggesting phycocyanin as a free radical quencher. Assessing calcium oxalate crystal retention in renal tissue using polarization microscopy and renal ultrastructure by electron microscopy reveals normal features in phycocyanin – pretreated groups. Thus the study presents positive pharmacological implications of phycocyanin against oxalate mediated nephronal impairment and warrants further work to tap this potential aquatic resource for its medicinal application. (Mol Cell Biochem xxx: 1–7, 2004)     

Termination of translation in eukaryotes is mediated by the quaternary eRF1*eRF3*GTP*Mg2+ complex. The biological roles of eRF3 and prokaryotic RF3 are profoundly distinct

GTP hydrolysis catalyzed in the ribosome by a complex of two polypeptide release factors, eRF1 and eRF3, is required for fast and efficient termination of translation in eukaryotes. Here, isothermal titration calorimetry is used for the quantitative thermodynamic characterization of eRF3 interactions with guanine nucleotides, eRF1 and Mg²⁺. We show that (i) eRF3 binds GDP (K_d = 1.9 μM) and this interaction depends only minimally on the Mg²⁺ concentration; (ii) GTP binds to eRF3 (K_d = 0.5 μM) only in the presence of eRF1 and this interaction depends on the Mg²⁺ concentration; (iii) GTP displaces GDP from the eRF1•eRF3•GDP complex, and vice versa; (iv) eRF3 in the GDP-bound form improves its ability to bind eRF1; (v) the eRF1•eRF3 complex binds GDP as efficiently as free eRF3; (vi) the eRF1•eRF3 complex is efficiently formed in the absence of GDP/GTP but requires the presence of the C-terminus of eRF1 for complex formation. Our results show that eRF1 mediates GDP/GTP displacement on eRF3. We suggest that after formation of eRF1•eRF3•GTP•Mg²⁺, this quaternary complex binds to the ribosomal pretermination complex containing P-site-bound peptidyl-tRNA and the A-site-bound stop codon. The guanine nucleotide binding properties of eRF3 and of the eRF3•eRF1 complex profoundly differ from those of prokaryotic RF3.     

Application of wavelet-based tools to study the dynamics of biological processes

The article makes use of three different examples (sensory information processing in the rat trigeminal complex, intracellular interaction in snail neurons and multimodal dynamics in nephron autoregulation) to demonstrate how modern approaches to time-series analysis based on the wavelet-transform can provide information about the underlying complex biological processes.     

New insights into tau-microtubules interaction revealed by isothermal titration calorimetry

Microtubule dynamic instability is tightly regulated by coordinated action of stabilizing and destabilizing microtubule associated proteins. Among the stabilizing proteins, tau plays a pivotal role in both physiological and pathological processes. Nevertheless, the detailed mechanism of tau-tubulin interaction is still subject to controversy. In this report, we studied for the first time tau binding to tubulin by a direct thermodynamic method in the absence of any tubulin polymerization cofactors that could influence this process. Isothermal titration calorimetry enabled us to evidence two types of tau-tubulin binding modes: one corresponding to a high affinity binding site with a tau:tubulin stoichiometry of 0.2 and the other one to a low affinity binding site with a stoichiometry of 0.8. The same stoichiometries were obtained at all temperatures tested (10-37°C), indicating that the mechanism of interaction does not depend on the type of tubulin polymer triggered upon tau binding. These findings allowed us to get new insights into the topology of tau on microtubules.     

Preparation and characterization of monoclonal antibodies to human adiponectin for its quantitative measurement in serum

Mouse Monoclonal antibodies against human adiponectin were produced by the routine method and the specificity of antibodies was verified. These monoclonal antibodies (MoAbs) interacted with the monomeric and trimeric forms of recombinant adiponectin according to the results of a Western blot analysis. Human blood serum was fractionated by gel filtration, and the protein of these fractions was stained using labeled MoAbs. It was established that a single high-molecular-weight form (HMW) of endogenous adiponectin was detected by this method. The use of competitive enzymelinked immunoassay on the basis of the obtained MoAbs allowed us to show that the sera of healthy male donors contains lower adiponectin concentrations than that of female donors (8.42 ± 1.59 μg/ml vs. 11.01 ± 2.58 μg/ml, p = 0.01). We also detected statistically significant lower adiponectin levels in the serum of patients with coronary artery disease for both men (6.01 ± 2.73 μg/ml vs. 8.42 ± 1.59 μg/ml, p = 0.015) and women (5.79 ± 2.98 μg/ml vs. 11.01 ± 2.58 μg/ml, p = 0.0003). Therefore, the developed methods for the analysis of the HMW form of adiponectin can be helpful in the diagnostics of the possible implications and assessment of unfavorable prognoses in patients with cardiovascular disorders.     

Auxin synthesis by the higher fungus Lentinus edodes (Berk.) sing in the presence of low concentrations of indole compounds

The auxin formation in a submerged culture of the xylotrophic basidiomycete Lentinus edodes (Berk.) Sing (Lentinula edodes (Berk.) Pegler) (shiitake) is studied. Biologically active substances of an indole nature are identified, “the effect of small doses” of which lies in not only the stimulation of growth of the mycelium (indole-3-acetic acid, 2 × 10⁻⁷–2 × 10⁻⁴ g/l), but also in the induction of tryptophan-independent paths of auxin biosynthesis. The above-mentioned path is realized in the presence of exogenous indole (1 × 10⁻³–1 × 10⁻⁴ g/l), as well as while inducing the biosynthesis of indole-3-acetic acid by its microadditives (1 × 10⁻⁵−1 × 10⁻⁸ g/l), and is accompanied by the formation of anthranilic acid (up to 1.5 mg/l). Induction of the generative development stage of shiitake by indole derivatives is revealed. It was found that among the studied compounds only indoleacetamide at a concentration of an order of ×10⁻⁴ g/l in the culture fluid of L. edodes had a pronounced stimulatory effect on the formation of shiitake’s brown mycelial film.     

Alpine plant functional group responses to fertiliser addition depend on abiotic regime and community composition

Background and aims

We ask how productivity responses of alpine plant communities to increased nutrient availability can be predicted from abiotic regime and initial functional type composition.

Methods

We compared four Caucasian alpine plant communities (lichen heath, Festuca varia grassland, Geranium-Hedysarum meadow, snow bed community) forming a toposequence and contrasting in productivity and dominance structure for biomass responses to experimental fertilization (N, P, NP, Ca) and irrigation for 4–5?years.

Results

The dominant plants in more productive communities monopolized added N and P, at the expense of their neighbors. In three out of four communities, N and P fertilizations gave greater aboveground biomass increase than N or P fertilization alone, indicating overall co-limitation of N and P, with N being most limiting. Relative biomass increase in NP treatment was negatively related to biomass in control plots across the four communities. Grasses often responded more vigorously to P, but sedges to N alone. Finally, we present one of the rare examples of a forb showing a strong N or NP response.

Conclusion

Our findings will help improve our ability to predict community composition and biomass dynamics in cool ecosystems subject to changing nutrient availability as induced by climate or land-use changes.     

Morphological Changes in the Midgut of Aedes aegypti L. (Diptera: Culicidae) Larvae Following Exposure to an Annona coriacea (Magnoliales: Annonaceae) Extract

Bioinsecticides are important in the control of disease vectors, but data regarding their physiological effects on target insects are incomplete. This study describes morphological changes that occur in the midgut of third instar Aedes aegypti L. (Diptera: Culicidae) following treatment with a methanolic extract of Annona coriacea (Magnoliales: Annonaceae). Dissected midguts were subdivided into anterior and posterior regions and analyzed by light and scanning electron microscopy. Insects exposed to the extract displayed intense, destructive cytoplasmic vacuolization in columnar and regenerative midgut cells. The apical surfaces of columnar cells exhibited cytoplasmic protrusions oriented toward the lumen, suggesting that these cells could be involved in apocrine secretory processes and/or apoptosis. We report that A. coriacea extracts induced morphological alterations in the midgut of A. aegypti midgut larvae, supporting the use of plant extracts for control of the dengue vector.     

Diagnostic system for studying generation of subterahertz radiation during beam-plasma interaction in the GOL-3 facility

The design principles and construction of the subterahertz radiometric spectral systems developed for the GOL-3 facility are described. The spectral systems are designed according to the quasi-optical scheme and use multilayer filters based on frequency-selective surfaces. The design and manufacturing technology of such elements are discussed. The results of measuring subterahertz radiation of plasma at the frequency close to the double plasma frequency are presented.