Role of the n+1 amino acid residue on the deamidation of asparagine in pentapeptides

Deamidation plays an important role in biochemical phenomena such as aging. The role of the n + 1 residue on the deamidation of asparagine (asparagine being the nth residue) in three pentapeptide chains (GGNGG, GGNMG and GGNIG) has been analysed with hybrid computational tools. Potentials of mean force at 300 K were calculated from the MD/replica exchange simulations using weighted histogram analysis (WHAM) in explicit water. The snapshots were clustered taking into account the requirements of the plausible deamidation mechanisms, as such the tautomerisation of the asparagine side chain as initial step has been confirmed, based on the proximity of water to the deamidation site. The ultimate goal being to gain an insight on the peptide backbone N-H acidity, quantum mechanical calculations have been carried out. For this purpose, the distribution of Φ/Ψ, Φ₂/Ψ and end-to-end distances deduced from the WHAM diagrams have been considered and a total of 110 structures have been sampled. These neutral pentapeptides as well as their corresponding anions have been optimised (B3LYP/6-31++G(d,p)) in implicit water in order to gain an insight on the peptide backbone N-H acidity. In this study, we have shown that the open conformations of the neutrals and the anions, which display a β sheet like structure are well populated and their pK_as rank in the same order as the deamidating half-lives, that is the peptides that deaminate fastest can more readily access conformations that are more acidic.     

Application of computer algebra to Jones polynomials

In this paper we apply computer algebra (Maple) techniques to calculate Jones polynomial of graphs of K(2,q)-Torus knots. For this purpose, a computer program was developed. When a positive integer q is given, the program calculate Jones polynomial of graph of K(2,q)-Torus knots.     

SERS-based sandwich immunoassay using antibody coated magnetic nanoparticles for Escherichia coli enumeration

A method combining immunomagnetic separation (IMS) and surface-enhanced Raman scattering (SERS) was developed to enumerate Escherichia coli (E. coli). Gold-coated magnetic spherical nanoparticles were prepared by immobilizing biotin-labeled anti-E. coli antibodies onto avidin-coated magnetic nanoparticles and used in the separation and concentration of the E. coli cells. Raman labels have been constructed using rod shaped gold nanoparticles coated with 5,5-dithiobis-(2-nitrobenzoic acid) (DTNB) and subsequently with a molecular recognizer. Then DTNB-labeled gold nanorods were interacted with gold-coated magnetic spherical nanoparticle-antibody-E. coli complex. The capture efficiency and calibration graphs were obtained and examined in different E. coli concentrations (10(1)-10(7) cfu mL(-1)). The correlation between the concentration of bacteria and SERS signal was found to be linear within the range of 10(1)-10(4) cfu mL(-1) (R(2) = 0.992). The limit of detection (LOD) and limit of quantification (LOQ) values of the developed method were found to be 8 and 24 cfu mL(-1), respectively. The selectivity of the developed immunoassay was examined with Enterobacter aerogenes, Enterobacter dissolvens, and Salmonella enteriditis which did not produce any significant response. The ability of the immunoassay to detect E. coli in real water samples was also investigated and the results were compared with the experimental results from plate-counting methods. There was no significant difference between the methods that were compared (p > 0.05). This method is rapid and sensitive to target organisms with a total analysis time of less than 70 min.     

Approximation properties of the generalized Szasz operators by multiple Appell polynomials via power summability method

In this paper some properties of the generalized Szasz operators by multiple Appell polynomials are given, using into consideration the power summability method. In the first section are given some direct estimation related to the generalized Szasz operators by multiple Appell polynomials, including Korovkin type theorem. In the second section, we give some results related to the weighted spaces of continuous functions and Voronovskaya type theorem. In the third section, we have proved some results related to the statistical convergence of the generalized Szasz operators by multiple Appell polynomials, using into consideration the A− transformation. At the end of the paper are given some illustrative computational examples which make such summability methods (for example, power series method) more useful and fruitful for applications of functional analysis in approximation theory.     

Photoluminescence spectral change in layered titanate oxide intercalated with hydrated Eu3+

A number of interesting photoluminescence properties of titanate layered oxide intercalated with hydrated Eu3+ have been demonstrated. Photoluminescence intensity of Eu3+ decreased rapidly with time during irradiation by UV light having energy higher than the band gap energy of the host TiO (Ti(1.81)O4) layer. This is presumably due to the decrease in energy transfer from the host TiO layer to Eu3+ as a result of the change in the hydration state of water molecules surrounding Eu3+, which is caused by the hole produced in the TiO valence band. When irradiation was discontinued, the emission intensity gradually recovered. The recovery time increased when the water in the interlayer is removed by heat treatment. This indicates that the state of interlayer water changes during irradiation and returns to its initial state after discontinuation of irradiation. The excitation spectra changed drastically at any given wavelength upon irradiation with UV light. A comparison of the excitation spectra before and after irradiation reveals that only the excitation peak at around the irradiation wavelength decreased upon irradiation, as in the case of spectral hole burning. The hydration state of water molecules surrounding Eu3+ presumably changes depending on the irradiation wavelength, leading to the above spectral change because the Eu/TiO film has a superlattice structure producing holes with different energies.     

Unified scaling law in the coherent noise model

The waiting time distribution between successive events and the unified scaling law is studied using the coherent noise model. It is shown that, although this model generates uncorrelated event sizes and does not exhibit criticality, it still provides the unified scaling law. We argue the role of characteristic kink observed in the unified scaling law and the meaning of the parameter C$C$ used to fix the peak of the kink to unity. Our results indicate that the parameter C$C$ is indeed a physical quantity localizing the end of the linear tendency in the scaling law, which corresponds to the completion of the dominance of correlated events in time.     

Ionic conductivity of PVdF-co-HFP/LiClO4 in terms of free volume defects probed by positron annihilation lifetime spectroscopy

ABSTRACT

Polymers based on ionic conducting materials have important interest because of their potential applications in polymer electrolytes and membranes for fuel cell application. PVdF-co-HFP poly(viniliden-co-hexafluoropropylene) was chosen as a polymer matrix because of its high ionic conductivity and better mechanical properties. Polymer matrix composites were prepared with various amounts of LiClO₄ salt by a solution casting method. The sample-ionic conductivity measurements were recorded by AC impedance analyzer at different frequencies from 0.1?Hz to 20?MHz and at different temperatures from 273 to 373?K.

The changes of nanoscopic free volume and free volume fraction in these materials were investigated in terms of temperature from 273 to 373?K using Positron Annihilation Lifetime Spectroscopy (PALS) and Simha-Somcynsky (SS) Hole Theory. The free volume had a bump at about 3% in weight percentage of the salt and there is a slight increase after 10%. The effects of weight percentages of LiClO₄ and temperature were investigated. The mechanism of the ac ionic conductivity was presented in terms of the free volume models, however thermo-occupancy function justifies the best accurate representation of the data.     

Tests of the CBM Rich readout and Daq prototype

The CBM RICH detector is an integral component of the future CBM experiment at FAIR, providing efficient electron identification and pion suppression necessary for the measurement of rare dileptonic probes in heavy ion collisions. An overview of the CBM RICH readout and DAQ system prototype is given, consisting of the PADIWA preamplifier-discriminator board, the TDC-HUB board TRBv3, and DAQ and analysis code in the CbmRoot framework. The laboratory setup built for studying the timing characteristics of the readout chain and the analysis results obtained using the laboratory measurements are presented. The fine time calibration and inter-channel delay correction techniques and their implementation and effect are discussed.     

Analysis of the alterations in porosity features of some natural stones due to thermal effect

Three types of commercially available carbonate rocks were used in the study to determine the effect of thermal treatment in the range from 100 °C to 500 °C on porosity features in terms of two different approaches such as pore shape factor and quality index values. The ratio of the ultrasonic velocity measurements before and after water saturation was used to differentiate porosity of pores from porosity of cracks under varying temperatures. It was found that, pores in Burdur Beige and Usak White are in the form of cracks, which are situated through inner structure. On the other hand, pores in Patara Limestone are in the form of porosity with lower pore shape factor values. Quality index calculation is another approach based on the comparison of the measured and theoretical ultrasonic velocity values. When the rocks were subjected to higher temperatures, internal stress was developed, crack lengths and numbers were increased and finally the higher pore shape factor and lower quality index values were obtained. This situation was proven by the higher water absorption values for all the stone types with the higher pore shape factor and lower quality index values depend on the noticeable increase in effective porosity values.     

Comparing the efficiencies of hydrazide labels in the study of protein carbonylation in human serum albumin

In this work, we establish a methodology for comparing the efficiencies of different hydrazide labels for detecting protein carbonyls. We have chosen acrolein-modified human serum albumin as a model. This system provides a convenient means of reproducibly generating carbonylated protein. Five hydrazide-based labels were tested. Three carry a biotin affinity tag, and the others are simple fatty acid hydrazides. For the biotin-based labels, the yield of the labeling reaction varies considerably, and the most commonly used label, biotin hydrazide, gives the lowest yield. The total tandem mass spectrometry (MS/MS) spectrum counts of modified peptides are similar for all of the biotin-based tags, indicating that factors beyond the labeling efficiency are important in determining the effectiveness of the label. In addition, there is a large variation in the number of spectra obtained for specific, modified peptides depending on the nature of the labeling group. This variation implies that the relative detectability of a particular modification site is highly dependent on the tagging reagent, and more importantly, titration schemes aimed at identifying the most reactive site based on its threshold concentration will be biased by the choice of tagging reagent. The fatty acid hydrazides are somewhat more effective than the biotin-based hydrazides in generating identifiable MS/MS spectra but offer no opportunity for enrichment. For the biotin-based tags, avidin affinity chromatography was used with the tryptic digests, and each tag led to similar enrichment levels.