Universal behavior of localization of residue fluctuations in globular proteins

Localization properties of residue fluctuations in globular proteins are studied theoretically by using the Gaussian network model. Participation ratio for each residue fluctuation mode is calculated. It is found that the relationship between participation ratio and frequency is similar for all globular proteins, indicating a universal behavior in spite of their different size, shape, and architecture.Comment: 4 pages, 3 figures. To appear in Phys. Rev.

Measurement Invariance of the Internet Addiction Test Among Hong Kong, Japanese, and Malaysian Adolescents

There has been increased research examining the psychometric properties on the Internet Addiction Test across different ages and populations. This population-based study examined the psychometric properties using Confirmatory Factory Analysis and measurement invariance using Item Response Theory (IRT) of the IAT in adolescents from three Asian countries. In the Asian Adolescent Risk Behavior Survey (AARBS), 2,535 secondary school students (55.91% girls) in Grade 7 to Grade 13 (Mean age = 15.61 years; SD=1.56) from Hong Kong (n=844), Japan (n=744), and Malaysia (n=947) completed a survey on their Internet use that incorporated the IAT scale. A nested hierarchy of hypotheses concerning IAT cross-country invariance was tested using multi-group confirmatory factor analysis. Replicating past finding in Hong Kong adolescents, the construct of IAT is best represented by a second-order three-factor structure in Malaysian and Japanese adolescents. Configural, metric, scalar, and partial strict factorial invariance was established across the three samples. No cross-country differences on Internet addiction were detected at latent mean level. This study provided empirical support to the IAT as a reliable and factorially stable instrument, and valid to be used across Asian adolescent populations

Bioremediation of mercury: not properly exploited in contaminated soils!

© 2017, Springer-Verlag Berlin Heidelberg. Contamination of land and water caused by heavy metal mercury (Hg) poses a serious threat to biota worldwide. The seriousness of toxicity of this neurotoxin is characterized by its ability to augment in food chains and bind to thiol groups in living tissue. Therefore, different remediation approaches have been implemented to rehabilitate Hg-contaminated sites. Bioremediation is considered as cheaper and greener technology than the conventional physico-chemical means. Large-scale use of Hg-volatilizing bacteria are used to clean up Hg-contaminated waters, but there is no such approach to remediate Hg-contaminated soils. This review focuses on recent uses of Hg-resistant bacteria in bioremediation of mercury-contaminated sites, limitation and advantages of this approach, and identifies the gaps in existing research

Information Loss in Coarse Graining of Polymer Configurations via Contact Matrices

Contact matrices provide a coarse grained description of the configuration omega of a linear chain (polymer or random walk) on Z^n: C_{ij}(omega)=1 when the distance between the position of the i-th and j-th step are less than or equal to some distance "a" and C_{ij}(omega)=0 otherwise. We consider models in which polymers of length N have weights corresponding to simple and self-avoiding random walks, SRW and SAW, with "a" the minimal permissible distance. We prove that to leading order in N, the number of matrices equals the number of walks for SRW, but not for SAW. The coarse grained Shannon entropies for SRW agree with the fine grained ones for n <= 2, but differs for n >= 3.Comment: 18 pages, 2 figures, latex2e Main change: the introduction is rewritten in a less formal way with the main results explained in simple term

Statistical Properties of Contact Maps

A contact map is a simple representation of the structure of proteins and other chain-like macromolecules. This representation is quite amenable to numerical studies of folding. We show that the number of contact maps corresponding to the possible configurations of a polypeptide chain of N amino acids, represented by (N-1)-step self avoiding walks on a lattice, grows exponentially with N for all dimensions D>1. We carry out exact enumerations in D=2 on the square and triangular lattices for walks of up to 20 steps and investigate various statistical properties of contact maps corresponding to such walks. We also study the exact statistics of contact maps generated by walks on a ladder.Comment: Latex file, 15 pages, 12 eps figures. To appear on Phys. Rev.

On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm

N-Acetyl-L-Glutamate Kinase (NAGK) is the structural paradigm for examining the catalytic mechanisms and dynamics of amino acid kinase family members. Given that the slow conformational dynamics of the NAGK (at the microseconds time scale or slower) may be rate-limiting, it is of importance to assess the mechanisms of the most cooperative modes of motion intrinsically accessible to this enzyme. Here, we present the results from normal mode analysis using an elastic network model representation, which shows that the conformational mechanisms for substrate binding by NAGK strongly correlate with the intrinsic dynamics of the enzyme in the unbound form. We further analyzed the potential mechanisms of allosteric signalling within NAGK using a Markov model for network communication. Comparative analysis of the dynamics of family members strongly suggests that the low-frequency modes of motion and the associated intramolecular couplings that establish signal transduction are highly conserved among family members, in support of the paradigm sequence→structure→dynamics→function © 2010 Marcos et al

Effect of nonstationarities on detrended fluctuation analysis

Detrended fluctuation analysis (DFA) is a scaling analysis method used to quantify long-range power-law correlations in signals. Many physical and biological signals are ``noisy'', heterogeneous and exhibit different types of nonstationarities, which can affect the correlation properties of these signals. We systematically study the effects of three types of nonstationarities often encountered in real data. Specifically, we consider nonstationary sequences formed in three ways: (i) stitching together segments of data obtained from discontinuous experimental recordings, or removing some noisy and unreliable parts from continuous recordings and stitching together the remaining parts -- a ``cutting'' procedure commonly used in preparing data prior to signal analysis; (ii) adding to a signal with known correlations a tunable concentration of random outliers or spikes with different amplitude, and (iii) generating a signal comprised of segments with different properties -- e.g. different standard deviations or different correlation exponents. We compare the difference between the scaling results obtained for stationary correlated signals and correlated signals with these three types of nonstationarities.Comment: 17 pages, 10 figures, corrected some typos, added one referenc

Bacteriophages in bathing wàters: A feasibility study on the development of a method based on bacteriophages for the determination of microbiological quality of bathing waters

Projecte: Project report. BCR Information. EU project KINA19506ENC_001. EUROPEAN COMMISSION. Community Research. DG XII/C - Competitive and Sustainable Growth Programme. Published by EU Directorate General ΧΠ - Science, Research and Development ISBN 92-828-9145-3Informe final projecte europeu aigües de bany i bacteriòfagsMethods for the detection and enumeration of somatic coliphages, F-specific RNA bacteriophages and bacteriophages infecting Bacteroides fragilis had been standardised and validated. Conditions for the preparation, transport and distribution of bacteriophage reference materials and preservation of samples had been defined. A method based on flocculation with Mg(OH2) with concentration efficiencies from about 40% was settled to concentrate phages from bathing waters. All methods were successfully implemented in routine laboratories all around the EU. Data on the occurrence of bacteriophages as compared to E. coli and Enterococci are available from diverse situations encountered in the EU. Results allow to conclude that the potential of phages for the determination of the microbiological quality of bathing waters merits to be considered since their determination is feasible and their behaviour in natural water differs from the behaviour of bacterial indicators and consequently they add valuable information

Enhancing tool life of hot isostatically pressed silicon nitride inserts in machining inconel 718 with different susceptors through hybrid microwave post sintering

Hybrid Microwave sintering has become a growing interest for heating and synthesizing ceramic materials due to its capabilities in successfully enhancing densification and improving mechanical and structural properties. Silicon Nitride (Si3N4) based cutting inserts have outstanding properties for machining hard materials such as cast iron, hard steel and nickel based super alloys. This research aims to analyze the effect of different susceptors on the tool life of various Si3N4 inserts (90Si3N4 4Y2O3 2.5MgO 2Al2O3 1.5SiO) that have been synthesized in machining Inconel 718. The Si3N4 inserts have been synthesized by means of Hot Isostatic Pressing (HIP) at 1800°C and followed by Hybrid Microwave (HMW) post-sintering at 200°C for 10 minutes with the aid of three different susceptors; Silicon Carbide (SiC), Graphite (G) and mixture of (SiC + G) powders. Density, hardness, micro structural properties and tool wear were analyzed. HMW post sintering for only 10 minutes using SiC, G and SiC+G susceptors enhanced the density (97-98%TD) and hardness (27-58%) significantly. Finer uniform grains and less porosities were produced particularly for Si3N4 inserts produced by HMW (SiC+G) when compared with HMW (SiC) and HMW (G). Tool life for the Si3N4 inserts were improved by 10-17% HMW(SiC), 20-53 % HMW(G) and 32-88% HMW(SiC+G) for the cutting speeds of 100, 125 and 160 m/min. Hence, the mixture of SiC +G powders as susceptors produced the best outcome for Si3N4 inserts with enhanced densification, hardness, wear resistance, and longer tool life (88% increment at 100 m/min) when compared with the commercial tool (RNGN 6060) in machining Inconel 718

Nonlinearity of Mechanochemical Motions in Motor Proteins

The assumption of linear response of protein molecules to thermal noise or structural perturbations, such as ligand binding or detachment, is broadly used in the studies of protein dynamics. Conformational motions in proteins are traditionally analyzed in terms of normal modes and experimental data on thermal fluctuations in such macromolecules is also usually interpreted in terms of the excitation of normal modes. We have chosen two important protein motors - myosin V and kinesin KIF1A - and performed numerical investigations of their conformational relaxation properties within the coarse-grained elastic network approximation. We have found that the linearity assumption is deficient for ligand-induced conformational motions and can even be violated for characteristic thermal fluctuations. The deficiency is particularly pronounced in KIF1A where the normal mode description fails completely in describing functional mechanochemical motions. These results indicate that important assumptions of the theory of protein dynamics may need to be reconsidered. Neither a single normal mode, nor a superposition of such modes yield an approximation of strongly nonlinear dynamics.Comment: 10 pages, 6 figure