Physiological changes induced by chromium stress in plants: an overview

This article presents an overview of the mechanism of chromium (Cr) stress in plants. Toxic effects of Cr on plant growth and development depend primarily on its valence state. Cr(VI) is highly toxic and mobile whereas Cr(III) is less toxic. Cr-induced oxidative stress involves induction of lipid peroxidation in plants that cause severe damage to cell membranes which includes degradation of photosynthetic pigments causing deterioration in growth. The potential of plants with the adequacy to accumulate or to stabilize Cr compounds for bioremediation of Cr contamination has gained engrossment in recent years.     

The Determination of Assay for Laccase of Bacillus subtilis WPI with Two Classes of Chemical Compounds as Substrates

Ligninolytic enzyme complexes are involved in lignin degradation. Among them laccases are outstanding because they use molecular oxygen as a co-substrate instead of hydrogen peroxide as used by peroxidases. Bacterial laccase of Bacillus genus was first reported in Claus and Filip (Microbiol Res 152:209–216, 1997), since then more bacterial laccases have been found. In this research, laccase-producing bacteria were screened from pulp and paper industry wastewater, bagass and sugarcane rhizosphere. Nutrient agar medium containing 0.5 mM of guaiacol was used. It was observed that the laccase-producing strains developed brown colour from which 16 strains of Bacillus were identified. One of the isolated strains was identified as Bacillus subtilis WPI based on the results of biochemical tests and 16S rDNA sequence analysis. This strain showed laccase-like activity towards the oxidizing substrates ABTS and guaiacol. In this study guaiacol was used as the substrate of laccase activity assay. For determination of laccase activity of this isolate guaiacol was used as a substrate of assay for the first time in this study. SDS-PAGE and Native-PAGE confirmed the presence of laccase.     

Role of active site rigidity in activity: MD simulation and fluorescence study on a lipase mutant

Relationship between stability and activity of enzymes is maintained by underlying conformational flexibility. In thermophilic enzymes, a decrease in flexibility causes low enzyme activity while in less stable proteins such as mesophiles and psychrophiles, an increase in flexibility is associated with enhanced enzyme activity. Recently, we identified a mutant of a lipase whose stability and activity were enhanced simultaneously. In this work, we probed the conformational dynamics of the mutant and the wild type lipase, particularly flexibility of their active site using molecular dynamic simulations and time-resolved fluorescence techniques. In contrast to the earlier observations, our data show that active site of the mutant is more rigid than wild type enzyme. Further investigation suggests that this lipase needs minimal reorganization/flexibility of active site residues during its catalytic cycle. Molecular dynamic simulations suggest that catalytically competent active site geometry of the mutant is relatively more preserved than wild type lipase, which might have led to its higher enzyme activity. Our study implies that widely accepted positive correlation between conformation flexibility and enzyme activity need not be stringent and draws attention to the possibility that high enzyme activity can still be accomplished in a rigid active site and stable protein structures. This finding has a significant implication towards better understanding of involvement of dynamic motions in enzyme catalysis and enzyme engineering through mutations in active site.     

Use of flux pre-analysis to enable ¹³C tracer studies in pyruvate kinase-deficient Escherichia coli

Pyruvate kinase-deficient Escherichia coli (PB25) is a low by-product-producing yet fast-growing mutant that has been shown to have technological potential. Determining the flux limits through finding the extreme point flux sets was previously reported to identify alternate metabolite trafficking scenarios. Previously, the extreme point flux sets were used to design tracer experiments; however, variation in extracellular measurements was not considered, and reaction reversibility was assumed to be low to moderate. In this study, we examined the utility of limiting the fluxes and predetermining the trafficking scenarios in PB25, including confirmation of quasi-linearity between extreme points to ensure sensitivity is maintained. The effects of variation in extracellular measurements and reaction reversibilities were also examined. Tightened flux limits reduced the nonlinearity between label distribution and fluxes. For low to moderate reversibility, contrast was also preserved. However, for highly reversible phosphoglucoisomerase activity, information from common analytes could lead to a flux solution that is biased towards one extreme point. Based on the PB25 model, some suggestions are provided for how predetermining flux limits and trafficking scenarios could enable flux identification in larger network problems.     

Gene regulatory network modeling using literature curated and high throughput data

Building on the linear matrix inequality (LMI) formulation developed recently by Zavlanos et al. (Automatica: Special Issue Syst Biol 47(6):1113–1122, 2011), we present a theoretical framework and algorithms to derive a class of ordinary differential equation (ODE) models of gene regulatory networks using literature curated data and microarray data. The solution proposed by Zavlanos et al. (Automatica: Special Issue Syst Biol 47(6):1113–1122, 2011) requires that the microarray data be obtained as the outcome of a series of controlled experiments in which the network is perturbed by over-expressing one gene at a time. We note that this constraint may be relaxed for some applications and, in addition, demonstrate how the conservatism in these algorithms may be reduced by using the Perron–Frobenius diagonal dominance conditions as the stability constraints. Due to the LMI formulation, it follows that the bounded real lemma may easily be used to make use of additional information. We present case studies that illustrate how these algorithms can be used on datasets to derive ODE models of the underlying regulatory networks.     

3D-QSAR studies of triazolopyrimidine derivatives of <Emphasis Type="Italic">Plasmodium falciparum</Emphasis> dihydroorotate dehydrogenase inhibitors using a combination of molecular dynamics,docking, and genetic algorithm-based methods

A series of 35 triazolopyrimidine analogues reported as Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors were optimized using quantum mechanics methods, and their binding conformations were studied by docking and 3D quantitative structure–activity relationship studies. Genetic algorithm-based criteria was adopted for selection of training and test sets while maintaining structural diversity of training and test sets, which is also very crucial for model development and validation. Both the comparative molecular field analyses ( q_\textLOO² = 0.841 q_{\text{LOO}}^2 = 0.{841} , r_\textncv² = 0.99 r_{\text{ncv}}^2 = 0.{99} ) and comparative molecular similarity indices analyses ( q_\textLOO² = 0.757 q_{\text{LOO}}^2 = 0.{757} , r_\textncv² = 0.943 r_{\text{ncv}}^2 = 0.{943} ) show excellent correlation and high predictive power. Furthermore, molecular dynamics simulations were performed to explore the binding mode of the two of the most active compounds of the series, 10 and 14. Harmonization in the two simulation results validate the analysis and therefore applicability of docking parameters based on crystallographic conformation of compound 14 bound to receptor molecule. This work provides useful information about the inhibition mechanism of this class of molecules and will assist in the design of more potent inhibitors of PfDHODH.     

Is Self-Rated Health an Independent Index for Mortality among Older People in Indonesia?

Background

Empirical studies on the association between self-rated health (SRH) and subsequent mortality are generally lacking in low- and middle-income countries. The evidence on whether socio-economic status and education modify this association is inconsistent. This study aims to fill these gaps using longitudinal data from a Health and Demographic Surveillance System (HDSS) site in Indonesia.

Methods

In 2010, we assessed the mortality status of 11,753 men and women aged 50+ who lived in Purworejo HDSS and participated in the INDEPTH WHO SAGE baseline in 2007. Information on self-rated health, socio-demographic indicators, disability and chronic disease were collected through face-to-face interview at baseline. We used Cox-proportional hazards regression for mortality and included all variables measured at baseline, including interaction terms between SRH and both education and socio-economic status (SES).

Results

During an average of 36 months follow-up, 11% of men and 9.5% of women died, resulting in death rates of 3.1 and 2.6 per 1,000 person-months, respectively. The age-adjusted Hazard Ratio (HR) for mortality was 17% higher in men than women (HR = 1.17; 95% CI = 1.04–1.31). After adjustment for covariates, the hazard ratios for mortality in men and women reporting bad health were 3.0 (95% CI = 2.0–4.4) and 4.9 (95% CI = 3.2–7.4), respectively. Education and SES did not modify this association for either sex.

Conclusions

This study supports the predictive power of bad self-rated health for subsequent mortality in rural Indonesian men and women 50 years old and over. In these analyses, education and household socio-economic status do not modify the relationship between SRH and mortality. This means that older people who rate their own health poorly should be an important target group for health service interventions.