Multi-tests for pore structure characterization-A case study using lamprophyre

The pore structure plays an important role to understand methane adsorption, storage and flow behavior of geological materials. In this paper, the multi-tests including N2 adsorption, mercury intrusion porosimetry (MIP) and CT reconstruction have been proposed on Tashan lamprophyre samples. The main findings are listed: (1) The pore size distribution has a broad range ranging from 2-100000nm, among which the adsorption pores (\u3c100nm) occupies the mainly specific surface areas and pore volume while the seepage pores (\u3e100nm) only account for 34% of total pore volume. (2) The lamprophyre open pores are mainly slit-like/plate-like and ink-bottle-shaped pores on a two-dimensional level. The lamprophyre 3D pore structure shows more stochastic and anisotropic extension on the z axis to form a complex pore system on a three-dimensional level. (3) The closed pores (\u3e647nm) occupy averaged 74.86% and 72.75% of total pores (\u3e647nm) volume and specific surface area indicating a poor connectivity pore system. The revealed results provide basic information for understanding the abnormal methane emission reasons in similar geological conditions with lamprophyre invasions

Genome-Wide Identification and Analysis of P-Type Plasma Membrane H+-ATPase Sub-Gene Family in Sunflower and the Role of HHA4 and HHA11 in the Development of Salt Stress Resistance

The P-type plasma membrane (PM) H+-ATPase plays a major role during the growth and development of a plant. It is also involved in plant resistance to a variety of biotic and abiotic factors, including salt stress. The PM H+-ATPase gene family has been well characterized in Arabidopsis and other crop plants such as rice, cucumber, and potato; however, the same cannot be said in sunflower (Helianthus annuus). In this study, a total of thirteen PM H+-ATPase genes were screened from the recently released sunflower genome database with a comprehensive genome-wide analysis. According to a systematic phylogenetic classification with a previously reported species, the sunflower PM H+-ATPase genes (HHAs) were divided into four sub-clusters (I, II, IV, and V). In addition, systematic bioinformatics analyses such as gene structure analysis, chromosome location analysis, subcellular localization predication, conserved motifs, and Cis-acting elements of promoter identification were also done. Semi-quantitative PCR analysis data of HHAs in different sunflower tissues revealed the specificity of gene spatiotemporal expression and sub-cluster grouping. Those belonging to sub-cluster I and II exhibited wide expression in almost all of the tissues studied while sub-cluster IV and V seldom showed expression. In addition, the expression of HHA4, HHA11, and HHA13 was shown to be induced by salt stress. The transgenic plants overexpressing HHA4 and HHA11 showed higher salinity tolerance compared with wild-type plants. Further analysis showed that the Na+ content of transgenic Arabidopsis plants decreased under salt stress, which indicates that PM H+ ATPase participates in the physiological process of Na+ efflux, resulting in salt resistance of the plants. This study is the first to identify and analyze the sunflower PM H+ ATPase gene family. It does not only lay foundation for future research but also demonstrates the role played by HHAs in salt stress tolerance

A Novel and Efficient Phthalate Hydrolase from <i>Acinetobacter</i> sp. LUNF3: Molecular Cloning, Characterization and Catalytic Mechanism

Phthalic acid esters (PAEs), which are widespread environmental contaminants, can be efficiently biodegraded, mediated by enzymes such as hydrolases. Despite great advances in the characterization of PAE hydrolases, which are the most important enzymes in the process of PAE degradation, their molecular catalytic mechanism has rarely been systematically investigated. Acinetobacter sp. LUNF3, which was isolated from contaminated soil in this study, demonstrated excellent PAE degradation at 30 °C and pH 5.0–11.0. After sequencing and annotating the complete genome, the gene dphAN1, encoding a novel putative PAE hydrolase, was identified with the conserved motifs catalytic triad (Ser201-Asp295-His325) and oxyanion hole (H127GGG130). DphAN1 can hydrolyze DEP (diethyl phthalate), DBP (dibutyl phthalate) and BBP (benzyl butyl phthalate). The high activity of DphAN1 was observed under a wide range of temperature (10–40 °C) and pH (6.0–9.0). Moreover, the metal ions (Fe2+, Mn2+, Cr2+ and Fe3+) and surfactant TritonX-100 significantly activated DphAN1, indicating a high adaptability and tolerance of DphAN1 to these chemicals. Molecular docking revealed the catalytic triad, oxyanion hole and other residues involved in binding DBP. The mutation of these residues reduced the activity of DphAN1, confirming their interaction with DBP. These results shed light on the catalytic mechanism of DphAN1 and may contribute to protein structural modification to improve catalytic efficiency in environment remediation

The Effect of <i>XPD</i> Polymorphisms on Digestive Tract Cancers Risk: A Meta-Analysis

<div><p>Background</p><p>The Xeroderma pigmento-sum group D gene (<i>XPD</i>) plays a key role in nucleotide excision repair. Single nucleotide polymorphisms (SNP) located in its functional region may alter DNA repair capacity phenotype and cancer risk. Many studies have demonstrated that <i>XPD</i> polymorphisms are significantly associated with digestive tract cancers risk, but the results are inconsistent. We conducted a comprehensive meta-analysis to assess the association between <i>XPD</i> Lys751Gln polymorphism and digestive tract cancers risk. The digestive tract cancers that our study referred to, includes oral cancer, esophageal cancer, gastric cancer and colorectal cancer.</p><p>Methods</p><p>We searched PubMed and EmBase up to December 31, 2012 to identify eligible studies. A total of 37 case-control studies including 9027 cases and 16072 controls were involved in this meta-analysis. Statistical analyses were performed with Stata software (version 11.0, USA). Odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of the association.</p><p>Results</p><p>The results showed that <i>XPD</i> Lys751Gln polymorphism was associated with the increased risk of digestive tract cancers (homozygote comparison (GlnGln <i>vs.</i> LysLys): OR = 1.12, 95% CI = 1.01–1.24, <i>P</i> = 0.029, <i>P</i>_{heterogeneity} = 0.133). We found no statistical evidence for a significantly increased digestive tract cancers risk in the other genetic models. In the subgroup analysis, we also found the homozygote comparison increased the susceptibility of Asian population (OR = 1.28, 95% CI = 1.01–1.63, <i>P</i> = 0.045, <i>P</i>_{heterogeneity} = 0.287). Stratified by cancer type and source of control, no significantly increased cancer risk was found in these subgroups. Additionally, risk estimates from hospital-based studies and esophageal studies were heterogeneous.</p><p>Conclusions</p><p>Our meta-analysis suggested that the <i>XPD</i> 751Gln/Gln genotype was a low-penetrate risk factor for developing digestive tract cancers, especially in Asian populations.</p></div

Forest plot of digestive cancer risk associated with the XPD Lys751Gln polymorphisms.

<p>Homozygote comparison.</p

Begg's funnel plot for publication bias test (Homozygote comparison).

<p>Each point represents a separate study for the indicated association.</p

Forest plot of digestive cancer risk associated with the XPD Lys751Gln polymorphisms in Asian subgroups (based on homozygote comparison).

<p>A fixed-effects model was used. The squares and horizontal lines correspond to the study-specific OR and 95% CI. The area of the squares reflects the weight (inverse of the variance). The diamond represents the summary OR and 95% CI.</p

Influence analysis of the summary odds ratio coefficients on the association between XPD Lys751Gln homozygote comparison with digestive tract cancers risk.

<p>Results were computed by omitting each study (left column) in turn. Bars, 95% CI.</p