Influences of low-head dams on the fish assemblages in the headwater streams of the Qingyi watershed, China

The influences of low-head dams on the fish assemblages were examined in this study, using fish data collected in six treatment and five reference sites at three low-head dams in the headwater streams of the Qingyi watershed, China. Comparing with those in the reference sites, local habitat variables were significantly altered by low-head dams in the treatment sites, involving wider channel (only in the impoundment area), deeper water and slower flow. Fish species richness varied significantly across seasons, not across site categories, suggesting that these low-head dams did not alter species richness. However, significant decreases in fish abundance and density were observed in the impoundment areas immediately upstream of dams, but not in the plunge areas downstream. Fish assemblage structures kept relative stability across seasons, and their significant difference between-site was only observed between the impoundment areas and the sites far from dams upstream. This variation in assemblage structures was due to the differing relative abundance of some co-occurring species; more lentic but less lotic fish was observed in the impoundment areas. The spatial and temporal patterns of fish assemblages were correlated with local habitat in this study area. Wetted width had negative correlation with fish species richness, abundance and density, respectively. Water temperature also positively affected species richness. In addition, wetted width, water depth, current velocity and substrate were the important habitat variables influencing assemblage structures. Our results suggested that, by modifying local habitat characteristics, low-head dams altered fish abundance and density in the impoundment areas immediately upstream of dam, not in the plunge areas immediately downstream, and thereby influenced fish assemblage structures in these stream segments.     

Improved protective efficacy of a chimeric Staphylococcus aureus vaccine candidate iron‐regulated surface determinant B (N126–P361)‐target of RNAIII activating protein in mice

The pathogen Staphylococcus aureus causes a wide range of serious infections, necessitating urgent development of a vaccine against this organism. However, currently developed vaccines are relatively ineffective because of the limited antigenic component that is contained in the vaccine formulations. To develop an effective S. aureus candidate vaccine, overlapping PCR was used to add the truncated immunodominant antigen iron‐regulated surface determinant B (IsdB)_{(N126–P361)} (tIsdB) to the N‐terminal of intact antigen target of RNAIII activating protein (TRAP) and thus construct a tIsdB‐TRAP chimera. The humoral and cellular immune responses against tIsdB‐TRAP were compared with those against single or combined formulations. tIsdB‐TRAP elicited significantly stronger humoral responses in mice (P < 0.05). As to cellular immune responses in mice, the tIsdB‐TRAP group resulted in a greater IL‐4 response than did other groups (P < 0.05). Greater amounts of IL‐2 and IFN‐γ were found in the tIsdB‐TRAP group. Mouse challenge also showed that tIsdB‐TRAP provided better protection against S. aureus than did the control groups. These results suggest that this chimeric protein may be a promising pathogen target for further vaccine development.     

Different coexpressions of arthritis-relevant genes between different body organs and different brain regions in the normal mouse population

Structural changes in different parts of the brain in rheumatoid arthritis (RA) patients have been reported. RA is not regarded as a brain disease. Body organs such as spleen and lung produce RA-relevant genes. We hypothesized that the structural changes in the brain are caused by changes of gene expression in body organs. Changes in different parts of the brain may be affected by altered gene expressions in different body organs. This study explored whether an association between gene expressions of an organ or a body part varies in different brain structures. By examining the association of the 10 most altered genes from a mouse model of spontaneous arthritis in a normal mouse population, we found two groups of gene expression patterns between five brain structures and spleen. The correlation patterns between the prefrontal cortex, nucleus accumbens, and spleen were similar, while the associations between the other three parts of the brain and spleen showed a different pattern. Among overall patterns of the associations between body organs and brain structures, spleen and lung had a similar pattern, and patterns for kidney and liver were similar. Analysis of the five additional known arthritis-relevant genes produced similar results. Analysis of 10 nonrelevant-arthritis genes did not result in a strong association of gene expression or clearly segregated patterns. Our data suggest that abnormal gene expressions in different diseased body organs may influence structural changes in different brain parts.     

A novel model for the molecular dynamics simulation study on mechanical properties of HMX/F2311 polymer-bonded explosive

The ‘insert’ model for β-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX)-based polymer-bonded explosive (PBX) was proposed for finding the relation of temperatures with mechanical properties. This model was simulated by using molecular dynamics models. The elastic constants and the effective moduli were calculated with static analysis method. Cauchy pressure was also calculated. It is found that the rigidity is weakened and the ductibility is improved by adding a small amount of F₂₃₁₁ in the crystalline HMX. The rigidity is also weakened with increasing temperature. However, the ductibility of HMX/F₂₃₁₁ PBX changes as a parabola with increasing temperature duo to the enhancement of F₂₃₁₁ molecular chain movement and simultaneously the increment of high energy conformation ratio in this molecular chain, i.e. the increment of the molecular chain rigidity.     

Involvement of Volume-Activated Chloride Channels in H2O2 Preconditioning Against Oxidant-Induced Injury Through Modulating Cell Volume Regulation Mechanisms and Membrane Permeability in PC12 Cells

The functions of chloride channels in preconditioning-induced cell protection remain unclear. In this report, we show that the volume-activated chloride channels play a key role in hydrogen peroxide (H₂O₂) preconditioning-induced cell protection in pheochromocytoma PC12 cells. The preconditioning with 100 μM H₂O₂ for 90 min protected the cells from injury induced by long period exposure to 300 μM H₂O₂. The protective effect was attenuated by pretreatment with the chloride channel blockers, 5-nitro-2-3-phenylpropylamino benzoic acid (NPPB) and tamoxifen. H₂O₂ preconditioning directly activated a chloride current, which was moderately outward-rectified and sensitive to the chloride channel blockers and hypertonicity-induced cell shrinkage. H₂O₂ preconditioning functionally up-regulated the activities of volume-activated chloride channels and enhanced the regulatory volume decrease when exposure to extracellular hypotonic challenges. In addition, acute application of H₂O₂ showed distinctive actions on cell volume and membrane permeability in H₂O₂ preconditioned cells. In H₂O₂ preconditioned cells, acute application of 300 μM H₂O₂ first promptly induced a decrease of cell volume and enhancement of cell membrane permeability, and then, cell volume was maintained at a relatively stable level and the facilitation of membrane permeability was reduced. Conversely, in control cells, 300 μM H₂O₂ induced a slow but persistent apoptotic volume decrease (AVD) and facilitation of membrane permeability. H₂O₂ preconditioning also significantly up-regulated the expression of ClC-3 protein, the molecular candidate of the volume-activated chloride channel. These results suggest that H₂O₂ preconditioning can enhance the expression and functional activities of volume-activated chloride channels, thereby modulate cell volume and cell membrane permeability, which may contribute to neuroprotection against oxidant-induced injury.     

Design and Synthesis of Fluoroacylshikonin as an Anticancer Agent

A series of shikonin derivatives, selectively acylated by various fluorinated carboxylic acids at the side chain of shikonin, were synthesized and their anticancer activity evaluated, in which eight compounds are reported for the first time. Among all the compounds tested, compound S7 showed the most potent anticancer activity against B16‐F10 (malignant melanoma cells), MG63 (human osteosarcoma cells), and A549 (lung cancer cells) with IC₅₀ 0.39 ± 0.01, 0.72 ± 0.04 and 0.58 ± 0.02 µmol/L. Docking simulation of compound S7 was carried out to position S7 into a tubulin active site to determine the probable binding conformation. All the results suggested that compound S7 may be a potential anticancer agent. Chirality 25:757–762, 2013. © 2013 Wiley Periodicals, Inc.     

Structure and function of the CBL–CIPK Ca2+-decoding system in plant calcium signaling

Calcium is a crucial messenger in many growth and developmental processes in plants. The central mechanism governing how plant cells perceive and respond to environmental stimuli is calcium signal transduction, a process through which cellular calcium signals are recognized, decoded, and transmitted to elicit downstream responses. In the initial decoding of calcium signals, Ca²⁺ sensor proteins that bind Ca²⁺ and activate downstream signaling components are implicated, thereby regulating specific physiological and biochemical processes. After calcineurin B-like proteins (CBLs) sense these Ca²⁺ signatures, these proteins interact selectively with CBL-interacting protein kinases (CIPKs), thereby forming CBL/CIPK complexes, which are involved in decoding calcium signals. Therefore, specificity, diversity, and complexity are the main characteristics of the CBL-CIPK signaling system. However, additional CBLs, CIPKs, and CBL/CIPK complexes remain to be identified in plants, and the specific functions of their abiotic and biotic stress signaling will need to be further dissected. Therefore, a much-needed synthesis of recent findings is important to further the study of CBL-CIPK signaling systems. Here, we review the structure of CBLs and CIPKs, discuss the current knowledge of CBL–CIPK pathways that decode calcium signals in Arabidopsis, and link plant responses to a variety of environmental stresses with specific CBL/CIPK complexes. This will provide a foundation for future research on genetically engineered resistant plants with enhanced tolerance to various environmental stresses.     

Community Structure and Role Analysis in Biological Networks

Abstract

Complex network analysis has received increasing interest in recent years, which provides a remarkable tool to describe complex systems of interacting entities, particular for biological systems. In this paper, we propose a methodology for identifying the significant nodes of the networks, including core nodes, bridge nodes and high-influential nodes, based on the idea of community and two new ranking measures, InterRank and IntraRank. The results show the significant nodes form a small number in biological networks, and uncover the relative small number of which has advantage for reducing the dimensions of the network and possibly help to define new biological targets.     

2D 1H and 31P NMR Spectra and Distorted A-DNA-Like Duplex Structure of a Phosphorodithioate Oligonucleotide

Abstract

Assignment of the ¹H and ³¹P NMR spectra of a phosphorodithioate modified oligonucleotide decamer duplex, d(CGCTTpS^? ₂AAGCG)₂ (10-mer-S; a site of dithioate substitution is designated with the symbols pS^? ₂), was achieved by two-dimensional homonuclear TOCSY, NOES Y and ¹H-³¹P Pure Absorption phase Constant time (PAC) heteronuclear correlation spectroscopy. In contrast to the parent palindromic decamer sequence (1) which has been shown to exist entirely in the duplex B-DNA conformation under comparable conditions (100 mM KCI), the dithiophosphate analogue forms a hairpin loop. However, the duplex form of the dithioate oligonucleotide can be stabilized at lower temperatures, higher salt and strand concentration. The solution structure of the decamer duplex was calculated by an iterative hybrid relaxation matrix method (MORASS) combined with 2D NOESY-distance restrained molecular dynamics. These backbone modified compounds, potentially attractive antisense oligonucleotide agents, are often assumed to possess similar structure as the parent nucleic acid complex. Importantly, the refined structure of the phosphorodithioate duplex shows a significant deviation from the parent unmodified, phosphoryl duplex. An overall bend and unwinding in the phosphorodithioate duplex is observed. The structural distortion of the phosphorodithioate duplex was confirmed by comparison of helicoidal parameters and groove dimensions. Especially, the helical twists of the phosphorodithioate decamer deviate significantly from the parent phosphoryl decamer. The minor groove width of phosphorodithioate duplex 10-mer-S varies between 8.4 and 13.3 Å which is much wider than those of the parent phosphoryl decamer d(CGCTTAAGCG)₂ (4.2～9.4Å). The larger minor groove width of 10-mer-S duplex contributes to the unwinding of the backbone and indicates that the duplex has an overall A-DNA-like conformation in the region surrounding the dithiophosphate modification.