Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies

The entry of human immunodeficiency virus (HIV) into cells depends on a sequential interaction of the gp120 envelope glycoprotein with the cellular receptors CD4 and members of the chemokine receptor family. The CC chemokine receptor CCR5 is such a receptor for several chemokines and a major coreceptor for the entry of R5 HIV type-1 (HIV-1) into cells. Although many studies focus on the interaction of CCR5 with HIV-1, the corresponding interaction sites in CCR5 and gp120 have not been matched. Here we used an approach combining protein structure modeling, docking and molecular dynamics simulation to build a series of structural models of the CCR5 in complexes with gp120 and CD4. Interactions such as hydrogen bonds, salt bridges and van der Waals contacts between CCR5 and gp120 were investigated. Three snapshots of CCR5-gp120-CD4 models revealed that the initial interactions of CCR5 with gp120 are involved in the negatively charged N-terminus (Nt) region of CCR5 and positively charged bridging sheet region of gp120. Further interactions occurred between extracellular loop2 (ECL2) of CCR5 and the base of V3 loop regions of gp120. These interactions may induce the conformational changes in gp120 and lead to the final entry of HIV into the cell. These results not only strongly support the two-step gp120-CCR5 binding mechanism, but also rationalize extensive biological data about the role of CCR5 in HIV-1 gp120 binding and entry, and may guide efforts to design novel inhibitors.

Structural and thermodynamic properties of different phases of supercooled liquid water.

Computer simulation results are reported for a realistic polarizable potential model of water in the supercooled region. Three states, corresponding to the low density amorphous ice, high density amorphous ice, and very high density amorphous ice phases are chosen for the analyses. These states are located close to the liquid-liquid coexistence lines already shown to exist for the considered model. Thermodynamic and structural quantities are calculated, in order to characterize the properties of the three phases. The results point out the increasing relevance of the interstitial neighbors, which clearly appear in going from the low to the very high density amorphous phases. The interstitial neighbors are found to be, at the same time, also distant neighbors along the hydrogen bonded network of the molecules. The role of these interstitial neighbors has been discussed in connection with the interpretation of recent neutron scattering measurements. The structural properties of the systems are characterized by looking at the angular distribution of neighboring molecules, volume and face area distribution of the Voronoi polyhedra, and order parameters. The cumulative analysis of all the corresponding results confirms the assumption that a close similarity between the structural arrangement of molecules in the three explored amorphous phases and that of the ice polymorphs I(h), III, and VI exists.

Structural and optical characterization of vertical GaAs/GaP core-shell nanowires grown on Si substrates

GaAs nanowires were grown on Si (111) substrates. By coating a thin GaAs buffer layer on Si surface and using a two-temperature growth, the morphology and crystal structure of GaAs nanowires were dramatically improved. The strained GaAs/GaP core-shell nanowires, based on the improved GaAs nanowires with a shell thickness of 25 nm, showed a significant shift in emission energy of 260 meV from the unstrained GaAs nanowires. © 2010 IEEE.

Growth, structural and optical properties of high quality gaAs nanowires for optoelectronics

We investigate how growth parameters may be chosen to obtain high quality GaAs nanowires suitable for optoelectronic device applications. Growth temperature and precursor flows have a significant effect on the morphology, crystallographic quality, intrinsic doping and optical properties of the resulting nanowires. Significantly, we find that low growth temperature and high arsine flow rate improve nanowire optical properties, reduce carbon impurity incorporation and drastically reduce planar crystallographic defects. Additionally, cladding the GaAs nanowire cores in an AlGaAs shell enhances emission efficiency. These high quality nanowires should create new opportunities for optoelectronic devices. © 2008 IEEE.

Structural and optical properties of III-V nanowires and nanowire heterostructures grown by metalorganic chemical vapour deposition

We have investigated the structural and optical properties of III-V nanowires grown by metalorganic chemical vapour deposition. Binary GaAs, InAs and InP nanowires, and ternary InGaAs and AlGaAs nanowires, have been fabricated and characterised. A variety of axial and radial heterostructures have also been fabricated, including GaAs/AlGaAs core-multishell and GaAs/InGaAs superlattice nanowires. GaAs/AlGaAs core-shell nanowires exhibit strong photoluminescence as the AlGaAs shell passivates the GaAs nanowire surface reducing the surface nonradiative recombination. © 2007 IEEE.

Growth, structural and optical properties of III-V nanowires for optoelectronic applications

We investigate the growth of III-V nanowires by MOCVD and the structural and optical properties of these nanowires. Binary and ternary nanowires of GaAs, InAs, InP, AlGaAs and InGaAs are achieved. We discuss the nucleation and growth issues involved in fabricating high quality nanowires suitable for device applications. We have fabricated and characterised a variety of axial and radial heterostructures including GaAs/InGaAs superlattices, and GaAs/AlGaAs core-shell and core-multishell nanowires. © 2007 IEEE.

Growth, structural and optical properties of GaAs/AlGaAs Core/shell nanowires with and without quantum well shells

We have investigated the growth, structural properties and photoluminescence of novel GaAs/AlGaAs radial heterostructure nanowires, fabricated by metalorganic chemical vapour deposition. The effect of growth temperature on nanowire morphology is discussed. Strong photoluminescence is observed from GaAs nanowires with AlGaAs shells. Core/multishell nanowires, of GaAs cores clad in several alternating layers of thick AlGaAs barrier shells and thin GaAs quantum well shells, exhibit a blue-shifted photoluminescence peak believed to arise from quantum confinement effects. A novel two-temperature growth procedure for obtaining GaAs cores is introduced, and other nanowire heterostructures are addressed. © 2006 IEEE.

Structural and optical properties of axial and radial heterostructure III-V nanowires grown by metalorganic chemical vapour deposition

We have investigated the structural properties and photoluminescence of novel axial and radial heterostructure III-V nanowires, fabricated by metalorganic chemical vapour deposition. Segments of InGaAs have been incorporated within GaAs nanowires, to create axial heterostructure nanowires which exhibit strong photoluminescence. Photoluminescence is observed from radial heterostructure nanowires (core-shell nanowires), consisting of GaAs cores with AlGaAs shells. Core-multishell nanowires, of GaAs cores clad in several alternating layers of thick AlGaAs barrier shells and thin GaAs quantum well shells, exhibit a blue-shifted photoluminescence peak arising from quantum confinement effects. © 2006 Crown Copyright.

Morphological and ultrastructural changes in tobacco BY-2 cells exposed to microcystin-RR

Tobacco BY-2 cells were exposed to microcystin-RR (MC-RR) at two concentrations, 60 mu g mL(-1) and 120 mu g mL(-1), to study the changes in morphology and ultrastructure of cells as a result of the exposure. Exposure to the lower concentration for 5 d led to typical apoptotic morphological changes including condensation of nuclear chromatin, creation of a characteristic 'half moon' structure, and cytoplasm shrinkage and decreased cell volume, as revealed through light microscopy. fluorescence microscopy, and transmission electron microscopy, respectively. Exposure to the higher concentration, on the other hand, led to morphological and ultrastructural changes typical of necrosis, such as rupture of the plasma membrane and the nuclear membrane and a marked swelling of cells. The presence of many vacuoles containing unusual deposits points to the involvement of vacuoles in detoxifying MC-RR. Results of the present study indicate that exposure of tobacco BY-2 cells to MC-RR at a lower concentration (60 mu g mL(-1)) results in apoptosis and that to a higher concentration (120 mu g mL(-1)), in necrosis. (C) 2009 Elsevier Ltd. All rights reserved.

Biochemical and ultrastructural changes of the liver and kidney of the phytoplanktivorous silver carp feeding naturally on toxic Microcystis blooms in Taihu Lake, China

Many experimental studies have documented the impact of microcystins (MC) on fish based on either intraperitoneal injection, or oral gavaging via the diet, but few experiments were conducted by MC exposure through natural food uptake in lakes. In this study, the phytoplanktivorous silver carp were stocked in a large pen set in Meiliang Bay of Taihu Lake where toxic Microcystis blooms occurred in the warm seasons. Fish samples were collected monthly and MC concentrations in liver and kidney of the fish were determined by LC-MS. The maximum MC concentrations in liver and kidney were present in July when damages in ultrastructures of the liver and kidney were revealed by electron microscope. In comparison with previous studies on common carp, silver carp showed less damage and presence of lysosome proliferation in liver and kidney. Silver carp might eliminate or lessen cell damage caused by MC through lysosome activation. Recovery in the ultrastructures of liver and kidney after Microcystis blooms was companied with a significant decrease or even disappearance of MC. Catalase and glutathione S-transferase in liver and kidney of silver carp during Microcystis blooms were significantly higher than before and after Microcystis blooms. The high glutathione pool in liver and kidney of silver carp suggests their high resistance to MC exposure. The efficient antioxidant defence may be an important mechanism of phytoplanktivorous fish like silver carp to counteract toxic Microcystis blooms. (C) 2007 Published by Elsevier Ltd.

In vivo studies on toxin accumulation in liver and ultrastructural changes of hepatocytes of the phytoplanktivorous bighead carp i.p.-injected with extracted microcystins

Phytoplanktivorous bighead carp were injected i.p. with extracted microcystins (mainly MC-RR and -LR) at two doses, 200 and 500 MC-LReq. mu g kg(-1) bw, and the changes in extractable MCs in liver and in the ultrastructure of hepatocytes were studied at 1, 3, 12, 24 and 48 h after injection. Quantitative and qualitative determinations of MCs in the liver were conducted by HPLC and LC-MS, respectively. MC concentration in the liver reached the maxima at 12 It (2.89 mu g MCs g(-1) dry weight at the lower dose) or at 3 h (5.43 mu g MCs g(-1) dry weight at the higher dose) post-injection, followed by sharp declines afterwards, whereas the ultrastructural changes of hepatocytes in both dose groups suggest progressive increases in severity toward the directions of apoptosis and necrosis from I to 24 h, respectively. There were two new findings in fish: widening of intercellular spaces was among the early ultrastructural changes induced by MCs and ultrastructural recovery of hepatocytes was evident at 48 h post-injection in both dose groups. Both the present and previous studies suggest that with in vivo or in vitro exposure to microcystins, hepatocyte damage in fish tends to proceed toward the direction of apoptosis at lower MC concentrations but toward the direction of necrosis at high MC concentrations. The temporal dynamics of MCs in the liver suggest that bighead carp may have a mechanism to degrade or bind MC-LR actively after it enters the blood system. (c) 2005 Elsevier Ltd. All rights reserved.

Use of PFU protozoan community structural and functional characteristics in assessment of water quality in a large, highly polluted freshwater lake in China

Structural and functional parameters of protozoan communities colonizing on PFU (polyurethane foam unit) artificial substrate were assessed as indicators of water quality in the Chaohu Lake, a large, shallow and highly polluted freshwater lake in China. Protozoan communities were sampled 1, 3, 6, 9 and 14 days after exposure of PFU artificial substrate in the lake during October 2003. Four study stations with the different water quality gradient changes along the lake were distinguishable in terms of differences in the community's structural (species richness, individual abundance, etc.) and functional parameters (protozoan colonization rates on PFU). The concentrations of TP, TN, COD and BOD as the main chemical indicators of pollution at the four sampling sites were also obtained each year during 2002-2003 for comparison with biological parameters. The results showed that the species richness and PFU colonization rate decreased as pollution intensity increased and that the Margalef diversity index values calculated at four sampling sites also related to water quality. The three functional parameters based on the PFU colonization process, that is, S-eq, G and T-90%, were strongly related to the pollution status of the water. The number of protozoan species colonizing on PFU after exposure of 1 to 3 days was found to give a clear comparative indication of the water quality at the four sampling stations. The research provides further evidence that the protozoan community may be utilized effectively in the assessment of water quality and that the PFU method furnishes rapid, cost-effective and reliable information that may be useful for measuring responses to pollution stress in aquatic ecosystems.