Molecular modeling on human CCR5 receptors and complex with CD4 antigens and HIV-1 envelope glycoprotein gp120

AIM: To investigate the interaction between human CCR5 receptors (CCR5) and HIV-1 envelope glycoprotein gp120 (HIV-1 gp120) and HIV-1 receptor CD4 antigens (CD4). METHODS: The structurally con served regions (SCR) of human CCR5 was built by the SYBYL/Biopolymer module using the corresponding transmembrane (TM) domain of bacteriorhodopsin (bR) as the template. The coordinates for amino-ter minal residue sequence, and carboxyl-terminal residue sequence, extracellular and cytoplasmic loops were generated using LOOP SEARCH algorithm. Subsequently the structural model was merged into the complex with HIV-1 gp120 and CD4. RESULTS: Human CCR5 interacted with both an HIV-1 gp120 and CD4. The N-terminal residues (especially Met1 and Gln4) of human CCR5, contacted with CD4 residues, mainly 7Nith one span (56 - 59) of CD4 in electrostatic interaction and hydrogen-bonds. The binding sites of human CCR5 were buried in a hydrophobic center surrounded by a highly basic periphery. On the other hand, direct interatomic contacts were made between ? CCR5 residues and 6 gp120 amino-acid residues, which included van der Waals contacts, hydrophobic interaction, and hydrogen bonds. CONCLUSION: The interaction model should be helpful for rational design of novel anti-HIV drugs.

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.

Effects of tetrabrominated diphenyl ether and hexabromocyclododecanes in single and complex exposure to hepatoma HepG2 cells

This study was designed to determine cytotoxic effects of PBDE-47 and HBCDs individually or with a mixture of both compounds exposure to Hep G2 cells. The results showed PBDE-47 and HBCDs induced increase of nitric oxide synthase (NOS) activity, release of NO. dissipation of mitochondria membrane potential and cell apoptosis. Exposure to HBCDs induced ROS formation. Moreover, preincubation with PTIO (NO scavanger) and N-acetylcysteine (ROS scavanger) partially reversed cytotoxic effects of these compounds. The possible mechanism is that PBDE-47 and HBCDs could boost generation of NO and/or ROS, impact mitochondria, and result in start-ups of apoptosis program. Cells exposed to mixture of both compounds and each of them showed non-apoptotic rate significant difference, but the combination of them caused more adverse effects on cells. These results Suggest that PBDE-47 and HBCDs in single and complex exposure have the cytotoxic activity of anti-proliferation and induction of apoptosis in tumor cells in vitro. (C) 2008 Elsevier B.V. All rights reserved.

Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation

Background: Short and long interspersed elements (SINEs and LINEs, respectively), two types of retroposons, are active in shaping the architecture of genomes and powerful tools for studies of phylogeny and population biology. Here we developed special protocol to apply biotin-streptavidin bead system into isolation of interspersed repeated sequences rapidly and efficiently, in which SINEs and LINEs were captured directly from digested genomic DNA by hybridization to bead-probe complex in solution instead of traditional strategy including genomic library construction and screening. Results: A new couple of SINEs and LINEs that shared an almost identical 3'tail was isolated and characterized in silver carp and bighead carp of two closely related species. These SINEs (34 members), designated HAmo SINE family, were little divergent in sequence and flanked by obvious TSD indicated that HAmo SINE was very young family. The copy numbers of this family was estimated to 2 x 10(5) and 1.7 x 10(5) per haploid genome by Real-Time qPCR, respectively. The LINEs, identified as the homologs of LINE2 in other fishes, had a conserved primary sequence and secondary structures of the 3'tail region that was almost identical to that of HAmo SINE. These evidences suggest that HAmo SINEs are active and amplified recently utilizing the enzymatic machinery for retroposition of HAmoL2 through the recognition of higher-order structures of the conserved 42-tail region. We analyzed the possible structures of HAmo SINE that lead to successful amplification in genome and then deduced that HAmo SINE, SmaI SINE and FokI SINE that were similar in sequence each other, were probably generated independently and created by LINE family within the same lineage of a LINE phylogeny in the genomes of different hosts. Conclusion: The presented results show the advantage of the novel method for retroposons isolation and a pair of young SINE family and its partner LINE family in two carp fishes, which strengthened the hypotheses containing the slippage model for initiation of reverse transcription, retropositional parasitism of SINEs on LINEs, the formation of the stem loop structure in 3'tail region of some SINEs and LINEs and the mechanism of template switching in generating new SINE family.

Meat and bone meal replacement in diets for juvenile gibel carp (Carassius auratus gibelio): effects on growth performance, phosphorus and nitrogen loading

A 11-week growth trial was conducted in a flow-through system with juvenile gibel carp Carassius auratus gibelio to evaluate the effects of gradual replacement of fish meal (FM) by meat and bone meal (MBM) on growth performance, phosphorus (P) and nitrogen (N) loading. Six isonitrogenous (crude protein: 410 g kg(-1)) and isoenergetic (gross energy: 18 kJ g(-1)) diets were formulated. FM was used as the control protein. In the other five diets, 20, 40, 60, 80 and 100% FM protein was substituted with MBM20, MBM40, MBM60, MBM80, MBM100, respectively. Total P content in the diets ranged from 16.0 to 28.3 g kg(-1) and the available P was 5.0-6.6 g kg(-1). The results showed that the best growth was achieved with fish fed on the control diet and MBM20. Final body weight, weight gain, feed efficiency, protein retention efficiency and energy retention efficiency decreased with increased dietary MBM. No significant differences were found in the feeding rate and hepatosomatic index between the groups. Apparent digestibility coefficient (ADC) of dry matter, protein and P decreased with increase in dietary MBM, while there were no significant differences in the ADC of energy. P and N retention decreased linearly while P and N loading increased linearly with the increased dietary MBM levels. No significant differences were observed in the activity of alkaline phosphatase, aspartate aminotransferase and alanine aminotransferase, as well as pyruvate kinase in liver or in serum. Total superoxide dismutase activity in MBM20 was significantly higher than that of MBM100.

Insecticide resistance in Chinese populations of the Culex pipiens complex through esterase overproduction

In most parts of China, mosquitoes have been subjected to organophosphate (OP) insecticide treatments since the mid-1960s, and resistance gene monitoring in the Culex pipiens complex (Diptera: Culicidae) started in only a few locations from the end of the 1980s. Many resistant alleles at the Ester locus have been found in field populations, including those commonly found around the world (Ester(B1) and Ester(2)), and those endemic to China (Ester(B6), Ester(B7), Ester(8), and Ester(9)). This situation is atypical, and may represent a complex situation for the evolution of insecticide resistance genes in China. To increase our understanding of the Chinese situation and our ability to manage resistance in the C. pipiens complex, a large study was performed. Twenty field populations were sampled from Beijing to Guangzhou. Bioassays with five insecticides (dichlorvos, parathion, chlorpyrifos, 2-sec-butylphenyl methyl carbamate, and propoxur) disclosed resistance levels variable according to the geographic origin, and up to 85-fold for dichlorvos. Six overproduced esterases were identified, including two that have not been previously described. Most of them were found in all samples, although at variable frequencies, suggesting variable selection or a transient situation, e.g., each one was recently restricted to a particular geographic area. The results are discussed in the context of recent alterations to insecticide campaigns, and of the evolution of resistance genes in Chinese C. pipiens populations.

Photoreduction of mercuric salt in UV/Fe (III)-oxalate complex system

In this paper, the photochemical reduction process of Hg (II) in aqueous solution containing ferric iron and oxalate (Ox) has been studied. Under the radiation of a low-pressure mercury lamp (lambda = 253.7 nm, 8W), Fe(III)-oxalate complexes undergo photolysis to produce ferrous ions and other organic reductive species, which reduce Hg(II) subsequently. For 0.1 mg/L Hg (II), the photoreduction efficiency is comparatively higher in the solution at pH 5.0 than that over the range of 3.0 similar to 8.0. The photoreduction efficiency of Ho (II) in aqueous solution increases with increasing, initial concentration of ferric ions from 0.02 mmol/L to 0.2 mmol/L and initial concentration of oxalate from 0.96 mmol/L to 4.8 mmol/L and then gradually approaches to a steady state. CH3OH also contributes the reduction of Hg (II). We investigate the increase of the ferric, oxalate and CH3OH concentrations resulting from the increase of reduction efficiency of Hg (II). It can be seen that ferrous ions and other reactive species are reductants of Hg (II), and the reaction product with oxalate is mainly volatile metallic mercury.

Partial and total replacement of fishmeal with poultry by-product meal in diets for gibel carp, Carassius auratus gibelio Bloch

Triplicate groups of gibel carp Carassius auratus gibelio Bloch (initial body weight: 4.89 g) were fed for 8 weeks at 24.8-30.8 degrees C with nine isonitrogenous and isoenergetic diets. The control diet (F1) used white fishmeal (FM) as the sole protein source. In the other eight diets (F2-F9), 40.5-100% of FM protein was substituted by poultry by-product meal (PBM) at 8.5% increments. The specific growth rate (SGR), feed efficiency ratio, protein efficiency ratio, protein retention efficiency and energy retention rate for fish fed PBM diets (F2-F9) were all higher, but not always significantly, than those for fish fed F1. All apparent digestibility coefficients for fish fed PBM diets were lower than those for fish fed F1. Fish fed F1 had a significantly higher hepatosomatic index value than fish fed PBM diets (P < 0.05). No significant (P > 0.05) effect of diet was found in whole-body moisture and fat content. Whole-body protein and energy content for fish fed PBM diets were slightly higher than that for fish fed F1. The optimal replacement level of FM by PBM was estimated by second-order polynomial regression to be 66.5% in protein.

Effects of live food and formulated diets on survival, growth and protein content of first-feeding larvae of Plelteobagrus fulvidraco

In recent years, much progress has been made in the rearing of fish larvae fed only artificial diets. A preliminary study was made in an attempt to evaluate the effects of live food and formulated diets on survival, growth and body protein content of first-feeding larvae of Plelteobagrus fulvidraco. Three test diets varying in protein level were formulated: Feed 1 containing 45% protein, Feed 2 with 50% protein and Feed 3 with 55% protein. Larvae fed live food (newly hatched Artemia, unenriched) were the control. The experiment started 3 days post-hatch and lasted for 23 days. At the end of the 23-day trial, survival was best in the control group (65.6%) whereby the final body weight and specific growth rate (SGR) were significantly lower than those in the test feed groups. At the same time, coefficients of variation for SGR and final body weight in the test groups were significantly higher than those in the control. Whole body protein content in all treatments showed a similar tendency during development: significantly higher 3 days post-hatch, then decreasing significantly, and then increasing unstatistically 10 days post-hatch. All results suggest that live food is still better for first-feeding larvae of P. fulvidraco, since live food leads to healthier larvae growth.

Complex mutation at a microsatellite locus in sturgeons: Acipenser sinensis, A-schrenckii, A-gueldenstaedtii and A-baerii

Cross-species amplifications of microsatellite locus Spl-106, which was originally screened from the genome of shovelnose sturgeon (Scaphirhynchus platorynchus) with a perfect TAGA repeat motif, were carried out in four other species of the genera Acipenser. A total of 34 polymerase chain reaction (PCR) products representing 16 different alleles of this locus was sequenced. Sequence analysis results showed that besides the number changes of repeat units, many mutational events, such as single-base substitutions and various insertion/deletion (indels) occurred not only at species level but also at individual level, even among the different alleles within the same individual. The repeat motifs varied from perfect (TAGA)n array to perfect compound (TAAA)m (GAAA)n and perfect or imperfect compound (TAAA)m (TAGA)n (TAAA)x arrays in different species and different individuals. The evolution dynamics of this locus in sturgeons was inferred in that it may evolve from a single perfect to different perfect or imperfect compounds.

Effects of animal-plant protein ratio in extruded and expanded diets on nitrogen and energy budgets of juvenile Chinese soft-shelled turtle (Pelodiscus sinensis Wiegmann)

In this study, we investigated the effects of animal-plant protein ratio in extruded and expanded diets on nutrient digestibility, nitrogen and energy budgets of juvenile soft-shelled turtle (Pelodiscus sinensis). Four extruded and expanded feeds (diets 1-4) were formulated with different animal-plant protein ratios (diet 1, 1.50:1; diet 2, 2.95:1; diet 3, 4.92:1; diet 4, 7.29:1). The apparent digestibility coefficients (ADCs) of dry matter and crude lipid for diet 1 were significantly lower than those for diets 2-4. There was no significant difference in crude protein digestibility among diets 1-4. The ADC of carbohydrate was significantly increased with the increase in animal-plant protein. Although nitrogen intake rate, faecal nitrogen loss rate and excretory nitrogen loss rate of turtles fed diet 1 were significantly higher than those fed diets 2-4, nitrogen retention rate, net protein utilization and biological value of protein in these turtles were significantly lower than those fed diets 2-4. In addition, energy intake rate, excretory energy loss rate and heat production rate of turtles fed diet 1 were also significantly higher than those fed diets 2-4. Faecal energy loss was significantly reduced with the increase in the animal-plant protein ratio. The ADC of energy and assimilation efficiency of energy significantly increased with a higher animal-plant protein ratio. The growth efficiency of energy in the group fed diet 1 was significantly lower than those in the groups fed diets 2-4. Together, our results suggest that the optimum animal-plant protein ratio in extruded and expanded diets is around 3:1.

Effect of replacement of fish meal by meat and bone meal and poultry by-product meal in diets on the growth and immune response of Macrobrachium nipponense

The potential use of poultry by-product meal (PBM) and meat and bone meal (MBM) as alternative dietary protein sources for juvenile Macrobrachium nipponense was studied by a 70-day growth trial. Triplicate groups of M. nipponense (initial body weight: 0.37 g) were fed at 20.7-22.4 degreesC on each of the five isoenergetic and isonitrogenous diets (protein content about 38%) with different replacement of fish meal by MBM or PBM. The control diet used white fish meal as the sole protein source, the other four diets were prepared with 15% or 50% fish meal protein substituted by either MBM (MBM15, MBM50) or PBM (PBM15, PBM50). The results showed that replacement of fish meal by MBM in diets did not affect growth performance of M. nipponense (P > 0.05), while specific growth rate in PBM15 was significantly higher than that in other groups (P < 0.05). Survival rates of shrimp fed with MBM15 diet were significantly higher than that in other groups (P < 0.05). No significant differences in immunological parameters, including total haemocyte count (THC), phenoloxidase activity (PO) and respiratory burst (O-2(-)), were observed between the shrimps that were fed five experimental diets, and all determined immunological parameters in control groups were slightly higher than those in replacement groups. In conclusion, either MBM or PBM investigated could replace up to 50% fish meal protein in diets for M. nipponense. (C) 2003 Elsevier Ltd. All rights reserved.