Secondary structural analysis of the mRNA regions encoding the hemagglutinin cleavage site basic amino acids of the avian influenza virus H5N1 subtype samples

Here we report the codon bias and the mRNA secondary structural features of the hemagglutinin (HA) cleavage site basic amino acid regions of avian influenza virus H5N1 subtypes. We have developed a dynamic extended folding strategy to predict RNA secondar

Site-directed PEGylation of trichosanthin retained its anti-HIV activity with reduced potency in vitro

Trichosanthin (TCS) was the first ribosome inactivating protein found to possess anti-HIV-1 activity. Phase I/II clinical trial of this compound had been done. Antigenicity and short plasma half-life were the major side effects preventing further clinical trial. Modification of TCS is therefore necessary to revive the interest to develop this compound as an anti-HIV agent. Three potential antigenic sites (Ser-7, Lys-173, and Gln-219) were identified by computer modeling. Through site-directed mutagenesis, these three antigenic amino acids were mutated to a cysteine residue resulting in 3 TCS mutants, namely S7C, K173C, and Q219C. These mutants were further coupled to polyethylene glycol with a molecular size of 20 kDa (PEG) via the cysteine residue. This produced another three TCS derivatives, namely PEG(20)k-S7C, PEG(20)k-K173C, and PEG(20)k-Q219C. PEGylation had been widely used recently to decrease immunogenicity by masking the antigenic sites and prolong plasma half-life by expanding the molecular size. The in vitro anti-HIV-1 activity of these mutants and derivatives was tested. Results showed that the anti-HIV-1 activity of S7C, K173C, and Q219C was decreased by about 1.5- to 5.5-fold with slightly lower cytotoxicity. On the other hand, PEGylation produced larger decrease (20- to 30-fold) in anti-HIV activity. Cytotoxicity was, however, weakened only slightly by about 3-fold. The in vitro study showed that the anti-HIV activity of PEGylated TCS was retained with reduced potency. The in vivo activity is expected to have only slightly changed due to other beneficial effects like prolonged half-life. (C) 2004 Elsevier Inc. All rights reserved.

Symmetrical 1-pyrrolidineacetamide showing anti-HIV activity through a new binding site on HIV-1 integrase

Aim: To characterize the functional and pharmacological features of a symmetrical 1-pyrrolidineacetamide, N,N'-(methylene-di-4,1-phenylene) bis-1-pyrrolidineacetamide, as a new anti-HIV compound which could competitively inhibit HIV-1 integrase (IN) bindi

Nest site selection by Black-necked Crane Grus nigricollis in the Ruoergai Wetland, China

From 5 May 2003 to early June 2005, nest site selection of Black-necked Cranes Grits nigricollis was studied at the Ruoergai Wetland Nature Reserve (RWNR), an important breeding area for the species in China. Results showed that the crane nests only in we

Molecular docking and 3D-QSAR study of pyranmycin derivatives against 16S rRNA A site

To understand pharmacophore properties of pyranmycin derivatives and to design novel inhibitors of 16S rRNA A site, comparative molecular field analysis (CoMFA) approach was applied to analyze three-dimensional quantitative structure-activity relationship (3D-QSAR) of 17 compounds. AutoDock 3.0.5 program was employed to locate the orientations and conformations of the inhibitors interacting with 16S rRNA A site. The interaction mode was demonstrated in the aspects of inhibitor conformation, hydrogen bonding and electrostatic interaction. Similar binding conformations of these inhibitors and good correlations between the calculated binding free energies and experimental biological activities suggest that the binding conformations of these inhibitors derived from docking procedure were reasonable. Robust and predictive 3D-QSAR model was obtained by CoMFA with q(2) values of 0.723 and 0.993 for cross-validated and noncross-validated, respectively. The 3D-QSAR model built here will provide clear guidelines for novel inhibitors design based on the Pyranmycin derivatives against 16S rRNA A site. (c) 2005 Elsevier B.V. All rights reserved.

Body loadings and health risk assessment of polychlorinated dibenzo-p-dioxins and dibenzofurans at an intensive electronic waste recycling site in China

This study is one of the very few investigating the dioxin body burden of a group of child-bearing-aged women at an electronic waste (e-waste) recycling site (Taizhou, Zhejiang Province) (24 +/- 2.83 years of age, 40% were primiparae) and a reference site (Lin'an city, Zhejiang Province, about 245 km away from Taizhou) (24 +/- 2.35 years of age, 100% were primiparae) in China. Five sets of samples (each set consisted of human milk, placenta, and hair) were collected from each site. Body burdens of people from the e-waste processing site (human milk, 21.02 +/- 13.81 pg WHO-TEQ(1998/g) fat (World Health Organization toxic equivalency 1998); placenta, 31.15 +/- 15.67 pg WHO-TEQ(1998/g) fat; hair, 33.82 +/- 17.74 pg WHO-TEQ(1998/g) dry wt) showed significantly higher levels of polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurnas (PCDD/Fs) than those from the reference site (human milk, 9.35 +/- 7.39 pg WHO-TEQ(1998/g) fat, placenta, 11.91 +/- 7.05 pg WHO-TEQ(1998/g) fat; hair, 5.59 +/- 4.36 pg WHO-TEQ(1998/g) dry wt) and were comparatively higher than other studies. The difference between the two sites was due to e-waste recycling operations, for example, open burning, which led to high background levels. Moreover, mothers from the e-waste recycling site consumed more foods of animal origin. The estimated daily intake of PCDD/Fs within 6 months by breast-fed infants from the e-waste processing site was 2 times higher than that from the reference site. Both values exceeded the WHO tolerable daily intake for adults by at least 25 and 11 times, respectively. Our results implicated that e-waste recycling operations cause prominent PCDD/F levels in the environment and in humans. The elevated body burden may have health implications for the next generation.

Site-directed gene integration in transgenic zebrafish mediated by cre recombinase using a combination of mutant Lox sites

With current gene-transfer techniques in fish, insertion of DNA into the genome occurs randomly and in many instances at multiple sites. Associated position effects, copy number differences, and multiple gene interactions make gene expression experiments difficult to interpret and fish phenotype less predictable. To meet different fish engineering needs, we describe here a gene targeting model in zebrafish. At first, four target zebrafish lines, each harboring a single genomic lox71 target site, were generated by zebrafish transgenesis. The zygotes of transgenic zebrafish lines were coinjected with capped Cre mRNA and a knockin vector pZklox66RFP. Site-specific integration event happened from one target zebrafish line. In this line two integrant zebrafish were obtained from more than 80,000 targeted embryos (integrating efficiency about 10(-4) to 10(-5)) and confirmed to have a sole copy of the integrating DNA at the target genome site. Genomic polymerase chain reaction analysis and DNA sequencing verified the correct gene target events where lox71 and lox66 have accurately recombined into double mutant lox72 and wild-type loxP. Each integrant zebrafish chosen for analysis harbored the transgene rfp at the designated egfp concatenates. Although the Cre-mediated recombination is site specific, it is dependent on a randomly placed target site. That is, a genomic target cannot be preselected for integration based solely on its sequence. Conclusively, an rfp reporter gene was successfully inserted into the egfp target locus of zebrafish genome by Cre-lox-mediated recombination. This site-directed knockin system using the lox71/lox66 combination should be a promising gene-targeting platform serving various purposes in fish genetic engineering.

Studies on the adsorption equilibrium and kinetics of pentachlorophenol on suspended particulate matter of Donghu Lake water

In this paper, the adsorption equilibrium and kinetic behaviors of pentachlorophenol (PCP) on suspended particulate matter (SPM) in Donghu Lake water were investigated. The Langmuir and Freundlich adsorption models were applied to describe the equilibrium isotherms and their constants were evaluated. The results indicated that the adsorption of PCP on Donghu Lake SPM followed the Freundlich isotherm. Furthermore, the first order Lagergren rate equation and the pseudo-second order rate equation were used to describe the kinetic behaviors of PCP adsorption on Donghu Lake SPM, the rate constants were determined, and the kinetic process of the adsorption of PCP on Donghu Lake SPM followed the second order kinetic model.

Hydrodynamics in an expanded bed of large size ion-exchange resin, and natural product adsorption

Successful applications of expanded bed adsorption (EBA) technology have been widely reported in the literature for protein purification. Little has been reported on the recovery of natural products and active components of Chinese herbal preparations using EBA technology. In this study, the hydrodynamic behavior in an expanded bed of cation resin, 001 x 7 Styrene-DVB, was investigated. Ephedrine hydrochloride (EH) was used as a model natural product to test the dynamic binding capacity (DBC) in the expanded bed. EBA of EH directly from a feedstock containing powdered herbs has also been investigated. These particles are different from commercially available expanded bed adsorbents by virtue of their large size (20S to 1030 gm). When the adsorbent bed is expanded to approximately 1.3 to 1.5 times its settled bed height, the axial liquid-phase dispersion coefficient was found to be of the order 10(-5) m(2) s(-1), which falls into the range 1.0 x 10(-6) to 1.0 X 10(-5) m(2) s(-1) observed previously in protein purification. Because of the favorable column efficiency (low axial dispersion coefficient), the recovery yield and purification factor values of EH directly from a feedstock reached 86.5% and 18, respectively. The results suggest that EBA technology holds promise for the recovery of natural products and active components of Chinese herbal preparations.

Microfabries of lacustrine sediments to pollutant adsorption from a polluted Eutrophic lake, the Yangtze delta region

Two types of microfabrics relating to pollutant adsorption were studied in the scanning electronic microscope (SEM) in a polluted, eutrophic lake, the Yangtze delta region. Agglutinational texture or the aggregates of small particles are composed of clay minerals and fine organic fragments among the silty grains and the coatings with a thickness about 1 mu m were on the surfaces of the silty grains in the sediments. The chemical constituents of the aggregates and the coatings are K, Na, Ca, Mg, Si, Al, O, Fe, Ti, C, N and P determined in X-ray energy spectrometry connected with the SEM. In some cases, Pb was detected in the aggregates in the top sediment. It is suggested that nutrients and metals are adsorbed to the aggregates, which were formed by electrostatic attraction of physicochemical floes. The coatings on the surface of quartz grains were formed by the interaction of dissociated Al, Si, Fe, etc from silicates with dissolved N, P and C nutrients in interstitial water, which was aroused by human pollution to the lake in recent two decades.

Analysis of steric mass-action model for protein adsorption equilibrium onto porous anion-exchange adsorbent

The ion-exchange equilibrium of bovine serum albumin (BSA) to an anion exchanger, DEAE Spherodex M, has been studied by batch adsorption experiments at pH values ranging from 5.26 to 7.6 and ionic strengths from 10 to 117.1 mmol/l. Using the unadjustable adsorption equilibrium parameters obtained from batch experiments, the applicability of the steric mass-action (SMA) model was analyzed for describing protein ion-exchange equilibrium in different buffer systems. The parametric sensitivity analysis was performed by perturbing each of the model parameters, while holding the rest constant. The simulation results showed that, at high salt concentrations or low pHs close to the isoelectric point of the protein, the precision of the model prediction decreased. Parametric sensitivity analysis showed that the characteristic charge and protein steric factor had the largest effects on ion-exchange equilibrium, while the effect of equilibrium constant was about 70%-95% smaller than those of characteristic charge and steric factor under all conditions investigated. The SMA model with the relationship between the adjusted characteristic charge and the salt concentration can well predict the protein adsorption isotherms in a wide pH range from 5.84 to 7.6. It is considered that the SMA model could be further improved by taking into account the effect of salt concentration on the intermolecular interactions of proteins. (c) 2006 Elsevier Ltd. All rights reserved.

Biotransfer of persistent organic pollutants from a large site in China used for the disassembly of electronic and electrical waste

Samples of groundwater, river water, river sediment, paddy soil, rice seeds, hen eggs, fish, umbilical cord blood, and newborn meconium were collected from October 2002 to October 2003 near a large site in China used for the disassembly of obsolete transformers and other electronic or electrical waste. Six indicator PCB congeners, three non-ortho dioxin-like PCB congeners, and six organochlorine pesticides were determined in the samples by GC with electron capture detector. The results demonstrated that the local environment and edible foods had been seriously polluted by toxic PCBs and organochlorine pesticides. The actual daily intakes (ADIs) of these pollutants were estimated for local residents living in the area. The intake data showed that the contents of PCBs in these local residents were substantial, as the ADI estimates greatly exceed the reference doses set by the World Health Organization and the United States Agency for Toxic Substances and Disease Registry. The presence of the indicator PCB congeners in the cord blood and the meconium samples, as well as significant correlations (r(2) > 0.80, p < 0.05) between these levels, suggests a potential biotransfer of these indicators from mothers to their newborns. This preliminary study showed that obsolete transformers and other electronic or electrical waste can be an important source for the emission of persistent organic pollutants into the local environment, such as through leakage, evaporation, runoff, and leaching. Contamination from this source appears to have reached the level considered to be a serious threat to environmental and human health around the disassembly site.