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.

Investigations into the perplexing interrelationship of the Genus Takifugu Abe, 1949 (Tetraodontiformes, Tetraodontidae)

The phylogenetic relationships within the genus Takifugu Abe, 1949 (Tetraodontiformes, Tetraodontidae) remain unresolved. Because of the use of Takifugu as model organisms, the resolution of these relationships is crucial for the interpretation of evolutionary trends in biology. Pufferfishes of this genus are comprised of a comparatively small number of species and are mainly distributed along the coastal region of the western part of the Sea of Japan and the coastline of China. Mitochondrial gene sequences were employed to test the phylogenetic hypotheses within the genus. Seventeen species of the genus were examined. Molecular phylogenetic trees were constructed using the maximum parsimony, neighbor-joining, maximum likelihood and Bayesian methods. Our hypothesis of internal relationships within the genus differs from previous hypotheses. Our results indicate that (1) the genus Takifugu is a monophyletic assemblage; (2) the genus is divided into 6 subgroups based on the molecular data; and (3) there is low genetic diversity among the species within this genus. In addition, speciation within Takifugu appears to be driven by hybridization and isolation by distribution. Our results also suggested that the taxonomy in the genus should be clarified based on both molecular and morphological data.

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.

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.