De novo RNA synthesis and homology modeling of the classical swine fever virus RNA polymerase

Classical swine fever virus (CSFV) non-structural protein 5B (NS5B) encodes an RNA-dependent RNA polymerase (RdRp), a key enzyme which initiates RNA replication by a de novo mechanism without a primer and is a potential target for anti-virus therapy. We expressed the NS5B protein in Escherichia coli. The rGTP can stimulate de novo initiation of RNA synthesis and mutation of the GDD motif to Gly-Asp-Asp (GAA) abolishes the RNA synthesis. To better understand the mechanism of viral RNA synthesis in CSFV, a three-dimensional model was built by homology modeling based on the alignment with several virus RdRps. The model contains 605 residues folded in the characteristic fingers, palm and thumb domains. The fingers domain contains an N-terminal region that plays an important role in conformational change. We propose that the experimentally observed promotion of polymerase efficiency by rGTP is probably due to the conformational changes of the polymerase caused by binding the rGTP. Mutation of the GDD to GAA interferes with the interaction between the residues at the polymerase active site and metal ions, and thus renders the polymerase inactive. (c) 2005 Elsevier B.V. All rights reserved.

Efficient RNA interference in zebrafish embryos using siRNA synthesized with SP6 RNA polymerase

Double-stranded RNA (dsRNA) has been shown to be a useful tool for silencing genes in zebrafish (Danio rerio), while the blocking specificity of dsRNA is still of major concern for application. It was reported that siRNA (small interfering RNA) prepared by endoribonuclease digestion (esiRNA) could efficiently silence endogenous gene expression in mammalian embryos. To test whether esiRNA could work in zebrafish, we utilized Escherichia coli RNaseIII to digest dsRNA of zebrafish no tail (ntl), a mesoderm determinant in zebrafish and found that esi-ntl could lead to developmental defects, however, the effective dose was so close to the toxic dose that esi-ntl often led to non-specific developmental defects. Consequently, we utilized SP6 RNA polymerase to produce si-ntl, siRNA designed against ntl, by in vitro transcription. By injecting in vitro synthesized si-ntl into zebrafish zygotes, we obtained specific phenocopies of reported mutants of ntl. We achieved up to a 59%no tail phenotype when the injection concentration was as high as 4 mu g/mu L. Quantitative reverse transcription-polymerase chain reaction (RT-PCR) and whole-mount in situ hybridization analysis showed that si-ntl could largely and specifically reduce mRNA levels of the ntl gene. As a result, our data indicate that esiRNA is unable to cause specific developmental defects in zebrafish, while siRNA should be an alternative for downregulation of specific gene expression in zebrafish in cases where RNAi techniques are applied to zebrafish reverse genetics.

Differential expression of vasa RNA and protein during spermatogenesis and oogenesis in the gibel carp (Carassius auratus gibelio), a bisexually and gynogenetically reproducing vertebrate

The RNA helicase Vasa is a germ cell marker in animals, and its homolog in vertebrates to date has been limited to bisexual reproduction. We cloned and characterized CagVasa, a Vasa homolog from the gibel carp, a fish that reproduces bisexually or gynogenetically. CagVasa possesses 14 RGG repeats and eight conserved motifs of Vasa proteins. In bisexually reproducing gibel carp, vasa is maternally supplied and its zygotic expression is restricted to gonads. By in situ hybridization on testicular sections, vasa is low in spermatogonia, high in primary spermatocytes, reduced in secondary spermatocytes, but disappears in spermatids and sperm. In contrast, vasa persists throughout oogenesis, displaying low-high-low levels from oogonia over vitellogenic oocytes to maturing oocytes. A rabbit anti-Vasa antibody (alpha Vasa) was raised against the N-terminal CagVasa for fluorescent immunohistochemistry. On testicular sections, Vasa is the highest in spermatogonia, reduced in spermatocytes, low in spermatids, and absent in sperm. In the ovary, Vasa is the highest in oogonia but persists throughout oogenesis. Subcellular localization of vasa and its protein changes dynamically during oogenesis. The aVasa stains putative primordial germ cells in gibel carp fry. It detects gonadal germ cells also in several other teleosts. Therefore, Cagvasa encodes a Vasa ortholog that is differentially expressed in the testis and ovary. Interestingly, the alpha Vasa in combination with a nuclear dye can differentiate critical stages of spermatogenesis and oogenesis in fish. The cross-reactivity and the ability to stain stage-specific germ cells make this antibody a useful tool to identify fish germ cell development and differentiation. (c) 2005 Wiley-Liss, Inc.

Species richness in a riparian plant community along the banks of the Xiangxi River, the Three Gorges region

The distribution of vascular plant species richness along an altitudinal gradient and their relationships with environmental variables, including slope, aspect, bank (flooding) height, and river width of the Xiangxi River, Hubei Province, were examined. Total vascular plant species richness changed with elevation: it increased at lower elevations, reached a maximum in the midreaches and decreased thereafter. In particular, tree and herbaceous species richness were related to altitude. Correlation analysis (Kendall's tau) between species richness and environmental variables indicated that the change in species richness in the riparian zone was determined by riparian environmental factors and characteristics of regional vegetation distribution along the altitudinal gradient. The low species richness at lower elevations resulted from seasonal flooding and human activities - agriculture and fuel collection - and the higher. Species richness ill (he midreaches reflected transitional zones ill natural vegetation types that had had little disturbance. These results oil species distribution in the riparian community could he utilized as a reference for restoration efforts to improve water quality of the emerging reservoir resulting from the Three Gorges Hydroelectric Dam project.

Biomarker responses and reproductive toxicity of the effluent from a Chinese large sewage treatment plant in Japanese medaka (Oryzias latipes)

The present study was conducted to assess the potential toxicity of the effluent from a large sewage treatment plant (GBD-STP) in Beijing. Japanese medakas (Oryzias latipes) at reproduction active period were exposed to a serial of graded concentrations of the effluent or 100 ng l(-1) of 17-alpha-ethinylestradiol (EE2, positive control). Growth, gonadosomatic index (GSI), hepatosomatic index (HSI), reproductive success, induction potency of vitellogenin (VTG) in male fish and that of 7-ethoxyresorufin-o-deethylase activity (EROD) in male fish liver were used as test endpoints. The growth suppression of fish was observed in a dose-dependent manner, resulting in significant differences in both body length and body weight of medaka above 5% effluent. This effluent can inhibit the growth of gonad of medakas and are more sensitive to male than to female. At exposure concentration of 40% and higher, there was an unexpected decrease of HSI values, which may be resulted from sub-lethal toxicity of effluent to fish liver. VTG of plasma in males were induced in all exposure concentration levels, but not in a dose-dependent manner. The concentration of 5% effluent would be the lowest observed adverse effect level (LOAEL) affecting reproductive success when examining fertile individuals, fecundity and fertilization rate. The overt CYP1A response and higher reproductive toxicity may be indicative of low process efficiency of this STP. (c) 2004 Elsevier Ltd. All rights reserved.

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.

The molecular characterization of RNA segment S9 of grass carp hemorrhage virus (GCHV), an aquareovirus

Although reovirus infection is one of the major virus diseases of grass carp in China, the available knowledge on the structure and function of genes and proteins of the virus is limited. The complete sequence of the S9 genome segment of grass carp hemorrhage virus (GCHV) was determined. The segment consists of 1130 nucleotides and has a large open reading frame (ORF) encoding a protein of 352 amino acids with predicted molecular mass of 37.7 kDa. Amino acid sequence comparison revealed that the deduced protein encoded by GCHV S9 is closely related to the sigma NS proteins of mammalian reovirus (MRV) and avian reovirus (ARV). Secondary structure analysis displayed that the form of alpha -helices (40.1%) and beta -sheets (49.4%) are the richest two contents in the protein encoded by S9, and this protein is predicted to be a nonstructural protein. (C) 2001 Elsevier Science B.V. All rights reserved.

Effects of the stocking density and body size of the mitten crab (Eriocheir sinensis) on aquatic plant biomass

Experiments in tanks and cages were conducted to examine the effects of stocking density and body size of the Mitten crab (Eriocheir sinensis) on transplanted submersed macrophyte biomass. The early juvenile crab with 7.0 +/-0.6 mm. carapace width (CW) had little effect on plant biomass, regardless of the stocking densities. However, larger crabs (CW: 18.0 +/-2.2,35.0 +/-3.6, and 60.0 +/-5.7 mm) significantly influenced plant biomass, especially at large stocking densities. Predictive models, using crab body size and stocking density, were generated to demonstrate effect of the mitten crab on the changes Of plant biomass. The results indicate that dense mitten crab populations may adversely affect aquatic plant communities, particularly when its animal food resources are scarce.

Utilization of several plant proteins by gibel carp (Carassius auratus gibelio)

Six isonitrogenous (gross protein content 35%) and isoenergetic (gross energy content 17 kJ g(-1)) diets were formulated to investigate the effects of inclusion of plant proteins on the gibel carp (Carassius auratus gibelio L.). The plant proteins tested were: soybean cake (SBC), potato protein concentrate (PPC), peanut cake (PNC), cottonseed cake (CSC) and rapeseed cake (RSC). Fish meal (FM) was used as control. In each diet, 27% of the protein was supplied by fish meal, and the rest supplied by the plant protein tested. Each diet was fed to three groups of gibel carp for 8 weeks in a recirculation system. Specific growth rate (SGR) in fish fed the control diet was significantly higher than those in the other groups, and SGR in fish fed the PPC was significantly lower than in fish fed other plant proteins. There was no significant difference in SGR among the other groups. Feeding rates were ranked in the order: RSC > CSC > FM > PNC > SBC > PPC. Conversion efficiency was highest in groups fed FM, SBC and PNC, followed by groups fed CSC and RSC, and was lowest in the group fed PPC. The fish fed PPC showed lower protein retention than those fed FM and SBC. FM showed highest energy retention while PPC showed lowest, There was no significant relationship between SGR and intake of digestible protein (g g(-1) day(-1)), digestible lysine (g g(-1) day(-1)), digestible methionine (g g(-1) day(-1)) or digestible total essential amino acids (g g(-1) day(-1)), suggesting that the differences in SGR could not alone account for any of these variables.

PURIFICATION AND CHARACTERIZATION OF A KINASE SPECIFIC FOR THE SERINE-RICH AND ARGININE-RICH PRE-MESSENGER-RNA SPLICING FACTORS

Members of the SR family of pre-mRNA splicing factors are phosphoproteins that share a phosphoepitope specifically recognized by monoclonal antibody (mAb) 104. Recent studies have indicated that phosphorylation may regulate the activity and the intracellular localization of these splicing factors. Here, we report the purification and kinetic properties of SR protein kinase 1 (SRPK1), a kinase specific for SR family members. We demonstrate that the kinase specifically recognizes the SR domain, which contains serine/arginine repeats. Previous studies have shown that dephosphorylated SR proteins did not react with mAb 104 and migrated faster in SDS gels than SR proteins from mammalian cells. We show that SRPK1 restores both mobility and mAB 104 reactivity to a SR protein SF2/ASF (splicing factor 2/alternative splicing factor) produced in bacteria, suggesting that SRPK1 is responsible for the generation of the mAb 104-specific phosphoepitope in vivo. Finally, we have correlated the effects of mutagenesis in the SR domain of SF2/ASF on splicing with those on phosphorylation of the protein by SRPK1, suggesting that phosphorylation of SR proteins is required for splicing.

Determining of the delay time for a heating ventilating and air-conditioning plant using two weighted neural network approach

This paper presents an two weighted neural network approach to determine the delay time for a heating, ventilating and air-conditioning (HVAC) plan to respond to control actions. The two weighted neural network is a fully connected four-layer network. An acceleration technique was used to improve the General Delta Rule for the learning process. Experimental data for heating and cooling modes were used with both the two weighted neural network and a traditional mathematical method to determine the delay time. The results show that two weighted neural networks can be used effectively determining the delay time for AVAC systems.

Determining of the delay time for a heating ventilating and air-conditioning plant using multi-weights neurons approach

This paper presents an multi weights neurons approach to determine the delay time for a Heating ventilating and air-conditioning (HVAC) plan to respond to control actions. The multi weights neurons is a fully connected four-layer network. An acceleration technique was used to improve the general delta rule for the learning process. Experimental data for heating and cooling modes were used with both the multi weights neurons and a traditional mathematical method to determine the delay time. The results show that multi weights neurons can be used effectively determining the delay time for HVAC systems.