一种四倍体鲤科鱼Sox基因的克隆和序列分析

为了研究重要功能基因在多倍体基因组中的演化情况,通过分子克隆的方法从四倍体大鳞结鱼(Tordouronensis)中获得13条Sox基因序列,分别为SoxB,SoxC和SoxE组成员.对大鳞结鱼Sox基因系统进化分析的结果支持鱼类特异的基因组重复的假说,同时表明,基因Sox19可能为真骨鱼特有的Sox基因家族成员.序列分析显示,与其他物种相比大鳞结鱼中Sox基因的碱基替代,绝大多数为同义替代.结果表明,所得到的Sox基因序列均受到净化选择,同时由多倍化所造成的重复基因对Sox4a,Sox9a和Sox9b受

Global civil aviation black carbon emissions.

Aircraft black carbon (BC) emissions contribute to climate forcing, but few estimates of BC emitted by aircraft at cruise exist. For the majority of aircraft engines the only BC-related measurement available is smoke number (SN)-a filter based optical method designed to measure near-ground plume visibility, not mass. While the first order approximation (FOA3) technique has been developed to estimate BC mass emissions normalized by fuel burn [EI(BC)] from SN, it is shown that it underestimates EI(BC) by >90% in 35% of directly measured cases (R(2) = -0.10). As there are no plans to measure BC emissions from all existing certified engines-which will be in service for several decades-it is necessary to estimate EI(BC) for existing aircraft on the ground and at cruise. An alternative method, called FOX, that is independent of the SN is developed to estimate BC emissions. Estimates of EI(BC) at ground level are significantly improved (R(2) = 0.68), whereas estimates at cruise are within 30% of measurements. Implementing this approach for global civil aviation estimated aircraft BC emissions are revised upward by a factor of ~3. Direct radiative forcing (RF) due to aviation BC emissions is estimated to be ~9.5 mW/m(2), equivalent to ~1/3 of the current RF due to aviation CO2 emissions.

Updated correlation between aircraft smoke number and black carbon concentration

Aircraft emissions of black carbon (BC) contribute to anthropogenic climate forcing and degrade air quality. The smoke number (SN) is the current regulatory measure of aircraft particulate matter emissions and quantifies exhaust plume visibility. Several correlations between SN and the exhaust mass concentration of BC (CBC) have been developed, based on measurements relevant to older aircraft engines. These form the basis of the current standard method used to estimate aircraft BC emissions (First Order Approximation version 3 [FOA3]) for the purposes of environmental impact analyses. In this study, BC with a geometric mean diameter (GMD) of 20, 30, and 60 nm and filter diameters of 19 and 35 mm are used to investigate the effect of particle size and sampling variability on SN measurements. For BC with 20 and 30 nm GMD, corresponding to BC emitted by modern aircraft engines, a smaller SN results from a given CBC than is the case for BC with 60 nm GMD, which is more typical of older engines. An updated correlation between CBC and SNthat accounts for typical size of BC emitted by modern aircraft is proposed. An uncertainty of ±25% accounts for variation in GMD in the range 20-30 nm and for the range of filter diameters. The SN-CBC correlation currently used in FOA3 underestimates by a factor of 2.5-3 for SN <15, implying that current estimates of aircraft BC emissions derived from SN are underestimated by the same factor. Copyright © American Association for Aerosol Research.

Sox genes evolution in closely related young tetraploid cyprinid fishes and their diploid relative

Previous study and analysis of cytochrome b suggested that polyploidization event in the genus Tor occurred about 10 Mya ago. In order to understand evolutionary fates of Sox gene in the early stage of genome duplication at the nucleotide level, PCR surveys for Sox genes in three closely related cyprinid fishes T douronensis (2n = 100), T qiaojiensis (2n = ?), T sinensis (2n = 100) and their relative T brevifilis (2n = 50) were performed. Totally, 52 distinct Sox genes were obtained in these four species, representing SoxB, SoxC, and SoxE group. As expected, isoforms of some Sox genes correspond with the ploidy of species, such as two copies of Sox9a exist in tetraploid species. Analysis indicated that duplicated Sox gene pairs caused by polyploidization evolved independently of each other within polyploid species. Results of substitution rate showed nearly equal rate of nonsynonymous substitution of duplicated Sox orthologs among different polyploid species and their diploid relative orthologs, suggesting at the early stage of genome duplicated Sox orthologs are under similar selective constraints in different polyploidy species and their diploid relative at the amino acid level. All PCR fragments of Sox genes obtained in this study are not accompanied by obvious increase in mutations and pseudogene formation which means that they are under strong purifying selection, suggesting that they are functional at the DNA level. Cenealogical analysis revealed that T qiaojiensis was tetraploid, and T douronensis, T qiaojiensis as well as T sinensis had an allotetraploid ancestor. (C) 2009 Elsevier B.V. All rights reserved.

Cloning and sequence analysis of Sox genes in a tetraploid cyprinid fish, Tor douronensis

A PCR survey for Sox genes in a young tetraploid fish Tor douronensis (Teleostei: Cyprinidae) was performed to access the evolutionary fates of important functional genes after genome duplication caused by polyploidization event. Totally 13 Sox genes were obtained in Tor douronensis, which represent SoxB, SoxC and SoxE groups. Phylogenetic analysis of Sox genes in Tor douronensis provided evidence for fish-specific genome duplication, and suggested that Sox19 might be a teleost specific Sox gene member. Sequence analysis revealed most of the nucleotide substitutions between duplicated copies of Sox genes caused by tetraploidization event or their orthologues in other species are silent substitutions. It would appear that the sequences are under purifying selective pressure, strongly suggesting that they represent functional genes and supporting selection against all null allele at either of two duplicated loci of Sox4a, Sox9a and Sox9b. Surprising variations of the intron length and similarities of two duplicated copies of Sox9a and Sox9b, suggest that Tor douronensis might be an allotetraploidy.

Dietary phosphorus requirement of juvenile black seabream, Sparus macrocephalus

A growth trial was conducted to estimate the optimum requirement of dietary available phosphorus (P) for black seabream (Sparus macrocephalus) in indoor net cages (1.5x1.0x1.0 m). Triplicate groups of black seabream (11.45 +/- 0.02 g) were fed diets containing graded levels (0.18, 0.36, 0.54, 0.72, 0.89 and 1.07%) of available P to satiation for 8 weeks. The basal diet (diet 1), containing 0.18% available P, was supplemented with graded levels of monosodium phosphate (NaH2PO4 2H(2)O) to formulate five experimental diets. The fish were fed twice daily (08:00 h and 16:00 h) and reared in seawater (salinity, 26-29 g l(-1)) at a temperature of 28 +/- 1 degrees C. Dissolved oxygen during the experiment was above 5 mg l(-1). The specific growth rate (SGR), weight gain (WG), feed efficiency (FE) and protein efficiency ratio (PER) were all significantly improved by dietary phosphorus up to 0.54% (P<0.05) and then leveled off beyond this level. Hepatosomatic index (HSI) was inversely correlated with dietary phosphorus levels (P< 0.05). Efficiency of P utilization stabled in fish fed diets containing 0.18%-0.54% available P and then decreased dramatically with further supplementation of dietary phosphorus. Body composition analysis showed that the whole-body lipid, ash, calcium and phosphorus contents were all significantly affected by dietary available P concentration (P<0.05), however, no significance were found in whole-body calcium/phosphorus (Ca/P) ratios among all the treatments (P>0.05). Dietary phosphorus levels also affected the mineralization of vertebrae, skin and scale (P<0.05). Ca/P ratios in vertebrae and scale were not influenced by dietary P supplementation, while skin Ca/P ratio increased statistically with dietary available P levels (quadratic effect, P<0.001). The blood chemistry analysis showed that dietary available P had distinct effects on enzyme activities of alkaline phosphatase (ALP) and plasma lysozyme (LSZ), as well as contents of triacyglycerol (TG) and total cholesterol (T-CHO) (P<0.05). Broken-line analysis showed maximum weight gain (WG) was obtained at dietary available P concentrations of 0.55%. Quadratic analysis based on P contents in whole fish, vertebrae or scale indicated that the requirements were 0.81, 0.87 and 0.88%, respectively. Signs of phosphorus deficiency were characterized by poor growth, slightly reduced mineralization and an increase in body lipid content. (C) 2008 Published by Elsevier B.V.

Sox genes in grass carp (Ctenopharyngodon idella) with their implications for genome duplication and evolution

The Sox gene family is found in a broad range of animal taxa and encodes important gene regulatory proteins involved in a variety of developmental processes. We have obtained clones representing the HMG boxes of twelve Sox genes from grass carp (Ctenopharyngodon idella), one of the four major domestic carps in China. The cloned Sox genes belong to group B1, B2 and C. Our analyses show that whereas the human genome contains a single copy of Sox4, Sox11 and Sox14, each of these genes has two co-orthologs in grass carp, and the duplication of Sox4 and Sox11 occurred before the divergence of grass carp and zebrafish, which support the "fish-specific whole-genome duplication" theory. An estimation for the origin of grass carp based on the molecular clock using Sox1, Sox3 and Sox11 genes as markers indicates that grass carp (subfamily Leuciscinae) and zebrafish (subfamily Danioninae) diverged approximately 60 million years ago. The potential uses of Sox genes as markers in revealing the evolutionary history of grass carp are discussed.

Influence of selected Indian immunostimulant herbs against white spot syndrome virus (WSSV) infection in black tiger shrimp, Penaeus monodon with reference to haematological, biochemical and immunological changes

Immunostimulants are the substances, which enhance the non-specific defence mechanism and provide resistance against the invading pathogenic micro-organism. In order to increase the immunity of shrimps against the WSSV, the methanolic extracts of five different herbal medicinal plants like Cyanodon dactylon, Aegle marmelos, Tinospora cordifolia, Picrorhiza kurooa and Eclipta alba were selected and mixed thoroughly in equal proportion. The mixed extract was supplemented with various concentrations viz. 100 (A), 200 (B), 400 (C), and 800 (D) mg kg(-1) through artificial diets individually. The prepared diets (A-D) were fed individually to WSSV free healthy shrimp Penaeus monodon with an average weight of 8.0 +/- 0.5 g for 25 days. Control diet (E), devoid of herbal extract was also fed to shrimps simultaneously. After 25 days of feeding experiment, the shrimps were challenged with WSSV, which were isolated and propagated from the infected crustaceans. The shrimps succumbed to death within 7 days when fed on no herbal immunostimulant diet (E). Among the different concentrations of herbal immunostimulant supplemented diets, the shrimps fed on diet D (800 mg kg(-1)) significantly (P < 0.0001) had more survival (74%) and reduction in the viral load. Also the better performance of haematological, biochemical and immunological parameters was found in the immunostimulant incorporated diets fed shrimps. The present work revealed that the application of herbal immunostimulants will be effective against shrimp viral pathogenesis and they can be recommended for shrimp culture. (c) 2006 Published by Elsevier Ltd.

Predictive entropy search for efficient global optimization of black-box functions

We propose a novel information-theoretic approach for Bayesian optimization called Predictive Entropy Search (PES). At each iteration, PES selects the next evaluation point that maximizes the expected information gained with respect to the global maximum. PES codifies this intractable acquisition function in terms of the expected reduction in the differential entropy of the predictive distribution. This reformulation allows PES to obtain approximations that are both more accurate and efficient than other alternatives such as Entropy Search (ES). Furthermore, PES can easily perform a fully Bayesian treatment of the model hyperparameters while ES cannot. We evaluate PES in both synthetic and real-world applications, including optimization problems in machine learning, finance, biotechnology, and robotics. We show that the increased accuracy of PES leads to significant gains in optimization performance.

Applications of factor-criteria system reconstruction analysis in the reproduction research on grass carp, black carp, silver carp and bighead in the Yangtze River

The natural reproduction of grass carp, black carp, silver carp, and bighead will be affected adversely by the Three Gorges Project in the Yangtze River. One of the methods to save the fish is to regulate the water levels, keeping them suited for the species to spawn. Nine factors associated with the scale of larvae-flood of the four species are classified into five levels, and the ranges of these factors producing larvae-floods are given by using the "factor-criteria system reconstruction analysis" method. Moderate beginning water levels and flow, with high daily increases in the rate of water level and flow, and a long duration of water level rising are important for the production of a large larvae-flood.