Genome-wide identification and characterization of cytochrome P450 monooxygenase genes in the ciliate Tetrahymena thermophila

Background: Cytochrome P450 monooxygenases play key roles in the metabolism of a wide variety of substrates and they are closely associated with endocellular physiological processes or detoxification metabolism under environmental exposure. To date, however, none has been systematically characterized in the phylum Ciliophora. T. thermophila possess many advantages as a eukaryotic model organism and it exhibits rapid and sensitive responses to xenobiotics, making it an ideal model system to study the evolutionary and functional diversity of the P450 monooxygenase gene family. Results: A total of 44 putative functional cytochrome P450 genes were identified and could be classified into 13 families and 21 sub-families according to standard nomenclature. The characteristics of both the conserved intron-exon organization and scaffold localization of tandem repeats within each P450 family clade suggested that the enlargement of T. thermophila P450 families probably resulted from recent separate small duplication events. Gene expression patterns of all T. thermophila P450s during three important cell physiological stages (vegetative growth, starvation and conjugation) were analyzed based on EST and microarray data, and three main categories of expression patterns were postulated. Evolutionary analysis including codon usage preference, sit-especific selection and gene-expression evolution patterns were investigated and the results indicated remarkable divergences among the T. thermophila P450 genes. Conclusion: The characterization, expression and evolutionary analysis of T. thermophila P450 monooxygenase genes in the current study provides useful information for understanding the characteristics and diversities of the P450 genes in the Ciliophora, and provides the baseline for functional analyses of individual P450 isoforms in this model ciliate species.

Identification of differentially expressed genes in Tetrahmena thermophila in response to dichlorodiphenyltrichloroethane (DDT) by suppression subtractive hybridization

The insecticide dichlorodiphenyltrichloroethane (DDT) is persistent in the environment, and continues to cause health problems. Tetrahymena has potential as a model organism for assaying low levels of DDT and for analysing the mechanisms of its toxicity. We constructed the suppression subtractive hybridization library of T thermophila exposed to DDT, and screened out 90 Expressed Sequence Tags whose expressions were significantly up- or downregulated with DDT treatment. From this, a series of important genes related to the DDT metabolism and detoxification were discovered, such as P450 gene, glutathione S-transferase gene and sterol carrier protein 2 gene. Furthermore, their expressions under different concentrations of DDT treatment were detected by real-time fluorescent quantitative PCR. The results show that Tetrahymena is a relevant and useful model organism for detecting DDT in the environment and for discovering biomarkers that can be used to develop specific bio-reporters at the molecular and genomic levels.

Advances in phylogenetic studies of Nematoda

Nematoda is a metazoan group with extremely high diversity only next to Insecta. Caenorhabditis elegans is now a favorable experimental model animal in modern developmental biology, genetics and genomics; studies. However, the phylogeny of Nematoda and the phylogenetic position of the phylum within animal kingdom have long been in debate. Recent molecular phylogenetic studies gave great challenges to the traditional nematode classification. The new phylogenies not only placed the Nematoda in the Ecdysozoan and divided the phylum into five clades, but also provided new insights into animal molecular identification and phylogenetic biodiversity studies. The present paper reviews major progress and remaining problems in the current molecular phylogenetic studies of Nematoda, and prospects the developmental tendencies of this field.

A SERINE KINASE REGULATES INTRACELLULAR-LOCALIZATION OF SPLICING FACTORS IN THE CELL CYCLE

Small nuclear ribonucleoprotein particles (snRNPs) and non-snRNP splicing factors containing a serine/arginine-rich domain (SR proteins) concentrate in 'speckles' in the nucleus of interphase cells(1). It is believed that nuclear speckles act as storage sites for splicing factors while splicing occurs on nascent transcripts(2). Splicing factors redistribute in response to transcription inhibition(3,4) or viral infection(5), and nuclear speckles break down and reform as cells progress through mitosis(6). We have now identified and cloned a kinase, SRPK1, which is regulated by the cell cycle and is specific for SR proteins; this kinase is related to a Caenorhabditis elegans kinase and to the fission yeast kinase Dsk1 (ref. 7). SRPK1 specifically induces the disassembly of nuclear speckles, and a high level of SRPK1 inhibits splicing in vitro. Our results indicate that SRPK1 mag have a central role in the regulatory network for splicing, controlling the intranuclear distribution of splicing factors in interphase cells, and the reorganization of nuclear speckles during mitosis.

Copper complexation by fulvic acid affects copper toxicity to the larvae of the polychaete Hydroides elegans

Copper toxicity is influenced by a variety of environmental factors including dissolved organic matter (DOM). We examined the complexation of copper by fulvic acid (FA), one of the major components of DOM, by measuring the decline in labile copper by anodic stripping voltammetrically (ASV). The data were described using a one-site ligand binding model, with a ligand concentration of 0.19 mu mol site mg(-1) C, and a logK' of 6.2. The model was used to predict labile copper concentration in a bioassay designed to quantify the extent to which Cu-FA complexation affected copper toxicity to the larvae of marine polychaete Hydroides elegans. The toxicity data, when expressed as labile copper concentration causing abnormal development, were independent of FA concentration and could be modeled as a logistic function, with a 48-h EC50 of 58.9 mu g 1(-1). However, when the data were expressed as a function of total copper concentration, the toxicity was dependent on FA concentration, with a 48-h EC50 ranging from 55.6 mu g 1(-1) in the no-FA control to 137.4 mu g 1(-1) in the 20 mg 1(-1) FA treatment. Thus, FA was protective against copper toxicity to the larvae, and such an effect was caused by the reduction in labile copper due to Cu-FA complexation. Our results demonstrate the potential of ASV as a useful tool for predicting metal toxicity to the larvae in coastal environment where DOM plays an important role in complexing metal ions. (c) 2007 Elsevier Ltd. All rights reserved.

Effects of exogenous double-stranded RNA on the basonuclin gene expression in mouse oocytes

In plants and less-advanced animal species, such as C.elegans, introduction of exogenous double-stranded RNA (dsRNA) into cells would trigger degradation of the mRNA with homologous sequence and interfere with the endogenous gene expression. It might represent an ancient anti-virus response which could prevent the mutation in the genome that was caused by virus infection or mobile DNA elements insertion. This phenomenon was named RNA interference, or RNAi. In this study, RNAi was used to investigate the function of basonuclin gene during oogenesis. Microinjection of dsRNA directed towards basonuclin into mouse germinal-vesicle-intact (GV) oocytes brought down the abundance of the cognate mRNA effectively in a time- and concentration-dependent manner. This reduction effect was sequence-specific and showed no negative effect on other non-homologous gene expression in oocytes, which indicated that dsRNA can recognize and cause the degradation of the transcriptional products of endogenous basonuclin gene in a sequence-specific manner. Immunofluorescence results showed that RNAi could reduce the concentration of basonuclin protein to some extent, but the effect was less efficient than the dsRNA targeting towards tPA and cMos which was also expressed in oocytes. This result might be due to the long half life of basonuclin protein in oocytes and the short reaction time which was posed by the limited life span of GV oocytes cultured in vitro. In summary, dsRNA could inhibit the expression of the cognate gene in oocytes at both mRNA and protein levels. The effect was similar to Knock-out technique which was based on homologous recombination. Furthermore, hairpin-style dsRNA targeting basonuclin gene could be produced by transcription from a recombinant plasmid and worked efficiently to deplete the cognate mRNA in oocytes. This finding offered a new way to study the function of basonuclin in the early stage of oogenesis by infection of primordial oocytes with the plasmid expressing hairpin-style basonuclin dsRNA.

三峡库区藻类水华调查及其毒理学研究

三峡水库一期工程蓄水近两年(2003年7月—2005年4月)期间,库区发生过多次藻类“水华”,尤其在阳光充足、气温回升的春季。经鉴定形成水华的藻类主要有拟多甲藻(Peridiniopsissp1,sp2),新星形冠盘藻(Stephanodiscusneoastraea),里海小环藻(Cyclotella caspia),湖沼红胞藻(Rhodomonas lacustris),实球藻(Pandorina morum)和空球藻(Eudorina elegans);其中以拟多甲藻水华涉及面积最大,持续时间最久,

秀丽锦龟——一种名贵的观赏龟

<正> 秀丽锦龟(Chr ysemys elegans)又称“红耳龟”,其原产地是南美洲的巴西,所以俗称巴西龟、巴西绿龟。由于其颜色非常艳丽,使它成为观赏龟中的姣姣者,过去在中、南美洲各地普遍饲养,作为一种动物宠物,被运往欧亚各国。作者在加拿大、美国的一些水族商店里都见到有此龟出售,价格昂贵。据记载秀丽锦龟于1987年从香港引入我国,运到上海、广州、南宁等大中城市销售。作者从上海花鸟市场购得数只,进行观察和饲养。秀丽锦龟的头部宽大,略像大头乌龟。

Identification of one intron loss and phylogenetic evolution of Dfak gene in the Drosophila melanogaster species group

Intron loss and its evolutionary significance have been noted in Drosophila. The current study provides another example of intron loss within a single-copy Dfak gene in Drosophila. By using polymerase chain reaction (PCR), we amplified about 1.3 kb fragment spanning intron 5-10, located in the position of Tyr kinase (TyK) domain of Dfak gene from Drosophila melanogaster species group, and observed size difference among the amplified DNA fragments from different species. Further sequencing analysis revealed that D. melanogaster and D. simulans deleted an about 60 bp of DNA fragment relative to other 7 Drosophila species, such as D. elegans, D. ficusphila, D. biarmipes, D. takahashii, D. jambulina, D. prostipennis and D. pseudoobscura, and the deleted fragment located precisely in the position of one intron. The data suggested that intron loss might have occurred in the Dfak gene evolutionary process of D. melanogaster and D. simulans of Drosophila melanogaster species group. In addition, the constructed phylogenetic tree based on the Dfak TyK domains clearly revealed the evolutionary relationships between subgroups of Drosophila melanogaster species group, and the intron loss identified from D. melanogaster and D. simulans provides a unique diagnostic tool for taxonomic classification of the melanogaster subgroup from other group of genus Drosophila.

Testate amoebae (Protozoa : Rhizopoda) from northwest Yunnan, China

A survey of the testate amoebae of northwest Yunnan in the Hengduan Mountains region of southwest China revealed 151 species belonging to 29 genera. Of these, three genera and 27 species were new to the testate amoebae fauna of China. The widely distributed and dominant species were Centropyxis aculeata aculeata, C aerophila aerophila, C. sylvatica, Difflugia elegans, D. globulosa, D. pristis, D. pulex, Phryganella hemisphaerica, Trinema enchelys, and T lineare. The most diverse genera were Difflugia (41 species), Centropyxis (31 species), Arcella (18 species), and Euglypha (11 species). The number of species in each sample varied greatly. It appears that species diversity of testate amoebae is related not only to macro-environments (e.g., geographic zonation) but also to microenvironments (e.g., microhabitats).

Morphology, biometry and distribution of Difflugia biwae Kawamura, 1918 (Protozoa : Rhizopoda)

The freshwater testate amoeba Difflugia biwae Kawamura, 1918, isolated from Mulan Lake, Hubei Province, China is investigated using light microscopy and scanning electron microscopy. The morphology, biometry and distribution of this little known species are supplied. After careful comparison with three other similar species, including D. delicatula Gauthier-Livre et Thomas, D. elegans Penard and D. oblonga caudata Stepanek, we believe that the characteristics of smooth fusiform shell, conspicuous great collar flare (always larger than body-width) around the aperture, constriction behind the aperture and a somewhat curved aboral horn set D. biwae apart from all other Difflugia species. This species shows a great diversity in total length, collar height and aboral horn length which have high variability (CV between 11.76 and 24.52). However, body width, collar diameter, neck width, body length and aperture diameter are fairly constant with low variability (CV between 5.34 and 8.79) which shows a remarkable uniformity of D. biwae. Also, the size frequency distributions of both body width and body length yield bell-shaped (normally distributed) curves and indicate that D. biwae is a size-monomorphic species, characterized by a main-size class and a small size range. D. biwae is probably endemic to East Asia (China and Japan) because it has such a large size (165-306 mu m) that it would have been easily found in Europe and North America, if it were there. Consequently, D. biwae must have a restricted geographical distribution, disproving the old hypothesis that microscopic organisms are cosmopolitan.

A conserved family of doublesex-related genes from fishes

The sex-determining gene Mab-3 of C. elegans and the doublesex gene of Drosophila each contain a common DM domain and share a similar role. Human doublesex-related gene DMRT1 also encodes a conserved DM-related DNA-binding domain. We present here the amplification of a broad range of DM domain sequences from three fish species using degenerate PCR. Our results reveal unexpected complexity of the DM domain gene family in vertebrates. (C) 2002 Wiley-Liss, Inc.

九寨沟核心景区湖泊硅藻的组成及其密度与环境因子的关系

九寨沟自然保护区地处四川盆地北部岷山山脉南段，属川西高原气候中的暖温带。保护区内分布着118 个串珠状排列的高山湖泊，核心景区共有湖泊20 个（组），集中在海拔2000 米到3000 米之间。水资源是九寨沟的灵魂，保护水生生态系统是九寨沟生态旅游可持续发展的立足之本。本研究以九寨沟湿地生物多样性保护项目为依托，于2007 年5 月～2008 年4 月对九寨沟核心景区湖泊水体硅藻植物进行调查，分析了其密度与环境因子的相互关系，旨在为九寨沟湖泊生态系统保护提供科学依据和基础资料。主要有以下几点结论： （1）九寨沟硅藻植物丰富，调查统计为2 纲6 目10 科35 属159 种（包括变种和变型），水体硅藻中真性浮游种类较少，着生种类多，羽纹纲的脆杆藻属、舟形藻属、桥弯藻属、异极藻属、曲壳藻属的种类最多，常为优势属组成湖泊硅藻群落，只在长海是小环藻属占绝对优势。 （2）九寨沟水体中硅藻细胞密度不大，多在4×104～30×104 个/L，长海最高，五花海最低。在年变化上，不同的湖泊水体中硅藻的生长高峰季节不尽相同，在夏季、秋末和冬末春初均有可能出现高密度。在空间上，整体看来密度与海拔有一定的正相关，但由于水温不是单一主导因素，密度受多种环境因子影响，在海拔梯度上呈现一定的波浪状变化。 （3）影响九寨沟湖泊水体硅藻细胞密度较重要的环境因子是海拔、水温和pH。硅藻细胞密度年变化幅度大的湖泊水体，年平均细胞密度大。因此，环境因素不太稳定的湖泊水体，更可能出现高的硅藻细胞密度。11 月份响应于水量剧烈的减少，细齿菱形藻大量出现在五彩池成为优势种群，造成水体硅藻细胞密度的大幅增加。 （4）九寨沟湖泊水体水质几乎达到国家地表水I 类标准，但是，硅藻商指数以及代表多样性的Cairns 指数计算的结果不能反映水质的情况，这是由于水质状况不是决定九寨沟湖泊水体中硅藻生存的种类和数量的主要因素。因此在用各种指数分析水质的时候，都应该先判断计算该指数的参数是否主要由水质状况决定，然后再综合理化性质等其他指标分析和比较。 （5）人类的活动对九寨沟湖泊水生态系统有一定的影响。一方面，在低海拔景点人类活动的干扰比海拔高处相对要大，干扰引起低海拔景点湖泊硅藻Cairns指数较高；另一方面，旺季的影响比淡季大，水体中出现了典型富营养种类。因此，应加强低海拔景点和旺季的管理，并限制淡季的人类活动以保证九寨沟生态系统的自我恢复。 Jiuzhaigou nature reserve is located in north Sichuan, at the south section of Minshan Mountain, having a warm temperate climate which belongs to West Sichuan plateau climate. It includes 118 mountain lakes, and 20 of them between 2000 and 3000 altitude degree constitute the core area of Jiuzhaigou. The water is Jiuzhaigou's soul, so it is the basis of sustainable tourism development of Jiuzhaigou to protect the water ecological environment. Research depends on Jiuzhaigou wetland biodiversity protection program in this paper, invested the diatom plants in 17 lakes at the core area from May 2007 to April 2008. The composition and the correlation of diatom density and the environment were studied, which could provide scientific and basic information for the protection of the ecological environment of Jiuzhaigou. The main conclusions were: 1 The diatom species were in abundance, investigation showed that there were 159 species belong to 10 families and 35 genera. Most diatoms were benthos, euplankton were less. Genera Fragilaria, Navicula, Cymbella, Gomphonema and Achnanthes had the most species, which always were the dominant genera. Only in The Long Lake genus Cyclotella possessed a predominant status. 2 The diatom cell density was not very high, always between 4×104 cell/L and 30×104 cell/L, highest in The Long Lake and lowest in The Colorful Lake. In one year's time, diatom in different lakes had different growth type. The maximum could be in summer, late autumn and late winter early spring. The cell density showed a positive correlation to altitude in the whole, but fluctuated in details along altitude because of comprehensive influence by many environmental factors. 3 Altitude, water temperature and pH were the more important factors to determine the cell density. There was a positive correlation between the range of cell density in one year and the average cell density. So high annual cell average density probably will appear in lakes which has an unstable environmental condition. The boom of Denticula elegans in The Jade-Colored Lake in November was corresponding to the large decrease in water quantity. 4 The water quality of Jiuzhaigou was near the National Surface Water Standard rank I, but the Diatom Quotient and the Cairns Index didn't reflect the water quality accordingly. It was because the water quality wasn't the most important factor here which determined the species number and species quantity, so the index based on these items would not reflect it. Therefore, it is recommended that, when we use indices to evaluate the water quality, we should know first whether the water quality is the main determinative factor inflects the items used to compute the indices, and then combined with other chemical indices to analyze and do comparison. 5 The tourists' activities had influenced the water ecosystem of Jiuzhaigou. On the one hand, disturbance was relatively high at the lower altitude, it resulted in higher Cairns index; on the other hand, influence in high season was more severe than in low season, some typical species indicating eutrophication were observed in the water. It is suggested that the management at lower altitude and in high season must be strengthen, and less people activity in low season is necessary to fulfill the recovery of the water ecosystem.

Knockdown and overexpression of Unc-45b result in defective myofibril organization in skeletal muscles of zebrafish embryos

We thank John Stubblefield for editing, Junling Li for the assistance in the Western blot analysis. This research was supported by a training grant from National Institutes of Health (#T32 AR07592) and a research grant MB-8713-08 from United States - Israel Binational Agriculture Research and Development Fund.

Novel antifouling and antimicrobial compound from a marine-derived fungus Ampelomyces sp.

In this study, using a bioassay-guided isolation and purification procedure, we obtained 3-chloro-2,5-dihydroxybenzyl alcohol from a marine-derived Ampelomyces species that effectively inhibited larval settlement of the tubeworm Hydroides elegans and of cyprids of the barnacle Balanus amphitrite. The inhibitive effect on larval settlement was nontoxic and the EC50 of 3-chloro-2,5-dihydroxybenzyl alcohol ranged from 3.19 mu g ml(-1) to 3.81 mu g ml(-1) while the LC50 was 266.68 lambda g ml(-1) for B. amphitrite cyprids; EC50 ranged from 0.67 mu g ml(-1) to 0.78 mu g ml(-1), and LC50 was 2.64 mu g ml(-1) for competent larvae of H. elegans, indicating that inhibitive effect of this compound was nontoxic. At a concentration of 50 mu g per disc, this compound showed strong inhibitive effects on the growth of 13 out of 15 marine bacterial species tested in disc diffusion bioassay. Overall, the high inhibitory activities against bacteria and larval settlement as well as the non- or low-toxic nature of this compound to the barnacle and polychaete larvae suggest this compound could be a potent antifoulant and/or antibiotic.