细胞色素b基因序列变异与东亚鲿科鱼类系统发育

采用PCR技术获得了中国鲿科鱼类线粒体DNA细胞色素b基因1138bp全序列.所得序列与GenBank中分布于日本、韩国和俄罗斯的鲿科2属9种鱼类同一基因序列排序,并选用鲇形目鲇科的大口鲇、钝头鮠科的鳗尾缺和伦氏(鱼央)以及脂鲤目的断线脂鲤作外类群.分析了细胞色素b基因序列,计算了Kimura双因子遗传距离和鲿科鱼类线粒体DNA的进化速率,用最大简约法和邻接法构建了鲿科鱼类分子系统树,得出如下结论:(1)线粒体DNA序列分析显示所测定的鲇形目鱼类细胞色素b基因序列中,存在3bp的缺失;(2)系统发育分析显

江汉平原农田生态系统B素循环及平衡分析

以江汉平原农田生态系统为研究对象 ,通过对当地农户小麦 -稻、稻 -稻、油菜 -大豆、油菜 -花生、小麦 -芝麻、小麦 -棉花、青椒 -大白菜、萝卜 -茄子 8种种植模式农田 B素的输入、输出和平衡研究。结果表明 ,B素的输出主要是作物收获 ,占 B素总输出量的 4 4.8%～ 6 4 .7% ;其次是淋溶损失占 2 5 %～ 4 1 .4 % ,B素流失占总输出量的 9.2 %～ 1 7.4 %。B素的主要输入途径是施有机肥和 B肥 ,此外 ,降雨也是 B素输入的主要途径 ,该区域各种类型农田生态系统

东亚低等鲤科鱼类细胞色素b基因序列测定及系统发育

采用PCR技术获得了14种主要分布于东亚的低等鲤科鱼类细胞色素b基因的全序列. 所得1 140 bp细胞色素b基因序列与10种取自GenBank, 分布在北美和欧洲的相关鲤科鱼类的同一基因序列一起排序后, 得到了24种鲤科鱼类的DNA序列矩阵. 此矩阵经过最大似然(maximum likelihood)法计算后获得了低等鲤科及相关种类的系统发育分支图解. 分支系统图显示鲤科的雅罗鱼亚科和亚科鱼类并不形成单系类群. 亚科鱼类中的马口鱼、等是原始的鲤科鱼类, 处于分支图的基部. 而其余的亚科鱼类则分散

PRELIMINARY STUDY ON MITOCHONDRIAL CYTOCHROME b DNA SEQUENCES AND PHYLOGENY OF FORMALIN FIXED SISORID FISHES(Teleostei: Siluriformes)

从９种科鱼类的福尔马林标本中获得了３３３ｂｐ的细胞色素ｂ基因片段的序列。这９个种分别代表科鱼类的８个属。３３３ｂｐ的ＤＮＡ序列经ＭＵＳＴ软件排序后，有１０１个变异位点，其中有３９个信息位点。序列在成对物种间的距离为８～４８。平均遗传距离为２４％～１４４％。简约分析产生了最大简约系统树，其步长是１６２（ＣＩ＝０７３５，ＲＩ＝０４９４）。在该系统树上，Ｂａｇａｒｉｕｓ是最原始的属，并与所有其他的物种形成姊妹群。其余８个属形成一个单系类群并分为二个姊妹群。尽管在形态上具有１３个离征，但在分子系统树上

福尔马林固定云南鲴的DNA提取及其细胞色素b基因序列分析

福尔马林固定云南鲴的ＤＮＡ提取及其细胞色素ｂ基因序列分析ＤＮＡＥＸＴＲＡＣＴＥＤＦＲＯＭＦＯＲＭＡＬＩＮ－ＦＩＸＥＤＸｅｎｏｃｙｐｒｉｓｙｕｎｎａｎｅｎｓｉｓＡＮＤＳＥＱＵＥＮＣＥＡＮＡＬＹＳＩＳＯＦＩＴＳＣＹＴＯＣＨＲＯＭＥＢＧＥＮＥ关键词福尔马林...

Growth of GaAs/InAs vertical nanowires on GaAs (111)B by metalorganic chemical vapor deposition

The growth mechanism and properties of GaAs/InAs nanowires prepared by metalorganic chemical vapor deposition are investigated. Vertical InAs nanowires on GaAs (111)B substrates are successfully grown despite the large lattice mismatch (-7.2%). The crystallographic perfection of InAs nanowires is confirmed by hexagonal or triangular cross section. An interesting L-shaping of GaAs/InAs heterostructure nanowire which could be useful for novel device application is observed. © 2005 IEEE.

Thermo-optical characterization of fluorescent rhodamine B based temperature-sensitive nanosensors using a CMOS MEMS micro-hotplate

A custom designed microelectromechanical systems (MEMS) micro-hotplate, capable of operating at high temperatures (up to 700 C), was used to thermo-optically characterize fluorescent temperature-sensitive nanosensors. The nanosensors, 550 nm in diameter, are composed of temperature-sensitive rhodamine B (RhB) fluorophore which was conjugated to an inert silica sol-gel matrix. Temperature-sensitive nanosensors were dispersed and dried across the surface of the MEMS micro-hotplate, which was mounted in the slide holder of a fluorescence confocal microscope. Through electrical control of the MEMS micro-hotplate, temperature induced changes in fluorescence intensity of the nanosensors was measured over a wide temperature range. The fluorescence response of all nanosensors dispersed across the surface of the MEMS device was found to decrease in an exponential manner by 94%, when the temperature was increased from 25 C to 145 C. The fluorescence response of all dispersed nanosensors across the whole surface of the MEMS device and individual nanosensors, using line profile analysis, were not statistically different (p < 0.05). The MEMS device used for this study could prove to be a reliable, low cost, low power and high temperature micro-hotplate for the thermo-optical characterisation of sub-micron sized particles. The temperature-sensitive nanosensors could find potential application in the measurement of temperature in biological and micro-electrical systems. The Authors. © 2013 Published by Elsevier B.V. All rights reserved.

Speciation and Phylogeography of Opsariichthys bidens (Pisces: Cypriniformes: Cyprinidae) in China: Analysis of the Cytochrome b Gene of mtDNA from Diverse Populations

Gao-Yan Li, Xu-Zhen Wang, Ya-Hui Zhao, Jie Zhang, Chun-Guang Zhang, and Shun-Ping He (2009) Speciation and phylogeography of Opsariichthys bidens (Pisces: Cypriniformes: Cyprinidae) in China: analysis of the cytochrome b gene of mtDNA from diverse populations. Zoological Studies 48(4): 569-583. The cyprinid fish Opsariichthys bidens Gunther is distributed in all major river systems of continental East Asia, and represents an attractive model for phylogeographic studies among cyprinid species or within a given species. In this study, we investigated the phylogeographic and demographic history of this species, using partial sequences of the cytochrome (cyt) b gene in mitochondrial (mt)DNA. Fish samples were collected from almost all major river systems where O. bidens is distributed in China. Sequence analysis showed remarkably high polymorphism, with 125 haplotypes in the 234 specimens examined, and with 89.8% of haplotypes occurring in only 1 specimen. A neutrality test indicated that some groups were not at mutation-drift equilibrium, suggesting a past population expansion. These results were supported by a mismatch distribution analysis. Based on our analysis, O. bidens consists of 4 groups belonging to 2 clades. The divergence time of the 2 clades was estimated to be 11.06-8.04 my. This value corresponds to the time of the 2nd uplift of the Qinghai-Tibet Plateau, the emergence of the East Asian monsoon, and the Epoch-6 Event. A two species scheme is proposed. http://zoolstud.sinica.edu.tw/Journals/48.4/569.pdf

Ultraviolet-B exposure induces photo-oxidative damage and subsequent repair strategies in a desert cyanobacterium Microcoleus vaginatus Gom.

Biological soil crusts are important in reversing desertification. Ultraviolet radiation, however, may be detrimental for the development of soil crusts. The cyanobacterium Microcoleus vaginatus can be a dominant species occurring in desert soil crusts all over the world. To investigate the physico-chemical consequences of ultraviolet-B radiation on M. vaginatus, eight parameters including the contents of chlorophyll a, reactive oxygen species, malondialdehyde and proline, as well as the activities of photosynthesis, superoxide dismutase (EC 1.15.1.1), peroxiclase (EC 1.11.1.7) and catalase (EC 1.11.1.6) were determined. As shown by the results of determinations, ultraviolet-B radiation caused decreases both in contents of chlorophyll a and in ratios of variable fluorescence over maximum fluorescence that indicate the growth and photosynthesis of M. vaginatus, besides, increases both in levels of reactive oxygen species and in contents of malondialdehyde and proline, while intensified activities of superoxide dismutase, peroxiclase and catalase reflecting the abilities of enzymatic preventive substances to oxidative stress of the treated cells. Therefore, ultraviolet-B radiation affects the growth of M. vaginatus and leads to oxidative stress in cells. Under ultraviolet-B radiation, the treated cells can improve their antioxidant abilities to alleviate oxidative injury. The change trends of reactive oxygen species, superoxide dismutase, peroxiclase and catalase are synchronous. These results suggest that a balance between the antioxidant system and the reactive oxygen species content may be one part of a complex stress response pathway in which multiple environmental factors including ultraviolet-B radiation affect the Survival of M. vaginatus. (C) 2009 Elsevier Masson SAS. All rights reserved.

Structure, organization and expression of common carp (Cyprinus carpio L.) NKEF-B gene

Natural killer (NK) cell enhancing factor (NKEF) belongs to the newly defined peroxiredoxin (Prx) family. Its functions are to enhance NK cell cytotoxicity and to protect DNA and proteins from oxidative damage. In this study, a partial cDNA sequence of carp NKEF-B was isolated from thymus cDNA library. Subsequently, the full-length cDNA of carp NKEF-B was obtained by means of 3' and 5' RACE, respectively. The full-length cDNA of carp NKEF-B was 1022 bp, consisting of a 73 bp 5'-terminal untranslated region (UTR), a 355 bp T-terminal UTR, and a 594 bp open reading frame coding for a protein of 197 amino acids. Carp NKEF-B contained two consensus Val-Cys-Pro (VCP) motifs and three consensus cysteine (Cys-51, Cys-70 and Cys-172) residues. Sequence comparison showed that the deduced amino acid sequence of carp NKEF-B had an overall similarity of 74-96% to that of other species homologues. Phylogenetic analysis revealed that carp NKEF-B forms a cluster with other known teleost NKEF-Bs. Then, by PCR we obtained a 5.1 -k long genomic DNA of carp NKEF-B containing six exons and five introns. Realtime RT-PCR results showed that carp NKEF-B gene was predominantly detected in kidney and head kidney under un-infected conditions. Whereas under SVCV-infection condition, the expression of NKEF-B gene was significantly increased in blood cells, gill, intestine and spleen, but maintained in liver, and decreased significantly in kidney and head kidney. Finally, the rNKEF-B was constructed and expressed in Escherichia coli. By using an antibody against carp rNKEF-B, immunohistochemical study further indicated that NKEF-B positive cells are mainly some RBCs and a few epithelial cells in gill and intestine, and that under SVCV-infection condition, these positive cells or positive products in their cytoplasm were mainly increased in gill and spleen sections of carp. The results obtained in the present study will help to understand the function of NKEF-B in teleost innate immunity. (C) 2008 Elsevier Ltd. All rights reserved.

Antimicrobial activity-specific to Gram-negative bacteria and immune modulation-mediated NF-kappa B and Sp1 of a medaka beta-defensin

Defensins are a group of cationic antimicrobial peptides which play an important role in the innate immune system by exerting their antimicrobial activity against pathogens. In this study, we cloned a novel beta-defensin cDNA from medaka (Oryzias latipes) by rapid amplification of cDNA ends (RACE) technique. The full-length cDNA consists of 480 bp, and the open reading frame (CRF) of 189 bp encodes a polypeptide of 63 amino acids (aa) with a predicted molecular weight of 7.44 kDa. Its genomic organization was analyzed, and Southern blot detection confirmed that only one copy of beta-defensin exists in the medaka HNI strain. RT-PCR, Western blot and immunohistochemistry detections showed that the beta-defensin transcript and protein could be detected in eyes, liver, kidney, blood, spleen and gill, and obviously prevalent expression was found in eyes. Antimicrobial activity of the medaka beta-defensin was evaluated, and the antibacterial activity-specific to Gram-negative bacteria was revealed. Furthermore, the lipopolysaccharide (LPS), a major component of the outer membrane of Gram-negative bacteria, was demonstrated to be able to induce about 13-fol up-regulation of the beta-defensin within first 12 h. In addition, promoter and promoter mutagenesis analysis were performed in the medaka beta-defensin. A proximal 100 base pair(bp) sequence (+26 to -73)and the next 1700 bp sequence (-73 to -1755) were demonstrated to be responsible for the basal promoter activity and for the transcription regulation. Three nuclear factor kappa B (NF-kappa B) cis-elements and a Sp1 cis-element were revealed by mutagenesis analysis to exist in the 5' flanking sequence, and they were confirmed to be responsible for the up-regulation of medaka beta-defensin stimulated by LPS. And, the Sp1 cis-element was further revealed to be related to the basal promoter activity, and transcriptional factor II D (TFIID) was found to be in charge of the gene transcription initiation. All the obtained data suggested that the novel medaka beta-defensin should have antimicrobial activity-specific to Gram-negative bacteria, and the antibacterial immune function should be modulated by NF-kappa B and Sp1. (C) 2008 Elsevier Ltd. All rights reserved.

UV-B-induced Oxidative Damage and Protective Role of Exopolysaccharides in Desert Cyanobacterium Microcoleus vaginatus

UV-B-induced oxidative damage and the protective effect of exopolysaccharides (EPS) in Microcoleus vaginatus, a cyanobacterium isolated from desert crust, were investigated. After being irradiated with UV-B radiation, photosynthetic activity (Fv/Fm), cellular total carbohydrates, EPS and sucrose production of irradiated cells decreased, while reducing sugars, reactive oxygen species (ROS) generation, malondialdehyde (MDA) production and DNA strand breaks increased significantly. However, when pretreated with 100 mg/L exogenous EPS, EPS production in the culture medium of UV-B stressed cells decreased significantly; Fv/Fm, cellular total carbohydrates, reducing sugars and sucrose synthase (SS) activity of irradiated cells increased significantly, while ROS generation, MDA production and DNA strand breaks of irradiated cells decreased significantly. The results suggested that EPS exhibited a significant protective effect on DNA strand breaks and lipid peroxidation by effectively eliminating ROS induced by UV-B radiation in M. vaginatus.

Expressional induction of Paralichthys olivaceus cathepsin B gene in response to virus, poly I:C and lipopolysaccharide

Cathepsin B is a lysosomal cysteine protease of the papain-like enzyme family with multiple biological functions. In this study, Paralichthys olivaceus cathepsin B (PoCatB) cDNA was isolated from flounder embryonic cells (FEC) treated with UV-inactivated grass carp hemorrhage virus (GCHV) and subsequently identified as a vitally induced gene. The full length cDNA of PoCatB is 1801 bp encoding 330-amino acids. The deduced protein has high homology to all known cathepsin B proteins, containing an N-terminal signal peptide, cysteine protease active sites, the occluding loop segment and a glycosylation site, all of which are conserved in the cathepsin B family. PoCatB transcription of FEC cells could be induced by turbot (Scophthalmus maximus) rhabdovirus (SMRV), UV-inactivated SMRV, UV-inactivated GCHV, poly I:C or lipopolysaccharide (LPS), and SMRV or poly I:C was revealed to be most effective among the five inducers. In normal flounder, PoCatB mRNA was detectable in all examined tissues. Moreover, SMRV infection could result in significant upregulation of PoCatB mRNA, predominantly in spleen, head kidney, posterior kidney, intestine, gill and muscle with 18.2,10.9, 24.7,12, 31.5 and 18 fold increases at 72 h post-infection respectively. These results provided the first evidence for the transcriptional induction of cathepsin B in fish by virus and LPS, indicating existence of a novel function in viral defense. (C) 2008 Elsevier Ltd. All rights reserved.

A fixed-grid b-spline finite element technique for fluid-structure interaction

We present a fixed-grid finite element technique for fluid-structure interaction problems involving incompressible viscous flows and thin structures. The flow equations are discretised with isoparametric b-spline basis functions defined on a logically Cartesian grid. In addition, the previously proposed subdivision-stabilisation technique is used to ensure inf-sup stability. The beam equations are discretised with b-splines and the shell equations with subdivision basis functions, both leading to a rotation-free formulation. The interface conditions between the fluid and the structure are enforced with the Nitsche technique. The resulting coupled system of equations is solved with a Dirichlet-Robin partitioning scheme, and the fluid equations are solved with a pressure-correction method. Auxiliary techniques employed for improving numerical robustness include the level-set based implicit representation of the structure interface on the fluid grid, a cut-cell integration algorithm based on marching tetrahedra and the conservative data transfer between the fluid and structure discretisations. A number of verification and validation examples, primarily motivated by animal locomotion in air or water, demonstrate the robustness and efficiency of our approach. © 2013 John Wiley & Sons, Ltd.

Molecular characterization and expression pattern of fetuin-B in gibel carp (Carassius auratus gibelio)

Fetuin-B has recently been cloned and identified from rats, mice, and humans; their expression patterns, however, have not been elucidated yet. In this study, Cagfetuin-B has been cloned in gibel carp. RT-PCR and Western blot detection revealed that Cagfetuin-B is first transcribed from the blastula stage and at a relatively stable level afterward during embryogenesis and the larval stage. Cagfetuin-B transcripts are predominantly distributed over the yolk syncytial layer in the early embryos and later restricted to the cells of liver and brain in newly hatched larvae. Moreover, a dynamic distribution of Cagfetuin-B protein was observed in brain, kidney, liver, and skin during morphogenesis. In adult fish, Cagfetuin-B transcripts are restricted in liver and ovary. Our work, for the first time, revealed the extra-hepatic transcription and a dynamic distribution of fetuin-B during embryogenesis and in adults, which indicates the potential roles of fetuin-B in fish organogenesis.