Molecular structure and expression patterns of flounder (Paralichthys olivaceus) Myf-5, a myogenic regulatory factor

Myf-5, a member of the myogenic regulatory factors (MRF), has been shown to be expressed in muscle precursors in early stage zebrafish embryos. The MRFs, including MyoD, Myf-5, Myogenin and MR-F4, belong to the basic Helix-Loop-Helix transcription factors that contain a conserved basic Helix-Loop-Helix (bHLH) domain. To better understand the role of Myf-5 in the development of fish muscles, we have isolated the Myf-5 genomic sequence and cDNA from Flounder (Paralichthys olivaceus), and analyzed its structures and patterns of expression. Promoter analysis identified several putative transcription factor binding sites such as an E-box, NF-Y sites that might confer muscle-specific expression. Myf-5 transcripts were first detected in the paraxial mesoderm that gives rise to slow muscles. During somitogenesis, Myf-5 expression was found in developing somites. Myf-5 expression decreased gradually in somites in the anterior region, but remained strong in the newly formed somites. In the hatching stage, the expression was also detected in other muscle cells such as head muscle and fin muscle. In the growing fish, RT-PCR results showed that Myf-5 was expressed in the skeletal muscle and intestine. (c) 2006 Elsevier Inc. All rights reserved.

牙鲆和大黄鱼经济性状候选基因的DNA分子标记研究

本文利用不同的分子标记方法，分别对牙鲆及大黄鱼不同养殖群体的生长、抗病等经济性状的候选基因进行了序列多态性研究，检测到了几个SNP位点和微卫星的多态性位点，并分析了它们与经济性状之间的相关性；同时，利用微卫星的多态性位点对牙鲆2个养殖群体的遗传变异进行了分析，这些均为海水鱼类遗传育种及标记辅助选育工作提供了基础数据。 在牙鲆胶南养殖群体中，以100个个体为实验材料，根据其生长激素（GH）基因的6个外显子序列设计引物，通过SSCP分析技术显示该群体GH基因的第4外显子存在多态性，检测到2种基因型，AA型和AB型。DNA测序结果表明，AB型在第1763位发生碱基突变，c→t，与AA型同源性达到99%。连锁分析结果表明：这2种基因型的个体在体重和头长上表现出显著的差异，AB型个体的体重和头长都明显大于AA型个体(P<0.05)，由此推测等位基因B是一个对牙鲆体重和头长都有利的等位基因；这2种基因型个体之间在其体型性状上也存在显著差异（P<0.05）；同时，该多态位点的Hardy-Weinberg平衡性检验结果表明，该群体处于Hardy-Weinberg平衡状态。在牙鲆GH基因第1外显子区域还发现了一个微卫星位点，对该位点进行多态性分析，检测到5种基因型、3种等位基因，one-way ANOVA统计结果显示，基因型AC个体的体重、头长和体高明显大于其它基因型个体（P<0.05），C是一个对体重、头长和体高有利的等位基因。 对2个大黄鱼养殖群体的GH基因进行SSCP分析后发现，浙江群体大黄鱼GH基因在第196位存在1个SNP（g→a）位点，检测到2种基因型，AA和AB。t检验结果表明，AA型个体的体高比AB型个体的高(P≤0.05)，但AB型个体在体长/体高上占优势(P≤0.05)，提示该突变位点可以作为大黄鱼体型性状的候选标记。福建群体大黄鱼GH基因在第692位有1个SNP位点(t→c)，共检测到2种基因型，CC型和CD型，其中，CD基因型个体的体重和全长显著大于CC基因型个体(P≤0.01)，提示该位点可以作为大黄鱼体重和头长性状的候选标记。 在牙鲆胶南和日照2个养殖群体中，采用牙鲆GHR基因5’端Promoter区的一个微卫星标记，进行了群体遗传变异的研究，并探索了该基因多态性位点与牙鲆生长性状之间的相关性。结果表明，2个群体在该位点检测到的等位基因数为12和9个，有效等位基因数为6.26和5.04个。两个群体该位点的Hardy-Weinberg遗传偏离指数均为正值，并没有显示出杂合子缺失，但各基因型分布频率都在一定程度上偏离Hardy-Weinberg平衡(P<0.01)。连锁分析发现，在胶南群体中，IM基因型对应的个体在全重、全长、体长、头长、体高和眼径形态学数据中均是最大的，但仅在体重上极其显著的大于全部其它基因型个体；在日照群体中，BC基因型对应的个体在全重、全长、体高、尾柄高、尾柄长和眼径数据中均是最大的；而CJ基因型对应的个体在体长和头长这两组数据中是最大的。由此认为，该位点IM基因型可以作为牙鲆体重性状的潜在标记。 在进行牙鲆抗病性状标记的筛选时，利用迟缓爱德华氏菌（Edwardsiella tarda）LSE40对牙鲆鱼进行攻毒感染实验，得到死亡群体和未死亡群体。选择Toll样受体基因中的TLR2、TLR3和TLR9基因作为候选基因，分别对这3个基因中的部分序列共设计7对引物进行扩增，同时对扩增产物进行RFLP多态性分析，目前只在TLR3基因内检测到一个EcoRI的酶切多态性位点，测序后发现，这是由于在TLR3基因第3806位的EcoRI酶切位点在某些个体中缺失所致。酶切产物共呈现出3种基因型，分别定义为AA，AB和BB。χ2检验证明该多态性位点与牙鲆抗迟缓爱德华氏菌LSE40的能力有一定关系。利用多因素非条件Logistic回归分析对死亡组和存活组牙鲆的各种形态学数据以及不同基因型之间进行了分析，发现体长、头长和体高均具有显著的相关性（P<0.05），而这几个因素与体重的相关性不显著（P>0.05）。多因素非条件Logistic分析后发现：AA基因型对死亡率具有显著的影响（P<0.05），是主要的危险因素，而AB基因型的作用不显著（P>0.05）；头长是主要的保护因素（P<0.05），体重对死亡率的影响很小。χ2检验证明，等位基因A是对死亡的主要危险等位基因，B是对存活有利的主要等位基因。推测该位点可以作为牙鲆抗迟缓爱德华氏菌的潜在标记。

靶向斑马鱼VEGF的shRNA表达载体的构建及其对斑马鱼胚胎血管发育的影响

血管内皮生长因子(vascular endothelial growth factor, VEGF)是一种多功能的细胞因子，其主要作用是促进血管内皮细胞增殖和增加血管通透性，是肿瘤及正常组织血管生成的中心调控因素，以VEGF为靶点的肿瘤血管靶向性治疗成为近几年肿瘤治疗的新途径。RNAi是近年来新发展的一项反向遗传学技术，是一种研究基因功能的有力工具。斑马鱼作为一种重要的模式生物，被广泛用于胚胎的分子发育机制、疾病模型的构建以及药物筛选等研究中。然而在斑马鱼中运用RNAi技术进行基因功能研究是一个相对较新的领域，研究资料较少，并且目前进行的斑马鱼RNAi实验中，siRNA大都是通过化学方法或体外转录合成的。体外合成的siRNA在进入体内后会被降解而无法达到持久阻抑基因表达的目的。因此本研究旨在探讨VEGF特异性siRNA表达载体对斑马鱼VEGF基因的沉默作用，通过分析表型及相关细胞因子的变化，阐明VEGF对斑马鱼胚胎血管生成的影响及作用机制。 研究通过计算机辅助设计软件，针对斑马鱼VEGF mRNA不同位点设计合成了4段含siRNA特异序列的DNA单链，经退火，克隆入pSilencer 4.1-CMV neo载体CMV启动子下游，构建了重组质粒pS1-VEGF、pS2-VEGF、pS3-VEGF及pS4-VEGF。 通过显微注射的方法将载体导入1-2细胞期斑马鱼体内，于胚胎发育的48 h采用RT-PCR的方法检测VEGF基因的表达量，研究不同干扰序列对VEGF基因表达的干涉作用。结果显示，针对不同位点的表达载体对VEGF基因表达的抑制效率有显著差异。它们对VEGF mRNA的抑制率分别为80.5%，42.8%，12.5%，40.7%。通过筛选我们得到了一条具有高效抑制作用的载体pS1-VEGF，该载体的相应序列靶向斑马鱼两个主要异构体VEGF165和VEGF121的共有外显子序列。 形态学检测结果显示，注射了pS1-VEGF的胚胎出现了心包膜水肿、血流速度减慢、循环红细胞堆积等症状。定量碱性磷酸酶染色显示，注射pS1-VEGF能够抑制斑马鱼胚胎新生血管的形成，当注射剂量为0.4 ng时，血管生成的抑制率为31.8%。NBT/BCIP血管染色显示，注射该载体后72 h，50%的斑马鱼肠下静脉、节间血管以及其它血管的发育受到不同程度的抑制。随着注射剂量的加大，血管发育受抑制的情况也随之加重，当注射剂量为1 ng时，只有心脏、头部及卵黄有血液循环。对干扰效果的特异性进行了研究，结果表明pS1-VEGF对斑马鱼内源基因胸苷酸合成酶（thymidylate synthase, TS）基因的表达没有明显的抑制作用。针对TS基因的shRNA表达载体及与斑马鱼没有同源性的对照载体对VEGF基因表达也没有明显的抑制作用。浓度梯度实验表明在0-1.2 ng的范围内干扰效果具有剂量依赖性。 以胚胎整体原位杂交的方法检测质粒对VEGF基因受体NRP1基因表达的影响，发现VEGF特异性shRNA表达载体能够引起NRP1基因表达的降低，说明斑马鱼中VEGF所介导的血管生成作用至少在部分上是依赖于NRP通路所调节的。 本研究工作为进一步研究斑马鱼基因功能、VEGF调控网络提供了一个快速、有效的手段，为阐明斑马鱼的血管生成机制提供了新的资料，为采用RNAi技术，以VEGF为靶点，以斑马鱼为模型对肿瘤进行基因治疗研究奠定了基础。

Cloning, characterization, and expression analysis of extracellular copper/zinc superoxide dismutase gene from bay scallop Argopecten irradians

Extracellular superoxide dismutase (ECSOD) is a major extracellular antioxidant enzyme that protects organs from damage by reactive oxygen species (ROS). We cloned a novel ECSOD from the bay scallop Argopecten irradians (AiECSOD) by 3' and 5' RACE. The full-length cDNA of AiECSOD was 893 bp with a 657 bp open reading frame encoding 218 amino acids. The deduced amino acid sequence contained a putative signal peptide of 20 amino acids, and sequence comparison showed that AiECSOD had low degree of homology to ECSODs of other organisms. The genomic length of the AiECSOD gene was about 5276 bp containing five exons and six introns. The promoter region contained many putative transcription factor binding sites such as c-Myb, Oct-1, Sp1, Kruppel-like, c-ETS, NF kappa B, GATA-1, AP-1, and Ubx binding sites. Furthermore, tissue-specific expressions of AiECSOD and temporal expressions of AiECSOD in haemocytes of bay scallops challenged with bacteria Vibrio anguillarum were quantified using qRT-PCR. High levels of expression were detected in haemocytes, but not in gonad and mantle. The expression of AiECSOD reached the highest level at 12 h post-injection with V. anguillarum and then returned to normal between 24 h and 48 h post-injection. These results indicated that AiECSOD was an inducible protein and that it may play an important role in the immune responses against V anguillarum. Crown Copyright (C) 2008 Published by Elsevier Ltd. All rights reserved.

Intracellular copper/zinc superoxide dismutase from bay scallop Argopecten irradians: Its gene structure, mRNA expression and recombinant protein

Superoxide dismutases are an ubiquitous family of enzymes that function to efficiently catalyze the dismutation of superoxide anions. Two unique and highly compartmentalized bay scallop Argopecten irradians superoxide dismutases: MnSOD and ecCuZnSOD, have been molecularly characterized in our previous study. To complete characterize the SOD family in A. irradians, a novel intracellular copper/zinc SOD from the A. irradians (Ai-icCuZnSOD) was obtained and characterized. The full-length cDNA of Ai-icCuZnSOD was 1047 bp with a 459 bp open reading frame encoding 152 amino acids. The genomic length of the Ai-icCuZnSOD gene was about 4279 bp containing 4 exons and 3 introns. The promoter region containing many putative transcription factor binding sites were analyzed. Furthermore, quantitative reverse transcriptase real-time PCR (qRT-PCR) analysis indicated that the highest expression of the Ai-icCuZnSOD was detected in gill and the expression profiles in hemocytes of bay scallops challenged with bacteria Vibrio anguillarum and lipopolysaccharide (LPS) were different. The result presented an increased expression after injection with LPS whereas no significant changes were observed after V. anguillarum injection. A fusion protein containing Ai-icCuZnSOD was produced in vitro. The rAi-icCuZnSOD is a stable enzyme, retaining more than 80% of its activity between 10 and 60 degrees C and keeping above 88% of its activity at pH values between 5.8 and 9. Ai-icCuZnSOD is more stable under alkaline than acidic conditions. Crown Copyright (C) 2009 Published by Elsevier Ltd. All rights reserved.

Molecular cloning, expression and biochemical property analysis of AtKP1, a kinesin gene from Arabidopsis thaliana

Kinesins are common in a variety of eukaryotic cells with diverse functions. A cDNA encoding a member of the Kinesin-14B subfamily is obtained using X-RACE technology and named AtKP1 (for Arabidopsis kinesin protein 1). This cDNA has a maximum open reading frame of 3.3 kb encoding a polypeptide of 1087 aa. Protein domain analysis shows that AtKP1 contains the motor domain and the calponin homology domain in the central and amino-terminal regions, respectively. The carboxyl-terminal region with 202 aa residues is diverse from other known kinesins. Northern blot analysis shows that AtKP1 is widely expressed at a higher level in seedlings than in mature plants. 2808 bp of the AtKP1 promoter region is cloned and fused to GUS. GUS expression driven by the AtKP1 promoter region shows that AtKP1 is mainly expressed in vasculature of young organs and young leaf trichomes, indicating that AtKP1 may participate in the differentiation or development of Arabidopsis thaliana vascular bundles and trichomes. A truncated AtKP1 protein containing the putative motor domain is expressed in E. coli and affinity-purified. In vitro characterizations indicate that the polypeptide has nucleotide-dependent microtubule-binding ability and microtubule-stimulated ATPase activity.

Graphitic nanofilaments as novel support of Ru-Ba catalysts for ammonia synthesis

A novel graphitic-nanofilament-(GNF-) supported Ru-Ba catalyst is prepared and used in ammonia synthesis reaction. The Ru-Ba/GNFs catalyst shows remarkably high activity and stability for ammonia synthesis, which can be attributed to high purity and graphitization of GNFs with unique structure. TEM micrographs of the Ru-Ba/GNFs catalysts show that Ru metal particles uniformly disperse on the outer wall of GNFs, and the particles become bigger than that before ammonia synthesis reaction after 50 h of operation at 500degreesC and 7.0 MPa, probably due to the Ru crystals covered by promoter and support materials and/or sintering of Ru crystals. (C) 2002 Elsevier Science (USA).

Comparative study by infrared spectroscopy and microcalorimetry of the CO adsorption over supported palladium catalysts

The adsorption of CO on Al(2)O(3), ZrO(2), ZrO(2)-SiO(2), and ZrO(2)-La(2)O(3) supported Pd catalysts was studied by adsorption microcalorimetry and infrared (TR) spectroscopy. Some interesting and new correlations between the results of microcalorimetry and IR spectroscopy have been found. The CO is adsorbed on palladium catalysts in three different modes: multibonded (3-fold), bridged (2-fold), both on Pd(lll) and (100) planes, and linear (1-fold) adsorbed species. The corresponding differential adsorption heats lie in the field of high (210-170 kJ/mol), medium (140-120 kJ/mol), and low (95-60 kJ/mol) values, respectively. The nature of the support, the reduction temperature, and the pretreatment conditions affect the surface structure of the Pd catalysts, resulting in variations in the site energy distribution, i.e., changes in the fraction of sites adsorbing CO with specific heats of adsorption. Moreover, the CeO(2); promoter addition weakens the adsorption strength of CO on palladium. Based on the exposed results, a correctness factor, which considers the percentages of various CO adsorption states, must be introduced when one calculates the Pd dispersion using CO adsorption data.

Thioreduction of cyclopentanone and hydrodesulfurization of dibenzothiophene over sulfided nickel or cobalt-promoted molybdenum on alumina catalysts

Two series of sulfided Ni or Co promoted Mo/alumina catalysts, having different Ni or Co loadings, were characterized by their activities for the transformation of cyclopentanone into cyclopentanethiol (flow reactor, 220 degrees C, atmospheric pressure) and for the hydrodesulfurization of dibenzothiophene (flow reactor, 340 degrees C, 3 MPa hydrogen pressure). The addition of the promoter increased significantly the activity of the Mo/alumina catalyst for both reactions, up to a maximum obtained with the catalysts having a (promoter)/(promoter+Mo) molar ratio equal to 0.3-0.4. This increase in activity was due in part to an increase in the hydrogenating properties of the Mo/alumina catalyst. However, an additional modification of the catalyst (basic and nucleophilic properties) must be considered to account for the spectacular effect of the promoter on the rate of the dibenzothiophene direct desulfurization reaction. (C) 1999 Elsevier Science B.V. All rights reserved.

Ammonia synthesis over Ru/C catalysts with different carbon supports promoted by barium and potassium compounds

Ammonia synthesis over ruthenium catalysts supported on different carbon materials using Ba or K compounds as promoters has been investigated. Ba(NO3)(2), KOH, and KNO3 are used as the promoter or promoter precursor, and activated carbon (AC), activated carbon fiber (ACF). and carbon molecular sieve (CMS) are used as the support. The activity measurement for ammonia synthesis was carried out in a flow micro-reactor under mild conditions: 350-450 degreesC and 3.0 MPa. Results show that KOH promoter was more effective than KNO3. and that Ba(NO3)(2) was the most effective promoter among the three. The roles of promoters can be divided into the electronic modification of ruthenium, the neutralization of surface functional groups on the carbon support and the ruthenium precursor. The catalyst with AC as the support gave the highest ammonia concentration in the effluent among the supports used, while the catalyst with ACF as the support showed the highest turnover-frequency (TOF) value. It seems that the larger particles of Ru on the carbon supports are more active for ammonia synthesis in terms of TOF value. (C) 2001 Elsevier Science B.V. All rights reserved.

Highly sensitive determination of the methylated p16 gene in cancer patients by microchip electrophoresis

The p16 tumor suppressor gene is inactivated by promoter region hypermethylation in many types of tumor. Recent studies showed that aberrant methylation of the p16 gene is an early event in many tumors, especially in lung cancer, and may constitute a new biomarker for early detection and monitoring of prevention trials. We detected tumor-associated aberrant hypermethylation of the p16 gene in plasma and tissue DNA from 153 specimens using a modified semi-nested methylation-specific PCR (MSP) combining plastic microchip electrophoresis or slab gel electrophoresis, respectively. Specimens were from 79 lung cancer patients, 15 abdominal tumor patients, 30 positive controls and 30 negative controls. The results showed that the positive rate obtained by microchip electrophoresis was more than 26.6% higher and the same speciticity was kept when compared with slab gel electrophoresis. The microchip electrophoresis can rapidly and accurately analyze the PCR products of methylated DNA and obviously improve the positive rate of diagnosis of cancer patients when compared with gel electrophoresis. This method with the high assay sensitivity might be used for detection of methylation of p16 gene and even to facilitate early diagnosis of cancer patients. (C) 2004 Elsevier B.V. All rights reserved.

Characterizations and activities of the nano-sized Ni/Al2O3 and Ni/La-Al2O3 catalysts for NH3 decomposition

A series of nano-sized Ni/Al2O3 and Ni/La-Al2O3 catalysts that possess high activities for NH3 decomposition have been successfully synthesized by a coprecipitation method. The catalytic performance was investigated under the atmospheric conditions and a significant enhancement in the activity after the introduction of La was observed. Aiming to study the influence of La promoter on the physicochemical properties, we characterized the catalysts by N-2 adsorption/desorption, XRD, H-2-TPR, chemisorption and TEM techniques. Physisorption results suggested a high specific surface area and XRD spectra showed that nickel particles are in a highly dispersed state. A combination of XRD, TEM and chemisorption showed that Ni-0 particles with the average size lower, than 5.0 nm are always obtained even though the Ni loading ranged widely from 4 to 63 %. Compared with the Ni/Al2O3 catalysts, the Ni/La-Al2O3 ones with an appropriate amount of promoter enjoy a more open mesoporous structure and higher dispersion of Ni. Reduction kinetic studies of prepared catalysts were investigated by temperature-programmed reduction (TPR) method and the fact that La additive partially destroyed the metastable Ni-Al mixed oxide phase was detailed. (c) 2005 Elsevier B.V. All rights reserved.

Exploitation of Ebola Virus VP35 Protein to identify new drugs counteracting its type I IFN antagonism

Ebolaviruses (EBOVs) are among the most virulent and deadly pathogens ever known, causing fulminant haemorrhagic fevers in humans and non-human primates. The 2014 outbreak of Ebola virus disease (EVD) in West Africa has claimed more lives than all previous EVD outbreaks combined. The EBOV high mortality rates have been related to the virus-induced impairment of the host innate immunity reaction due to two virus-coded proteins, VP24 and VP35. EBOV VP35 is a multifunctional protein, it is essential for viral replication as a component of the viral RNA polymerase and it also participates in nucleocapsid assembly. Early during EBOV infection, alpha-beta interferon (IFN-α/β) production would be triggered upon recognition of viral dsRNA products by cytoplasmic retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs). However, this recognition is efficiently prevented by the double-stranded RNA (dsRNA) binding activity of the EBOV VP35 protein, which hides RLRs binding sites on the dsRNA phosphate backbone as well the 5’-triphosphate (5’-ppp) dsRNA ends to RIG-I recognition. In addition to dsRNA binding and sequestration, EBOV VP35 inhibits IFN-α/β production preventing the activation of the IFN regulatory factor 3 (IRF-3) by direct interaction with cellular proteins. Previous studies demonstrated that single amino acid changes in the VP35 dsRNA binding domain reduce EBOV virulence, indicating that VP35 is an attractive target for antiviral drugs development. Within this context, here we report the establishment of a novel method to characterize the EBOV VP35 inhibitory function of the dsRNA-dependent RIG-I-mediated IFN-β signaling pathway in a BLS2 cell culture setting. In such system, a plasmid containing the promoter region of IFN-β gene linked with a luciferase reporter gene was transfected, together with a EBOV VP35 mammalian expression plasmid, into the IFN-sensitive A549 cell line, and the IFN-induction was stimulated through dsRNA transfection. Through alanine scanning mutational studies with biochemical, cellular and computational methods we highlighted the importance of some VP35 residues involved in dsRNA end-capping binding, such as R312, K282 and R322, that may serve as target for the development of small-molecule inhibitors against EBOV. Furthermore, we identified a synthetic compound that increased IFN-induction only under antiviral response stimulation and subverted VP35 inhibition, proving to be very attractive for the development of an antiviral drug. In conclusion, our results provide the establishment of a new assay as a straightforward tool for the screening of antiviral compounds that target i) dsRNA-VP35 or cellular protein-VP35 interaction and ii) dsRNA-dependent RIG-I-mediated IFN signaling pathway, in order to potentiate the IFN response against VP35 inhibition, setting the bases for further drug development.

Hugh Blaker: Doing his Bit for the Moderns

Meyrick, Robert, 'Hugh Blaker: Doing his Bit for the Moderns', Journal of the History of Collections (2004) 16(2):173-189 RAE2008

Molecular analysis of the anaerobic rumen fungus Orpinomyces - insights into an AT-rich genome

Matthew J. Nicholson, Michael K. Theodorou and Jayne L. Brookman. (2005). Molecular analysis of the anaerobic rumen fungus Orpinomyces - insights into an AT-rich genome. Microbiology, 151 (1), 121-133. Sponsorship: BBSRC RAE2008