In silico assessment of EpCAM transcriptional expression and determination of the prognostic biomarker for human lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC)

Epithelial cell adhesion molecule (EpCAM) is a transmembrane glycoprotein which is involved in cell signaling, proliferation, maturation, and movement, all of which are crucial for the proper development of cells and tissues. Cleavage of the EpCAM protein leads to the up-regulation of c-myc, e-fabp, and cyclins A and E which promote tumorigenesis. EpCAM can act as potential diagnostic and prognostic biomarker for different types of cancers as it is also found to be expressed in epithelia and epithelial-derived neoplasms. Hence, we aimed to analyze the EpCAM gene expression and any associated feedback in the patients of two major types of lung cancer (LC) i.e., lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), based on the publicly available online databases. In this study, server-based gene expression analysis represents the up-regulation of EpCAM in both LUAD and LUSC subtypes as compared to the corresponding normal tissues. Besides, the histological sections revealed the over-expression of EpCAM protein in cancerous tissues by depicting strong staining signals. Furthermore, mutation analysis suggested missense as the predominant type of mutation both in LUAD and LUSC in the EpCAM gene. A significant correlation (P-value < 0.05) between the higher EpCAM expression and lower patient survival was also found in this study. Finally, the co-expressed genes were identified with their ontological features and signaling pathways associated in LC development. The overall study suggests EpCAM to be a significant biomarker for human LC prognosis.     

盐芥谷胱甘肽过氧化物酶基因（ThGPX6）的克隆及表达分析

谷胱甘肽过氧化物酶在植物响应盐胁迫中具有重要作用。依据盐芥EST序列进行RACE实验,获得1个新的谷胱甘肽过氧化物酶基因,命名为ThGPX6(GenBank注册号为FJ357244)。该基因的cDNA全长892 bp,包含1个长为702bp的开放读码框,编码234个氨基酸。生物信息学分析表明,该蛋白具有植物GPX的典型结构,即GPX催化活性区(NVASKCGLT)和标志性基序(ILAFPCNQF),以及PHGPX特有序列(KWNF(S/T)KFL)。实时荧光定量PCR分析结果表明,ThGPX6在盐芥叶片和根中表达,其表达受NaCl诱导,显示ThGPX6在植物高盐响应中发挥作用。亚细胞定位结果表明,ThGPX6存在于线粒体和内体中的可能性最大,预示着ThGPX6在清除ROS过程中起着重要作用。     

一个巨大的多烯抗生素基因簇中聚酮合酶(PKS)基因单元在大肠杆菌中的双重诱导超量表达

根据序列分析信息,将链霉菌FR－008中与多烯大环内酯抗生素生物合成直接有关的PKS基因簇内长2671bp的一个PKS单元以正确框架克隆于表达载体pET－15b中P（T7）启动子下游的BamHI位点上,经IPTG诱导只得到微量PKS表达。同样地克隆于pBV220中PRPL启动子下游的PKS基因在42℃诱导后也不能超量表达出PKS蛋白。然而克隆于串联启动子PRP（T7）或PRPLP（T7）下游的PKS基因却得到了超量表达。在PRPLP（T7）下游PKS基因的超量表达依赖于IPTG及42℃两个条件的双重诱导,而42℃及IPTG单独诱导只得到常量表达。而在PRP（T7）启动子下游时PKS基因在42℃、IPTG单独诱导或42℃＋IPTG双重诱导时均可获得超量表达。据此构建了启动子PR、P（T7）串联排列的表达载体pH2330。外源基因克隆于该载体起始密码子下游的多克隆位点时,表达的外源蛋白可用Ni（＋＋）"柱亲和纯化。此外,用在大肠杆菌中表达的PKS蛋白作为抗原免疫大白兔制备了特异性的抗体,Westernblotting实验证明该抗体是PKS特异性的,可用于PKS基因簇及PKS异源表达的深入研究。     

亚洲玉米螟神经肽羽化激素基因cDNA的克隆及组织表达

羽化激素对调节昆虫的蜕皮和发育起关键作用。亚洲玉米螟Ostrinia furnacalis是亚洲农业重要害虫之一,本实验研究了亚洲玉米螟羽化激素基因cDNA的分子结构和表达模式。利用兼并性引物RT-PCR技术,克隆了亚洲玉米螟羽化激素基因cDNA的中间片段,然后再用RACE方法,获得羽化激素基因的 cDNA全长序列。结果表明： 亚洲玉米螟羽化激素基因cDNA全长986 bp（GenBank登录号： DQ668369）,开放阅读框为267 bp,编码88个氨基酸的前体蛋白,其中包括前26个氨基酸组成的信号肽和62个氨基酸的成熟肽。亚洲玉米螟羽化激素基因与烟草天蛾、棉铃虫和家蚕已报道同源基因的同源性较高,分别为79.5%、77.3%和67.0%,与黑腹果蝇同源基因的同源性最低,仅45.5%。亚洲玉米螟羽化激素基因mRNA只在脑中表达,在咽下神经节、胸神经节、腹神经节等神经组织中检测不到,在非神经组织如中肠、脂肪体和表皮中也不表达。     

RNA 检测技术在法医病理学中的应用研究

DNA技术广泛应用于法医学中,RNA分析技术为调查疾病和死亡原因提供依据,RNA检测可以作为法医病理学检测一个有效的工具。RNA还可以应用在损伤时间和死亡后间隔时间的检测。在法医案件分析中,体液中细胞特异mRNA的表达的分子检测已经为DNA分析的重要补充手段。本文综述了RNA检测技术在法医病理学中的研究进展及其应用。     

A review of <Emphasis Type="Italic">Piper</Emphasis> spp. (Piperaceae) phytochemistry,insecticidal activity and mode of action

The tropical plant family Piperaceae has provided many past and present civilizations with a source of diverse medicines and food grade spice. The secondary plant compounds that produce these desired qualities function also as chemical defenses for many species in the genus Piper. The compounds with the greatest insecticidal activity are the piperamides. Many studies have shown the effectiveness of Piper spp. extracts for the control of stored products pests and recently studies from our laboratory group have tested the extracts of Piper. nigrum, P. guineense and P. tuberculatum against insect pests of the home and garden. These results and those from investigations that examined the biochemical and molecular modes of action of the piperamides singly or in combination will be the focus of this review. The conclusions of our current work with Piperaceae are that Piper extracts offer a unique and useful source of biopesticide material for controlling small-scale insect out-breaks and reducing the likelihood of resistance development when applied as a synergist with other botanical insecticides such as pyrethrum.     

Ribosomal RNA genes structure in somePopulus spp. (Salicaceae) and their hybrids

The tandemly repeated multigene families encoding 18S and 25S rRNAs were studied at the restriction enzyme level inPopulus alba L.,Populus deltoides Bartr. exMarsh.,Populus trichocarpa Torr. & Gray and in the hybrids between the last two mentioned species. The analysis of single and double digestion with EcoRI, BamHI, XbaI, and SstI endonucleases showed the presence of single repetitive unit types of 12.25 and 11.75kb inP. alba andP. trichocarpa, respectively.P. deltoides showed two rDNA gene types having the same length (12.25Kb) but different nucleotide sequence in the IGS. The rDNAs genes ofP. deltoides andP. triochocarpa are inherited codominantly in their hybrids.     

香蕉（‘威廉斯突变体’）苯丙氨酸解氨酶基因克隆、表达及酶活性分析

选用抗枯萎病突变体‘威廉斯突变体(Musa spp.AAA,Williams Mutant)'为试材,用RT-PCR技术从香蕉叶中克隆得到一个长为1 504 bp,编码501个氨基酸的苯丙氨酸解氨酶(PAL)基因cDNA序列.序列分析与其它植物PAL蛋白有较高同源性,尤其是麻疯树和柑橘属同源性高达93%.半定量PCR和酶活性测定被采用研究威廉斯突变体在接种枯萎病菌Fusarium oxysporum f. sp.cubense.roce 4(FOC4)茎中PAL表达的变化,结果显示茎中PAL活性呈规律性变化,且均高于同期对照,与其它植物相关研究结果类似,表明PAL与香蕉抗枯萎病密切相关.     

Cloning and characteristics of the antibacterial peptide gene abaecin in the bumblebee Bombus lantschouensis (Hymenoptera: Apidae)

Among the antimicrobial peptides, abaecin is rich in proline content and plays a vital role in insect innate immune defense. Here, the full-length gene of abaecin from the bumblebee Bombus lantschouensis was cloned, and its expression profiles for different tissues, developmental stages and reproductive statuses were analyzed by RT-qPCR. Meanwhile, the responses of abaecin to a bacterium (Escherichia coli) and a fungus (Beauveria bassiana) were tested. The full length of abaecin cDNA was 470 bp, and the open reading frame (ORF) was 258 bp, encoding a polypeptide of 85 amino acids. The abaecin gene consists of three exons and two introns. Phylogenetic analysis showed that Bombus ignitus was the closest species to B. lantschouensis base on putative Abaecin protein sequence. Expression analysis showed that abaecin was expressed broadly in different tissues, with the highest expression in fat bodies and extremely low expression in antennae. Regarding developmental stage, low expression of abacein was detected in eggs and larvae, and high expression was detected in pupal stages. The highest expression was observed at the Pw pupal stage (pupae with an unpigmented body cuticle and white eyes), and the expression then decreased from the Pp (pupae with pink eyes) to the Pdd (dark-eye pupae with a dark-pigmented cuticle) stages. In addition, the expression of abaecin was higher in egg-laying than in non-egg-laying female bumblebees. Both E. coli and B. bassiana infections induced the expression of abaecin. Our results indicated that the abaecin gene plays important roles in the development, reproduction and immune responses of bumblebees. During the artificial rearing of bumblebees, a good environment should be created to avoid infection with bacteria or fungi.     

基因表达系列分析法(SAGE)的改进及其在植物功能基因组研究中的应用

基因表达系列分析方法(SAGE)是一种新的基因表达分析方法,与基因芯片技术一样具有高通量的特点,可测定特定组织的基因表达水平,在全基因组水平上同时定量检测数万个基因表达模式;可在未知目的基因的前提下,分析来自一个细胞的全部转录本信息;对已知或未知基因表达进行定性和定量分析.目前,虽然在疾病、发育、细胞凋亡、药物筛选等多个领域已有利用SAGE方法进行的研究,但该方法在植物功能基因组研究中的应用相对较少.本文主要综述了该方法在RNA用量、PCR循环次数、SAGE效能和可靠性、标签长度和未知标签分析等方面的改进及其在植物中构建SAGE文库、筛选新基因、基因表达图谱分析等方面的应用,从而为其在植物功能基因组研究中的进一步应用提供理论参考.     

丹参肉桂醇脱氢酶基因（SmCAD）的克隆及表达分析

肉桂醇脱氢酶（cinnamyl alcohol dehydrogenase,CAD）依赖于NADPH还原肉桂醛及其衍生物,是催化木质素单体生物合成途径的最后一步关键酶。通过分析丹参转录组数据库,从丹参中获得一条肉桂醇脱氢酶基因,命名为SmCAD（Genebank注册号：HQ162287）。该序列包含一个长为1083 bp的开放阅读框,有3个内含子和4个外显子,编码360个氨基酸,含有NADP（H）结合域,Zn1和Zn2锌结合位点。利用BD walking的方法获得其启动子序列1202 bp,序列分析结果表明,SmCAD启动子区包含茉莉酸甲酯（MeJA）、脱落酸（ABA）、赤霉素（GA3）响应元件以及MYB结合位点。利用实时荧光定量PCR分析表明,该基因在丹参根、茎、叶中均有表达,且其表达受到MeJA的诱导和GA3的抑制,推测该基因可能参与了丹参对外源信号的应答反应。研究结果可为进一步研究SmCAD基因在丹参中的具体功能提供理论依据。     

菊芋Na+/H+逆向转运蛋白基因的克隆与表达分析

根据同源序列设计简并引物,通过RT-PCR及RACE的方法从菊芋中克隆了Na /H 逆向转运蛋白基因。序列分析表明,该基因全长2148 bp,开放读码框为1647 bp,可编码长549个氨基酸的多肽,与其它植物已克隆的Na /H 逆向转运蛋白具有很高的同源性。系统发育分析表明该蛋白(HtNHX1)与液泡型Na /H 逆向转运蛋白的亲缘关系较近,与质膜型Na /H 逆向转运蛋白亲缘关系较远。NaCl胁迫条件下RT-PCR检测结果表明,HtNHX1随NaCl浓度增加和处理时间延长表达持续增强,但到了第3天表达量开始下降。HtNHX1逆向转运蛋白基因的转录调控可能是决定菊芋耐盐能力的一个重要因素。     

Performance of a Prototype Baited-trap in Attracting and Infecting the Tick Amblyomma variegatum (Acari: Ixodidae) in Field Experiments

Investigations were commenced to study the potential use of the fungi, Beauveria bassiana, Metarhizium anisopliae, and the attraction-aggregation-attachment pheromone (AAAP) for the control of Ambloyomma variegatum as an environmentally friendly technology. The objective of the study was to develop and test a device, which could be used for pheromone and carbon dioxide delivery and infection of ticks with the fungi in an attempt to control the tick populations in the vegetation. Using a pheromone-baited device treated with the fungi mixture, 79% of the ticks released were attracted and exposed to the fungi and of these, 78% died during incubation in the laboratory. In another set of experiments, of the released ticks that were similarly exposed to fungi using the pheromone-baited device and left in the vegetation, 33.8% were recovered compared to recoveries of between 76 and 84% in the controls. These results were significantly different at the 5% level, an indication that the pheromone/fungi mixtures had significant effect in reducing the tick population in the field.     

草鱼瘦素受体基因片段序列的克隆及其组织表达分析

根据斑马鱼、大西洋鲑和人等物种巴知的瘦素受体基因核苷酸保守区序列设计一对简并引物,通过RT-PCR法从草鱼肝胰脏中首次克隆获得草鱼瘦素受体基因的片段序列.该片段序列长713 bp,编码237个氨基酸,氨基酸序列分析表明草鱼瘦素受体基因片段氨基酸序列与其他物种的相似性在35％ -86％之间.通过邻接法(Neighbor Joining,NJ)构建系统进化树显示,鱼类的瘦素受体独立聚成一支,草鱼与金鱼、斑马鱼聚成一支,再与日本青鳉、黑点青鳉、红鳍东方鲀和大西洋鲑聚成一支.通过实时荧光定量PCR分析草鱼瘦素受体基因的组织差异表达,结果表明,草鱼瘦素受体基因在肝胰脏、肌肉、脑、心脏、脾和肠系膜脂肪组织中均有表达,其中在脾脏组织中表达量最多,显著高于其他组织(P＜0.05),其次是心脏、脑、肌肉和肠系膜脂肪组织,在肝胰脏组织中表达量最低,且显著低于其他组织(P＜0.05).     

Construction and evaluation of pMycoFos, a fosmid shuttle vector for Mycobacterium spp. with inducible gene expression and copy number control

Molecular tools for Gram-positive bacteria such as Mycobacterium are less well-developed than those for Gram-negatives such as Escherichiacoli. This has slowed the molecular-genetic characterisation of Mycobacterium spp, which is unfortunate, since this genus has high medical, environmental and industrial significance. Here, we developed a new Mycobacterium shuttle vector (pMycoFos, 12.5 kb, Km^R) which combines desirable features of several previous vectors (controllable copy number in E. coli, inducible gene expression in Mycobacterium) and provides a new multiple cloning site compatible with large inserts of high-GC content DNA. Copy number control in E. coli was confirmed by the increased Km^R of cultures after arabinose induction and the greater DNA yield of vector from arabinose-induced cultures. Measurement of beta-galactosidase activity in pMycoFos clones carrying the lacZ gene showed that in Mycobacterium smegmatis mc²-155, expression was inducible by acetamide, but in E. coli EPI300, the expression level was primarily determined by the vector copy number. Examination of protein profiles on SDS-PAGE gels confirmed the beta-galactosidase assay results. Construction of a fosmid library with the new vector confirmed that it could carry large DNA inserts. The new vector enabled the stable cloning and expression of an ethene monooxygenase gene cluster, which had eluded previous attempts at heterologous expression.     

Molecular cloning and expression of a major surface protein (the 75-kDa protein) of Porphyromonas (Bacteroides) gingivalis in Escherichia coli

A major immunodominant surface protein (the 75-kDa protein) of Porphyromonas (Bacteroides) gingivalis 381 has been purified and its amino-terminal amino acid sequence has been determined. Using oligonucleotide probes corresponding to the sequence, we identified a recombinant plasmid clone carrying a single 4.2-kb BamHI fragment from pUC19 libraries of P. gingivalis. The BamHI fragment transferred to the bacteriophage T7 RNA polymerase/promoter expression vector system produced a slightly larger (77-kDa) protein, a precursor form, immunoreactive to the antibody against the 75-kDa protein, suggesting that the cloned DNA fragment probably carried an entire gene for the 75-kDa protein. Genomic Southern analysis revealed a single copy of the 75-kDa protein gene per genome among all P. gingivalis strains tested, and that no homologous genes are present in other black-pigmented Bacteroides species. These observations suggest that the 75-kDa protein gene may be useful as a specific DNA probe to classify or to detect this organism.