MicroRNA‐guided gene expression in prostate cancer: Literature and database overview

Insight into the aberrant expression of microRNAs (miRNAs) and the genes that they regulate during the progression of cancer in general and prostate cancer (PCa) in particular is one of the most important issues in current molecular biomedicine and allows for the discovery of therapeutic or diagnostic miRNA targets. The present study aimed to analyze the available data regarding the direct or indirect effects of miRNAs on the expression of the mRNAs involved in carcinogenesis and to enable updating and optimizing the selection of the corresponding targets. The present review focuses on the data related to the genes with miRNA‐dependent expression during the development of PCa. The data used in this review have been extracted from research papers and the databases STRING, PANTHER and TargetScan, with a special focus on the genes directly associated with cell transformation and the maintenance of the transformed genotype, as well as tumor invasion and spread. The search for miRNA markers of PCa and therapeutically active molecules should rely on bioinformatics resources, such as data from recent experimental studies, as well as meta‐analysis and cross‐analysis of the data on the state of the tumor, patient status, histological/immunohistological data and data on mRNA–miRNA coexpression.     

中华蜜蜂OBP3基因的克隆、原核表达及组织表达谱

【目的】气味结合蛋白质（odorant binding proteins, OBPs）参与气味分子的识别,在蜜蜂嗅觉中扮演重要的角色。本研究旨在克隆中华蜜蜂 Apis cerana cerana OBP3基因,以制备多克隆抗体。【方法】运用RT-PCR技术从中华蜜蜂头部总RNA中扩增OBP3基因,将该基因亚克隆入原核表达载体pET-28a并转入大肠杆菌Escherichia coli Rosetta (DE3)中诱导表达获得融合蛋白质,融合蛋白质经纯化后免疫新西兰白兔制备多克隆抗体,最后分别用间接ELISA和Western Blot检测抗体的效价和特异性,并采用荧光定量PCR检测OBP3基因在中蜂不同组织中的表达。【结果】克隆得到了中华蜜蜂OBP3基因AccOBP3（GenBank登录号KJ026357）,大小为444 bp。 SDS-PAGE结果显示融合蛋白成功表达。制备的多克隆抗体效价高于1∶40 000,且具有很高的特异性。荧光定量PCR结果表明,AccOBP3基因在腿部和触角中显著高表达（P<0.01）,胸部中次之（P<0.01）,头部和腹部中显著低表达,后两者表达量差异不显著（P>0.05）。【结论】OBP3基因在中蜂触角有高转录活性。本研究实现了中蜂OBP3基因的原核表达,并制备了兔抗中蜂OBP3多克隆抗体,为深入研究中蜂OBP3基因的功能奠定基础 。     

Depth‐dependent plasticity in opsin gene expression varies between damselfish (Pomacentridae) species

Phenotypic plasticity plays an important role in adapting the visual capability of many animal species to changing sensory requirements. Such variability may be driven by developmental change or may result from environmental changes in light habitat, thereby improving performance in different photic environments. In this study, we examined inter‐ and intraspecific plasticity of visual sensitivities in seven damselfish species, part of the species‐rich and colourful fish fauna of the Great Barrier Reef in Australia. Our goal was to test whether the visual systems of damselfish were tuned to the prevailing light environment in different habitats and/or other aspects of their lifestyle. More specifically, we compared the opsin gene expression levels from individuals living in different photic habitats. We found that all species expressed rod opsin (RH1) used for dim‐light vision, and primarily three cone opsins (SWS1, RH2B and RH2A) used for colour vision. While RH1 levels changed exclusively following a diurnal cycle, cone opsin expression varied with depth in four of the seven species. Estimates of visual pigment performance imply that changes in opsin expression adjust visual sensitivities to the dominant photic regime. However, we also discovered that some species show a more stable opsin expression profile. Further, we found indication that seasonal changes, possibly linked to changes in the photic environment, might also trigger opsin expression. These findings suggest that plasticity in opsin gene expression of damselfish is highly species‐specific, possibly due to ecological differences in visual tasks or, alternatively, under phylogenetic constraints.     

Ontogeny of gene expression in Pomoxis (pisces: Centrarchidae)

The regulation of gene expression during embryogenesis was investigated in white and black crappie (Pomoxis spp.) and their reciprocal interspecific F₁ hybrids. The schedule of morphological development and the timing of isozyme expression were compared among the two species and both reciprocal maternal half-sibling F₁ hybrids. Although absolute rates of morphological development differed in response to incubation temperature, relative rates of morphological development (normalized to the onset of retinal pigment deposition) were similar among all crosses. Furthermore, these relative rates were similar to those previously documented for other centrarchid species. To assess differences in ontogenetic patterns of gene expression among the crosses, we examined expression for 39 enzymeencoding loci. Expression was not detected in the embryos for 16 loci due to low or nonexistent activity. Enzymatic activity from eight other loci were continuously detected throughout embryogenesis as a result of maternal enzyme in the egg. However, 15 loci initiated expression during the early development period investigated (fertilization through yolk sac absorption). We observed temporal variability in expression of these 15 loci among the crosses, either in the form of differential expression between parental species or as disturbances in the ontogeny of expression in interspecific hybrids. Such variability in expression suggests that some of the gene regulating mechanisms have diverged since Pomoxis species shared a common ancestral genome. © 1994 Wiley-Liss, Inc.     

Population genetics of the olive‐winged bulbul (Pycnonotus plumosus) in a tropical urban‐fragmented landscape

With increasing urbanization, urban‐fragmented landscapes are becoming more and more prevalent worldwide. Such fragmentation may lead to small, isolated populations that face great threats from genetic factors that affect even avian species with high dispersal propensities. Yet few studies have investigated the population genetics of species living within urban‐fragmented landscapes in the Old World tropics, in spite of the high levels of deforestation and fragmentation within this region. We investigated the evolutionary history and population genetics of the olive‐winged bulbul (Pycnonotus plumosus) in Singapore, a highly urbanized island which retains <5% of its original forest cover in fragments. Combining our own collected and sequenced samples with those from the literature, we conducted phylogenetic and population genetic analyses. We revealed high genetic diversity, evidence for population expansion, and potential presence of pronounced gene flow across the population in Singapore. This suggests increased chances of long‐term persistence for the olive‐winged bulbul and the ecosystem services it provides within this landscape.     

飞蝗发育相关基因Omb的克隆、原核表达及时空表达分析

【目的】本研究克隆飞蝗Locusta migratoria发育相关的optomotor-blind(Omb)基因,并对其进行序列和表达分析,旨在更好地了解Omb基因在飞蝗翅发育中的作用及为进一步蝗灾的治理和防治提供新的理论依据。【方法】利用RT-RCR扩增飞蝗Omb基因cDNA序列,采用生物信息学软件分析该基因的核苷酸和氨基酸序列,利用MEGA 6. 0构建昆虫纲分子系统进化树;构建重组表达载体pET-30a/LmOmb,转化到大肠杆菌Escherichia coli BL21(DE3)中,SDS-PAGE及Western blot鉴定重组表达蛋白;基于qPCR技术分析Omb基因在飞蝗不同发育时期及成虫不同组织中的表达谱。【结果】克隆获得飞蝗Omb基因部分cDNA序列,命名为LmOmb(GenBank登录号:MG867658),其长792 bp,编码264个氨基酸,在第37-219位氨基酸之间存在一个T-box superfamily保守结构域。同源序列比对分析表明Lm Omb与褐飞虱Nilaparvata lugens Nl Omb氨基酸序列一致性为93%。在IPTG诱导下目标蛋白以6×His标签融合蛋白的形式在宿主菌中得到稳定表达。荧光定量PCR结果显示LmOmb基因在飞蝗不同发育时期均有表达,其中胚胎期的表达量最高,进入若虫期后表达量下降,且各龄若虫之间表达量相对平稳。Lm Omb基因在雌性和雄性成虫的胸部、足、腹部和翅中都有表达,且雌性和雄性之间表达量明显不同。【结论】LmOmb基因可能参与了飞蝗的胚胎发育。研究结果为进一步研究飞蝗LmOmb的功能提供了依据。     

Enhanced expression of the human chitinase 3-like 2 gene (YKL-39) but not chitinase 3-like 1 gene (YKL-40) in osteoarthritic cartilage

The knowledge of molecular alterations in osteoarthritic cartilage is important to identify novel therapeutic targets or to develop new diagnostic tools. We aimed to characterize the molecular response to cartilage degeneration by identification of differentially expressed genes in human osteoarthritic versus normal cartilage. Gene fragments selectively amplified in osteoarthritic cartilage by cDNA representational difference analysis included YKL-39 and the oesophageal-cancer-related-gene-4 (ECRG4). YKL-39 expression was significantly upregulated in cartilage from patients with osteoarthritis (n=14) versus normal subjects (n=8) according to real-time PCR (19-fold, p=0.009) and cDNA array analysis (mean 15-fold, p<0.001) and correlated with collagen 2 up-regulation. In contrast, the homologous cousin molecule YKL-40 (chitinase 3-like 1), which is elevated in serum and synovial fluid of patients with arthritis, showed no significant regulation in OA cartilage. Enhanced levels of YKL-40 may, therefore, be derived from synovial cells while modulation of YKL-39 and collagen 2 expression reflected the cartilage metabolism in response to degradation.     

The ornithine aminotransferase gene in gyrate,atrophy of the retina: Analysis of expression and gross structure of this gene in cultured fibroblasts

Summary Gyrate atrophy (GA), a degenerative disease of the human chorioretina, is associated with a deficiency of ornithine aminotransferase (OAT) activity, hyperornithinemia, and ornithinuria. We have characterized a cDNA clone for OAT (HLOAT) that was isolated from a cDNA library constructed from mRNA prepared from Hep G2, cells, a human hepatoma cell line. We have used HLOAT and a nearly full length OAT cDNA clone isolated from, a rat liver library (RLOAT) to examine in cultured fibroblasts from individuals with GA and control individuals, the expression of OAT mRNA and the gross structure of the OAT gene. Northern blot analyses of total cellular RNA indicated that 3 of 3 control cell lines and 5 of 6 GA cell lines are capable of expressing an OAT related mRNA of approximately 2100 bases, the size of OAT mRNA. To date, this is the only case of GA in which a complete lack of OAT mRNA has been observed. Southern blot analyses of DNA isolated from these cell lines indicated that the gross structure of the OAT gene is usually not detectably altered in individuals with GA. However, a unique pattern, of restriction fragments was observed upon digestion with Eco RI or Hind III of DNA from the GA cell line that does not express OAT mRNA. These unique Eco RI and Hind III fragments arise from the OAT structural gene and will serve as useful molecular markers that allow this particular defective OAT allele to be identified. When the cellular DNAs were digested with Hinf I and examined with a probe that corresponds to at least a portion of the active site of the enzyme, i. e., the pyridoxal phosphate binding site, identical patterns of fragments were detected in all samples. Therefore, it appears unlikely that the loss of OAT activity associated with these GA cases, 4 of which are pyridoxal phosphate responders, is the result of insertions or deletions in this region of the OAT gene. This study indicates that the lack of OAT enzyme activity associated with GA is the result of a variety of different molecular defects within the OAT gene. This project was initiated in the laboratory of H. C. P. and was supported by grants CA07175, CA22484, and 5 T32 CA09020 from the National Cancer Institute and Postdoctoral Fellowship PF-2414 from the American Cancer Society. The continuing work in the laboratory of J. D. S. was supported by grants CA36727 and HD24189 from the National, Institutes of Health, grants SIG-16, ACS-IN165A, and a Junior Faculty Research Award (JFRA-227) from the American Cancer Society, and by University of Nebraska Medical Center Seed Research Grant 88-10.     

Embryonic stages and eye‐specific gene expression of the local cyprinoid fish Anabarilius grahami in Fuxian Lake,China

Anabarilius grahami is a cyprinoid fish endemic to Fuxian Lake, Yunnan, China. In this study, a comprehensive staging series of A. grahami was produced. The embryonic development of A. grahami was divided into six main periods: zygote period, cleavage period, blastula period, gastrula period, segmentation period and hatching period. Its embryonic development is essentially similar to that of zebrafish Danio rerio but relatively slower. The expression patterns of A. grahami sox2, pax6a, six3a and rx2 genes were also cloned and checked during eye development. The four genes showed similar expression patterns to their D. rerio homologues, suggesting the evolutionary conservation of the regulatory network of eye development.     

Serum withdrawal up‐regulates human SIRT1 gene expression in a p53‐dependent manner

SIRT1, a nicotinamide adenine dinucleotide (NAD⁺)‐dependent histone/protein deacetylase, has been extensively studied recently for its critical role in the regulation of physiology, calorie restriction and aging. Studies on laboratory mice showed that expression of SIRT1 can be induced by starvation in a p53‐dependent manner and requires the p53‐binding sites present in the Sirt1 promoter. However, it remains to be determined whether these findings based on rodents apply to human beings. In this paper, we characterized a putative p53‐binding element in the human SIRT1 promoter that might be required for the up‐regulation of SIRT1 in response to nutritional stress. The p53‐binding site in the promoter of human SIRT1 is more deviant from the consensus sequence than the corresponding sequence in the mouse Sirt1. There is a C to A change at the second half site in human SIRT1, thus disrupting the core‐binding element CWWG in the canonical RRRCWWGYYY. To test whether such sequence change would affect its binding with p53 and the SIRT1 expression under stress, we studied various human cell lines with different p53 status and cells with ectopic expression of functionally distinct p53. We found that serum withdrawal also up‐regulates human SIRT1 gene expression in a p53‐dependent manner and that the p53‐binding element in SIRT1 is required for the up‐regulation. Thus, the mechanism responsible for the regulation of SIRT1 expression by p53 is conserved between mice and human beings.     

Bisphosphonates induce the osteogenic gene expression in co‐cultured human endothelial and mesenchymal stem cells

Bisphosphonates (BPs) are known to affect bone homeostasis and also to have anti-angiogenic properties. Because of the intimate relationship between angiogenesis and osteogenesis, this study analysed the effects of Alendronate (AL) and Zoledronate (ZL) in the expression of endothelial and osteogenic genes on interacting endothelial and mesenchymal stem cells, an issue that was not previously addressed. Alendronate and ZL, 10⁻¹²–10⁻⁶ M, were evaluated in a direct co-culture system of human dermal microvascular endothelial cells (HDMEC) and human bone marrow mesenchymal stem cells (HMSC), over a period of 14 days. Experiments with the respective monocultures were run in parallel. Alendronate and ZL caused an initial dose-dependent stimulation in the cell proliferation in the monocultures and co-cultures, and did not interfere with their cellular organization. In HDMEC monocultures, the expression of the endothelial genes CD31, VE-cadherin and VEGFR2 was down-regulated by AL and ZL. In HMSC monocultures, the BPs inhibited VEGF expression, but up-regulated the expression of the osteogenic genes alkaline phosphatase (ALP), bone morphogenic protein-2 (BMP-2) and osteocalcin (OC) and, to a greater extent, osteoprotegerin (OPG), a negative regulator of the osteoclastic differentiation, and increased ALP activity. In co-cultured HDMEC/HMSC, AL and ZL decreased the expression of endothelial genes but elicited an earlier and sustained overexpression of ALP, BMP-2, OC and OPG, compared with the monocultured cells; they also induced ALP activity. This study showed for the first time that AL and ZL greatly induced the osteogenic gene expression on interacting endothelial and mesenchymal stem cells.     

棉卷叶野螟泛素基因的克隆、序列分析及原核表达

本研究用RT-PCR方法,克隆了棉卷叶野螟Haritalodes derogata (Fabricius)泛素基因编码区,GenBank登录号为EU580145。序列分析表明,该编码区长228 bp,编码76个氨基酸,推测的编码蛋白的相对分子质量和等电点分别为8.53 kD和5.83。同源性比较发现,棉卷叶野螟泛素基因与其他10种昆虫泛素基因在氨基酸水平上具有93%以上的相似性。系统发育树显示棉卷叶野螟与斜纹夜蛾Spodoptera litura (Fabricius)遗传距离较近,通过同源建模获得了该棉卷叶野螟基因编码蛋白的理论三维结构。将棉卷叶野螟泛素基因与pET-32a(+)连接,构建原核表达载体pET-32a-ub,经IPTG诱导,棉卷叶野螟泛素基因在大肠杆菌BL21(DE3) 中高效表达。本研究成功克隆了棉卷叶野螟泛素基因的编码区,并经Western blotting分析证明实现了该基因的原核表达,为进一步研究其在该昆虫体内的作用机理奠定了基础。     

扶桑绵粉蚧组织蛋白酶B基因的克隆、原核表达和不同发育阶段表达分析

昆虫组织蛋白酶B在昆虫代谢过程中发挥重要作用。本研究利用RACE技术克隆了扶桑绵粉蚧Phenacoccus solenopsis Tinsley组织蛋白酶B基因的开放阅读框（ORF）序列, 命名为PsCb （GenBank登录号: JQ727999）。生物信息学分析表明, 该基因的开放阅读框包含927 bp的片段, 编码308个氨基酸。多序列比对表明, 该基因编码的蛋白在N端变异较大, 在C端保守性高。组织蛋白酶B基因的系统进化树结果表明扶桑绵粉蚧组织蛋白酶独自成为一支。原核表达电泳检测到一条大约35 kDa的目的条带, 与预测的蛋白分子量相符。组织蛋白酶B基因在扶桑绵粉蚧各个虫态均有表达, 卵期表达量相对较低, 2龄若虫期达到最高峰, 然后下降。本研究为进一步研究该基因的功能并开发出组织蛋白酶抑制剂, 从而研制出扶桑绵粉蚧杀卵剂和胚胎发育抑制剂等提供理论依据。     

沙葱萤叶甲核糖体蛋白基因GdRpS3a的克隆、分子特性及表达分析

核糖体蛋白(ribosomal protein,Rp)是一类参与蛋白质合成、细胞代谢、机体免疫及信号传导等重要功能的蛋白质.本研究旨在克隆沙葱萤叶甲Galeruca daurica核糖体蛋白S3a基因cDNA全长序列,分析其分子特性和表达模式,以期为进一步研究其在沙葱萤叶甲生长发育及滞育中的作用提供必要的基础.根据现有...