A Systems Biology Approach to Study the Biology Characteristics of Esophageal Squamous Cell Carcinoma by Integrating microRNA and Messenger RNA Expression Profiling

Esophageal squamous cell carcinoma (ESCC) is one of the most malignant tumors. The aim of this study was to investigate the biology characteristics of ESCC by analyzing microRNA and mRNA expression profile. We used BRB-array tools to analyze the deregulated microRNA and mRNA between esophageal squamous cell carcinomas and paired normal adjacent tissues. We used miRTrail and protein–protein interaction methods to explore the related pathways and networks of deregulated microRNA and mRNA. By combining the results of pathways and networks, we found that the deregulated microRNA and their deregulated target mRNA are enriched in the following pathways: DNA replication, cell cycle, ECM-receptor interaction, focal adhesion, mismatch repair, and pathways in cancer. The results showed that many deregulated microRNAs and mRNAs may play a vital role in the pathogenesis of ESCC, and the systems biology approach is very helpful to explore molecular mechanism of ESCC.     

RNA and Macronuclear transcription in the ciliate Stylonychia mytilus

Nuclear and cytoplasmic RNA of Stylonychia mytilus were analyzed on denaturing polyacrylamide gels. The molecular weight of rRNA precursor molecules is within a range of 2.1×10⁶ daltons. A comparison between the electrophoretic pattern of nuclear non-ribosomal RNA and cytoplasmic mRNA indicates that a considerable amount of nuclear RNA sequences is of higher molecular weight than cytoplasmic RNA sequences. The molecular weight distribution of cytoplasmic RNA supports the assumption that also in Stylonychia an average sized mRNA molecule contains 1,200–1,500 nucleotides according to a molecular weight of 4×10⁵ to 5×10⁵ daltons. The size of the polyadenylic acid fragment of poly-A⁺ RNA molecules is about 120 nucleotides. The total mass of cytoplasmic RNA is around 7.5/10¹⁰ g/cell, corresponding to 1.2×10⁷ average sized mRNA molecules per cell. RNA excess hybridization experiments show that 60% of the DNA sequences are transcribed into nuclear RNA and that the cytoplasmic mRNA sequences are homologous to about 40% of macronuclear DNA sequences. There is no indication of different frequency classes within the mRNA. The number of different mRNA species in a Stylonychia cell is 1.2–1.5×10⁴. On the average each of them is present about 1,000 times in every cell.     

Analysis of the temperature-dependent temporal pattern of heat-shock-protein synthesis in fish cells

Continuous exposure of Chinook salmon embryo cells to an elevated incubation temperature of 24°C induces the transient expression of a set of heat-shock or stress proteins whereas maintenance of the cells at a higher incubation temperature of 28°C produces a continuous synthesis of these stress proteins. In vitro translation studies suggest that the temperature-dependent temporal pattern of stress-protein synthesis is correlated with the levels of stress-protein mRNA. This was verified using a recombinant-DNA probe complementary to the 70K heat-shock-protein mRNA. A transient increase in the level of the fish heat-shock 70K mRNA was observed in RNA samples isolated from cells continuously exposed at 24°C However, a constant increase in the level of this specific mRNA was found in RNA preparations obtained from cells maintained at 28°C Therefore, the temperature-dependent pattern of fish heat-shockprotein synthesis appears to be directly related to the level of heat-shock-protein mRNA.     

Possible Correlation of Selenoprotein W with Inflammation Factors in Chicken Skeletal Muscles

The aim of the present study was to investigate the possible correlation of selenoprotein W (SelW) with inflammatory injury induced by dietary selenium (Se) deficiency in chicken. One-day-old male chickens were fed either a commercial diet or a Se-deficient diet for 55 days. Then, the expression levels of SelW messenger RNA (mRNA) and inflammation-related genes (NF-κB, TNF-α, iNOS, COX-2, and PTGES) in chicken skeletal muscles (wing muscle, pectoral muscle, and thigh muscle) were determined at 15, 25, 35, 45, and 55 days old, respectively. In addition, the correlation between SelW mRNA expression and inflammation-related genes were assessed. The results showed that dietary Se deficiency reduced the mRNA expression of SelW in chicken wing, pectorals, and thigh muscles. In contrast, Se deficiency increased the mRNA expression levels of inflammation-related genes in chicken skeletal muscle tissues at different time points. The Pearson’s correlation coefficients showed that the mRNA expression levels of inflammation-related genes were significantly negative related to SelW (p?相似文献   

Progressive induction of β-glucuronidase in individual kidney epithelial cells

The magnitude and kinetics of β-glucuronidase induction in mouse kidney are determined by a cis-acting regulatory gene, Gus-r, that is closely linked to the enzyme structural gene. The accumulation of β-glucuronidase mRNA during induction is much slower than the turnover time of the mRNA, suggesting progressive acquisition of mRNA synthesizing capacity during induction. Counts of the numbers of induced cells present at various times of induction in strains carrying three different alleles of Gus-r show that all potentially responsive cells respond immediately. The level of induction is progressive in individual cells and does not involve continued recruitment of new cells into the induced population. It appears that during induction each chromosome becomes progressively more active in directing the synthesis of β-glucuronidase.     

The action of exogenous gibberellic acid on polysome formation and translation of mRNA in germinating castor-bean seeds

The amount of protein synthesis in germinating castor-bean seeds has been estimated by the quantitative and qualitative exmainatin of polysomes from the seeds in the presence and absence of gibberellic acid (GA₃). Careful optimisation of polysome extraction procedures was required to minimise the ribonuclease activity in the extracts. Ribonuclease activity in seed extracts increased fourfold over the first 5 d of germination. Gibberellic acid stimulated polysome formation about twofold during the first 4 d of germination. It also stimulated the amount of mRNA associated with polysomes by about twofold during the first 3 d of germination. Between days 1 and 5 of germination, polysome formation was primarily limited by mRNA availability. During the period 0–24 h, polysome formation was independent of mRNA levles. The increase in enzyme activities stimulated by GA₃ was probably the result of an increase in the amount of cellular mRNA. No evidence was obtained for an action of GA₃ on translation other than on the increased production of RNA. Examination of the recruitment of isocitrate-lyase mRNA into polysomes showed that GA₃ did not specifically stimulate production of this enzyme.     

Gibberellic-acid-regulated expression of α-amylase and six other genes in wheat aleurone layers

The effect of gibberellic acid (GA₃) on gene expression in wheat aleurone cells has been characterised. In-vitro translation of polyadenylated RNA indicated that α-amylase and other messenger-RNA (mRNA) species increase in relative concentration in GA₃-treated tissue. At least one mRNA species declines in relative level in response to GA₃. There is also a GA₃-dependent, four-fold increase in the level of polyadenylated RNA. This effect is largely the result of increased levels of many mRNA species which are also present in untreated tissue. Seven GA₃-induced polyadenylated RNA species including the Amyl α-amylase gene product have been cloned as complementary DNA in the plasmid pBR322. These cloned DNAs have been used as hybridisation probes to show that the GA₃-induced increase in α-amylase mRNA is more prolonged than the accumulation of the other GA₃-regulated mRNA species. A polyadenylated-RNA sequence showing reduced concentration in GA₃-treated tissue has also been cloned.     

Relative mRNA expression and immunolocalization for transforming growth factor-beta (TGF-β) and their effect on in vitro development of caprine preantral follicles

This study aimed to evaluate the immunolocalization and messenger RNA (mRNA) expression for transforming growth factor-beta (TGF-β) and its receptors (TGF-βRI and RII), as well as mRNA expression for P450 aromatase and FSH receptor in caprine preantral follicles. The effects of TGF-β, FSH alone, or in association on the in vitro follicular development were also assessed. Immunohistochemical analyses showed the expression of TGF-β and its receptors in oocytes of all follicle stages and granulosa cells of primary and secondary follicles. mRNA for TGF-β receptors and for FSH receptor (FSHR) was present in preantral follicles as well as in oocytes and granulosa cells of antral follicles. Isolated secondary follicles were cultured in α-minimum essential medium (MEM) alone or supplemented with either FSH (100 ng/ml), TGF-β (10 ng/ml), or TGF-β + FSH for 18 d. TGF-β increased significantly oocyte diameter when compared to FSH alone and control. After 18 d of culture, all groups showed a significant reduction in P450 aromatase and FSHR mRNA levels in comparison to fresh control. In contrast, treatment with FSH significantly increased the mRNA expression for TGF-β in comparison to fresh control and other treatments. In conclusion, the findings showed that TGF-β and its receptors are present in caprine ovarian follicles. Furthermore, they showed a positive effect on oocyte growth in vitro.     

Polysome assembly and RNA synthesis during phytochrome-mediated photomorphogenesis in mustard cotyledons

The effect of phytochrome (high irradiance reaction, elicited by continuous far-red light) on cellular polysome levels was investigated using ribosome-isolation procedures which prevent the methodological artifacts inherent in previous studies on polysomes. By including the large pool of ribosomal subunits in the analysis and using the ratio (polysomes: monomers + subunits) as a quantitative estimate of the translational capacity of the ribosomes in mustard (Sinapis alba L.) cotyledons, we found the following results: 1) After a lag-phase of less than 30 min, phytochrome induces a massive increase in the relative amount of cytosolic (free) polysomes at the expense of ribosomal subunits. 2) Cytosolic and membrane-bound polysomes are increased by phytochrome in constant proportions (constant ratio of 65:35 in light and darkness). 3) Simultaneously with the light-mediated increase of the polysome level there is an increased incorporation of newly synthesized (labeled) non-ribosomal RNA, presumably mRNA, into the polysomes which can be kinetically discriminated from the slower incorporation of newly synthesized (labeled) rRNA. 4) Cordycepin strongly inhibits the synthesis of RNA and completely prevents the light-mediated increase of polysomes. 5) The electrophoretic patterns of the in-vitro translation products obtained with polysomal polyadenylated RNA from dark-grown and light-grown cotyledons showed no significant qualitative differences. We conclude from these results that photomorphogenesis of mustard cotyledons is related to a massive increase of newly synthesized mRNA leading to a correspondingly increased recruitment of ribosomal subunits into polysomes. The phytochrome-induced increase of translatable mRNA involves mainly quantitative changes in the production of mRNA species which are also present in the dark-grown cotyledons.     

Molecular characterization of argininosuccinate synthase and argininosuccinate lyase from the liver of the African lungfish Protopterus annectens,and their mRNA expression levels in the liver,kidney, brain and skeletal muscle during aestivation

Argininosuccinate synthase (Ass) and argininosuccinate lyase (Asl) are involved in arginine synthesis for various purposes. The complete cDNA coding sequences of ass and asl from the liver of Protopterus annectens consisted of 1,296 and 1,398 bp, respectively. Phylogenetic analyses revealed that the deduced Ass and Asl of P. annectens had close relationship with that of the cartilaginous fish Callorhinchus milii. Besides being strongly expressed in the liver, ass and asl expression were detectable in many tissues/organs. In the liver, mRNA expression levels of ass and asl increased significantly during the induction phase of aestivation, probably to increase arginine production to support increased urea synthesis. The increases in ass and asl mRNA expression levels during the prolonged maintenance phase and early arousal phase of aestivation could reflect increased demand on arginine for nitric oxide (NO) production in the liver. In the kidney, there was a significant decrease in ass mRNA expression level after 6 months of aestivation, indicating possible decreases in the synthesis and supply of arginine to other tissues/organs. In the brain, changes in ass and asl mRNA expression levels during the three phases of aestivation could be related to the supply of arginine for NO synthesis in response to conditions that resemble ischaemia and ischaemia–reperfusion during the maintenance and arousal phase of aestivation, respectively. The decrease in ass mRNA expression level, accompanied with decreases in the concentrations of arginine and NO, in the skeletal muscle of aestivating P. annectens might ameliorate the potential of disuse muscle atrophy.