All-Trans Retinoic Acid Induces DU145 Cell Cycle Arrest through Cdk5 Activation

All-trans retinoic acid (ATRA), the active form of vitamin A, plays an important role in the growth arrest of numerous types of cancer cells. It has been indicated that cyclin-dependent kinase 5 (Cdk5) activity can be affected by ATRA treatment. Our previous results demonstrate the involvement of Cdk5 in the fate of prostate cancer cells. The purpose of this study is to examine whether Cdk5 is involved in ATRA-induced growth arrest of the castration-resistant cancer cell line DU145 through up-regulating Cdk inhibitor protein, p27

SpliceInfo: an information repository for mRNA alternative splicing in human genome

We have developed an information repository named SpliceInfo to collect the occurrences of the four major alternative-splicing (AS) modes in human genome; these include exon skipping, 5′-alternative splicing, 3′-alternative splicing and intron retention. The dataset is derived by comparing the nucleotide and protein sequences available for a given gene for evidence of AS. Additional features such as the tissue specificity of the mRNA, the protein domain contained by exons, the GC-ratio of exons, the repeats contained within the exons, and the Gene Ontology are annotated computationally for each exonic region that is alternatively spliced. Motivated by a previous investigation of AS-related motifs such as exonic splicing enhancer and exonic splicing silencer, this resource also provides a means of identifying motifs candidates and this should help to identify potential regulatory mechanisms within a particular exonic sequence set and its two flanking intronic sequence sets. This is carried out using motif discovery tools to identify motif candidates related to alternative splicing regulation and together with a secondary structure prediction tool, will help in the identification of the structural properties of such regulatory motifs. The integrated resource is now available on http://SpliceInfo.mbc.NCTU.edu.tw/

miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs), small non-coding RNAs of 19 to 25 nt, play important roles in gene regulation in both animals and plants. In the last few years, the oligonucleotide microarray is one high-throughput and robust method for detecting miRNA expression. However, the approach is restricted to detecting the expression of known miRNAs. Second-generation sequencing is an inexpensive and high-throughput sequencing method. This new method is a promising tool with high sensitivity and specificity and can be used to measure the abundance of small-RNA sequences in a sample. Hence, the expression profiling of miRNAs can involve use of sequencing rather than an oligonucleotide array. Additionally, this method can be adopted to discover novel miRNAs.</p> <p>Results</p> <p>This work presents a systematic approach, miRExpress, for extracting miRNA expression profiles from sequencing reads obtained by second-generation sequencing technology. A stand-alone software package is implemented for generating miRNA expression profiles from high-throughput sequencing of RNA without the need for sequenced genomes. The software is also a database-supported, efficient and flexible tool for investigating miRNA regulation. Moreover, we demonstrate the utility of miRExpress in extracting miRNA expression profiles from two Illumina data sets constructed for the human and a plant species.</p> <p>Conclusion</p> <p>We develop miRExpress, which is a database-supported, efficient and flexible tool for detecting miRNA expression profile. The analysis of two Illumina data sets constructed from human and plant demonstrate the effectiveness of miRExpress to obtain miRNA expression profiles and show the usability in finding novel miRNAs.</p

i-Genome: A database to summarize oligonucleotide data in genomes

BACKGROUND: Information on the occurrence of sequence features in genomes is crucial to comparative genomics, evolutionary analysis, the analyses of regulatory sequences and the quantitative evaluation of sequences. Computing the frequencies and the occurrences of a pattern in complete genomes is time-consuming. RESULTS: The proposed database provides information about sequence features generated by exhaustively computing the sequences of the complete genome. The repetitive elements in the eukaryotic genomes, such as LINEs, SINEs, Alu and LTR, are obtained from Repbase. The database supports various complete genomes including human, yeast, worm, and 128 microbial genomes. CONCLUSIONS: This investigation presents and implements an efficiently computational approach to accumulate the occurrences of the oligonucleotides or patterns in complete genomes. A database is established to maintain the information of the sequence features, including the distributions of oligonucleotide, the gene distribution, the distribution of repetitive elements in genomes and the occurrences of the oligonucleotides. The database can provide more effective and efficient way to access the repetitive features in genomes

Development of the Swimbladder Surfactant System and Biogenesis of Lysosome-Related Organelles Is Regulated by BLOS1 in Zebrafish

Hermansky-Pudlak syndrome (HPS) is a human autosomal recessive disorder that is characterized by oculocutaneous albinism and a deficiency of the platelet storage pool resulting from defective biogenesis of lysosome-related organelles (LROs). To date, 10 HPS genes have been identified, three of which belong to the octamer complex BLOC-1 (biogenesis of lysosome-related organelles complex 1). One subunit of the BLOC-1 complex, BLOS1, also participates in the BLOC-1-related complex (BORC). Due to lethality at the early embryo stage in BLOS1 knockout mice, the function of BLOS1 in the above two complexes and whether it has a novel function are unclear. Here, we generated three zebrafish mutant lines with a BLOC-1 deficiency, in which melanin and silver pigment formation was attenuated as a result of mutation of bloc1s1, bloc1s2, and dtnbp1a, suggesting that they function in the same complex. In addition, mutations of bloc1s1 and bloc1s2 caused an accumulation of clusters of lysosomal vesicles at the posterior part of the tectum, representing a BORC-specific function in zebrafish. Moreover, bloc1s1 is highly expressed in the swimbladder during postembryonic stages and is required for positively regulating the expression of the genes, which is known to govern surfactant production and lung development in mammals. Our study identified BLOS1 as a crucial regulator of the surfactant system. Thus, the zebrafish swimbladder might be an easy system to screen and study genetic modifiers that control surfactant production and homeostasis.</p

LPS诱导的肺纤维细胞PTEN基因表达和Akt磷酸化蛋白表达的研究

Objective: To investigate PTEN gene expression and the Akt phosphorylation of protein expression in the LPS-induced lung fibroblast, to initially reveal the relation between PTEN gene and the Akt phosphorylated proteins to LPS-induced lung fibroblast proliferation mechanism. Methods: BrdU experiments was performed to evaluate the LPS-induced lung fibroblast proliferation,  RT-PCR and Western Blot analysis were used to analyze the PTEN gene expression and Western blot was performed to analyze Akt phosphorylated protein expression. Results: PTEN mRNA level of the experimental group were significantly lower than the control group (P&lt;0.05) with LPS simulation for 24h and 72h , and there were no significant difference between the experimental group and control group the experimental group and control group (P&gt;0.05) . PTEN protein expression levels of the experimental group were significantly lower than the control group (P&lt;0.05) , at 72h, and PTEN mRNA levels had no significant differences between these of the experimental and control group at 6h,12h and 24h(p&gt;0.05). Phosphorylation Akt protein level (relative to total Akt protein) was significantly higer than the control group (P&lt;0.05) at 24h and 72h, and phosphorylation Akt protein levels had no significant differences between these of the experimental and control group at 6h and 12h (P&gt;0.05) .Conclusion: PTEN gene and phosphorylation Akt protein involve in LPS-induced lung fibroblast proliferation signal transduction pathway.目的  探讨LPS诱导肺成纤维细胞PTEN基因表达和Akt磷酸化蛋白表达，初步揭示LPS诱导的肺成纤维细胞增殖机制中PTEN基因和Akt磷酸化蛋白的变化情况。方法  通过BrdU实验评价LPS诱导肺成纤维细胞增殖情况，通过RT-PCR和Western Blot分析LPS诱导LPS诱导肺成纤维细胞增殖后细胞内PTEN mRNA水平和蛋白表达情况，通过Western Blot分析LPS诱导肺成纤维细胞增殖后细胞Akt磷酸化蛋白表达情况。结果  在6h、12h时实验组和对照组PTEN mRNA转录水平差异无显著性（P&gt;0.05），24h和72h时实验组PTEN mRNA转录水平显著低于对照组（P&lt;0.05）。在6h、12h和24h时实验组和对照组PTEN mRNA转录水平差异无显著性（P&gt;0.05），在72h时实验组PTEN蛋白表达水平显著低于对照组（P&lt;0.05）。在6h、12h时实验组和对照组Akt磷酸化蛋白（相对总Akt蛋白）差异无显著性（P&gt;0.05），在24h和72h实验组Akt磷酸化蛋白（相对总Akt蛋白）显著低于对照组（P&lt;0.05）。结论  PTEN基因和Akt磷酸化蛋白参与了LPS诱导的肺成纤维细胞增殖信号转导途径

Asymptotic Analytical Solutions of First-Passage Rate to Quasi- Nonintegrable Hamiltonian Systems

The first-passage problem of quasi-nonintegrable Hamiltonian systems subject to light linear/nonlinear dampings and weak external/parametric random excitations is investigated here. The motivation is to acquire asymptotic analytical solution of the firstpassage rate or the mean first-passage time based on the averaged Itô stochastic differential equation for quasi-nonintegrable Hamiltonian systems. By using the probability current equation and the Laplace integral method, a new method is proposed to obtain the asymptotic analytical expressions for the first-passage rate in the case of high passage threshold. The associated functions such as the reliability function and the probability density function of first-passage time can then be obtained from the first-passage rate. High passage threshold is the crucial condition for the validity of the proposed method. The random bistable oscillator is studied as an illustrative example using the method. The analytical result obtained from the asymptotic analysis shows its consistency with the Kramers formula. A coupled two-degree-of-freedom (2DOF) nonlinear oscillator subjected to stochastic excitations is studied to illustrate the procedure of acquiring the asymptotic analytical solution. The results obtained from the analytical solution agree well with those from numerical simulation, which verifies the accuracy of the proposed method