-
[show abstract]
[hide abstract]
ABSTRACT: Piwi-interacting RNAs (piRNAs) and their partner PIWI proteins play an essential role in fertility, germline stem cell development, as well as the basic control and evolution of animal genomes. However, research was rare with regard to piRNA population in sea urchin, a model animal intensively used for development and genetics studies. Utilizing Solexa sequencing, we present an identification of 13,051 piRNA-like RNAs expressed in male gonad of Strongylocentrotus nudus. Out of 202 tested RNAs, 94 sequences were confirmed to express in female gonad using microarray assay, suggesting that both male and female gonads are piRNA-like RNA-enriched organs. These RNAs with "U" at the 5' end or "A" at position of 10, in size from 26 to 30 nucleotides, were predominantly 28 nt in length and tend to be clustered in small regions in genome, achieving the longest piRNA-like RNA-enriched region about 5.5 kb in scaffold78427. Alignment results showed 11 RNAs were homologous to the known piRNAs. Furthermore, BLASTn searching against sea urchin repeat element database showed these piRNA-like RNAs matched to 101 types of DNA transposons and retrotransposons, of which SPRP1, Harbinger-N2, piggyBac-N10, SINE2-1, and piggyBac-N11 were the most frequent hit elements, suggesting a transposon silencing function of these piRNA-like RNAs.
Marine Biotechnology 12/2011; 14(4):459-67. · 3.43 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Adipose differentiation-related protein (ADRP) is a protein which induced during the early onset of the adipose differentiation program and is expressed at high level in mature adipocytes. In the present study, 1311 bp of ADRP in Peking duck (Anas platyrhynchos) was cloned by reverse transcription (RT)-PCR. The cloned sequence of ADRP was highly conserved, although relevant changes with respect to human, mouse and chicken were identified. Real-time quantitative PCR was used to determine if the ADRP was expressed in different tissues of male and female Peking ducks. The expression of ADRP was widely distributed in all examined tissues. The expression level of it was highest in abdominal fat and lowest (only few) in lung of male and female Peking ducks.
Molecular Biology Reports 11/2010; 38(4):2479-84. · 2.93 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Peroxisome proliferators-activated receptors (PPARs) plays important role in regulate a variety of target genes which involves in lipid metabolism. In the present study, 1,430 bp of PPARalpha and 1,650 bp of PPARgamma in Peking duck (Anas platyrhynchos) were cloned by reverse transcription (RT)-PCR. The cloned sequences of PPARalpha and PPARgamma were highly conserved, although relevant changes with respect to human, mouse, chicken, and goose were identified. Real-time quantitative RT-PCR was used to determine if the PPARalpha and PPARgamma were expressed in different tissues of male and female Peking ducks. The expression of PPARalpha and PPARgamma were widely distributed in all examined tissues. The expression level of PPARalpha was highest in liver and lowest in kidney in male and female ducks. And it was highest in abdominal fat and lowest in small intestine of PPARgamma in male and female ducks.
Molecular Biology Reports 04/2009; 37(3):1235-40. · 2.93 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Human Bocavirus (HBoV) is a novel virus which can cause respiratory tract disease in infants or children. In this study, the codon usage bias and the base composition variations in the available 11 complete HBoV genome sequences have been investigated. Although, there is a significant variation in codon usage bias among different HBoV genes, codon usage bias in HBoV is a little slight, which is mainly determined by the base compositions on the third codon position and the effective number of codons (ENC) value. The results of correspondence analysis (COA) and Spearman's rank correlation analysis reveals that the G+C compositional constraint is the main factor that determines the codon usage bias in HBoV and the gene's function also contributes to the codon usage in this virus. Moreover, it was found that the hydrophobicity of each protein and the gene length are also critical in affecting these viruses' codon usage, although they were less important than that of the mutational bias and the genes' function. At last, the relative synonymous codon usage (RSCU) of 44 genes from these 11 HBoV isolates is analyzed using a hierarchical cluster method. The result suggests that genes with same function yet from different isolates are classified into the same lineage and it does not depend on geographical location. These conclusions not only can offer an insight into the codon usage patterns and gene classification of HBoV, but also may help in increasing the efficiency of gene delivery/expression systems.
Biosystems 07/2008; 92(3):207-14. · 1.78 Impact Factor
