Computational Detection of piRNA in Human Using Support Vector Machine.

BACKGROUND: Piwi-interacting RNAs (piRNAs) are small non-coding RNAs (ncRNAs), with a length of about 24-32 nucleotides, which have been discovered recently. These ncRNAs play an important role in germline development, transposon silencing, epigenetic regulation, protecting the genome from invasive transposable elements, and the pathophysiology of diseases such as cancer. piRNA identification is challenging due to the lack of conserved piRNA sequences and structural elements. METHODS: To detect piRNAs, an appropriate feature set, including 8 diverse feature groups to encode each RNA was applied. In addition, a Support Vector Machine (SVM) classifier was used with optimized parameters for RNA classification. According to the obtained results, the classification performance using the optimized feature subsets was much higher than the one in previously published studies. RESULTS: Our results revealed 98% accuracy, Mathew' correlation coefficient of 98% and 99% specificity in discriminating piRNAs from the other RNAs. Also, the obtained results show that the proposed method outperforms its competitors. CONCLUSION: In this paper, a prediction method was proposed to identify piRNA in human. Also, 48 heterogeneous features (sequence and structural features) were used to encode RNAs. To assess the performance of the method, a benchmark dataset containing 515 piRNAs and 1206 types of other RNAs was constructed. Our method reached the accuracy of 99% on the benchmark dataset. Also, our analysis revealed that the structural features are the most contributing features in piRNA prediction.

Estrogen receptor alpha gene expression in breast cancer tissues from the Iranian population--a pilot study.

Estrogen receptor alpha (ERα) is one of the major sub-types of estrogen receptors. ERα plays an important role in cellular proliferation and differentiation, chiefly in mammary tissues. In the present study we aimed to quantify of ERα mRNA and protein expression in breast tissues from the Iranian population using a real-time PCR assay. Twenty nine breast tissues including 19 adenocarcinomas and 10 normal controls were recruited from the Iranian population. mRNA extraction and cDNA synthesis were performed from these tissues using commercial kits. ERα mRNA and protein expression was quantified using real-time PCR and immunohistochemistry respectively. The results showed high expression of ERα mRNA (68%) and protein (53%) in the majority of breast cancer tissues compared to normal breast tissues (p=0.035). Also, high ERα mRNA was associated with tumour size of breast carcinomas. In this study, we first reported the expression of ERα in Iranian patients with breast cancers and demonstrated prevalence of the expression to be similar to breast cancers noted in other populations.

Wool characteristics in the third generation of Arkharmerino × Ghezel and Arkharmerino × Moghani crossbreed sheep.

This investigation was conducted to evaluate the comparative productive performances and effect of some environmental factors on wool characteristics of Arkharmerino × Ghezel (Ar × Gh) and Arkharmerino × Moghani (Ar × Mo) crossbreed sheep. The mid-side fleece samples taken from animals during 2 years (2007-2008) were analyzed. Each sample was measured for average fiber diameter, fiber diameter variability, staple length, proportion of medullated fiber, proportion of kemp, and comfort factor. The comparative values for these fleece characteristics in F(3) generation Ar × Gh were 28.78 ± 0.48 µm, 36.84 ± 1.16%, 11.94 ± 0.35 cm, 7.07 ± 0.93%, 1.02 ± 0.23%, and 68.93%, respectively; while those traits were 29.79 ± 0.43 µm, 41.86 ± 1.16%, 11.96 ± 0.37 cm, 8.13 ± 1.06%, 2.71 ± 0.45%, and 63.33 ± 3.66% for Ar × Mo, respectively. The effects of genotype, sex, birth type, and year of birth were analyzed. Genotype had a significant (P < 0.01) effect on average fiber diameter and proportion of kemp, and Ar × Gh crossbreeds had lower diameter with less proportion of kemp. The two differences in fiber characteristics that were attributable to sex were fiber diameter variability and proportion of medullated fiber, and females had higher measure than males for both traits. Statistical analysis showed that crossbreeding with Arkharmerino generally had positive effects on the fleece favored to be used in the hand woven authentic carpet production.