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

Transient expression of foot and mouth disease virus [FMDV] coat protein in tobacco [Nicotiana tabacom] via agroinfiltration

Transient and stable transformation of host plants are the common techniques to produce transgenic plants. However, the main drawback of stable transformation is the fact that it takes quite a long time to produce a transgenic line. While, transient gene expression is a quick method to produce recombinant proteins in plants. The main goal of the present study was to evaluate efficient agroinfiltration as an efficient and rapid method for production of recombinant antigen of FMDV. Tobacco leaves were transformed via agroinfiltration using a needle-free syringe. Presence of the gene cassette was verified by polymerase chain reaction [PCR]. Expression of the foreign gene was evaluated using Real Time PCR, protein dot blot and enzyme-linked immunosorbent assay [ELISA]. PCR analysis confirmed successful transformation of plant leaves. Expression of foreign protein was confirmed at both transcription and translation levels. Results of Real Time PCR assay indicated that the foreign gene was transcribed in transformed leaves. ELISA results showed that the foreign gene was expressed in the transformed leaves in high level. Here, the efficacy of agroinfiltration for transient expression of FMDV coat protein in tobacco was illustrated. Accordingly, transient agroinfilteration expedites the process of recombinant antigens expression in plant tissues

Quantiation of IL-4, IL-10 and IFN-gamma genes expression after immunization of mice with CFP-10 and ESAT-6 containing vectors

Tuberculosis is a disease with high morbidity, caused mainly by Mycobaterium tuberculosis [M.tb.]. DNA vaccines show a promising future due to their unique advantages over conventional methods. The early-secreted antigen target [ESAT]-6 and culture filtrate protein [CFP]-10 of M.tb. antigens have been identified as vaccine candidates against Mycobacteria and used as subunit vaccines, DNA or protein, in different studies. To investigate the potential of pcDNA3.1+ plasmid containing CFP-10 and ESAT-6 genes in induction of local immune responses after intramuscular injection in BALB/c mice. pcDNA 3.1+ CFP-10 and pcDNA3.1+ ESAT-6 plasmids were prepared and defined groups of mice were injected intramuscularly with the plasmids both separately and in combination. The RNA was extracted from muscles after one month and cDNA was made using RT-PCR. The expressions of IL-4, IL-10 and IFN-gamma genes cytokines were evaluated using comparative real time PCR. Expression of IL-4 and IL-10 increased in the injection site of the mice groups which received plasmids encoding ESAT-6 and CFP-10 individually or together. More than 10-fold increase in IFN-gamma expression was found in samples taken from mice groups inoculated by plasmids encoding ESAT-6 and CFP-10 individually or together. pcDNA 3.1+ESAT-6 and pcDNA3.1+CFP-10 plasmids can increase the expression of IFN-gamma in mice after immunization.