Journal of Genetic Resources
Volume:4 Issue: 1, Winter-Spring 2018

Emerging evidence implicates that a large fraction of human genome was transcribed but the transcripts known as long non coding RNA are not translated into proteins. They are contributing in different cellular processes, including cellular proliferation and apoptosis. LncRNAs were found to play critical roles in many diseases and act as key regulators in malignancies. In this study, we investigated the expression and clinical significance of ZEB1-AS1 in colorectal cancer. In the present study, 64 samples including 32 samples of colorectal tumor and 32 matched tumor marginal samples were obtained from Iran National Tumor Bank (Tehran, Iran). RNA extraction was performed with TRIzol reagent and cDNA was synthesized using MMULV reverse transcriptase enzyme. The expression of ZEB1-AS1 in tumors and marginal tissues was determined by using real time PCR. We found that the expression level of ZEB1-AS1 was much higher in tumor tissues compared to marginal samples. Moreover, in tumor group, ZEB1-AS1 expression was significantly upregulated in high-grade tumors in comparison to low-grade ones. Additionally, we observed the expression of  ZEB1-AS1 was much higher in lymph node metastatic tumors compared to non-lymph node metastatic ones. Our data showed that the ZEB1-AS1 was dramatically overexpressed in colorectal cancer tissues. The results of the study revealed that the expression of ZEB1-AS1 is correlated with tumor stage, lymph node metastasis and vascular invasion. Based on our findings, we suggested that ZEB1-AS1 might be considered as a tumor marker with potential diagnostic, prognostic and therapeutic value for aggressive and metastatic colorectal cancers.

Booroola gene is one of the major genes in the enhancement of ovulation rate and could be an attractive candidate gene for ovulation rate in sheep. Molecular technologies have been widely used for discovery of mutations in animal species. These mutations have major effects on the important economic traits of sheep and goats. This study was conducted to identify the mutation in FecXG region of exon 2 of BMP15 gene which is associated with twining using polymerase chain reaction-restriction fragment length polymorphism method in Hisari Sheep. For this purpose, blood samples were obtained from 110 sheep. DNA was extracted using the salting out method and quantity and quality properties of DNA were determined using electrophoresis gel. Afterward, a 141 bp fragment, which contains the given polymorphic site of BMP15 gene, was amplified by the specific primers. Restriction enzyme (HinfI G/ANTC) cuts the "wild-type" allele and as a result of digestion, 112 and 29 bp fragments produced. Mutant type allele is not cut because of the removal of the intended cutting site. All the samples showed the similar monomorphic of genotype (+/+) (wild genotype). Results of this study indicate that the investigated polymorphism is not present in the hisari sheep

In order to compare the efficiency of morphological traits and molecular markers in distinguishing the Consolida species, molecular analysis using nrDNA ITS and cpDNA trnL-trnF with maximum parsimony and Bayesian methods were done in a total of 34 species and forma representing 28 species of Consolida, 6 species of Aconitella, plus two species of Delphinium and two species of Aconitum as out groups.  Beside phenetic analysis for 20 quantitative morphological traits in 17 species of Consolida in Iran are performed. The molecular analysis, based on successive reweighting by rescaled consistency index, revealed that Maximum parsimony method and Bayesian analysis gave very similar results based on individual and combine data sets. In the combined analysis (chloroplast and nuclear DNA) recovered most parsimonious trees (L= 558 steps, CI=0.695, RI=0.827). The ITS results revealed that Consolida is not monophyletic and the genus Aconitella is clearly nested within Consolida. Our results confirms the decrease of C. paradoxa Bunge to a forma of C. rugulosa also confirmed the decrease of C. kabulica as a variety of C. stokciana. One way ANOVA, principal component analysis (PCA) and cluster analysis were used in phenetic analysis to visualize the species among different traits. Most of the quantitative morphological traits which showed significant differences between populations were deleted. PCA and cluster analysis carried out for morphological traits divided the Consolida species in to two cluster and A. barbata has separated from other species. Aconitella species are located in separate cluster and location of other species are almost similar to molecular results.

The NorA efflux pump considered as one of the contributors to antibiotic resistance in Staphylococcus aureus strains. One of the challenges of the researchers is finding natural plant compounds with the ability to inhibit the pumps. The aim of this study was to investigate the inhibitory effect of thyme (Thymus vulgaris) extract on NorA efflux pump in ciprofloxacin-resistant strains of S. aureus. Here, by using polymerase chain reaction (PCR), the presence of norA efflux pump was identified in 10 clinical and standard ciprofloxacin-resistant strains of S. aureus. The extract of thyme (T. vulgaris) was prepared using ethanol solvent and the effect of the extract against norA efflux pump was investigated by ethidium bromide method. In the following, after exposure to sub minimum inhibitory concentration of the extract, norA gene expression was evaluated using real-time polymerase chain reaction. Finally, we used the gas chromatography mass spectrometry (GC-mass) method to characterize the compounds with antibacterial properties. The results of PCR showed that all strains had a norA efflux pump, and ethidium bromide phenotypic method indicated that thyme extract had an inhibitory effect on all resistant strains with norA efflux pump. The norA gene expression in ciprofloxacin-resistant strains also decreased in sub minimum inhibitory concentration of the extract. By using gas chromatography- mass spectrometric, five chemical compounds of thymol, carvacrol, indole, 2-methoxy-4-methylphenol and quinic acid were determined as the dominant compounds of thyme (T. vulgaris) extract. Due to the antiefflux pump effect of thyme extract, it seems that this plant extract can be used as a good antibacterial component in the pharmaceutical industry of Iran.

Beta-thalassemia is one of the most common autosomal recessive disorders in the world population resulting from over 200 different mutations of HBB gene. Beta-thalassemias are caused by point mutations or, more rarely, deletions in the HBB gene leading to reduced (beta+) or absent (beta0) synthesis of the beta chains of hemoglobin (Hb). High-resolution melting of polymerase chain reaction (PCR) products can detect heterozygous and most homozygous mutations without electrophoretic or chromatographic separations. In the current study, blood samples collected from 20 individuals carrying minor thalassemia were genotyped using HRM technique. The genotype of each sample had been previously determined via the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP)/ amplification-refractory mutation system (ARMS) or sequencing method. This study aimed to determine the specificity and sensitivity of HRM method in the diagnosis of carriers of FSC 36-37 (-T) mutation from carriers who do not have this mutation. DNA extraction from peripheral blood was performed and HRM method was used to genotype samples. The results were analyzed according to the normalized and difference plot. High-resolution melting analysis could correctly identify all carriers of FSC 36-37 (-T) from who did not have this mutation. In summary, HRM is a technique associated with high sensitivity and specificity. Therefore, HRM is an appealing technique for the identification of FSC 36-37 (-T) mutation.

Cadmium (Cd), as a widespread metal pollutant, readily accumulates in the food chain due to its easy absorption and high mobility. The endophytic fungi are cosmopolitan microorganisms that occur widely in association with plants in a heavy metal stress environment. A current pot experiment was conducted to evaluate the influence of Piriformospora indica, as a root endosymbiotic fungus, on the biomass and biochemical responses of sunflower cv. Zaria under excessive Cd concentrations (0, 40, 80 and 120 mg Cd/kg) in the soil, in a 2 × 4 factorial randomized block design in five replicates. In response to increasing Cd levels in soil, root colonization, growth parameters, and total chlorophyll and carotenoids contents were significantly reduced (P < 0.05), whereas root and leaf Cd accumulation, malondialdehyde (MDA) amount and the antioxidant enzymes activities of catalase (CAT), guaiacol peroxidase (POD), ascorbate peroxidase (APX) and superoxide dismutase (SOD) were increased (P < 0.05). Under different levels of Cd in soil, presence of P. indica (in inoculated sunflowers) had a significant increase (P < 0.05) on growth rate, photosynthesis pigments content, root Cd accumulation, and activities of CAT, POD, APX and SOD in compare to absence of P. indica (in non-inoculated ones). Also, P. indica-inoculated plants showed a reduced MDA concentration and leaf Cd accumulation than un-inoculated sunflowers. The results indicated that P. indica, as an appropriate fungal association, can improve tolerance of sunflower to Cd toxicity through increased levels of photosynthesis pigments and antioxidants, and reduced Cd accumulation and MDA content of the leaf. Therefore, this root endophyte can be modulated cadmium toxicity in Helianthus annuus under excessive cadmium in soil, and recommended as a complement crop-growing strategy in the fields under Cd-contaminated soils, for other studies.

Now, it is clear that protein is just one of the most functional products produced by the eukaryotic genome. Indeed, a major part of the human genome is transcribed to non-coding sequences than to the coding sequence of the protein. In this study, we selected three long non-coding RNAs namely AK082072, AK043754 and AK082467 which show brain expression and local region conservation among vertebrates. Thus, the sequences of these genes are appropriate for phylogenetic analysis. In order to evaluate the evolutionary and molecular trend of lncRNAs in vertebrates, phylogenetic analysis and natural selection process were analyzed during evolution. The nucleotide sequences of selected long non-coding RNAs from different vertebrates were aligned and the phylogenetic trees were constructed using Neighbor Joining method with maximum sequence differences of 0.75. Our analysis of nucleotide sequences to find closely evolved organisms with high similarity by NCBI-BLAST tools and MEGA7 showed that the selected sequence of AK082072 in human and M. fascicularis (macaque) were placed into the same cluster and they may originate from a common ancestor. In addition, the human sequence of AK082467 and AK043754 had the closest similarity with cow. Also, bioinformatic analysis showed that the dN/dS ratio is lower than 1 for all three genes which demonstrates purifying selection for the longest predicted ORF of each lncRNA. Together, these results indicate that lncRNAs act as regulatory genes that have important roles in development.