Journal of Genetic Resources
Volume:6 Issue: 1, winter-spring 2020

The prokaryotic residents of the Tis solar saltern in the southeast of Iran on the shore of Oman Sea were investigated by the culture-dependent methods. Sequencing of the PCR-amplified fragments of 16S rRNA genes revealed that bacterial populations were related to Actinobacteria, Bacteroidetes, Balneolaeota, Firmicutes, and Proteobacteria. They were phylogenetically identified as members of Bacillus (35%), Aliifodinibius (15%), Longibacter (10%), Halomonas (10%), Arthrobacter (5%), Luteimonas (5%), Ornithinibacillus (5%), Rhodovibrio (5%), Staphylococcus (5%),and Tamilnaduibacter (5%). All archaeal isolates were belonged to the order Halobacteriales in the following genera: Haloferax (33%), Haloarcula (27%), Halogeometricum (11%), Halococcus (5%), Halomicroarcula (5%), Halorubrum (5%), Halostagnicola (5%), and Natronoarchaeum (5%). Semi-quantitative evaluation of six hydrolytic enzymes, including amylase, cellulase, lipase, pectinase, protease, and urease among these strains, revealed that urease (47%) and amylase (41%) had the highest production frequency. The average production rates were observed for lipase (25%) and protease (30%), while the pectinase (12%) and cellulase (4%) productions were rare among these halophiles. The most potent bacterial/archaeal strains for the enzymes production were as: Longibacter/Natronoarchaeum (amylase), Bacillus/ non archaeum (cellulase), Tamilnaduibacter/ Haloferax (lipase), Bacillus/ Haloferax (pectinase), Bacillus/ Haloferax (protease), and Staphylococcus/ Halococcus (urease). This first report about the prokaryote populations of the solar salterns in Iran demonstrated its high microbial diversity and potentials for the production of industrially interesting enzymes.

Mints are herbaceous perennial plants with aromatic leaves that are cultivated for their essential oils. The essential oil of Mint used in pharmaceutical, perfumery and cosmetics applications. The aim of this study was to analyze the relationship between nine different genotypes of Mentha spicata and M. piperita collected from different regions of Iran according to the seed storage protein profile using the SDS-PAGE method. The electropherogram showed a total of 31 bands of proteins with the molecular weight ranging from 12 kDa to 103 kDa. Among the genotypes G1, G5 and G9 showed the maximum number (26) of protein bands while the minimum number (9) of bands was present in genotype G7. Cluster analysis based on the seed storage protein profile, using the Euclidean distance matrix and the UPGMA method, grouped the evaluated genotypes into three clusters. Five genotypes (G1, G4, G5, G8, and G9) were in group 1, group two contained genotype G3 and the rest of the genotypes were in the third group (G2, G6, G7). Cluster analysis showed that some of the genotypes of two different species of M. piperita and M. spicata were closely related to each other and were in the same group. With regard to M. piperita is a natural hybrid of M. spicata and M.aquatica, this result is expected. The protein variability analysis clearly showed that there was divergence among and within the studied genotypes. It was concluded that this study will be useful for the future breeding and conservation program of Mentha genotypes.

This study was conducted to evaluate the effect of different extraction solvents, including hydro-alcoholic (H-A), ethanolic (Et-OH), and methanolic (Me-OH), on chemical composition and synergistic antibacterial activity of Frangula alnus extract against Staphylococcus aureus and Escherichia coli. The chemical composition of the F. alnus bark extract was evaluated using FTIR, UV-Vis spectroscopy, and GC/MS analysis. The synergistic antimicrobial effect of the extracts with Ciprofloxacin (CIP) and Erythromycin (ERY) was evaluated using minimum inhibitory concentrations, combined disc, and checkerboard titration method. F. alnus contained alkanes, alkenes, phenols, alcohols, esters, terpenes, fatty acid, tetrazole, halo-alkane, anthraquinone as well aromatic, and plasticizer compounds in the ethanolic, methanolic, and hydro-alcoholic extracts. Total phenolic compounds for ethanolic, hydro-alcoholic and methanolic extracts were recorded 110.92±0.01, 95.27±0.01 and 126.6±0.02 g/L Gallic acid, respectively. Et-OH and H-A extracts in both combined and synergistic forms significantly inhibited bacterial growth. Concerning the antibacterial activity of the extracts, it was assumed that the compounds present in the plant extracts would destroy the bacterial cell membranes and consequently cause leakage of intracellular contents. Therefore these antibiotics in combination with the extracts would be able to affect their target sites (CIP; DNA gyrase and ERY; 50S subunit) more effectively. According to the results, H-A, Me-OH, and Et-OH extract efficiently in the synergistic state with erythromycin and ciprofloxacin can be a promising candidate to be used against bacterial pathogens.

In the current investigation, karyotype analysis and chromosome characteristics of six populations of Calendula officinalis L.(pot marigold) from Iran are studied. Results showed that all populations were diploid (2n= 2x= 32), and had symmetrical karyotypes composing mainly of metacentric and submetacentric chromosomes. The mean chromosome length ranged from 1.05 in Karaj to 1.50 μm in Masjed Soleyman 1. Haploid genome length was in the range of 16.89 to 24.07 μm and mean centromeric index (CI) of complements varied from 0.38 to 0.44, indicating the role of the quantitative genomic changes in the diversification of C. officinalis populations. Cluster analysis using chromosomal parameters and based on the UPGMA method classified studied populations into three major groups. In addition, the principal component analysis revealed the first two components account for 99.8% of the total variance. The results of the present study revealed the natural variation in six populations of C. officinalis, which can further serve conservation and breeding planning.

Antifungal agents are causing different problems in the agriculture industry. Plants are using various defense mechanisms for resistance against fungal pathogens. Some examples of these mechanisms are making physical barriers, producing chemical components and pathogenesis-related proteins such as lipid transfer protein (LTP) and Osmotin which can inhibit the growth of fungi at micro-molar concentrations. In this study, Osmotin and LTP genes were fused by the EAAAK linker to produce a single-fused gene construct. An in silico approach was used to predict and analyze Osmotin-EAAAK-LTP fused protein. Secondary and tertiary structure and mRNA formation of fused protein were predicted using bioinformatics tools. The designed construct was chemically synthesized and cloned in the pUC57 cloning vector. To express the fused protein gene was subcloned in expression vector pET-21b (+) with a hexahistidine tag. This gene was used for prokaryotic expression in E. coliBL21 (DE3) host. Different expression conditions were examined for expressing of fused protein. The fused protein was expressed with 1 mM IPTG after 3 hours of incubation at 28°C. The expression of 36.5 kDa protein was confirmed by western blotting. The study of antifungal activity of expressed fused protein was achieved by radial diffusion assay. This protein was able to exhibit antifungal activity towards experimented plant pathogenic fungi under in vitro conditions.

Osteosarcoma is the most frequent malignant bone tumor with a peak incidence in the second and third decades of life. Diagnosis of patients with osteosarcoma is limited to clinico-pathological parameters whereas molecular markers of tumor initiation and promotion have not yet been identified. We aimed to study the expression of the anti-apoptotic survivin gene in osteosarcoma specimens. A total of 35 formalin-fixed, paraffin-embedded (FFPE) specimens including 25 tumoral and 20 non-tumoral paired-margins were collected. The expression of survivin was evaluated by employing real-time PCR and immunohistochemistry. Our data showed that survivin is differently expressed in osteosarcoma samples rather than non-tumoral margins. Real-time PCR showed that survivin is up-regulated in osteosarcoma specimens compared to margins (p<0.01). Furthermore, IHC confirmed that the survivin protein is significantly found in malignant parts of paraffin blocks. Our data show that survivin expression is modulated in osteosarcoma and may be considered as a diagnostic marker for further studies. Our data showed that survivin is differently expressed in osteosarcoma samples rather than non-tumoral margins. Real-time PCR showed that survivin is up-regulated in osteosarcoma specimens compared to margins (p<0.01). Furthermore, IHC confirmed that the survivin protein is significantly found in malignant parts of paraffin blocks. Our data show that survivin expression is modulated in osteosarcoma and could be considered as a diagnostic marker for further studies.

Tuberculosis is a vagarious infectious disease that generally affects the lungs. Accordingly, in some cases, it can also affect the liver and kidney. Host genetic may affect tuberculosis caused by bacillus Mycobacterium tuberculosis. The main risk factors for the disease are a weakened immune system because of diabetes, some cancers, HIV/AIDS, severe kidney disease, cancer treatment, and malnutrition. Il-33 is involved in the activation of eosinophils, mast cells, basophils, and natural killer cells and the maturation of T helper type2 cells. The developments of CD4 (+) TH1 and CD8 (+) T cell responses are involved in protection against TB, IL-33 promotes the development of these cells. The purpose of the present research was to investigate the association between Mycobacterium tuberculosis infection and IL-33 gene polymorphisms (rs1157505C/G and rs11792633C/T) with tuberculosis in the cases and controls from the area of high tuberculosis prevalence in Iran. In this study, 100 patients with tuberculosis disease and 91 healthy controls were included. Polymorphisms of the IL-33 gene were genotyped using T-ARMS-PCR. The analysis of the haplotype combinations among IL-33 polymorphisms demonstrated that the magnitude of the association was higher for the combined CC/CT genotypes. The CT genotype related to C/T polymorphism of the IL-33 gene increased the risk of tuberculosis. The combined CG+GG genotypes related to C/G polymorphism of the IL-33 gene also increased the risk of tuberculosis, but the difference was not statistically significant. In conclusion, IL-33 gene polymorphisms may be considered as important contributors to tuberculosis in Iran.

Gastric cancer is one of the most common cancers in the world. Late diagnosis is the main cause of the high rate of treatment failure and death among patients with gastric cancer; therefore identifying the molecular basis of cancer initiation and metastasis is so critical for developing efficient methods for early diagnosis and therapy. long non-coding RNAs (lncRNAs) are the largest group of noncoding RNAs, which are involved in cancer pathogenesis. Regarding the roles of lncRNA-HNF1A-AS1 and lncRNA-MVIH in cancer pathogenesis and progression, we aimed to evaluate expression profiles and clinicopathological relevance of these two genes in human gastric cancer. Real-time PCR was performed to assess relative gene expressions in 60 tumoral and non-tumoral gastric tissues. The association between gene expressions and clinicopathological characteristics were also analyzed. Expression and clinicopathological data of the lncRNA-HNF1A-AS1 from 318 gastric cancer patients were also downloaded from the TCGA database. HNF1A-AS1 was down-regulated in GC tissues and MVIH did not show any significant differential expression in GC tissues. Otherwise, the expression of lncRNA-HNF1A-AS1 was significantly higher in TCGA tumor samples. Furthermore, lncRNA-HNF1A-AS1 expression was associated with tumor metastasis and that of lncRNA-MVIH showed association with tumor grade and stage. lncRNA-HNF1A-AS1 expression status did not show any significant correlation with GC overall survival. In conclusion, lncRNA-HNF1A-S1 and lncRNA-MVIH genes may play a critical role in gastric cancer progression. Functional studies on the mechanism of action of these two lncRNAs could help to understand their role in gastric cancer progression.

The importance of grain cultivation especially wheat is obvious in terms of providing human and animal food and its impact on the economy of human societies. The reduction of genetic diversity in cultivars prevents increasing yields in line with rising demand and consumption. Therefore, it is necessary to improve the compatibility of them and increase their genetic extent. In the current, the genetic diversity of Iranian wheat genotypes was investigated at the DNA level using RAPD and ISSR markers. 17 RAPD primers and 16 ISSR primers generated 86 (86/99= %86.86) and 56 (56/64= %57.5) polymorphic bands respectively. The cluster analysis based on UPGMA and dendrogram plotted using NTSYSpc 2.02 software revealed three main clusters. The highest genetic distance was between CD-89-2 and CD-89-7 genotypes and the minimum genetic distance was between CD-89-2 and CD-89-3 genotypes. Based on Nei's genetic distance matrix, the mean number of effective bands, the Shannon index, and polymorphism content were 1.381, 0.332, and % 87.12, respectively. Our results showed that RAPD and ISSR analysis are suitable methods to study genetic diversity and relationships among T. aestivum genotypes.

Breast cancer is a serious health problem worldwide in women. MicroRNAs are small non-coding RNAs of 18–25 nucleotides in length that post-transcriptionally modulate gene expression. MiR-490 has been reported as a tumor suppressor and oncomiR microRNA in breast cancer with two separate targets, NFAT and Rho. NFAT is one of the targets for miR-490 but the relationship between hsa-miR-490 and NFATc3, NFATc4 are not clear yet. Except for NFAT5, the other members of NFAT are activated by Ca2+ influx in the cell, either via the PLC-γ pathway or via store-operated Ca2+ entry, typically in T lymphoid cells. In a cross-sectional comparative study, peripheral blood samples were collected from 30 subjects with breast cancer and 30 healthy individuals as a control group. Gene expression analysis of peripheral blood mononuclear cells (PBMCs) was performed using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to study the NFATc3, NFATc4, and hsa-miR-490-5p gene expression alterations.   As per the obtained results, a significant decrease was observed in the expression level of NFATc4 (P<0.05), while hsa-miR-490-5p expression found to be elevated in PBMCs of breast cancer patient (P<0.05).  Expression changes were not significant for NFATc3 gene (P>0.05). Taken together findings of this study indicated that serum hsa-miR-490-5p acts as an oncomiR by direct targeting the NFATc4.