فصلنامه ژنتیک نوین
سال شانزدهم شماره 2 (پیاپی 65، تابستان 1400)

The present research studied biochemical responses and expression of two important genes in the biosynthetic pathway of steviol glycosides (SGs) of stevia at various levels of salicylic acid (SA) (0, 25, 50, 75 and 100 mM) and of yeast extract (YE) (0, 1, 2, 3 and 5 g/L) under different tissue culture conditions using a completely randomized design with three replications. After 4 weeks of culture, biochemical properties including H2O2, soluble carbohydrates, DPPH, total phenol and total protein contents and expression levels of the DXS and CPPS genes were measured. The results of ANOVA showed that both SA and YE had significant effects on all the studied biochemical traits. There was a linear relationship between DPPH and total phenol contents so that their highest amounts were recorded at 100 mM SA and 5 g/L YE. The highest contents of soluble protein and soluble carbohydrates were recorded at 75 mM and 3 g/L concentrations of the two elicitors. The results of gene expression studies indicated that the elicitors had positive effects on expression levels of the genes. Their highest expression levels were recorded at 50 mM SA and 2 g/L YE. We can conclude from these results that the use of SA and YE is a suitable method for increasing biosynthesis of the bioactive compounds in stevia.

Today, machine-learning approaches are widely used in the analysis of massive data. Due to new technology and the production of high-throughput data in biology (such as next-generation sequencing data), the use of machine learning methods on large biological data can help to understand the mechanism of complex diseases such as cancer. Extraction of candida genes as a therapeutic target or biomarkers from high-throughput biological data such as gene expression data considered as the first step in cancer treatment. Therefore, developing an efficient approach to analyzing such data plays a key role in bioinformatics and computational biology. In this paper, we try to identify lung cancer-related genes as potential biomarkers by applying the WCC algorithm and SVM to lung cancer gene expression data. The data from RNA-Seq technology used for lung cancer samples as well as healthy tissue samples obtained from the TCGA database. These data include the expression of mRNA genes in cancerous and healthy tissue samples. The results of the study led to important findings such as CASZ1 and ASNS, which according to previously published articles have an important role in the formation of cancer and their role in the formation of lung cancer can be examined in future studies. In addition, the validation results of the proposed method show the power of machine learning-based methods in analyzing gene expression data.

Wheat (Triticum aestivum) is one of the most important crops in the world which has strategic importance in providing human food. Bread wheat is an allohexaploid (AABBDD) produced during two hybridizations with its wild ancestors that Aegilops tauschii is considered to be the donor of wheat D genome. In this study, the evolutionary relationship between bread wheat and Ae. tauschii has been discussed using the study of their common miRNAs and target genes. An examination of bread wheat chromosomes and Ae. tauschii shows that the corresponding chromosomes are largely the same in terms of length and number of genes. In this study, five miRNAs transcript from D genome of wheat and common with Ae. tauschii and three new miRNAs identified by bioinformatics approach of RNA Seq were analyzed. Alignment analysis of the desired miRNA sequences in monocotyledon showed that these miRNAs are most similar in wheat and Ae. tauschii and it seems that during the evolution, these genes have been conserved from Ae. tauschii to wheat. The study of the target genes of common miRNAs between wheat and Aegilops tauschii showed that they were very similar in terms of gene anthology as well as the proteins produced from them. Therefore, it seems that these miRNAs have a similar role and functions in these related plants. The findings of this study can be used to better understand the mechanism and function of miRNAs of wheat and Ae. tauschii and their use in wheat breeding projects through their wild relatives.

Barbels Barbus spp. is one of the most important and complex genus of the Cyprinidae family, but some species that are similar in appearance, making it difficult for researchers to identify and separate species or populations of this genus. Nowadays, new methods of DNA-based identification can solve many of the common problems that we face in morphological studies. In the present study, in order to identify and prepare a distribution map of Barbus species in Iran, Namak, Kavir, Caspian, Urmia and Tigris basins were sampled using electro-fisher. After sequencing the COI mitochondrial gene, phylogenetic trees were reconstructed using the Bayesian inference method and Maximum likelihood estimation of phylogeny. According to the results, the presence of four species of B. lacerta, B. karunensis, B. cyri and B. miliaris in the inland water basins of Iran was confirmed. In addition, the results of the mean genetic distance of K2P between species of the genus Barbus in Iran, showed that the highest genetic distance was 3.48 between two species of B. lacerta and B. miliaris and the lowest was 1.17 for two species. Also, according to the results B. urmianus regard as a synonym of B. cyri.

Weeds such as wild mustard are a serious problem in crop production. Herbicide resistance in weeds and wild mustard has become a common threat in agriculture and endangers global food security. In this experiment, the ALS gene of wild weed suspected of weeding due to field screening and PCR-based methods from Kermanshah provincechr('39')s wheat fields was investigated. The ALS gene was then identified, isolated and cloned. For this purpose, primers were designed according to the information available in the NCBI database and ALS gene was amplified using RT-PCR. The gene ALS cloned in pTZ57R / T vector within E. coli bacteria, DH5α strain and sequenced. Based on PCR-based molecular results, six biotypes showed mutations in the target site. PCR-based sequencing results confirm the nucleotide mutations of Asp376-Gly (GAC to GGC), Pro197-Ser (CCT to TCT), Trp574-Leu (TGG to TTG), and Ala122-Thr (GCA to ACA) in six biotypes. These mutation sites were confirmed by sequencing. According to the study, herbicide resistance in wild mustard could be related to resistance in the target site due to the mentioned nucleotide mutations in the active site of the enzyme, the binding site of ALS inhibitors and its family, or due to the resistance of the target site that can cause conformational changes. Changes in the level of the protein reaction site with herbicides and as a result changes in activity and enzyme-herbicide binding. This means that the molecular levels of the mutant enzyme are less likely to come into contact with herbicides, and the herbicide cannot stop the enzyme from working and cause herbicide resistance.

Feverfew (Tanacetum parthenium) is an herbaceous plant belonging to the Asteraceae family, which is one of the valuable medicinal plants that its usage effect has been confirmed in preventing migraine remedy by reducing the swelling, pain and the spasm of the blood vessels. Parthenolide is one of the most important sesquiterpene lactone in feverfew, which contains more than 85% of the total sesquiterpene in this plant and is known as the effective material in this plant. The aim of the present study was to investigate the gene expression of Germacrene A Synthase Tp (GAS) in Feverfew plants under salinity stress and Parthenolide amount changes by HPLC and essence compound by GC/MS method. In the present study, young leaves of Feverfew were placed under different salinity levels (zero salinity EC=3.2, mild salinity EC=6.1, average salinity EC=8.4 and severe salinity EC=10.2). Additionally, the changes in the expression of Germacrene A Synthase Tp (GAS) was investigated using Real Time PCR. The content of produced Parthenolide in leaves was measured by HPLC extraction and essence percentage was measured using GC/MS instrument. The results demonstrated that there was a significant increase in the expression of the studied genes in the leaves of plants under salinity stress compared to the control plants (p≤0.01). Moreover, the highest expression of GAS gene was observed in severe and moderate salinity treatments. Significantly changes in gene expression was accordance with changes in the amount of produced Parthenolide in leaves. Moreover, the essence percentage under stress condition (0.66%) was more than control (0.49%).

Evaluation of genetic diversity in a gene pool contributes to the effective selection of genotypes and shortens the plant breeding programes time. Genetic diversity plays a very important role in reducing genetic vulnerability during breeding process. In the present study, 96 durum wheat breeding line was evaluated for genotypic diversity using 12 SCoT primers. Our results revealed that the SCoT primers generated 76 polymorphic bands, with an average of 5.42 fragments per primer. The values of marker index (MI) and polymorphism information content (PIC) indicated that SCoT markers were efficient for detection of genetic diversity in durum wheat germplasm. The average of PIC and MI values for the SCoT markers were 0.46 and 2.51, respectively. According to Shannon’s index (I), Nei’s genetic diversity (He), the observed (Na) and effective (Ne) number of alleles, the ICARDA population had a higher level of genetic diversity than the CIMMYT’s population. Genetic relationships inferred from a nighbour-joining’s dendrogram clustered all the investigated lines into seven main groups. This clustering was supported by a principal coordinate analysis (PCoA). Our Results indicated a desirable genetic diversity among studied lines and confirmed that the SCoT technique is a suitable tool for studying genetic diversity in durum wheat germplasm.

Cold spring frost is considered as the most important environmental constraint for almond and due to damage to reproductive tissues annually, it causes significant damage to its product. Since little information is available regarding the molecular response of this plant to the frost stress and considering the important role of regulatory microRNA (miRNAs) in many regulatory networks, based on the data from RNA and sRNA sequencing analysis of almond, three microRNA namely, PdumiR160a, PdumiR168 and PdumiR171a with their target genes were selected as cold stress-responsive microRNA. Confirmation of miRNAs expression patterns by quantitative real-time PCR (RT-qPCR) was performed in reproductive tissues of cold-tolerant genotype (H) alongside a sensitive variety (Sh12) under two stress conditions of 0 and -2 ° C. The results showed the negative regulatory role of two miRNAs in response to both cold stresses, but unlike the H genotype, the positive regulatory role of PdumiR168 and PdumiR171a were revealed under cold stress in both reproductive tissues of Sh12 variety. Pearson correlation test showed a negative correlation between PdumiR160a and PduARF18 under both cold stress treatments in the reproductive tissues of Sh12 variety. However, the negative correlation was observed between PdumiR168 and PduAGO1 in ovary tissue of H genotype under two cold stress conditions. Also, in this study, the negative regulatory role of PdumiR171a on the PduSCL6 target gene was revealed under -2 ° C in ovary tissue of H genotype and both reproductive tissues of Sh12 variety.

The spread of resistance to gram-negative bacteria, especially strains of Escherichia coli, has reduced the effectiveness of antibiotics, including ciprofloxacin in the treatment of infectious diseases. The main target of this antibiotic in Escherichia coli is DNA gyrase. GyrI is one of the inhibitors of DNA gyrase that binds to DNA gyrase to prevent the binding of ciprofloxacin. Therefore, the aim of this study was to investigate the expression of gyrI in a ciprofloxacin resistant mutant of Escherichia coli following treatment with ciprofloxacin. To evaluate gyrI expression, cell RNA was extracted at the exponential phase of growth and after cDNA synthesis, gyrI gene expression of ciprofloxacin resistant mutant was measured as compared to wild type strain by Real Time PCR. The results of Real Time PCR showed that the expression of gyrI gene was increased in ciprofloxacin resistant mutant in exponential phase of growth. Increased expression of gyrI in presence and absence of ciprofloxacin in comparison to the wild type strain was significant (P<0.05). Increased expression of this gene in presence and absence of ciprofloxacin in the mutant cell was 63 and 8 times of that in wild type strain, respectively. In conclusion, it seems that in ciprofloxacin resistant mutant GyrI overexpression in exponential phase of growth especially in the presence of ciprofloxacin is an important factor in DNA gyrase inhibition and resistance to ciprofloxacin.