Saad Badday Betti; Mojtaba Tahmoorespur; Ali Javadmanesh
Abstract
Long non-coding RNAs (lncRNAs) compose a plentiful category of transcripts that have gained increasing importance because of their roles in different biological processes. Although the function of most lncRNAs remains unclear. They are implicated in epigenetic regulation of gene expression, including ...
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Long non-coding RNAs (lncRNAs) compose a plentiful category of transcripts that have gained increasing importance because of their roles in different biological processes. Although the function of most lncRNAs remains unclear. They are implicated in epigenetic regulation of gene expression, including muscle development and differentiation. We aimed to identify the effect of novel lncRNAs (Alternatively spliced) and their target genes on two stages of sheep skeletal muscle growth and development. FastQC files have been used to examine the quality control and the Trimmomatic program for trimming low-quality reads from twelve longissimus dorsal muscle tissue samples (including six young and six old from Texel sheep). Hisat2, Cufflink, Cuffmerge, and Cuffdiff investigated the expression levels. Novel lncRNAs (Alternative spliced) were distinguished using NONCODE databases and Cuffcompare software. In addition, the lncRNA–mRNA interactions and regulatory network visualization were identified via RIsearch and Cytoscape software, respectively. Those 139 novel lncRNA (Alternative spliced) transcripts had been recognized, probably 65 lncRNAs interacted with their target genes and regulated sheep skeletal muscle growth and development. Three novel lncRNA transcripts (TCONS_00041386, TCONS_00050059, and TCONS_00056428) showed a strong association and five transcripts (TCONS_00055761, TCONS_00055762, TCONS_00055763, TCONS_00055764, and TCONS_00055770) had made complex network correlations with mRNAs. Our research provided more knowledge of the associated mechanisms with novel lncRNAs, which could play a role in regulating sheep skeletal muscle tissue development and growth.
Seyedeh Nahid Fotuhi; Mohammad Khalaj-Kondori; Hadis Karimi
Abstract
Patients with ovarian cancer are mostly diagnosed at advanced stages which leads to poor prognosis and high mortality rate. Deregulation of lncRNA HOXD-AS1 expression associates with cancer development and metastasis. However, the expression level of this lncRNA in ovarian cancer ...
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Patients with ovarian cancer are mostly diagnosed at advanced stages which leads to poor prognosis and high mortality rate. Deregulation of lncRNA HOXD-AS1 expression associates with cancer development and metastasis. However, the expression level of this lncRNA in ovarian cancer is not determined.50paired ovarian tumors and their adjusted normal tissues were included in the study. Total RNA was extracted by TRIzol® Reagent and reverse-transcribed to cDNA using PrimeScript II cDNA synthesis kit. The expression levels of HOXD-AS1 were quantified by qRT-PCR and compared. The Roc curve analysis was used to evaluate the capacity of HOXD-AS1 as a biomarker for ovarian cancer. We observed that lncRNA HOXD-AS1 was significantly upregulated in ovarian tumors compared to their adjusted normal tissues (p <0.003). Moreover, the ROC curve analysis revealed that the lncRNA HOXD-AS1 expression level could discriminate tumoral and non-tumoral tissues with 85% sensitivity and 88% specificity. The lncRNA HOXD-AS1 expression level might be considered as a potential biomarker for ovarian cancer development.
Mina Jahandideh; Ebrahim Barzegari
Abstract
MicroRNAs are interesting as cancer diagnostic and prognostic biomarkers because of their unique tissue expression profiles, higher stability in the blood in comparison to mRNAs, and the possibility for reliable quantification. In the case of prostate cancer (PCa), it is currently ...
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MicroRNAs are interesting as cancer diagnostic and prognostic biomarkers because of their unique tissue expression profiles, higher stability in the blood in comparison to mRNAs, and the possibility for reliable quantification. In the case of prostate cancer (PCa), it is currently emphasized to explore new biomarkers, particularly from microRNAs which are freely available in the bloodstream. In this study, the gene expression omnibus database (GEO), a repository of microarray data for PCa circulating extracellular vesicle-free microRNAs profiling, was analyzed for differentially expressed miRNAs (DE-miRs). Top 20 most differentially expressed miRs with significant (adjusted p-value < 0.01) high expression (fold change) levels were extracted by the simultaneous application of different filtering criteria. Then, microRNA-gene networks were constructed for the two sets of positively (n=20) or negatively (n=20) regulated miRNAs. Gene ontology annotations of the target gene sets were also extracted and analyzed. Results indicated that human miR-1587, miR-223-3p, miR-3125, and miR-642b-3p are highly significant DE-miRs in PCa. In addition, human miR-4459, miR-1273g, miR 642a-3p, and miR-642b-3p were identified as top-ranked hubs in the relevant miRNA-gene networks. FOXK1, PML, CD24, ATN1, BAZ2A, CDKN1A, NUFIP2, and HARNPU were identified as microRNA target genes with significant dysregulation. miR-4459, miR-1273g-3p, miR-3135b, miR-5001-5p, and miR-1587 were proposed as novel microRNAs with the potential to be utilized as diagnostic biomarkers of prostate cancer among circulating vesicle-free miRNAs.
Alireza Mirzaei; Sara Dezhsetan; Gholamreza Kavoosi; Mahdi Behnamian
Abstract
Stevia rebaudiana bertoni is a plant with sweetening properties. This medicinal plant is perennial and from Asteraceae family. Its leaves contain glycoside compounds of a sugar part and non-sugar sectors. One of the glycosides compounds is RebaudiosideA which has a greater importance in market. Several ...
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Stevia rebaudiana bertoni is a plant with sweetening properties. This medicinal plant is perennial and from Asteraceae family. Its leaves contain glycoside compounds of a sugar part and non-sugar sectors. One of the glycosides compounds is RebaudiosideA which has a greater importance in market. Several key regulating genes including copalyl diphosphate synthase (CPPS) (AF034545.1), geranylgeranyl diphosphate synthase (GGDPS) (DQ432013.3), (E)-4-hydroxy-3-methylbut-2-enyl diphosphate synthase (HDS) (FJ755689.1), UDP glucosyltranserase 85C2(UGT85C2)(AY345978.1), UDPglucosyltranserase–74G1 (UGT74G1) (AY345982.1) and UDP glucosyltranserase–76G1 (UGT76G1) (KC631816.1) are involved in the biosynthesis Rebaudioside A. This experiment was conducted to evaluate the effect of silver oxide Ag2O on the mRNA level of these genes in the stevia rebaudiana. The experiments repeated 3 times and with concentrations of 50, 100 and 200 µM. Increasing concentrations of 50 micromoles of silver oxide up to 100 micromoles leads to an increase in the expression levels of all the studied genes. Also according to the expression profile of these genes and the results of HPLC there is a significant increase on the expression level of the genes and production of RebaudiosideA under Ag2O treatment. In general, it was found that increasing the concentration of Ag2O can lead to an increase in the level of mRNA for the chosen genes. On the other hand, the low expression of the genes studied under control conditions (No Treatment), compared to the treatment with Ag2O, revealed that the treatment can lead to higher sweetener glycoside components in the Stevia leaves. The physiological assay showed that Ag2O treatment in concentrations of 100 and 200 µM have more positive effect on chlorophyll, protein, carbohydrates and carotenoids in Stevia.
Nasrin moshtaghi; Robab Ghahremanzadeh; Seyyed Hasan Marashi
Abstract
Saffron (Crocus sativus L.) is an indigenous and the most valuable and marginal plant in Iran. However,
limited knowledge exists on its molecular biology. The importance of this plant is due to the color, flavor and
medicinal properties of its red stigmas. Saffron stigmas contain a high amount of carotenoids ...
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Saffron (Crocus sativus L.) is an indigenous and the most valuable and marginal plant in Iran. However,
limited knowledge exists on its molecular biology. The importance of this plant is due to the color, flavor and
medicinal properties of its red stigmas. Saffron stigmas contain a high amount of carotenoids such as crocetin
and crocin. Two genes, bch and pds, have essential role in carotenoid production. In this study, the effect of
four different irrigation regimes was evaluated on the expression of bch and pds genes. Semi-quantitative RTPCR
showed no significant difference in the expression levels of genes of interest related to the internal
standard (18S rRNA). Results of Real-Time PCR assays showed that the expression of bch and pds genes were
affected by irrigation treatments as their expression decreased in irrigated plants in comparison to non irrigated
ones, exept for one irrigation treatment (one irrigation in September) where the pds gene expression showed
higher level. However, the expression profile of the genes was almost the same in all treatments. The
comparison between results of two techniques indicated that the Real-Time PCR is more accurate for
determination of the level of transcript in the Iranian saffron. It was interesting that by decreasing of irrigation,
the expression level of these two genes increased indicating that abiotic stress and drought can affect on the
gene expression relating to the saffron color.
