Prebiotic Oligosaccharides: Special Focus on Fructooligosaccharides,Its Biosynthesis and Bioactivity

MicroRNAs (miRNAs) are important nonprotein-coding genes involved in almost all biological processes during biotic and abiotic stresses in plants. To investigate the miRNA-mediated plant response to drought stress, two drought-tolerant (C-306 and NI-5439) and two drought-sensitive (HUW-468 and WL-711) wheat genotypes were exposed to 25 % PEG 6000 for 1, 12 and 24 h. Temporal expression patterns of 12 drought-responsive miRNAs and their corresponding nine targets were monitored by quantitative real-time PCR (qRT-PCR). The results showed differential expression of miRNAs and their targets with varying degree of upregulation and downregulation in drought-sensitive genotypes. Likewise, in drought-tolerant wheat genotypes, maximum accumulation of miR393a and miR397a was observed at 1 h of stress. In addition, nearly perfect negative correlation was observed in four miRNA and target pairs (miR164-NAC, miR168a-AGO, miR398-SOD and miR159a-MYB) across all the temporal period studied which could be a major player during drought response in wheat. We, for the first time, validated the presence of miR529a and miR1029 in wheat. These findings gives a clue for temporal and variety-specific differential regulation of miRNAs and their targets in wheat in response to osmotic shock and could help in defining the potential roles of miRNAs in plant adaptation to osmotic stress in future.     

Exosome based miRNA delivery strategy for disease treatment

miRNA, which is a common non-coding RNA, can target various m RNAs to regulate their physiological activities. Therefore, mi RNAs play an important role in various physiological and pathological processes,and so they have been proposed as a powerful tool to treat different diseases efficiently. However, the characteristic of mi RNA degradation in vivo limits its further clinical application. Exosomes have the advantage of crossing the biological barrier and achieving long-distance communication ...     

In silico prediction of human genes as potential targets for rice miRNAs

BackgroundExogenous microRNAs (miRNAs) enter the human body through food, and their effects on metabolic processes can be considerable. It is important to determine which miRNAs from plants affect the expression of human genes and the extent of their influence.MethodThe binding sites of 738Oryza sativa miRNAs (osa-miRNAs) that interact with 17 508 mRNAs of human genes were determined using the MirTarget program.ResultThe characteristics of the binding of 46 single osa-miRNAs to 86 mRNAs of human genes with a value of free energy (ΔG) interaction equal 94%–100% from maximum ΔG were established. The findings showed that osa-miR2102-5p, osa-miR5075-3p, osa-miR2097-5p, osa-miR2919 targeted the largest number of genes at 38, 36, 23, 19 sites, respectively. mRNAs of 86 human genes were identified as targets for 93 osa-miRNAs of all family osa-miRNAs with ΔG values equal 94%–98% from maximum ΔG. Each miRNA of the osa-miR156-5p, osa-miR164-5p, osa-miR168-5p, osa-miR395-3p, osa-miR396-3p, osa-miR396-5p, osa-miR444-3p, osa-miR529-3p, osa-miR1846-3p, osa-miR2907-3p families had binding sites in mRNAs of several human target genes. The binding sites of osa-miRNAs in mRNAs of the target genes for each family of osa-miRNAs were conserved when compared to flanking nucleotide sequences.ConclusionTarget mRNA human genes of osa-miRNAs are also candidate genes of cancer, cardiovascular and neurodegenerative diseases.     

Sequence-based analysis of 5′UTR and coding regions of CASP3 in terms of miRSNPs and SNPs in targetting miRNAs

Apoptosis is described as a mechanism of cell death occurring after adequate cellular harm. Deregulation of apoptosis occurs in many human conditions such as autoimmune disorders, ischemic damage, neurodegenerative diseases and different cancer types. Information relating miRNAs to cancer is increasing. miRNAs can affect development of cancer via many different pathways, including apoptosis. Polymorphisms in miRNA genes or miRNA target sites (miRSNPs) can change miRNA activity. Although polymorphisms in miRNA genes are very uncommon, SNPs in miRNA-binding sites of target genes are quite common. Many researches have revealed that SNPs in miRNA target sites improve or decrease the efficacy of the interaction between miRNAs and their target genes. Our aim was to specify miRSNPs on CASP3 gene (caspase-3) and SNPs in miRNA genes targeting 5′UTR and coding exons of CASP3, and evaluate the effect of these miRSNPs and SNPs of miRNA genes with respect to apoptosis. We detected 141 different miRNA binding sites (126 different miRNAs) and 7 different SNPs in binding sites of miRNA in 5′UTR and CDS of CASP3 gene. Intriguingly, miR-339-3p’s binding site on CASP3 has a SNP (rs35372903, G/A) on CASP3 5′UTR and its genomic sequence has a SNP (rs565188493, G/A) at the same nucleotide with rs35372903. Also, miR-339-3p has two other SNPs (rs373011663, C/T rs72631820, A/G) of which the first is positioned at the binding site. Here, miRSNP (rs35372903) at CASP3 5′UTR and SNP (rs565188493) at miR-339-3p genomic sequence cross-matches at the same site of binding region. Besides, miR-339-3p targets many apoptosis related genes (ZNF346, TAOK2, PIM2, HIP1, BBC3, TNFRSF25, CLCF1, IHPK2, NOL3) although it had no apoptosis related interaction proven before. This means that miR-339-3p may also have a critical effect on apoptosis via different pathways other than caspase-3. Hence, we can deduce that this is the first study demonstrating a powerful association between miR-339-3p and apoptosis upon computational analysis.     

Os(VI)bipy-based electrochemical assay for detection of specific microRNAs as potential cancer biomarkers

Recently, altered expression levels of microRNAs (miRNAs) – short noncoding RNA molecules which bind to mRNAs and thus regulate gene expression – were observed in many cancer cells. miRNA expression profiling is therefore of great interest, but current standard methods are still considered relatively laborious and expensive. Electrochemistry has a potential to become quick and inexpensive alternative. Here, we describe modification of miRNA with an electroactive complex composed of six-valent osmium and 2,2′-bipyridine, Os(VI)bipy, specifically binding to the 3′-end of the ribose, which is detectable at hanging mercury drop electrode at femtomole level due to an electrocatalytic nature of a resulting signal. By combining miRNA labeling step with magnetic beads-based hybridization assay, detection of specific miRNA sequence from a mixture of other noncomplementary miRNAs was possible.     

Expression of miRNAs Targeting <Emphasis Type="Italic">mTOR</Emphasis> and <Emphasis Type="Italic">S6K1</Emphasis> Genes of mTOR Signaling Pathway Including miR-96, miR-557, and miR-3182 in Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC) is a highly aggressive form of breast cancer. Aberrant expression of genes in mTOR pathway and their targeting miRNAs plays an important role in TNBC. The aim of this study was to determine the expression of mTOR and S6K1 and their targeting miRNAs in breast cancer cell lines and clinical samples. miRNAs targeting 3′-UTR of mTOR and S6K1 mRNAs were predicted using bioinformatic algorithms. MDA-MB-231, MCF-7, and MCF-10A as well as 20 TNBC samples were analyzed for gene and miRNA expression using quantitative real-time PCR (RT-qPCR). A receiver operating characteristic (ROC) curve analysis was performed for evaluation of candidate miRNAs as diagnostic biomarkers. miR-96 and miR-557 targeting mTOR and S6K1 mRNAs, respectively, were selected, and miR-3182 was selected as the miRNA targeting both genes. The miRNAs were down-regulated in cell lines, while their target mRNAs were up-regulated. Similar findings were observed in clinical samples. The ROC curve analysis revealed decline in expression of these miRNAs. We suggest that miR-96, miR-557, and miR-3182 can be used as inhibitory agents for mTOR and S6K1 in TNBC-targeted therapy.     

Computational Approach for Identification of Anopheles gambiae miRNA Involved in Modulation of Host Immune Response

MicroRNAs (miRNAs) are small, noncoding RNAs that play key roles in regulating gene expression in animals, plants, and viruses, which involves in biological processes including development, cancer, immunity, and host–microorganism interactions. In this present study, we have used the computational approach to identify potent miRNAs involved in Anopheles gambiae immune response. Analysis of 217,261 A. gambiae ESTs and further study of RNA folding revealed six new miRNAs. The minimum free energy of the predicted miRNAs ranged from ?27.2 to ?62.63 kcal/mol with an average of ?49.38 kcal/mol. While its A + U % ranges from 50 to 65 % with an average value of 57.37 %. Phylogenetic analysis of the predicted miRNAs revealed that aga-miR-277 was evolutionary highly conserved with more similarity with other mosquito species. Observing further the target identification of the predicted miRNA, it was noticed that the aga-miR-2304 and aga-miR-2390 are involved in modulation of immune response by targeting the gene encoding suppressin and protein prophenoloxidase. Further detailed studies of these miRNAs will help in revealing its function in modulation of A. gambiae immune response with respect to its parasite.     

<Superscript>1</Superscript>H-nuclear magnetic resonance spectroscopy-based metabolic assessment in a rat model of obesity induced by a high-fat diet

MicroRNAs (miRNAs) are a class of small noncoding RNAs ∼22 nt in length that regulate gene expression and play fundamental roles in multiple biological processes, including cell differentiation, proliferation and apoptosis as well as disease processes. The study of miRNA has thus become a rapidly emerging field in life science. The detection of miRNA expression is a very important first step in miRNA exploration. Several methodologies, including cloning, northern blotting, real-time RT-PCR, microRNA arrays and ISH (in situ hybridization), have been developed and applied successfully in miRNA profiling. This review discusses the main existing microRNA detection technologies, while emphasizing microRNA arrays.