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High-Throughput Profiling in the Hematopoietic System

The expression profile of microRNAs significantly varies in physiological and pathological conditions. Increasing evidence from the literature shows that abnormalities of the miRNome (defined as the full spectrum of miRNAs expressed in a genome) occur in almost all human diseases ...

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MicroRNA Cloning from Cells of the Immune System

MicroRNAs have emerged as – important posttranscriptional regulators of gene expression. Small RNA cloning is a powerful method to identify new microRNAs (miRNAs) and to profile miRNA expression. In addition, it reveals end heterogeneity that may be important in miRNA function. Here, we d ...

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Measuring MicroRNA Expression in Size-Limited FACS-Sorted and Microdissected Samples

MicroRNAs (miRNAs) are small noncoding RNAs of an average length of 22 nucleotides, which repress translation of a large number of target mRNAs. The particular importance of this group of small RNAs arises from the ever growing evidence that they control many biological processes, such as diff ...

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MicroRNA Detection in Bone Marrow Cells by LNA-FISH

The protocol reported in this chapter describes a method for the detection and spatial localisation of microRNAs (miRNAs) in cryopreserved primary leukaemic suspension cells using digoxigenin (DIG)-labelled, Locked Nucleic Acid (LNA)-modified probes, and fluorescence in si ...

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Normalization of MicroRNA Quantitative RT-PCR Data in Reduced Scale Experimental Designs

Proper normalization of quantitative RT-PCR (qRT-PCR) data is a crucial component of gene �expression analysis. Although arbitrarily selected housekeeping genes have been used to normalize many published mRNA RT-PCR datasets, there is a growing awareness that such normalizers sh ...

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A Rapid, Quantitative Assay for Direct Detection of MicroRNAs and Other Small RNAs Using Splinted Ligation

This protocol describes a method that uses splinted ligation for in-solution, direct labeling of small RNAs from total RNA. The liquid phase hybridization method makes it possible to achieve sensitive, specific, and quantitative detection while eliminating a number of time-consumi ...

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Identification and Validation of the Cellular Targets of Virus-Encoded MicroRNAs

Since the identification of the first virus-encoded microRNA (miRNA) in Epstein–Barr virus (EBV)-infected B cells in 2004, viral miRNAs have been found in different groups of herpesviruses. Viral miRNAs play an important role in regulating both viral and cellular gene expression. Ident ...

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Large-Scale Integration of MicroRNA and Gene Expression Data for Identification of Enriched MicroRNAmRNA Associations in Biological Systems

The discovery of microRNAs (miRNAs) revealed a hidden layer of gene regulation that is able to integrate multiple genes into biologically meaningful networks. A number of computational prediction programs have been developed to identify putative miRNA targets. Collectively, the m ...

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Computational Prediction of MicroRNA Targets

One critical step in miRNA functional studies is to identify the gene targets that are directly regulated by miRNAs. In this chapter, we describe a computational algorithm and an online database, miRDB, for miRNA target prediction. In miRDB, flexible Web search interface has been developed for ...

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MiRNA Editing

RNA editing by A-to-I modification is a widespread mechanism in complex organisms that leads to the posttranscriptional alteration of protein coding as well as noncoding sequences. MiRNA transcripts have been recognized as a major target for RNA editing enzymes, and single-nucleoti ...

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Solution Structure of miRNA:mRNA Complex

The use of contemporary nuclear magnetic resonance (NMR) methods in the studies of model systems between microRNA (miRNA) and messenger RNA (mRNA) is reviewed. We describe our studies on structural features of 33-nt RNA model construct between let-7 miRNA and lin-41 mRNA at the second binding s ...

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Lentivirus-Mediated Antagomir Expression

MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation via hybridisation to mRNAs. miRNA function can be inhibited by the so-called “antagomirs” – anti-sense RNA oligonucleotides complementary to individual miRNAs. Since, in principle, ...

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Expression of miRNAs in Lymphocytes: A Review

In this chapter, we provide a review on the functions of the most important miRNAs in lymphocytes. Most of them are involved in lymphopoiesis, immune response, and lymphoid malignancies, highlighting the importance of miRNAs in these cells.

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Monitoring MicroRNA Activity and Validating MicroRNA Targets by Reporter-Based Approaches

An essential requirement for discovering microRNAs that may be relevant to an immune cell’s function is to identify the microRNAs that are active in the cell and the genes they target. As several chapters in this volume describe, there are a number of technologies available for profiling microR ...

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Generation of Parasite Antigens for Use in Toll-Like Receptor Research

Pathogen recognition is a central activity of the Toll-like receptor (TLR) family. Molecules from various pathogens have been widely used in TLR research as natural ligands for the receptors. TLR ligands from bacteria, viruses, and fungi are widely available from commercial companies and ...

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Innate Immunity, Toll-Like Receptors, and Atherosclerosis: Mouse Models and Methods

Chronic inflammation and aberrant lipid metabolism represent hallmarks of atherosclerosis. Innate immunity critically depends upon Toll-like receptor (TLR) signalling. Recent data directly implicate signalling by TLR4 and TLR2 in the pathogenesis of atherosclerosis. T ...

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Biomarkers Measuring the Activity of Toll-Like Receptor Ligands in Clinical Development Programs

Efforts to develop therapeutic approaches based on stimulation of Toll-like receptor (TLR) pathways have increased in recent years (Nat Med 13:552–559). The effectiveness of TLR agonists is currently being tested in diseases such as cancer, asthma, allergic rhinitis, and viral infect ...

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Toll-Like Receptor-Dependent Immune Complex Activation of B Cells and Dendritic Cells

High titers of autoantibodies reactive with DNA/RNA molecular complexes are characteristic of autoimmune disorders such as systemic lupus erythematosus (SLE). In vitro and in vivo studies have implicated Toll-like receptor 9 (TLR9) and Toll-like receptor 7 (TLR7) in the activation of ...

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Practical Techniques for Detection of Toll-Like Receptor-4 in the Human Intestine

The human intestine has evolved in the presence of a diverse array of luminal microorganisms. In order to maintain intestinal homeostasis, mucosal immune responses to theses microorganisms must be tightly regulated. The intestine needs to be able to respond to pathogenic organisms whi ...

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Toll-Like Receptors and Rheumatoid Arthritis

Rheumatoid arthritis (RA) is a chronic inflammatory disease that ultimately leads to the progressive destruction of cartilage and bone in numerous joints. There is mounting evidence for an important function of innate immunity in the pathogenesis of RA. Activation of cells by microbial ...

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