Methods in molecular biology
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Identification of phosphoproteins or phosphopeptides as cancer biomarkers is an emerging field in phosphoproteomics. Owing to the low stoichiometric nature of protein phosphorylation, phosphoproteins or phosphopeptides must be enriched prior to downstream mass spectrometry analysis. Titanium dioxide (TiO2) has been prevalently used to enrich phosphopeptides from complex proteome samples due to its high affinity for phosphopeptides, and the method is straightforward. ⋯ Phosphopeptides are eluted using an ammonia solution at high pH. Use of NH4Glu significantly reduces nonspecific bindings while a high recovery rate (84 %) of phosphopeptides is retained. The method is optimized for large-scale phosphoproteomic analysis and phosphoprotein biomarker discovery starting from sub-milligram or milligrams of proteome samples.
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Complex, interrelated systems exist to maintain the fluidity of the blood in the vascular system while allowing for the rapid formation of a solid blood clot to prevent hemorrhaging subsequent to blood vessel injury. These interrelated systems are collectively referred to as haemostasis. The components involved in the haemostatic mechanism consist of vessel walls, platelets, coagulation factors, inhibitors, and the fibrinolytic system. ⋯ Once the fibrin clot is formed, the fibrinolytic system ensures that the clot is lysed so that it does not become a pathological complication. Taken together, the systems exist to balance each other and maintain order. The balance of coagulation and fibrinolysis keeps the haemostatic system functioning efficiently.
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Fibrinogen is the final essential building block of the clotting process. Thus, all of the preliminary "cause and effect" events in the clotting cascade rely on the work of this molecule to measure their success. The most commonly used laboratory method for measuring fibrinogen is the Clauss fibrinogen assay. ⋯ The following chapter includes detailed information on the Clauss fibrinogen assay. Other fibrinogen assays used include fibrinogen levels derived from prothrombin time assays and antigenic methods. Fibrinogen measurements using the prothrombin time and antigenic based assays are described in brief.
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Studies of DNA methylation in Arabidopsis have rapidly advanced from the analysis of a single reference accession to investigations of large populations. The goal of emerging population studies is to detect differentially methylated regions (DMRs) at the genome-wide scale, and to relate this variation to gene expression and phenotypic diversity. Whole-genome bisulfite sequencing (WGBS-seq) has established itself as a gold standard in DNA methylation analysis due to its high accuracy and single cytosine measurement resolution. ⋯ However, detection can be susceptible to strong signal distortions resulting from a combination of dye bias and the CG content of effectively unmethylated genomic regions. We show that these issues can be easily bypassed by taking appropriate data preparation steps and applying suitable analysis tools. We conclude that MeDIP-chip is a reasonable alternative to WGBS-seq in emerging Arabidopsis population epigenetic studies.
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Promoter deletion analysis is a useful tool for identifying important regulatory regions involved in transcriptional control of gene expression. In this approach, a series of promoter deletion fragments are fused to a reporter gene, such as chloramphenicol acetyltransferase or luciferase gene in a vector, and then transfected into cells for induction. Screening the expression level of the reporter gene using either a qualitative or a quantitative assay, allows to identify the regulatory regions of interest (e.g., cis-acting elements or enhancer) in the promoter. ⋯ Therefore, the enzymatic activities of firefly and Renilla luciferases can be sequentially measured in a single sample by controlling reaction conditions. Here, we describe a dual-luciferase reporter assay, where the promoter of interest is fused to a firefly luciferase reporter and is co-transfected into cells with an internal control vector (pRL-CMV) to express Renilla luciferase. Both the Firefly and Renilla luciferases are measured using a dual-luciferase reporter assay system which improves experimental accuracy.