Most antibodies generated against the HA recognize the variable portion of the HA

Most antibodies generated against the HA recognize the variable portion of the HA. the complete set of RNA transcripts that are produced by the genome (under specific circumstances or in a specific cell or group of cells) using high-throughput sequencing. Comparing transcriptomes within groups enables the identification of genes that are differentially expressed in specific cell populations or in response to different treatments. Technologies used to conduct transcriptomics include microarrays and RNA sequencing. Microarrays are a fixed-probe technology, while RNA sequencing is more dynamic, and measures both known as well as new transcripts in a given sample. Microarrays measure the relative amount of mRNA activity of target genes with existing sequences. RNA sequencing uses high-throughput sequencing to record all transcripts and provides information regarding the gene sequence in addition to the expression level. Such tools generate a transcriptional profile (gene expression signature), representing a snapshot of genes expressed at a specific point in time. The steps involved in transcriptomics utilizing Gatifloxacin hydrochloride RNA sequencing are outlined in Figure 1. Briefly, after sample collection, cells of interest are isolated, RNA is extracted, and converted to a library consisting of cDNA fragments. Each molecule is then sequenced with or without amplification. The resulting reads are then aligned to a reference genome or transcripts (or assembled de novo) to produce a genome-scale transcription map that consists of the level of expression for each gene. RNA sequencing data can produce over 109 short DNA sequences, which must then be analyzed using bioinformatics. Open Gatifloxacin hydrochloride in a separate window Figure 1. Steps involved in transcriptomic analyses using RNA sequencing. Transcriptomics has revolutionized our Gatifloxacin hydrochloride understanding of how genes are expressed, by providing a comprehensive, unbiased and integrated analysis of the complexities of cellular activity. However, transcriptomic analyses require significant computation and proper experimental design to produce meaningful data, and this technology assumes that mRNA transcription is a proxy for protein products of a cell, which is not always the case. Not only is RNA unstable, but post-transcriptional modifications further modulate protein synthesis, such that mRNA and protein abundance do not always Gatifloxacin hydrochloride correlate. Gatifloxacin hydrochloride Further, gene expression is highly tissue-specific, and caution is needed in interpretation of gene expression patterns from a mix of cell populations. Transcriptomics is emerging as an important tool in immunological and infectious diseases research. The transcriptomic study of peripheral blood mononuclear cells C including B cells, T cells, monocytes, dendritic cells, and natural DUSP8 killer cells C can provide a comprehensive summary of the immune response to infection. More recently, newer platforms enable whole blood analysis and single cell sorting to allow for a more comprehensive analysis, and immune cells found in respiratory secretions are being used to study the local host response to influenza infection. Immunopathology of influenza infection Complex co-ordinated immune responses are triggered in the host following an acute influenza infection, involving both innate and adaptive immunologic processes. Innate immune response The first mechanisms of defense against influenza infection come into play at the portal of entry in the respiratory tract. The virus must cross the mucous layer that covers the respiratory epithelium in order to attach to the cell membrane and invade the cell. Infected epithelial cells, tissue macrophages and plasmacytoid dendritic cells (pDC) identify the viral RNA as a foreign element through pattern recognition receptors (PRRs), which activate an innate immune cascade resulting in the downstream secretion of type I interferons, other inflammatory cytokines, and chemokines.1-3 The type I interferons stimulate hundreds of genes collectively known as interferon-stimulated genes (ISGs) in the surrounding cells, establishing potent innate local antiviral activity.4 The inflammatory mediators released at this stage of infection may result in systemic symptoms including fever and malaise. They also instruct the adaptive immune response. The chemokines released by epithelial cells and local immune cells attract natural killer cells (NKs), monocytes and neutrophils at the site of infection..