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SUMMARY High-throughput RNA sequencing (RNA-seq) is rapidly emerging as a major quantitative transcriptome profiling platform. Here, we present DEGseq, an R package to identify differentially expressed genes or isoforms for RNA-seq data from different samples. In this package, we integrated three existing methods, and introduced two novel methods based on(More)
The endoplasmic reticulum (ER) is the primary organelle for folding and maturation of secretory and transmembrane proteins. Inability to meet protein-folding demand leads to "ER stress," and activates IRE1α, an ER transmembrane kinase-endoribonuclease (RNase). IRE1α promotes adaptation through splicing Xbp1 mRNA or apoptosis through incompletely understood(More)
Depending on endoplasmic reticulum (ER) stress levels, the ER transmembrane multidomain protein IRE1α promotes either adaptation or apoptosis. Unfolded ER proteins cause IRE1α lumenal domain homo-oligomerization, inducing trans autophosphorylation that further drives homo-oligomerization of its cytosolic kinase/endoribonuclease (RNase) domains to activate(More)
In cells experiencing unrelieved endoplasmic reticulum (ER) stress, the ER transmembrane kinase/endoribonuclease (RNase)-IRE1α-endonucleolytically degrades ER-localized mRNAs to promote apoptosis. Here we find that the ABL family of tyrosine kinases rheostatically enhances IRE1α's enzymatic activities, thereby potentiating ER stress-induced apoptosis.(More)
A compression scheme of defect image based on wavelet analysis is proposed, according to characteristic of MFL (Magnetic Flux Leakage) signal, in which new wavelet base functions are redesigned by adjusting its zeros and apices of the orthogonal function. The functions are used to transform the defect image and all the wavelet coefficients are scaled(More)
Under endoplasmic reticulum stress, unfolded protein accumulation leads to activation of the endoplasmic reticulum transmembrane kinase/endoRNase (RNase) IRE1α. IRE1α oligomerizes, autophosphorylates and initiates splicing of XBP1 mRNA, thus triggering the unfolded protein response (UPR). Here we show that IRE1α's kinase-controlled RNase can be regulated in(More)
High-throughput RNA sequencing (RNA-seq) technology provides a revolutionary approach to studying splicing events de novo. However, identifying splice junctions with high sensitivity and specificity remains a challenge. In the present study, we proposed a new tool named SeqSaw to detect splice junctions with or without the canonical GT-AG splicing signal.(More)
BACKGROUND Hepatitis B viral infection-induced hepatocellular carcinoma (HCC) is a major threat to human health in China. Hepatitis B virus X protein (HBX), an HBV protein, has been reported to be involved in regulating the cellular activities of the host cells and is responsible for HCC oncogenesis. METHODS AND RESULTS In this study, we performed(More)
BACKGROUND To observe the effects of the minimally invasive removal of an intracerebral hematoma on the glutamate concentration, blood-brain barrier (BBB) permeability and brain water content in the brain tissue surrounding the hematoma and to provide a theoretical basis for minimally invasive removal of intracerebral hematomas. METHODS Thirty rabbits(More)
Protein lysine acetylation plays an important role in the normal functioning of cells, including gene expression regulation, protein stability and metabolism regulation. Although large amounts of lysine acetylation sites have been identified via large-scale mass spectrometry or traditional experimental methods, the lysine (K)-acetyl-transferase (KAT)(More)