SOHSite: incorporating evolutionary information and physicochemical properties to identify protein S-sulfenylation sites

Distribution of KEGG pathway annotations for S-sulfenylated proteins. (DOCX 15 kb

Enhancement of brain-type creatine kinase activity ameliorates neuronal deficits in Huntington's disease

AbstractHuntington's disease (HD) is a hereditary neurodegenerative disorder caused by a CAG repeat expansion in the huntingtin (HTT) gene. Brain-type creatine kinase (CKB) is an enzyme involved in energy homeostasis via the phosphocreatine–creatine kinase system. Although downregulation of CKB was previously reported in brains of HD mouse models and patients, such regulation and its functional consequence in HD are not fully understood. In the present study, we demonstrated that levels of CKB found in both the soma and processes were markedly reduced in primary neurons and brains of HD mice. We show for the first time that mutant HTT (mHTT) suppressed the activity of the promoter of the CKB gene, which contributes to the lowered CKB expression in HD. Exogenous expression of wild-type CKB, but not a dominant negative CKB mutant, rescued the ATP depletion, aggregate formation, impaired proteasome activity, and shortened neurites induced by mHTT. These findings suggest that negative regulation of CKB by mHTT is a key event in the pathogenesis of HD and contributes to the neuronal dysfunction associated with HD. In addition, besides dietary supplementation with the CKB substrate, strategies aimed at increasing CKB expression might lead to the development of therapeutic treatments for HD

Intra- and Inter-Individual Variance of Gene Expression in Clinical Studies

BACKGROUND: Variance in microarray studies has been widely discussed as a critical topic on the identification of differentially expressed genes; however, few studies have addressed the influence of estimating variance. METHODOLOGY/PRINCIPAL FINDINGS: To break intra- and inter-individual variance in clinical studies down to three levels--technical, anatomic, and individual--we designed experiments and algorithms to investigate three forms of variances. As a case study, a group of "inter-individual variable genes" were identified to exemplify the influence of underestimated variance on the statistical and biological aspects in identification of differentially expressed genes. Our results showed that inadequate estimation of variance inevitably led to the inclusion of non-statistically significant genes into those listed as significant, thereby interfering with the correct prediction of biological functions. Applying a higher cutoff value of fold changes in the selection of significant genes reduces/eliminates the effects of underestimated variance. CONCLUSIONS/SIGNIFICANCE: Our data demonstrated that correct variance evaluation is critical in selecting significant genes. If the degree of variance is underestimated, "noisy" genes are falsely identified as differentially expressed genes. These genes are the noise associated with biological interpretation, reducing the biological significance of the gene set. Our results also indicate that applying a higher number of fold change as the selection criteria reduces/eliminates the differences between distinct estimations of variance

The role of TonEBP in regulation of AAD expression and dopamine production in renal proximal tubule cells upon hypertonic challenge

a b s t r a c t Renal proximal tubule cells overexpress aromatic L-amino acid decarboxylase (AAD) to produce dopamine, which inhibits salt absorption in the hypertonic environment. We examined the effect of TonEBP on AAD expression in human proximal tubule epithelial cells, HK-2 cell line. Confocal microscopy showed that after 2 h of exposure to the hypertonic medium, TonEBP accumulation in nuclei increased as compared to the isotonic control. The activated TonEBP enhanced the mRNA expression of the representative downstream genes (i.e., SMIT and TauT). Meanwhile, AAD protein abundance also increased with TonEBP activation. EMSA and luciferase reporter assay showed that TonEBP was involved in transcriptional regulation of AAD upon hypertonic stress. Inactivation of TonEBP by the p38 inhibitor SB203580, or TonEBP shRNA significantly reduced AAD expression, which was rescued by re-expressing Myc-tagged TonEBP. Up-regulation of AAD increased dopamine synthesis, and dopamine inhibited NKA activity in hypertonic condition. These results suggested that TonEBP played an important role in the epithelial cells of renal proximal tubule upon hypertonic stress by enhancing AAD expression, which could promote dopamine secretion to negative regulate NKA activity. The elucidation of a new mechanism described in this study combined with previous findings provides more insights into this issue

Development of a P300 Brain–Machine Interface and Design of an Elastic Mechanism for a Rehabilitation Robot

This paper focuses on the development of a P300 speller and the design of a rehabilitation robot using a brain-machine interface. The combined feature set provides a norm that can be used to assess trends of the user’s increased or decreased independence. The combined feature set is found to maintain a 90% sorting rate; it can also reduce the relationship of individual independence for each subject. Among the results, the highest P300 classification accuracy can be increased by 36.04%. A novel adaptive coupled elastic actuator (ACEA) is proposed that uses adjustable characteristics to adapt to the applied output and input forces, thus ensuring safe human-machine interaction without the use of complex control strategies. The proposed robotic system uses variable impedance to achieve adaptability and safety in dynamic unstructured environments. This paper discusses the design, model, control, and performance of the ACEA. </p