ROKU: a novel method for identification of tissue-specific genes

BACKGROUND: One of the important goals of microarray research is the identification of genes whose expression is considerably higher or lower in some tissues than in others. We would like to have ways of identifying such tissue-specific genes. RESULTS: We describe a method, ROKU, which selects tissue-specific patterns from gene expression data for many tissues and thousands of genes. ROKU ranks genes according to their overall tissue specificity using Shannon entropy and detects tissues specific to each gene if any exist using an outlier detection method. We evaluated the capacity for the detection of various specific expression patterns using synthetic and real data. We observed that ROKU was superior to a conventional entropy-based method in its ability to rank genes according to overall tissue specificity and to detect genes whose expression pattern are specific only to objective tissues. CONCLUSION: ROKU is useful for the detection of various tissue-specific expression patterns. The framework is also directly applicable to the selection of diagnostic markers for molecular classification of multiple classes

Effects of stressors on the expression of virulence factors and cell survival in Clostridium perfringens

[原著/Originals] 平成24年5月16日受付,平成24年6月14日受理

Global regulation of gene expression in response to cysteine availability in Clostridium perfringens

<p>Abstract</p> <p>Background</p> <p>Cysteine has a crucial role in cellular physiology and its synthesis is tightly controlled due to its reactivity. However, little is known about the sulfur metabolism and its regulation in clostridia compared with other firmicutes. In <it>Clostridium perfringens</it>, the two-component system, VirR/VirS, controls the expression of the <it>ubiG </it>operon involved in methionine to cysteine conversion in addition to the expression of several toxin genes. The existence of links between the <it>C. perfringens </it>virulence regulon and sulfur metabolism prompted us to analyze this metabolism in more detail.</p> <p>Results</p> <p>We first performed a tentative reconstruction of sulfur metabolism in <it>C. perfringens </it>and correlated these data with the growth of strain 13 in the presence of various sulfur sources. Surprisingly, <it>C. perfringens </it>can convert cysteine to methionine by an atypical still uncharacterized pathway. We further compared the expression profiles of strain 13 after growth in the presence of cystine or homocysteine that corresponds to conditions of cysteine depletion. Among the 177 genes differentially expressed, we found genes involved in sulfur metabolism and controlled by premature termination of transcription via a cysteine specific T-box system (<it>cysK</it>-<it>cysE</it>, <it>cysP1 </it>and <it>cysP2</it>) or an S-box riboswitch (<it>metK </it>and <it>metT</it>). We also showed that the <it>ubiG </it>operon was submitted to a triple regulation by cysteine availability via a T-box system, by the VirR/VirS system via the VR-RNA and by the VirX regulatory RNA.</p> <p>In addition, we found that expression of <it>pfoA </it>(theta-toxin), <it>nagL </it>(one of the five genes encoding hyaluronidases) and genes involved in the maintenance of cell redox status was differentially expressed in response to cysteine availability. Finally, we showed that the expression of genes involved in [Fe-S] clusters biogenesis and of the <it>ldh </it>gene encoding the lactate dehydrogenase was induced during cysteine limitation.</p> <p>Conclusion</p> <p>Several key functions for the cellular physiology of this anaerobic bacterium were controlled in response to cysteine availability. While most of the genes involved in sulfur metabolism are regulated by premature termination of transcription, other still uncharacterized mechanisms of regulation participated in the induction of gene expression during cysteine starvation.</p

Assessment of Growth Disturbance in Japanese Children with IBD

In Japan, there is as yet no report on growth retardation in children with IBD. We therefore investigated the cause of growth retardation in Japanese children with IBD. We investigated the height, body weight, serum levels of albumin, IGF-I, CRP, and cytokines, and the amount of corticosteroid administered in children with Crohn's disease (CD, n = 15) and ulcerative colitis (UC, n = 18). Our results suggest that growth retardation is already present before the initial visit in children with CD, and chronic inflammation may be responsible this growth disturbance. Moreover, the amount of PSL used may contribute to growth retardation by decreasing the serum levels of IGF-I in children with IBD

926-24 Clinical and Electrophysiological Characteristics in Patients with Exercise Induced Idiopathic Multiform Ventricular Tachycardia. Differential Effects of Atrial Pacing and Isoproterenol Infusion on QTc Interval and Induction of Ventricular Arrhythmia

Idiopathic multiform ventricular tachycardia (VT) is characterized by normal QT interval at restand 3 or more distinct QRS configuration during VT, which has been distinguished from torsade de pointes in long QT syndrome. Facilitation by exercise and suppression by β-antagonist of this VT suggest that it may depend on rapid heart rate (HR) or increased sympathetic tone. To determine which factors is responsible, we performed atrial pacing (120/min) and isoproterenol (ISP) infusion (0.5 or 1.0μg to attain HR 120/min) in 6 patients (2 males/4 females, mean 15.8 years) and 10 control (4 males/6 females, mean 22.8 years). Inducibility of premature ventricular contraction (PVC) or VT, and response of QTc interval (QT/√RR) were evaluated during the procedures.controlmultiform VTp valuePVCNT inductionAtrial pacing0/71/6n.s.Isoproterenol0/86/60.001OTc (secl/2)Rest0.40±0.02 (n=10)0.40±0.03n.s.Atrial pacing0.43±0.02 (n=7)0.47±003&lt;0.01Isoproterenol0.44±0.01 (n=8)0.50±0.05&lt;0.001ConclusionAlthough both rapid HR and increased sympathetic tone may be responsible for this VT, contribution of the latter is predominant. Differential response of QT interval to atrial pacing and isoproterenol infusion may have a possible role for the occurrence of this VT

Prediction of Carbohydrate-Binding Proteins from Sequences Using Support Vector Machines

Carbohydrate-binding proteins are proteins that can interact with sugar chains but do not modify them. They are involved in many physiological functions, and we have developed a method for predicting them from their amino acid sequences. Our method is based on support vector machines (SVMs). We first clarified the definition of carbohydrate-binding proteins and then constructed positive and negative datasets with which the SVMs were trained. By applying the leave-one-out test to these datasets, our method delivered 0.92 of the area under the receiver operating characteristic (ROC) curve. We also examined two amino acid grouping methods that enable effective learning of sequence patterns and evaluated the performance of these methods. When we applied our method in combination with the homology-based prediction method to the annotated human genome database, H-invDB, we found that the true positive rate of prediction was improved

Phosphodiesterase Inhibitors Suppress Lactobacillus casei Cell-Wall-Induced NF-κB and MAPK Activations and Cell Proliferation through Protein Kinase A—or Exchange Protein Activated by cAMP-Dependent Signal Pathway

Specific strains of Lactobacillus have been found to be beneficial in treating some types of diarrhea and vaginosis. However, a high mortality rate results from underlying immunosuppressive conditions in patients with Lactobacillus casei bacteremia. Cyclic AMP (cAMP) is a small second messenger molecule that mediates signal transduction. The onset and progression of inflammatory responses are sensitive to changes in steady-state cAMP levels. L. casei cell wall extract (LCWE) develops arteritis in mice through Toll-like receptor-2 signaling. The purpose of this study was to investigate whether intracellular cAMP affects LCWE-induced pathological signaling. LCWE was shown to induce phosphorylation of the nuclear factor κB (NF-κB) and mitogen-activated protein kinase (MAPK) signaling pathways and cell proliferation in mice fibroblast cells. Theophylline and phosphodiesterase inhibitor increased intracellular cAMP and inhibited LCWE-induced cell proliferation as well as phosphorylation of NF-κB and MAPK. Protein kinase A inhibitor H89 prevented cAMP-induced MAPK inhibition, but not cAMP-induced NF-κB inhibition. An exchange protein activated by cAMP (Epac) agonist inhibited NF-κB activation but not MAPK activation. These results indicate that an increase in intracellular cAMP prevents LCWE induction of pathological signaling pathways dependent on PKA and Epac signaling

Prevention of pin tract infection with titanium-copper alloys

金沢大学医薬保健研究域医学系The most frequent complication in external fixation is pin tract infection. To reduce the incidence of implant-associated infection, many published reports have looked at preventing bacterial adhesion by treating the pin surface. This study aimed to evaluate the antibacterial activity of a Titanium-Copper (Ti-Cu) alloy on implant infection, and to determine the potential use of the Ti-Cu alloy as a biomaterial. Two forms of Ti-Cu alloys were synthesized: one with 1% Cu and the other with 5% Cu. For analyzing infectious behavior, the implants were exposed to Staphylococcus aureus and Escherichia coli. The reaction of pathogens to the Ti-Cu alloys was compared with their reaction to stainless steel and pure titanium as controls. Both Ti-Cu alloys evidently inhibited colonization by both bacteria. Conversely, cytocompatibility studies were performed using fibroblasts and colony formation on the metals was assessed by counting the number of colonies. Ti-1% Cu alloy showed no difference in the number of colonies compared with the control. External fixator pins made of Ti-Cu alloys were evaluated in a rabbit model. The tissue-implant interactions were analyzed for the presence of infection, inflammatory changes and osteoid-formation. Ti-1% Cu alloy significantly inhibited inflammation and infection, and had excellent osteoid-formation. Copper blood levels were measured before surgery and at 14 days postoperatively. Preoperative and postoperative blood copper values were not statistically different. Overall, it was concluded that Ti-Cu alloys have antimicrobial activity and substantially reduce the incidence of pin tract infection. Ti-1% Cu alloy shows particular promise as a biomaterial. © 2009 Wiley Periodicals, Inc