DNA motif elucidation using belief propagation

Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ∼10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors’ websites: e.g. http://www.cs.toronto.edu/∼wkc/kmerHMM.     

Acidosis antagonizes intracellular calcium response to kappa -opioid receptor stimulation in the rat heart

To study the effects of -opioid receptor stimulation onintracellular Ca²⁺ concentration([Ca²⁺]_i)homeostasis during extracellular acidosis, we determined the effects of-opioid receptor stimulation on[Ca²⁺]_iresponses during extracellular acidosis in isolated single ratventricular myocytes, by a spectrofluorometric method. U-50488H (10-30 µM), a selective -opioid receptor agonist, dosedependently decreased the electrically induced[Ca²⁺]_itransient, which results from the influx ofCa²⁺ and the subsequentmobilization of Ca²⁺ from thesarcoplasmic reticulum (SR). U-50488H (30 µM) also increased theresting[Ca²⁺]_iand inhibited the[Ca²⁺]_itransient induced by caffeine, which mobilizesCa²⁺ from the SR, indicating thatthe effects of the -opioid receptor agonist involved mobilization ofCa²⁺ from its intracellular poolinto the cytoplasm. The Ca²⁺responses to 30 µM U-50488H were abolished by 5 µMnor-binaltorphimine, a selective -opioid receptorantagonist, indicating that the event was mediated by the -opioidreceptor. The effects of the agonist on[Ca²⁺]_iand the electrically induced[Ca²⁺]_itransient were significantly attenuated when the extracellular pH(pH_e) was loweredto 6.8, which itself reduced intracellular pH(pH_i) and increased[Ca²⁺]_i.The inhibitory effects of U-50488H were restored during extracellular acidosis in the presence of 10 µM ethylisopropyl amiloride, a potentNa⁺/H⁺exchange blocker, or 0.2 mM Ni²⁺,a putativeNa⁺/Ca²⁺exchange blocker. The observations indicate that acidosismay antagonize the effects of -opioid receptor stimulation viaNa⁺/H⁺andNa⁺/Ca²⁺exchanges. When glucose at 50 mM, known to activate theNa⁺/H⁺exchange, was added, both the resting[Ca²⁺]_iand pH_i increased. Interestingly,the effects of U-50488H on [Ca²⁺]_iand the electrically induced[Ca²⁺]_itransient during superfusion with glucose were significantly attenuated; this mimicked the responses during extracellular acidosis. When a high-Ca²⁺ (3 mM) solutionwas superfused, the resting[Ca²⁺]_iincreased; the increase was abolished by 0.2 mMNi²⁺, but thepH_i remained unchanged. Like theresponses to superfusion with high-concentration glucose andextracellular acidosis, the responses of the[Ca²⁺]_iand electrically induced[Ca²⁺]_itransients to 30 µM U-50488H were also significantly attenuated. Results from the present study demonstrated for the first time thatextracellular acidosis antagonizes the effects of -opioid receptorstimulation on the mobilization ofCa²⁺ from SR. Activation of bothNa⁺/H⁺andNa⁺/Ca²⁺exchanges, leading to an elevation of[Ca²⁺]_i,may be responsible for the antagonistic action of extracellular acidosis against -opioid receptor stimulation.

     

Protein tyrosine kinase-dependent modulation of voltage-dependent potassium channels by genistein in rat cardiac ventricular myocytes

Effects of the isoflavone protein tyrosine kinase (PTK) inhibitor genistein on voltage-dependent K(+) currents, i.e., transient outward K(+) current (I(to)), sustained K(+) current (I(ss)), and inward rectifier K(+) current (I(K1)) were studied in rat cardiac ventricular myocytes. It was found that I(to) was reversibly inhibited by genistein in a concentration-dependent manner (IC(50)=28.1 microM), while I(ss) was suppressed by genistein with IC(50) of 18.5 microM. In addition, I(K1) (at -50 mV) was significantly decreased by 36.3+/-4.4% with 25 microM genistein. The inhibition of I(to), I(ss), and I(K1) by genistein was significantly reversed by the application of the protein tyrosine phosphatase inhibitor sodium orthovanadate (1 mM). However, I(to), I(ss), and I(K1) were not affected by the non-isoflavone PTK inhibitor tyrphostin A23 (100 microM) and PP2 (1 microM). These results indicate that activation of I(to), I(ss), and I(K1) channels is modulated by genistein-sensitive PTKs in rat ventricular myocytes.     

Forskolin fails to activate L-type calcium current in hypertrophied cardiomyocytes of chronically hypoxic rats

We have shown that the contractile, cytosolic calcium ([Ca2+]i) and cyclic AMP (cAMP) responses to beta-adrenoceptor stimulation are attenuated in ventricular myocytes of chronically hypoxic (CH) rats. The aim of this study was to examine the effect of forskolin on the L-type Ca2+ current in CH hypertrophied ventricular myocytes. Patch-clamp recording of the L-type Ca2+ current was measured in right ventricular myocytes of normoxic control and CH rats exposed to 10% inspired oxygen for 4 weeks. The breadth, but not the length, of CH myocytes was significantly greater than that of the control group. Activation of beta-adrenoceptor with isoproterenol (0.1 microM) increased the peak Ca2+ current by 83% in the normoxic control but the increase of peak Ca2+ current was not significant in the CH myocytes. Forskolin (0.1 - 1 microM), an activator of adenylyl cyclase, increased the peak Ca2+ current by 49% - 102% in the normoxic controls but it did not cause significant change of the peak Ca2+ current in CH myocytes. These results suggest an absence of forskolin-induced activation of Ca2+ current in hypertrophied ventricular myocytes during chronic hypoxia. The failure of activation of the Ca2+ current is consistent with the idea that adenylyl cyclase function is down-regulated in CH hypertrophied myocytes.     

雌激素的心脏保护作用——与β1-肾上腺素受体的相互作用及其信号通路

雌激素是女性体内主要的类固醇性激素。对于心肌缺血性伤害,切除卵巢的成年雌性大鼠在β-肾上腺素受体激动时,比正常雌性大鼠呈现更严重的心肌损伤：而去卵巢后的雌激素替补组大鼠对β-肾上腺素受体激动时心肌缺血性伤害的反应则又回复到正常雌性大鼠水平,这为雌激素对抗缺血性伤害的心脏保护作用提供了证据。雌激素的这种保护作用是通过下调β1-肾上腺素受体的表达来实现的。也有研究证明,雌激素能抑制蛋白激酶A（protein kinaseA,PKA）的表达和活性,PKA是Gs蛋白／腺苷酸环化酶（adenylyl cyclase,AC）／cAMP／PKA通路的第二信使,而该通路最终影响心肌的收缩功能。有初步证据表明雌激素还能抑制β1-肾上腺素受体通路下游的另一种第二信使钙调蛋白激酶Ⅱ．δc（Ca^2＋/calmodulin kinaseⅡ-δc,CaMKⅡ-δc）的活性,而CaMKII-δc参与PKA非依赖性的细胞凋亡。即时给予生理浓度雌激素可不通过雌激素受体而直接抑制心肌β1-肾上腺素受体并减弱Ca^2＋内流。此外,脑研究也显示雌激素能抑制负责调节动脉血压脑区的β1-肾上腺素受体活性。因此,雌激素和β1-肾上腺素受体之间的相互作用及其信号通路十分复杂。雌激素不仅主导性别决定,在机体其它功能例如心脏保护方面也具有重要作用。     

雌激素的心脏保护作用——与β1-肾上腺素受体的相互作用及其信号通路

雌激素是女性体内主要的类固醇性激素.对于心肌缺血性伤害,切除卵巢的成年雌性大鼠在β-肾上腺素受体激动时,比正常雌性大鼠呈现更严重的心肌损伤;而去卵巢后的雌激素替补组大鼠对β-肾上腺素受体激动时心肌缺血性伤害的反应则又回复到正常雌性大鼠水平,这为雌激素对抗缺血性伤害的心脏保护作用提供了证据.雌激素的这种保护作用是通过下调β1-肾上腺素受体的表达来实现的.也有研究证明,雌激素能抑制蛋白激酶A(protein kinase A,PKA)的表达和活性,PKA是Gs蛋白/腺苷酸环化酶(adenylyl cyclase,AC)/cAMP/PKA通路的第二信使,而该通路最终影响心肌的收缩功能.有初步证据表明雌激素还能抑制β1-肾上腺素受体通路下游的另一种第二信使钙调蛋白激酶Ⅱ-δc(Ca2+/calmodulin kinase Ⅱ-δc,CaMKⅡ-δc)的活性,而CaMKⅡ-δc参与PKA非依赖性的细胞凋亡.即时给予生理浓度雌激素可不通过雌激素受体而直接抑制心肌β1-肾上腺素受体并减弱Ca2+内流.此外,脑研究也显示雌激素能抑制负责调节动脉血压脑区的β广肾上腺素受体活性.因此,雌激素和β1-肾上腺素受体之间的相互作用及其信号通路十分复杂.雌激素不仅主导性别决定,在机体其它功能例如心脏保护方面也具有重要作用.