Efficient experimental design and analysis of real-time PCR assays.

Real-time polymerase chain reaction (qPCR) is currently the standard for gene quantification studies and has been extensively used in large-scale basic and clinical research. The operational costs and technical errors can become a significant issue due to the large number of sample reactions. In this paper, we present an experimental design strategy and an analysis procedure that are more efficient requiring fewer sample reactions than the traditional approach. We verified mathematically and experimentally the new design on a well-characterized model, to evaluate the gene expression levels of CACNA1C and CACNA1G in hypertrophic ventricular myocytes induced by phenylephrine treatment.

Differential regulation of low and high voltage-activated calcium channels in neonatal rat myocytes following chronic PKA modulation.

The biophysical properties of voltage-dependent cardiac calcium channels (VDCC) can be modulated by protein kinases. In this study, we investigate whether long-term treatment with protein kinase A (PKA) modulators alters the VDCC activity in neonatal ventricular myocytes. Using whole-cell patch-clamp recordings, we found an increase in high-voltage activated (HVA) current density and a corresponding decrease in low-voltage activated (LVA) current density in neonatal rat ventricular myocytes up to 6 days in culture. Long-term exposure to 8Br-cAMP, a PKA stimulator, increased the HVA current density at 7 and 24 hours. In contrast, H89, a PKA inhibitor, caused a biphasic change in the HVA, an initial reduction at 7 hours exposure followed by an increase up to 4 days. In addition, H89 caused a sustained increase in LVA currents from 7 hours to 4 days. These findings suggest that chronic exposure to H89 changes LVA and HVA calcium current activities in cardiac myocytes. PKA is a key target of ß-adrenoceptor activiation, thus, our findings suggest long-term repeated use of ß-adrenergic drugs may induce unexpected functional alteration of VDCCs.

Differential sensitivities of CaV1.2 IIS5-S6 mutants to 1,4-dihydropyridine analogs.

1,4-Dihydropyridines (DHPs), L-type calcium channel (Ca(V)1) blockers, are known to interact with Ca(V)1.2 subunits through their binding site located at IIIS5-S6 and IVS6 regions. We recently identified two domain II residues (S666 and A752) critical for nifedipine blockade (Kwok et al., 2008). In this study, we examined the blockade effects of two DHP analogues, nemadipine and nicardipine, on wildtype, M1161A (in IIIS6), S666V (in IIS5) and A752T (in IIS6) mutants of the rat alpha(1C) subunit transiently expressed with beta(2a) and alpha(2)delta in cultured tsA201 cells. We found that the IC(50) ratio of the mutants to the wildtype channel was similar in S666V and M1161A mutants for both drugs, but in A752T it was lower for nemadipine than nicardipine (P<0.05). At saturating drug concentrations, not all the current was completely blocked in the mutants. The residual current recorded in 100 microM nemadipine was approximately 10% of the total current for the A752T channel, which was significantly higher than that in 100 microM nicardipine (approximately 2%). In wildtype, S666V and M1161A, there was no significant difference in residual current between nemadipine and nicardipine, although it was greater in S666V (approximately 15%) and M1161A approximately 30%) as compared to the wildtype channel (<5%). Taken together, our findings suggest that the domain II residues alter the DHP effect in a structure-specific manner and may be involved in a pathway downstream of DHP binding.

A genetic screen for dihydropyridine (DHP)-resistant worms reveals new residues required for DHP-blockage of mammalian calcium channels.

Dihydropyridines (DHPs) are L-type calcium channel (Ca(v)1) blockers prescribed to treat several diseases including hypertension. Ca(v)1 channels normally exist in three states: a resting closed state, an open state that is triggered by membrane depolarization, followed by a non-conducting inactivated state that is triggered by the influx of calcium ions, and a rapid change in voltage. DHP binding is thought to alter the conformation of the channel, possibly by engaging a mechanism similar to voltage dependent inactivation, and locking a calcium ion in the pore, thereby blocking channel conductance. As a Ca(v)1 channel crystal structure is lacking, the current model of DHP action has largely been achieved by investigating the role of candidate Ca(v)1 residues in mediating DHP-sensitivity. To better understand DHP-block and identify additional Ca(v)1 residues important for DHP-sensitivity, we screened 440,000 randomly mutated Caenorhabditis elegans genomes for worms resistant to DHP-induced growth defects. We identified 30 missense mutations in the worm Ca(v)1 pore-forming (alpha(1)) subunit, including eleven in conserved residues known to be necessary for DHP-binding. The remaining polymorphisms are in eight conserved residues not previously associated with DHP-sensitivity. Intriguingly, all of the worm mutants that we analyzed phenotypically exhibited increased channel activity. We also created orthologous mutations in the rat alpha(1C) subunit and examined the DHP-block of current through the mutant channels in culture. Six of the seven mutant channels examined either decreased the DHP-sensitivity of the channel and/or exhibited significant residual current at DHP concentrations sufficient to block wild-type channels. Our results further support the idea that DHP-block is intimately associated with voltage dependent inactivation and underscores the utility of C. elegans as a screening tool to identify residues important for DHP interaction with mammalian Ca(v)1 channels.

Fibrocystin/polyductin modulates renal tubular formation by regulating polycystin-2 expression and function.

Autosomal recessive polycystic kidney disease is caused by mutations in PKHD1, which encodes the membrane-associated receptor-like protein fibrocystin/polyductin (FPC). FPC associates with the primary cilia of epithelial cells and co-localizes with the Pkd2 gene product polycystin-2 (PC2), suggesting that these two proteins may function in a common molecular pathway. For investigation of this, a mouse model with a gene-targeted mutation in Pkhd1 that recapitulates phenotypic characteristics of human autosomal recessive polycystic kidney disease was produced. The absence of FPC is associated with aberrant ciliogenesis in the kidneys of Pkhd1-deficient mice. It was found that the COOH-terminus of FPC and the NH2-terminus of PC2 interact and that lack of FPC reduced PC2 expression but not vice versa, suggesting that PC2 may function immediately downstream of FPC in vivo. PC2-channel activities were dysregulated in cultured renal epithelial cells derived from Pkhd1 mutant mice, further supporting that both cystoproteins function in a common pathway. In addition, mice with mutations in both Pkhd1 and Pkd2 had a more severe renal cystic phenotype than mice with single mutations, suggesting that FPC acts as a genetic modifier for disease severity in autosomal dominant polycystic kidney disease that results from Pkd2 mutations. It is concluded that a functional and molecular interaction exists between FPC and PC2 in vivo.

NCS-1 differentially regulates growth cone and somata calcium channels in Lymnaea neurons.

Local voltage-gated calcium channels, which regulate intracellular Ca2+ levels by allowing Ca2+ influx, play an important role in guiding and shaping growth cones, and in regulating the outgrowth and branching of neurites. Therefore, elucidating the mechanisms that regulate the biophysical properties of whole-cell calcium currents in the growth cones and somata of growing neurons is important to improving our understanding of neuronal development and regeneration. In this study, taking advantage of the large size of the pedal A (PeA) neurons in Lymnaea stagnalis, we compared the biophysical properties of somata and growth cone whole-cell calcium channel currents using Ba2+ and Ca2+ as current carriers. We found that somata and growth cone currents exhibit similar high-voltage activation properties. However, Ba2+ and Ca2+ currents in growth cones and somata are differentially affected by a dominant-negative peptide containing the C-terminal amino acid sequence of neuronal calcium sensor-1 (NCS-1). The peptide selectively reduces the peak and sustained components of current densities and the slope conductance in growth cones, and shifts the reversal potential of the growth cone currents to more hyperpolarized voltages. In contrast, the peptide had no significant effect on the somata calcium channels. Thus, we conclude that NCS-1 differentially modulates Ca2+ currents in the somata and growth cones of regenerating neurons, and may serve as a key regulator to facilitate the growth cone calcium channel activity.

Neuronal calcium sensor-1 modulation of optimal calcium level for neurite outgrowth.

Neurite extension and branching are affected by activity-dependent modulation of intracellular Ca2+, such that an optimal window of [Ca2+] is required for outgrowth. Our understanding of the molecular mechanisms regulating this optimal [Ca2+]i remains unclear. Taking advantage of the large growth cone size of cultured primary neurons from pond snail Lymnaea stagnalis combined with dsRNA knockdown, we show that neuronal calcium sensor-1 (NCS-1) regulates neurite extension and branching, and activity-dependent Ca2+ signals in growth cones. An NCS-1 C-terminal peptide enhances only neurite branching and moderately reduces the Ca2+ signal in growth cones compared with dsRNA knockdown. Our findings suggest that at least two separate structural domains in NCS-1 independently regulate Ca2+ influx and neurite outgrowth, with the C-terminus specifically affecting branching. We describe a model in which NCS-1 regulates cytosolic Ca2+ around the optimal window level to differentially control neurite extension and branching.

Zn2+ sensitivity of high- and low-voltage activated calcium channels.

The essential cation zinc (Zn2+) blocks voltage-dependent calcium channels in several cell types, which exhibit different sensitivities to Zn2+. The specificity of the Zn2+ effect on voltage-dependent calcium channel subtypes has not been systematically investigated. In this study, we used a transient protein expression system to determine the Zn2+ effect on low- and high-voltage activated channels. We found that in Ba2+, the IC50 value of Zn2+ was alpha1-subunit-dependent with lowest value for CaV1.2, and highest for CaV3.1; the sensitivity of the channels to Zn2+ was approximately ranked as CaV1.2>CaV3.2>CaV2.3>CaV2.2=CaV 2.1>or=CaV3.3=CaV3.1. Although the CaV2.2 and CaV3.1 channels had similar IC50 for Zn2+ in Ba2+, the CaV2.2, but not CaV3.1 channels, had approximately 10-fold higher IC50 to Zn2+ in Ca2+. The reduced sensitivity of CaV2.2 channels to Zn2+ in Ca2+ was partially reversed by disrupting a putative EF-hand motif located external to the selectivity filter EEEE locus. Thus, our findings support the notion that the Zn2+ block, mediated by multiple mechanisms, may depend on conformational changes surrounding the alpha1 pore regions. These findings provide fundamental insights into the mechanism underlying the inhibitory effect of zinc on various Ca2+ channel subtypes.

The role of synaptotagmin I C2A calcium-binding domain in synaptic vesicle clustering during synapse formation.

Synaptic vesicles aggregate at the presynaptic terminal during synapse formation via mechanisms that are poorly understood. Here we have investigated the role of the putative calcium sensor synaptotagmin I in vesicle aggregation during the formation of soma-soma synapses between identified partner cells using a simple in vitro synapse model in the mollusc Lymnaea stagnalis. Immunocytochemistry, optical imaging and electrophysiological recording techniques were used to monitor synapse formation and vesicle localization. Within 6 h, contact between appropriate synaptic partner cells up-regulated global synaptotagmin I expression, and induced a localized aggregation of synaptotagmin I at the contact site. Cell contacts between non-synaptic partner cells did not affect synaptotagmin I expression. Application of an human immunodeficiency virus type-1 transactivator (HIV-1 TAT)-tagged peptide corresponding to loop 3 of the synaptotagmin I C2A domain prevented synaptic vesicle aggregation and synapse formation. By contrast, a TAT-tagged peptide containing the calcium-binding motif of the C2B domain did not affect synaptic vesicle aggregation or synapse formation. Calcium imaging with Fura-2 demonstrated that TAT-C2 peptides did not alter either basal or evoked intracellular calcium levels. These results demonstrate that contact with an appropriate target cell is necessary to initiate synaptic vesicle aggregation during nascent synapse formation and that the initial aggregation of synaptic vesicles is dependent on loop 3 of the C2A domain of synaptotagmin I.

Permeable ions differentially affect gating kinetics and unitary conductance of L-type calcium channels.

Although ion permeation and gating of L-type Ca(2+) channels are generally considered separate processes controlled by distinct components of the channel protein, ion selectivity can vary with the kinetic state. To test this possibility, we studied single-channel currents (cell-attached) of recombinant L-type channels (Ca(V)1.2, beta(2a), and alpha(2)delta) transiently expressed in tsA201 cells in the presence of the channel agonist BayK 8644 which promotes long channel openings (Mode 2 openings). We found that both the brief (Mode 1) and long (Mode 2) mean open times in the presence of Ca(2+) were relatively longer than those with Ba(2+). The unitary slope conductance with Ba(2+) was significantly larger (p<0.05) in Mode 2 openings than for brief Mode 1 openings, whereas the conductance with Ca(2+) did not vary with mode gating. Consequently, the gamma(Ba):gamma(Ca) ratio was greater for Mode 2 than Mode 1 openings. Our findings indicate that both ion permeation and gating kinetics of the L-type channel are differentially modulated by permeable ions. Ca(2+) binding to the L-type channel may stabilize the alteration of channel ion permeability mediated by gating kinetics, and thus, play a role in preventing excessive ion entry when the activation gating of the channel is promoted to the prolonged open state.

Biophysical properties of menthol-activated cold receptor TRPM8 channels.

The temperature-sensitive transient receptor potential channel, TRPM8, was recently cloned and found to be activated by cold and menthol. Whole-cell recordings show that TRPM8 is permeable to multiple cations and exhibits a strong outward rectification. Here, we examine the mechanism underlying menthol-evoked current rectification of TRPM8 transiently expressed in tsA-201 cells at room temperature ( approximately 25 degrees C). Whole-cell currents (ruptured, bath: Na(+), K(+), Ca(2+), or Ba(2+); pipette: KCl) exhibited a strong outward rectification in the presence of menthol, consistent with previous studies. The outward K(+) current was reduced in the presence of external Ca(2+) or Ba(2+). Single-channel recordings (cell-attached) showed that menthol induced brief channel openings with two conducting states in the voltage range between -80 and +60mV. The small current (i(S)) conducted both monovalent and divalent ions, and the large one (i(L)) predominantly monovalent ions. The i-V plot for Ca(2+) was weakly outward rectifying, whereas those for monovalent ions were linear. The i(S) may result in the divalent ion-induced reduction of the whole-cell outward current. The open probability (P(o)) in all ion conditions tested was low at negative voltages and increased with depolarization, accounting for the small inward currents observed at the whole-cell level. In conclusion, our results indicate that menthol induced steep outward rectification of TRPM8 results from the voltage-dependent open channel probability and the permeating ion-dependent modulation of the unitary channel conductance.

Thermodynamics of heat activation of single capsaicin ion channels VR1.

Temperature affects functions of all ion channels, but few of them can be gated directly. The vanilloid receptor VR1 provides one exception. As a pain receptor, it is activated by heat >42 degrees C in addition to other noxious stimuli, e.g. acids and vanilloids. Although it is understood how ligand- and voltage-gated channels might detect their stimuli, little is known on how heat could be sensed and activate a channel. In this study, we characterized the heat-induced single-channel activity of VR1, in an attempt to localize the temperature-dependent components involved in the activation of the channel. At <42 degrees C, openings were few and brief. Raising the ambient temperature rapidly increased the frequency of openings. Despite the large temperature coefficient of the apparent activity (Q(10) approximately 27), the unitary current, the open dwell-times, and the intraburst closures were all only weakly temperature dependent (Q(10) < 2). Instead, heat had a localized effect on the reduction of long closures between bursts (Q(10) approximately 7) and the elongation of burst durations (Q(10) approximately 32). Both membrane lipids and solution ionic strength affected the temperature threshold of the activation, but neither diminished the response. The thermodynamic basis of heat activation is discussed, to elucidate what makes a thermal-sensitive channel unique.

Conotoxins as sensors of local pH and electrostatic potential in the outer vestibule of the sodium channel.

We examined the block of voltage-dependent rat skeletal muscle sodium channels by derivatives of mu-conotoxin GIIIA (muCTX) having either histidine, glutamate, or alanine residues substituted for arginine-13. Toxin binding and dissociation were observed as current fluctuations from single, batrachotoxin-treated sodium channels in planar lipid bilayers. R13X derivatives of muCTX only partially block the single-channel current, enabling us to directly monitor properties of both muCTX-bound and -unbound states under different conditions. The fractional residual current through the bound channel changes with pH according to a single-site titration curve for toxin derivatives R13E and R13H, reflecting the effect of changing the charge on residue 13, in the bound state. Experiments with R13A provided a control reflecting the effects of titration of all residues on toxin and channel other than toxin residue 13. The apparent pKs for the titration of residual conductance are shifted 2-3 pH units positive from the nominal pK values for histidine and glutamate, respectively, and from the values for these specific residues, determined in the toxin molecule in free solution by NMR measurements. Toxin affinity also changes dramatically as a function of pH, almost entirely due to changes in the association rate constant, kon. Interpreted electrostatically, our results suggest that, even in the presence of the bound cationic toxin, the channel vestibule strongly favors cation entry with an equivalent local electrostatic potential more negative than -100 mV at the level of the "outer charged ring" formed by channel residues E403, E758, D1241, and D1532. Association rates are apparently limited at a transition state where the pK of toxin residue 13 is closer to the solution value than in the bound state. The action of these unique peptides can thus be used to sense the local environment in the ligand--receptor complex during individual molecular transitions and defined conformational states.

Dependence of mu-conotoxin block of sodium channels on ionic strength but not on the permeating [Na+]: implications for the distinctive mechanistic interactions between Na+ and K+ channel pore-blocking toxins and their molecular targets.

Mu-conotoxins (mu-CTXs) are Na+ channel-blocking, 22-amino acid peptides produced by the sea snail Conus geographus. Although K+ channel pore-blocking toxins show specific interactions with permeant ions and strong dependence on the ionic strength (mu), no such dependence has been reported for mu-CTX and Na+ channels. Such properties would offer insight into the binding and blocking mechanism of mu-CTX as well as functional and structural properties of the Na+ channel pore. Here we studied the effects of mu and permeant ion concentration ([Na+]) on mu-CTX block of rat skeletal muscle (mu1, Nav1.4) Na+ channels. Mu-CTX sensitivity of wild-type and E758Q channels increased significantly (by approximately 20-fold) when mu was lowered by substituting external Na+ with equimolar sucrose (from 140 to 35 mm Na+); however, toxin block was unaltered (p > 0.05) when mu was maintained by replacement of [Na+] with N-methyl-d-glucamine (NMG+), suggesting that the enhanced sensitivity at low mu was not due to reduction in [Na+]. Single-channel recordings identified the association rate constant, k(on), as the primary determinant of the changes in affinity (k(on) increased 40- and 333-fold for mu-CTX D2N/R13Q and D12N/R13Q, respectively, when symmetric 200 mm Na+ was reduced to 50 mm). In contrast, dissociation rates changed <2-fold for the same derivatives under the same conditions. Experiments with additional mu-CTX derivatives identified toxin residues Arg-1, Arg-13, and Lys-16 as important contributors to the sensitivity to external mu. Taken together, our findings indicate that mu-CTX block of Na+ channels depends critically on mu but not specifically on [Na+], contrasting with the known behavior of pore-blocking K+ channel toxins. These findings suggest that different degrees of ion interaction, underlying the fundamental conduction mechanisms of Na+ and K+ channels, are mirrored in ion interactions with pore-blocking toxins.

Capsaicin activation of the pain receptor, VR1: multiple open states from both partial and full binding.

Capsaicin, the pungent ingredient of hot peppers, has long been used to identify nociceptors. Its molecular target, the vanilloid receptor VR1, was recently cloned and confirmed functionally as a polymodal detector of multiple pain stimuli: heat, acid, and vanilloids. Previous electrophysiology studies have focused on whole-cell characteristics of the receptor. Here, we provide the first in-depth single-channel kinetic study of VR1 to understand its activation mechanism. At low to medium concentrations, channel activity appeared as bursts. Not only did the durations of the interburst gaps vary with capsaicin, the bursts also appeared ligand-dependent, with high capsaicin prolonging bursts and stabilizing openings. Gating involved at least five closed and three open states, with strong correlations between short closures and long openings, and long closures and short openings. Increasing capsaicin reduced the long closures with little effect on short ones. The open time constants changed little with capsaicin concentration, though their relative proportions varied. These results suggest that 1), the channel contains multiple capsaicin binding sites; 2), both partial and full binding are capable of opening the channel; 3), when activated, multiple open states are accessible irrespective of the level of binding; and 4), capsaicin association occurs preferentially to the closed channel.

Electrostatic and steric contributions to block of the skeletal muscle sodium channel by mu-conotoxin.

Pore-blocking toxins are valuable probes of ion channels that underlie electrical signaling. To be effective inhibitors, they must show high affinity and specificity and prevent ion conduction. The 22-residue sea snail peptide, mu-conotoxin GIIIA, blocks the skeletal muscle sodium channel completely. Partially blocking peptides, derived by making single or paired amino acid substitutions in mu-conotoxin GIIIA, allow a novel analysis of blocking mechanisms. Replacement of one critical residue (Arg-13) yielded peptides that only partially blocked single-channel current. These derivatives, and others with simultaneous substitution of a second residue, were used to elucidate the structural basis of the toxin's blocking action. The charge at residue-13 was the most striking determinant. A positive charge was necessary, though not sufficient, for complete block. Blocking efficacy increased with increasing residue-13 side chain size, regardless of charge, suggesting a steric contribution to inhibition. Charges grouped on one side of the toxin molecule at positions 2, 12, and 14 had a weaker influence, whereas residue-16, on the opposite face of the toxin, was more influential. Most directly interpreted, the data suggest that one side of the toxin is masked by close apposition to a binding surface on the pore, whereas the other side, bearing Lys-16, is exposed to an aqueous cavity accessible to entering ions. Strong charge-dependent effects emanate from this toxin surface. In the native toxin, Arg-13 probably presents a strategically placed electrostatic barrier rather than effecting a complete steric occlusion of the pore. This differs from other well-described channel inhibitors such as the charybdotoxin family of potassium channel blockers and the sodium channel-blocking guanidinium toxins (tetrodotoxin and saxitoxin), which appear to occlude the narrow part of the pore.