Modeling the dynamic behaviors of the COPI vesicle formation regulators, the small GTPase Arf1 and its activating Sec7 guanine nucleotide exchange factor GBF1 on Golgi membranes

The components and subprocesses underlying the formation of COPI-coated vesicles at the Golgi are well understood. The coating cascade is initiated after the small GTPase Arf1 is activated by the Sec7 domain–containing guanine nucleotide exchange factor GBF1 (Golgi brefeldin A resistant guanine nucleotide exchange factor 1). This causes a conformational shift within Arf1 that facilitates stable association of Arf1 with the membrane, a process required for subsequent recruitment of the COPI coat. Although we have atomic-level knowledge of Arf1 activation by Sec7 domain–containing GEFs, our understanding of the biophysical processes regulating Arf1 and GBF1 dynamics is limited. We used fluorescence recovery after photobleaching data and kinetic Monte Carlo simulation to assess the behavior of Arf1 and GBF1 during COPI vesicle formation in live cells. Our analyses suggest that Arf1 and GBF1 associate with Golgi membranes independently, with an excess of GBF1 relative to Arf1. Furthermore, the GBF1-mediated Arf1 activation is much faster than GBF1 cycling on/off the membrane, suggesting that GBF1 is regulated by processes other than its interactions Arf1. Interestingly, modeling the behavior of the catalytically inactive GBF1/E794K mutant stabilized on the membrane is inconsistent with the formation of a stable complex between it and an endogenous Arf1 and suggests that GBF1/E794K is stabilized on the membrane independently of complex formation.

0746 Dynamics of Sleep Stage Transitions in Patients with Narcolepsy and Other Hypersomnias

Introduction

Narcolepsy is a chronic sleep disorder characterized by excessive daytime sleepiness and abnormal REM sleep phenomena. Narcolepsy can be distinguished into type 1 (NT1; with cataplexy) and type 2 (NT2; without cataplexy). It has been reported that sleep stage sequences at sleep-onset as well as sleep-wake dynamics across the night may be useful in the differential diagnosis of hypersomnia. Here we studied dynamic features of sleep stage transitions during whole night sleep in patients with NT1, NT2, and other types of hypersomnia (o-HS).

Methods

Twenty patients with NT1, 14 patients with NT2, and 35 patients with o-HS underwent overnight PSG. Transition probabilities between sleep stages (wake, N1, N2, N3, and REM) and survival curves of continuous runs of each sleep stage were compared between groups. Transition-specific survival curves of continuous runs of each sleep stage, dependent on the subsequent stage of the transition, were also compared.

Results

The probability of transitions from N1-to-wake was significantly greater in NT1 than in NT2 and o-HS while that from N1-to-N2 was significantly smaller in NT1 than in NT2 and o-HS. The probability of transitions from N2-to-REM was significantly smaller in NT1 than in o-HS. Wake and N1 were significantly more continuous in NT1 than in NT2; specifically, N1 followed by N2 was significantly more continuous in NT1 than in NT2 and o-HS. N2 was significantly less continuous in NT1 and NT2 than in o-HS; this was specifically confirmed for N2 followed by N1/wake. REM sleep was significantly less continuous in NT1 than in NT2 and o-HS; specifically, REM sleep followed by wake was significantly less continuous in NT1 than in o-HS. Continuity of N3 did not differ significantly between groups.

Conclusion

Dynamics of sleep stage transitions differed between NT1, NT2, and o-HS. Dynamic features of sleep such as sleep instability, persistency of wake/N1, and REM fragmentation may differentiate NT1 from NT2, while N2 continuity may differentiate narcolepsy from o-HS. The results suggest that sleep transition analysis may be of clinical utility and provide insights into the underlying pathophysiology of hypersomnia and narcolepsy.

Support

JSPS KAKENHI (18K17891 to AK).

Feeding catheter gastrostomy with the round ligament of the liver prevents mechanical bowel obstruction after esophagectomy

Jejunostomy, which requires the fixation of the jejunum to the abdominal wall, is commonly used as an enteral feeding access after esophagectomy. However, this procedure sometimes causes severe complications, such as mechanical bowel obstruction. In 2009, we developed a modified approach to insert an enteral feeding tube through the reconstructed gastric tube using the round ligament of the liver. The aim of this study is to investigate the usefulness of this approach as compared to the approach through jejunostomy. Between January 2005 and March 2015, 420 patients with thoracic esophageal cancer underwent esophagectomy via thoracotomy and laparotomy. Of these, 214 underwent feeding jejunostomy (FJ group) and 206 patients underwent feeding via gastric tube with round ligament of the liver (FG group). Catheter-related complications, other postoperative complications, and mortality were compared between the two groups. The incidence of catheter site infection during catheterization in the FG group was significantly lower (n = 1/206, 0.5%) compared to the FJ group (n = 11/214, 5.1%) (P < 0.01). The postoperative bowel obstruction did not occur in the FG group, while it occurred in eight patients (3.7%) in the FJ group (P < 0.01). The incidences of other catheter-related and postoperative complications were similar between the two groups. Feeding catheter gastrostomy with the round ligament of the liver can be a useful enteral feeding access after esophagectomy, because the incidence rate of severe catheter-related complications, such as surgical site infection and mechanical obstruction tend to be lower with this technique compare to jejunostomy.

External Carotid Artery Embolization of Dural Arteriovenous Malformations Involving the Cavernous Sinus; Outcome and Role of Venous Thrombosis

Nine patients with dural arteriovenous malformations (AVMs) in the region of the cavernous sinus were treated by means of external carotid artery (ECA) embolization using polyvinyl alcolhol. All AVMs received vascular supply from both the ECA and the internal carotid artery. Seven cases were clinically cured after embolization, while 2 cases with cortical venous drainage and high flow through the shunt were not completely cured. Venous thrombosis was observed in 5 cases before and in 9 after embolization. In 6 cases the drainage pattern changed owing to venous thrombosis. Complete thrombosis of the cavernous sinus was found on a follow-up angiography in 2 cases. Formation of venous thrombosis and occlusion of feeding arteries are crucial factors for success of ECA embolization. Dural AVMs with cortical venous drainage and high flow cannot be relieved by ECA embolization alone owing to difficulty in obtaining thrombosis of the veins.

Optical levitation of a microdroplet containing a single quantum dot

We demonstrate the optical levitation or trapping in helium gas of a single quantum dot (QD) within a liquid droplet. Bright single photon emission from the levitated QD in the droplet was observed for more than 200 s. The observed photon count rates are consistent with the value theoretically estimated from the two-photon-action cross section. This Letter presents the realization of an optically levitated solid-state quantum emitter.

Cytokines induce MMP-3-regulated proliferation of embryonic stem cell-derived odontoblast-like cells

OBJECTIVES

Matrix metalloproteinase (MMP)-3 expression increases after pulpectomy and accelerates angiogenesis in rat dental pulp by an uncharacterised mechanism. Odontoblasts, a major component of dental pulp, could represent a therapeutic target. We investigated whether MMP-3 activity is induced by cytokines and/or is associated with cell proliferation and apoptosis in embryonic stem cell-derived odontoblast-like cells.

MATERIALS AND METHODS

We used reverse transcriptase polymerase chain reaction, western blotting, an MMP-3 activity assay, a BrdU-cell proliferation enzyme-linked immunosorbent assay and DNA fragmentation analysis to evaluate siRNA-mediated downregulation of MMP-3 expression and activity, and any changes in the proliferative and apoptotic responses associated with this reduced expression.

RESULTS

Pro-inflammatory cytokines (interleukin-1β, tumour necrosis factor-α and interferon-γ, at relatively low concentrations) induced MMP-3 mRNA and protein expression, and increased MMP-3 activity and cell proliferation, but not apoptosis. MMP-3 silencing produced a potent and significant suppression of cytokine-induced MMP-3 expression and activity, decreased cell proliferation and increased apoptosis. These effects were rescued by application of exogenous MMP-3.

CONCLUSIONS

Our results suggest that pro-inflammatory cytokines induce MMP-3-regulated cell proliferation and anti-apoptosis effects in odontoblast-like cells derived from embryonic stem cells, in addition to their well-documented destructive role in inflammation.

Momentum transfer in nonequilibrium steady states

When a Brownian object interacts with noninteracting gas particles under nonequilibrium conditions, energy dissipation associated with Brownian motion causes an additional force on the object as a "momentum transfer deficit." This principle is demonstrated first by a new nonequilibrium steady state model and then applied to several known models such as an adiabatic piston for which a simple explanation has been lacking.

High-density lipoprotein cholesterol is positively associated with hypertension in apparently healthy Japanese men and women

Among five components of metabolic syndrome, high-density lipoprotein (HDL) cholesterol is unique because it is not significantly associated with blood pressure. This study looks at cross-sectional relationships between HDL cholesterol and hypertension using medical check-up data from 1803 apparently healthy Japanese men aged 49.9 +/- 9.0 years, and 1150 Japanese women aged 49.5 +/- 9.0 years. Pearson's correlation coefficients between systolic blood pressure (SBP)/diastolic blood pressure (DBP) and HDL cholesterol were -0.01 (ns)/-0.01 (ns) in men and -0.04 (ns)/-0.01 (ns) in women. The standardised partial regression coefficient of HDL cholesterol for SBP/DBP (mmHg) controlling for age, body mass index (BMI), fasting plasma glucose (FPG), triglycerides, high-sensitivity C-reactive protein (hs-CRP) and low-density lipoprotein (LDL) cholesterol were 0.15 (P < 0.0001)/0.15 (P < 0.0001) in men and 0.10 (P < 0.0001)/0.12 (P < 0.0001) in women. The odds ratio (OR; 95% confidence interval [CI]) of a 1 mg/dL increment of HDL cholesterol for hypertension controlling for age, BMI, FPG, triglycerides, hs-CRP, LDL cholesterol, metabolic syndrome, diabetes, exercise status, drinking status, and smoking status was 1.03 (1.02-1.04; P < 0.001) in men and 1.03 (1.01-1.05; P = 0.002) in women. Thus, HDL cholesterol was independently positively associated with hypertension in apparently healthy Japanese men and women.

Efficiency at maximum power of low-dissipation Carnot engines

We study the efficiency at maximum power, η*, of engines performing finite-time Carnot cycles between a hot and a cold reservoir at temperatures Th and Tc, respectively. For engines reaching Carnot efficiency ηC=1-Tc/Th in the reversible limit (long cycle time, zero dissipation), we find in the limit of low dissipation that η* is bounded from above by ηC/(2-ηC) and from below by ηC/2. These bounds are reached when the ratio of the dissipation during the cold and hot isothermal phases tend, respectively, to zero or infinity. For symmetric dissipation (ratio one) the Curzon-Ahlborn efficiency ηCA=1-√Tc/Th] is recovered.

Quantum-dot Carnot engine at maximum power

We evaluate the efficiency at maximum power of a quantum-dot Carnot heat engine. The universal values of the coefficients at the linear and quadratic order in the temperature gradient are reproduced. Curzon-Ahlborn efficiency is recovered in the limit of weak dissipation.

Comparative pharmacokinetics of RAD001 (everolimus) in normal and tumor-bearing rodents

PURPOSE

Comparative pharmacokinetic (PK) analysis of the mTOR inhibitor RAD001 (everolimus) in rats and mice.

METHODS

Blood cell partitioning, plasma protein binding and PK parameters of RAD001 in blood and tissues (including brain) of both mice and rats were determined. PK modeling predicted plasma/blood and tumor levels from a variety of regimens and these were compared with the known human PK profile. DCE-MRI was used to compare tumor vascularity between mice and rats. Estimation of IC50 values in vitro and ED50 values in vivo were used to provide an indication of anti-tumor activity.

RESULTS

The PK properties of RAD001 differed between mice and rats, including erythrocyte partitioning, plasma protein binding, plasma/blood t(1/2), oral bioavailability, volume of distribution, tissue/tumor penetration and elimination. Modeling of tumor and blood/plasma PK suggested that in mice, multiple daily administrations result in a 2-fold increase in tumor levels of RAD001 at steady state, whereas in rats, a 7.9-fold increase would occur. Weekly high-dose regimens were predicted not to facilitate tumor accumulation in either species. Total tumor levels of RAD001 were four- to eight-fold greater in rats than in mice. Rat tumors had a >2-fold greater plasma content and permeability compared to mouse tumors, which could contribute to differences in tumor drug uptake. Maximal antitumor effects (T/C of 0.04-0.35) were observed in both species after daily administration with similar C(max) and AUC values of unbound (free) RAD001. These free levels of RAD001 are exceeded in serum from cancer patients receiving clinically beneficial daily regimens. In rodents, brain penetration of RAD001 was poor, but was dose-dependent and showed over-proportional uptake in rats with a longer t(1/2) compared to the systemic circulation.

CONCLUSIONS

The PK of RAD001 differed between mice and rats, with rats having a PK profile closer to that of humans. High intermittent doses of RAD001 may be more appropriate for treatment of brain tumors.

Inertial effects in Büttiker-Landauer motor and refrigerator at the overdamped limit

We investigate the energetics of a Brownian motor driven by position-dependent temperature, commonly known as the Büttiker-Landauer motor. Overdamped models (M=0) predict that the motor can attain Carnot efficiency. However, the overdamped limit (M-->0) contradicts the previous prediction due to the kinetic energy contribution to the heat transfer. Using molecular dynamics simulation and numerical solution of the inertial Langevin equation, we confirm that the motor can never achieve Carnot efficiency and verify that the heat flow via kinetic energy diverges as M{-1/2} in the overdamped limit. The reciprocal process of the motor, namely, the Büttiker-Landauer refrigerator, is also examined. In this case, the overdamped approach succeeds in predicting the heat transfer only when there is no temperature gradient. Its found that the Onsager symmetry between the motor and refrigerator does not suffer from the singular behavior of the kinetic energy contribution.

Continuous and discontinuous phase transitions and partial synchronization in stochastic three-state oscillators

We investigate both continuous (second-order) and discontinuous (first-order) transitions to macroscopic synchronization within a single class of discrete, stochastic (globally) phase-coupled oscillators. We provide analytical and numerical evidence that the continuity of the transition depends on the coupling coefficients and, in some nonuniform populations, on the degree of quenched disorder. Hence, in a relatively simple setting this class of models exhibits the qualitative behaviors characteristic of a variety of considerably more complicated models. In addition, we study the microscopic basis of synchronization above threshold and detail the counterintuitive subtleties relating measurements of time-averaged frequencies and mean-field oscillations. Most notably, we observe a state of suprathreshold partial synchronization in which time-averaged frequency measurements from individual oscillators do not correspond to the frequency of macroscopic oscillations observed in the population.

Fluctuation theorem for entropy production during effusion of an ideal gas with momentum transfer

We derive an exact expression for entropy production during effusion of an ideal gas driven by momentum transfer in addition to energy and particle flux. Following the treatment in Cleuren [Phys. Rev. E 74, 021117 (2006)], we construct a master equation formulation of the process and explicitly verify the thermodynamic fluctuation theorem, thereby directly exhibiting its extended applicability to particle flows and hence to hydrodynamic systems.

Effects of disorder on synchronization of discrete phase-coupled oscillators

We study synchronization in populations of phase-coupled stochastic three-state oscillators characterized by a distribution of transition rates. We present results on an exactly solvable dimer as well as a systematic characterization of globally connected arrays of N types of oscillators (N=2,3,4) by exploring the linear stability of the nonsynchronous fixed point. We also provide results for globally coupled arrays where the transition rate of each unit is drawn from a uniform distribution of finite width. Even in the presence of transition rate disorder, numerical and analytical results point to a single phase transition to macroscopic synchrony at a critical value of the coupling strength. Numerical simulations make possible further characterization of the synchronized arrays.

Dissipation: the phase-space perspective

We show, through a refinement of the work theorem, that the average dissipation, upon perturbing a Hamiltonian system arbitrarily far out of equilibrium in a transition between two canonical equilibrium states, is exactly given by <W{diss}> =W-DeltaF=kTD(rho||rho[over ])=kT<ln(rho/rho[over ])>, where rho and rho[over ] are the phase-space density of the system measured at the same intermediate but otherwise arbitrary point in time, for the forward and backward process. D(rho||rho[over ]) is the relative entropy of rho versus rho[over ]. This result also implies general inequalities, which are significantly more accurate than the second law and include, as a special case, the celebrated Landauer principle on the dissipation involved in irreversible computations.

Ethnic sensitivity study of fingolimod in white and Asian subjects

OBJECTIVE

The authors compared the pharmacokinetics and pharmacological effects of the immunomodulator fingolimod in healthy white and Asian subjects for potential ethnic differences.

METHODS

White and Asian (Japanese) healthy subjects were demographically matched for sex, age and weight. Subjects received single 1.25 mg doses of fingolimod (6 ethnic pairs), 2.5 mg (7 pairs), 5 mg (6 pairs) or 5 mg/day for 7 days (6 pairs). The pharmacokinetics of fingolimod, major metabolites, peripheral blood lymphocyte counts and heart rate were characterized over 1 month after single-dose and 2 months after multiple-dose administration.

RESULTS

There were no clinically relevant differences in the fingolimod dose Cmax or dose AUC relationships between Asian subjects (slopes 0.84 and 1.05) versus white subjects (slopes 1.13 and 1.26) after single-dose administration. During multiple-dose administration, there were no clinically relevant interethnic differences in fingolimod accumulation ratios (6.6 +/- 0.4 for whites, 7.0 +/- 0.7 for Asians), area under the concentration-time curve (390 +/- 73 versus 382 +/- 106 ng x h/ml), or elimination half-life (7.4 +/- 0.8 versus 7.9 +/- 2.0 days). The acute decrease in lymphocyte counts after single- and multiple-dose fingolimod were similar in the two ethnic groups. The lymphocyte recovery rate to baseline after a 5 mg single dose and 5 mg/day multiple dose was reduced by 36 and 15% in Asian subjects compared with white subjects. The transient, acute decrease in heart rate after the first dose of fingolimod and the subsequent return to baseline was similar in the two ethnic groups.

CONCLUSION

There were no marked differences between healthy white and Asian subjects in fingolimod single-dose and multiple-dose pharmacokinetics, lymphocyte trafficking and heart rate responses.

Critical behavior and synchronization of discrete stochastic phase-coupled oscillators

Synchronization of stochastic phase-coupled oscillators is known to occur but difficult to characterize because sufficiently complete analytic work is not yet within our reach, and thorough numerical description usually defies all resources. We present a discrete model that is sufficiently simple to be characterized in meaningful detail. In the mean-field limit, the model exhibits a supercritical Hopf bifurcation and global oscillatory behavior as coupling crosses a critical value. When coupling between units is strictly local, the model undergoes a continuous phase transition that we characterize numerically using finite-size scaling analysis. In particular, we explicitly rule out multistability and show that the onset of global synchrony is marked by signatures of the XY universality class. Our numerical results cover dimensions d=2, 3, 4, and 5 and lead to the appropriate XY classical exponents beta and nu, a lower critical dimension dlc=2, and an upper critical dimension duc=4.

Fluctuation theorem for the effusion of an ideal gas

The probability distribution of the entropy production for the effusion of an ideal gas between two compartments is calculated explicitly. The fluctuation theorem is verified. The analytic results are in good agreement with numerical data from hard disk molecular dynamics simulations.

Brownian molecular motors driven by rotation-translation coupling

We investigated three models of Brownian motors which convert rotational diffusion into directed translational motion by switching on and off a potential. In the first model a spatially asymmetric potential generates directed translational motion by rectifying rotational diffusion. It behaves much like a conventional flashing ratchet. The second model utilizes both rotational diffusion and drift to generate translational motion without spatial asymmetry in the potential. This second model can be driven by a combination of a Brownian motor mechanism (diffusion driven) or by powerstroke (drift driven) depending on the chosen parameters. In the third model, elements of both the Brownian motor and powerstroke mechanisms are combined by switching between three distinct states. Relevance of the model to biological motor proteins is discussed.

Brownian refrigerator

Onsager symmetry implies that a Brownian motor, driven by a temperature gradient, will also perform a refrigerator function upon loading. We analytically calculate the corresponding heat flow for an exactly solvable microscopic model and compare it with molecular dynamics simulations.

On and off membrane dynamics of the endoplasmic reticulum-golgi tethering factor p115 in vivo

The mechanisms regulating membrane recruitment of the p115 tethering factor in vivo are unknown. Here, we describe cycling of p115 between membranes and cytosol and document the effects of Golgi matrix proteins, Rab1, and soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptors (SNAREs) on this process. Rapid membrane/cytosol exchange is shown by swift (t1/2 approximately 20 s) loss of Golgi-localized p115-green fluorescent protein (GFP) after repeated photobleaching of cell periphery and rapid (t1/2 approximately 13 s) fluorescence recovery after photobleaching Golgi-localized p115-GFP. p115 mutant missing the GM130/giantin binding site exhibits analogous fluorescence recovery after photobleaching (FRAP) (t1/2 approximately 13 s), suggesting that GM130 and giantin are not major determinants of p115 membrane dynamics. In contrast, p115-GFP exchanges more rapidly (t1/2 approximately 8 s) in cells expressing the inactive Rab1/N121I mutant, indicating that p115 cycling is influenced by Rab1. p115-GFP dynamics is also influenced by the assembly status of SNAREs. In cells expressing an ATPase-deficient NSF/E329Q mutant that inhibits SNARE complex disassembly, the cycling kinetics of p115-GFP are significantly slower (t1/2 approximately 21 s). In contrast, in cells incubated at reduced temperature (10 degrees C) that inhibits vesicular traffic, the cycling kinetics of p115-GFP are faster (t1/2 approximately 7 s). These data suggest that p115-binding sites on the membrane are provided by unassembled SNAREs. In agreement, biochemical studies show increased p115 recruitment to membranes in the presence of NSF and alpha-SNAP. Our data support a model in which recruitment of tethers is directly regulated by the assembly status of SNAREs.

Universality of synchrony: critical behavior in a discrete model of stochastic phase-coupled oscillators

We present the simplest discrete model to date that leads to synchronization of stochastic phase-coupled oscillators. In the mean field limit, the model exhibits a Hopf bifurcation and global oscillatory behavior as coupling crosses a critical value. When coupling between units is strictly local, the model undergoes a continuous phase transition which we characterize numerically using finite-size scaling analysis. In particular, the onset of global synchrony is marked by signatures of the XY universality class, including the appropriate classical exponents beta and nu, a lower critical dimension d(lc) = 2, and an upper critical dimension d(uc) = 4.

Fluctuation and dissipation of work in a Joule experiment

We elucidate the connection between various fluctuation theorems by a microcanonical version of the Crooks relation. We derive the microscopically exact expression for the work distribution in an idealized Joule experiment, namely, for a convex object moving at constant speed through an ideal gas. Analytic results are compared with molecular dynamics simulations of a hard disk gas.

Microscopic analysis of a thermal brownian motor

We study a genuine Brownian motor by hard disk molecular dynamics and calculate analytically its properties, including its drift speed and thermal conductivity, from microscopic theory.

Macroscopic limit cycle via pure noise-induced phase transitions

Bistability generated via a pure noise-induced phase transition is reexamined from the view of bifurcations in macroscopic cumulant dynamics. It allows an analytical study of the phase diagram in more general cases than previous methods. In addition, using this approach we investigate spatially extended systems with two degrees of freedom per site. For this system, the analytic solution of the stationary Fokker-Planck equation is not available and a standard mean field approach cannot be used to find noise-induced phase transitions. A different approach based on cumulant dynamics predicts a noise-induced phase transition through a Hopf bifurcation leading to a macroscopic limit cycle motion, which is confirmed by numerical simulation.

An efficient synthesis of nucleotides via the phosphoramidite method using a triflic acid salt of an imidazole-related compound as a promoter

N-Phenylimidazolium triflate and N-methylbenzimidazolium triflate, new imidazole-related compound/triflic acid-complex type of promoters in the phosphoramidite method, has been developed. These reagents are, particularly, useful for internucleotide-bond formation with lowly reactive reactants and have allowed an efficient, high-yield synthesis of oligodeoxyribonucleotides both in a solution phase and on a solid supports.

Drift by dichotomous Markov noise

We derive explicit results for the asymptotic probability density and drift velocity in systems driven by dichotomous Markov noise, including the situation in which the asymptotic dynamics crosses unstable fixed points. The results are illustrated on the problem of the rocking ratchet.

The role of the putative catalytic base in the phosphoryl transfer reaction in a protein kinase: first-principles calculations

Protein kinases are important enzymes controlling the majority of cellular signaling events via a transfer of the gamma-phosphate of ATP to a target protein. Even after many years of study, the mechanism of this reaction is still poorly understood. Among many factors that may be responsible for the 1011-fold rate enhancement due to this enzyme, the role of the conserved aspartate (Asp166) has been given special consideration. While the essential presence of Asp166 has been established by mutational studies, its function is still debated. The general base catalyst role assigned to Asp166 on the basis of its position in the active site has been brought into question by the pH dependence of the reaction rate, isotope measurements, and pre-steady-state kinetics. Recent semiempirical calculations have added to the controversy surrounding the role of Asp166 in the catalytic mechanism. No major role for Asp166 has been found in these calculations, which have predicted the reaction process consisting of an early transfer of a substrate proton onto the phosphate group. These conclusions were inconsistent with experimental observations. To address these differences between experimental results and theory with a more reliable computational approach and to provide a theoretical platform for understanding catalysis in this important enzyme family, we have carried out first-principles structural and dynamical calculations of the reaction process in cAPK kinase. To preserve the essential features of the reaction, representations of all of the key conserved residues (82 atoms) were included in the calculation. The structural calculations were performed using the local basis density functional (DFT) approach with both hybrid B3LYP and PBE96 generalized gradient approximations. This kind of calculation has been shown to yield highly accurate structural information for a large number of systems. The optimized reactant state structure is in good agreement with X-ray data. In contrast to semiempirical methods, the lowest energy product state places the substrate proton on Asp166. First-principles molecular dynamics simulations provide additional support for the stability of this product state. The latter also demonstrate that the proton transfer to Asp166 occurs at a point in the reaction where bond cleavage at the PO bridging position is already advanced. This mechanism is further supported by the calculated structure of the transition state in which the substrate hydroxyl group is largely intact. A metaphoshate-like structure is present in the transition state, which is consistent with the X-ray structures of transition state mimics. On the basis of the calculated structure of the transition state, it is estimated to be 85% dissociative. Our analysis also indicates an increase in the hydrogen bond strength between Asp166 and substrate hydroxyl and a small decrease in the bond strength of the latter in the transition state. In summary, our calculations demonstrate the importance of Asp166 in the enzymatic mechanism as a proton acceptor. However, the proton abstraction from the substrate occurs late in the reaction process. Thus, in the catalytic mechanism of cAPK protein kinase, Asp166 plays a role of a "proton trap" that locks the transferred phosphoryl group to the substrate. These results resolve prior inconsistencies between theory and experiment and bring new understanding of the role of Asp166 in the protein kinase catalytic mechanism.

Efficient liquid-phase synthesis of short-length nucleotides via the phosphoramidite method using stoichiometric amounts of reactants

The condensation of a nucleoside phosphoramidite and a nucleoside by the aid of a suitable promoter in stoichiometric use is achieved in acetonitrile in the presence of molecular sieves 3A or 4A to give a desired coupling product in an excellent yield. This strategy is particularly useful for the large-scale synthesis of short nucleotides.

Activation of striated muscle: nearest-neighbor regulatory-unit and cross-bridge influence on myofilament kinetics

We have formulated a three-compartment model of muscle activation that includes both strong cross-bridge (XB) and Ca(2+)-activated regulatory-unit (RU) mediated nearest-neighbor cooperative influences. The model is based on the tight coupling premise--that XB retain activating Ca(2+) on the thin filament. Using global non-linear least-squares, the model produced excellent fits to experimental steady-state force-pCa and ATPase-pCa data from skinned rat soleus fibers. In terms of the model, nearest-neighbor influences over the range of Ca(2+) required for activation cause the Ca(2+) dissociation rate from regulatory-units (k(off)) to decrease and the cross-bridge association rate (f) to increase each more than ten-fold. Moreover, the rate variations occur in separate Ca(2+) regimes. The energy of activation governing f is strongly influenced by both neighboring RU and XB. In contrast, the energy of activation governing k(off) is less affected by neighboring XB than by neighboring RU. Nearest-neighbor cooperative influences provide both an overall sensitization to Ca(2+) and the well-known steep response of force to free Ca(2+). The apparent sensitivity for Ca(2+)-activation of force and ATPase is a function of cross-bridge kinetic rates. The model and derived parameter set produce simulated behavior in qualitative agreement with steady-state experiments reported in the literature for partial TnC replacement, increased [P(i)], increased [ADP], and MalNEt-S1 addition. The model is an initial attempt to construct a general theory of striated muscle activation-one that can be consistently used to interpret data from various types of muscle manipulation experiments.

Nonlinear response with dichotomous noise

Dichotomous noise appears in a wide variety of physical and mathematical models. It has escaped attention that the standard results for the long time properties cannot be applied when unstable fixed points are crossed in the asymptotic regime. We show how calculations have to be modified to deal with these cases and present as a first application full analytic results for hypersensitive transport.

Collective behavior of parametric oscillators

We revisit the mean-field model of globally and harmonically coupled parametric oscillators subject to periodic block pulses with initially random phases. The phase diagram of regions of collective parametric instability is presented, as is a detailed characterization of the motions underlying these instabilities. This presentation includes regimes not identified in earlier work [I. Bena and C. Van den Broeck, Europhys. Lett. 48, 498 (1999)]. In addition to the familiar parametric instability of individual oscillators, two kinds of collective instabilities are identified. In one the mean amplitude diverges monotonically while in the other the divergence is oscillatory. The frequencies of collective oscillatory instabilities in general bear no simple relation to the eigenfrequencies of the individual oscillators nor to the frequency of the external modulation. Numerical simulations show that systems with only nearest-neighbor coupling have collective instabilities similar to those of the mean-field model. Many of the mean-field results are already apparent in a simple dimer [M. Copelli and K. Lindenberg, Phys. Rev. E 63, 036605 (2001)].

Histologic examination of dislocated lenses

PURPOSE

To examine histological changes resulting from dislocated and subluxated lenses.

CASES

The subjects consisted of 16 patients (aged 52-89 years) who underwent total lens extraction for lens dislocation or subluxation in the Department of Ophthalmology at Fukui Medical University during the period between April 1991 and June 1998. There were 5 patients (6 eyes) with traumatic dislocation and 11 patients (11 eyes) with idiopathic dislocation.

RESULT

Rupture of the cortical fibers and migration of the epithelial cells toward the posterior pole of the lens were more frequently noted in patients with traumatic dislocation than in the idiopathic group, and both findings were often simultaneously observed. Rupture of the cortical fibers was considered attributable to external pressure transmitted to the lens.

CONCLUSION

We speculate that the concurrent migration and dislocation of the equatorial bow architecture toward the posterior pole was caused by inhibition of differentiation of the epithelial cells to fiber cells by external pressure on the equatorial region.

Acid/azole complexes as highly effective promoters in the synthesis of DNA and RNA oligomers via the phosphoramidite method

The utility of various kinds of acid salts of azole derivatives as promoters for the condensation of a nucleoside phosphoramidite and a nucleoside is investigated. Among the salts, N-(phenyl)imidazolium triflate, N-(p-acetylphenyl)imidazolium triflate, N-(methyl)benzimidazolium triflate, benzimidazolium triflate, and N-(phenyl)imidazolium perchlorate have shown extremely high reactivity in a liquid phase. These reagents serve as powerful activators of deoxyribonucleoside 3'-(allyl N,N-diisopropylphosphoramidite)s or 3'-(2-cyanoethyl N,N-diisopropylphosphoramidite)s employed in the preparation of deoxyribonucleotides, and 3'-O-(tert-butyldimethylsilyl)ribonucleoside 2'-(N,N-diisopropylphosphoramidite)s or 2'-O-(tert-butyldimethylsilyl)ribonucleoside 3'-(N,N-diisopropylphosphoramidite)s used for the formation of 2'-5' and 3'-5' internucleotide linkages between ribonucleosides, respectively. The azolium salt has allowed smooth and high-yield condensation of the nucleoside phosphoramidite and a 5'-O-free nucleoside, in which equimolar amounts of the reactants and the promoter are employed in the presence of powdery molecular sieves 3A in acetonitrile. It has been shown that some azolium salts serve as excellent promoters in the solid-phase synthesis of oligodeoxyribonucleotides and oligoribonucleotides. For example, benzimidazolium triflate and N-(phenyl)imidazolium triflate can be used as effective promoters in the synthesis of an oligodeoxyribonucleotide, (5')CGACACCCAATTCTGAAAAT(3') (20mer), via a method using O-allyl/N-allyloxycarbonyl-protected deoxyribonucleoside 3'-phosphoramidites or O-(2-cyanoethyl)/N-phenoxyacetyl-protected deoxyribonucleotide 3'-phosphoramidite as building blocks, respectively, on high-cross-linked polystyrene resins. Further, N-(phenyl)imidazolium triflate is useful for the solid-phase synthesis of oligoribonucleotides, such as (5')AGCUACGUGACUACUACUUU(3') (20mer), according to an allyl/allyloxycarbonyl-protected strategy. The utility of the azolium promoter has been also demonstrated in the liquid-phase synthesis of some biologically important substances, such as cytidine-5'-monophosphono-N-acetylneuraminic acid (CMP-Neu5Ac) and adenylyl(2'-5')adenylyl(2'-5')adenosine (2-5A core).

Nucleotide synthesis via methods without nucleoside-base protection

Oligonucleotide synthesis via methods without nucleobase protection (N-unprotected methods) is briefly reviewed. The N-unprotected methods are advantageous in the following respects over conventional approaches that use protectors, generally, acyl protectors for the nucleobase (N-protected method). Two steps, introduction and removal of the protecting groups, are eliminated, and consequently use of undesirable reagents involved in these steps are avoided. In the synthesis of DNA oligomers, the risk of depurination of deoxyadenosine and deoxyguanosine derivatives, which is a serious problem in the N-protected methods, is considerably reduced. The range of synthesizable artificial analogues bearing base-labile functions is extended because harsh base treatment for the deprotection is eliminated.

N-phenylimidazolium triflate as a highly effective promoter for the interribonucleotide-bond formation via the phosphoramidite method

N-Phenylimidazolium triflate has been invented as an extremely effective promoter for the construction of interribonucleotide linkage according to the phosphoramidite strategy.

Ethyl(methyl)dioxirane as an efficient reagent for the oxidation of nucleoside phosphites into phosphates under nonbasic anhydrous conditions

A convenient method for the oxidation of nucleoside phosphites into phosphates under nonbasic and nonaqueous conditions using commercially available ethyl(methyl)dioxirane has been developed. This oxidation is effective with both N-protected and N-unprotected strategies.