Walker Type Research Articles

Effect of partition line on jamming transition in pedestrian counter flow

Abstract The effect of partition line on the pedestrian counter flow is investigated under the open boundaries by using the lattice-gas model of biased random walkers. There are two types of walkers without the back step: the one is the walker going to the right and the other is the walker going to the left. The right (left) walker prefers to move within (outside) the partition line. Right walkers interfere with left walkers near the partition line. When the density of right walkers increases under a constant value of left-walker density, the jamming transition between the freely moving phase and the stopped state occurs at a critical density depending on the left-walker density. The critical density is compared with that without the partition line. The partition line has an important effect on the jamming transition.

Lattice Gas Simulation of Pedestrian Flow in a Channel.

A lattice gas model with biased random walkers is presented to mimic the pedestrian counter flow in a channel under the open boundary condition of constant density. There are two types of walkers without the back step : the one is the random walker going to the right and the other is the random walker going to the left. It is found that a dynamical jamming transition from the freely i moving state at low density to the stopped state at high density occurs at the critical density. The density profiles of walkers are calculated over the channel. It is shown that the pedestrian counter flow can be simulated by the lattice gas model.

Intracellular ATP Increases Capsaicin-Activated Channel Activity by Interacting with Nucleotide-Binding Domains

Capsaicin (CAP)-activated ion channel plays a key role in generating nociceptive neural signals in sensory neurons. Here we present evidence that intracellular ATP upregulates the activity of capsaicin receptor channel. In inside-out membrane patches isolated from sensory neurons, application of CAP activated a nonselective cation channel (i(cap)). Further addition of ATP to the bath caused a significant increase in i(cap), with a K(1/2) of 3.3 mm. Nonhydrolyzable analogs of ATP, adenylimidodiphosphate and adenosine 5'-O-(3-thio)-triphosphate, also increased i(cap). Neither Mg(2+)-free medium nor inhibitors of various kinases blocked the increase in i(cap) induced by ATP. The enhancing effect of ATP was also observed in inside-out patches of oocytes expressing vanilloid receptor 1, a cloned capsaicin receptor. Single point mutations (D178N, K735R) within the putative Walker type nucleotide-binding domains abolished the effect of ATP. These results show that ATP increases i(cap) in sensory neurons by direct interaction with the CAP channel without involvement of phosphorylation.

Jamming transition of pedestrian traffic at a crossing with open boundaries

Pedestrian traffic at a crossing is investigated under the open boundary condition by the use of the lattice gas model of biased random walkers without the back step. The four types of walkers interact with each other at the crossing where there are random walkers going to the right, left, up, and down. It is found that a dynamical jamming transition from the moving state at low density to the stopped state at high density occurs at the critical density. The transition point depends on the strength of drift and decreases with increasing drift. The transition point does not depend on the length of roads connecting the crossing for the long road. Also, the pedestrian traffic with two types of walkers is studied where there are random walkers going to the right and up. It is compared with the pedestrian traffic with the four types of random walkers.

Constraining the cosmic equation of state from old galaxies at high redshift

New limits on the cosmic equation of state are derived from age measurements of three recently reported old high-redshift galaxies (OHRG). The results are based on a flat Friedmann–Robertson–Walker (FRW) type cosmological model driven by non-relativistic matter plus a smooth component parametrized by its equation of state pxωρx (ω−1). The range of ω is strongly dependent on the matter density parameter. For ΩM∼0.3, as indicated from dynamical measurements, the age estimates of the OHRG restrict the cosmic parameter to ω−0.27. However, if ΩM is the one suggested by some studies of field galaxies, i.e., ΩM≃0.5, only a cosmological constant (ω=−1) may be compatible with these data.

Wave packets and initial conditions in quantum cosmology

We discuss the construction of wave packets resulting from the solutions of a class of Wheeler–DeWitt equations in Robertson–Walker type cosmologies. We present an ansatz for the initial conditions which leads to a unique determination of the expansion coefficients in the construction of the wave packets with probability distributions which, in an interesting contrast to some of the earlier works, agree well with all possible classical paths. The possible relationship between these initial conditions and signature transition in the context of classical cosmology is also discussed.

Plasmid and chromosome partitioning: surprises from phylogeny.

Plasmids encode partitioning genes (par) that are required for faithful plasmid segregation at cell division. Initially, par loci were identified on plasmids, but more recently they were also found on bacterial chromosomes. We present here a phylogenetic analysis of par loci from plasmids and chromosomes from prokaryotic organisms. All known plasmid-encoded par loci specify three components: a cis-acting centromere-like site and two trans-acting proteins that form a nucleoprotein complex at the centromere (i.e. the partition complex). The proteins are encoded by two genes in an operon that is autoregulated by the par-encoded proteins. In all cases, the upstream gene encodes an ATPase that is essential for partitioning. Recent cytological analyses indicate that the ATPases function as adaptors between a host-encoded component and the partition complex and thereby tether plasmids and chromosomal origin regions to specific subcellular sites (i.e. the poles or quarter-cell positions). Two types of partitioning ATPases are known: the Walker-type ATPases encoded by the par/sop gene family (type I partitioning loci) and the actin-like ATPase encoded by the par locus of plasmid R1 (type II partitioning locus). A phylogenetic analysis of the large family of Walker type of partitioning ATPases yielded a surprising pattern: most of the plasmid-encoded ATPases clustered into distinct subgroups. Surprisingly, however, the par loci encoding these distinct subgroups have different genetic organizations and thus divide the type I loci into types Ia and Ib. A second surprise was that almost all chromosome-encoded ATPases, including members from both Gram-negative and Gram-positive Bacteria and Archaea, clustered into one distinct subgroup. The phylogenetic tree is consistent with lateral gene transfer between Bacteria and Archaea. Using database mining with the ParM ATPase of plasmid R1, we identified a new par gene family from enteric bacteria. These type II loci, which encode ATPases of the actin type, have a genetic organization similar to that of type Ib loci.

A novel SMC protein complex in Schizosaccharomyces pombe contains the Rad18 DNA repair protein.

In Schizosaccharomyces pombe, rad18 is an essential gene involved in the repair of DNA damage produced by ionizing radiation and in tolerance of UV-induced DNA damage. The Rad18 protein is a member of the SMC (structural maintenance of chromosomes) superfamily, and we show that, like the other SMC proteins in condensin and cohesin, Rad18 is a component of a high-molecular-weight complex. This complex contains at least six other proteins, the largest of which is Spr18, a novel SMC family member closely related to Rad18, and likely to be its heterodimeric partner. SMC proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. We show that the N-terminal ATP-binding domain of Rad18 is essential for all functions, and overexpression of an N-terminal mutant has a dominant-negative effect. We have identified an important mutation (S1045A) near the C-terminus of Rad18 that separates its repair and essential roles. Potential models for the role of the Rad18-Spr18 complex during DNA repair are discussed.

Mutation in the Magnesium Binding Site of hMSH6 Disables the hMutSα Sliding Clamp from Translocating along DNA

In human cells, binding of base/base mismatches and small insertion/deletion loops is mediated by hMutSalpha, a heterodimer of hMSH2 and hMSH6. In the presence of ATP and magnesium, hMutSalpha dissociates from the mismatch by following the DNA contour in the form of a sliding clamp. This process is enabled by a conformational change of the heterodimer, which is driven by the binding of ATP and magnesium in the Walker type A and B motifs of the polypeptides, respectively. We show that a purified recombinant hMutSalpha variant, hMutSalpha 6DV, which contains an aspartate to valine substitution in the Walker type B motif of the hMSH6 subunit, fails to undergo the conformational change compatible with translocation. Instead, its direct dissociation from the mismatch-containing DNA substrate in the presence of ATP and magnesium precludes the assembly of a functional mismatch repair complex. The "translocation-prone" conformation of wild type hMutSalpha could be observed solely under conditions that favor hydrolysis of the nucleotide and mismatch repair in vitro. Thus, whereas magnesium could be substituted with manganese, ATP could not be replaced with its slowly or nonhydrolyzable homologues ATP-gammaS or AMPPNP, respectively. The finding that ATP induces different conformational changes in hMutSalpha in the presence and in the absence of magnesium helps explain the functional differences between hMutSalpha variants incapable of binding ATP as compared with those unable to bind the metal ion.

Jamming transition in two-dimensional pedestrian traffic

Jamming transitions of pedestrian traffic are investigated under the periodic boundary condition on the square lattice by the use of the lattice gas model of biased random walkers without the back step. The two cases are presented: the one with two types of walkers and the other with four types of walkers. In the two types of walkers, the first is the random walker going to the right and the second is the random walker going up. In the four types of walkers, the first, second, third, and fourth are, respectively, the random walkers going to the right, left, up, and down. It is found that the dynamical jamming transitions occur at the critical densities. The transition points do not depend on the system size for large system but depend strongly on the strength of drift. The jamming transitions are compared with that obtained by the cellular automaton model of car traffic.

DUAL NATURE OF RICCI SCALAR AND MODELS OF THE EARLY UNIVERSE

In some of the earlier papers, it was noticed that at a high energy level Ricci scalar behaved in dual manner: (a) like a matter field and (b) like a geometrical field. In this letter, dual nature of the Ricci scalar is also obtained from a gravitational action where R2 and R3 terms dominate the Einstein–Hilbert Lagrangian in the gravitational action. Cosmological models are derived using dual role of the Ricci scalar. In an expanding model of the universe, local gravitational effect of a compact object is ignored. These models are interesting in the sense that these have capability of exhibiting gravitational effect of compact objects also in an expanding universe. Moreover, these models provide an inhomogeneous generalization of Robertson–Walker type models. Another important feature of the letter is the derivation of these models through physical theories like phase transition and spontaneous symmetry breaking, not through conventional approach of solving complicated Einstein's field equations.

Jamming transition in pedestrian counter flow

A lattice gas model with biased random walkers is presented to mimic the pedestrian counter flow in a channel under the open boundary condition of constant density. There are two types of walkers without the back step: the one is the random walker going to the right and the other is the random walker going to the left. It is found that a dynamical jamming transition from the freely moving state at low density to the stopped state at high density occurs at the critical density. The transition point is given by p c =0.45±0.01, not depending on the system size. The transition point depends on the strength of drift and decreases with increasing drift. Also, we present the extended model to take into account the traffic rule in which a pedestrian walks preferably on the right-hand side of the channel.

An Aspartic Acid Residue Near the Second Transmembrane Segment of ATP Receptor/ Channel Regulates Agonist Sensitivity

Charged or polarized amino acid residues near or within the second transmembrane (M2) segment of neuronal ATP receptor/channels (P2X2receptors) were neutralized by site-directed mutagenesis, and the properties of the mutants were electrophysiologically characterized usingXenopusoocytes. When Asp315was substituted with Val (D315V), the sensitivity to ATP was reduced by about 60-fold. The sensitivity to ATP was not affected by the neutralization of Lys324, which is involved in a Walker type A ATP-binding sequence, Lys366, Tyr330, or Asn333. With D315V channels, the sensitivities to other agonists (ADP, ATPγS, and 2-methylthio ATP) were also reduced. The sensitivities to antagonists (suramin and Cibacron Blue F3GA) were, however, not affected by this neutralization. The results suggest that Asp315, which is assumed to be present in the extracellular region near the M2 segment of P2X2receptor/channels, serves to maintain agonist sensitivity.

29] High-level expression of mouse Mdr3 P-glycoprotein in yeast Pichia pastoris and characterization of ATPase activity

This chapter characterizes the ATPase activity of mouse P-glycoproteins (Pgp) following selective detergent solubilization and reconstitution in Escherichia coli lipids of Pgp-rich membranes fractionated on sucrose gradients. Pgps, which are eukaryotic members of the adenosine triphosphate-binding cassette (ABC) superfamily of transporters, cause cellular resistance to a wide variety of structurally unrelated cytotoxic drugs, including Vinca alkaloids, anthracyclins, colchicine, and ionophore peptides, such as valinomycin and gramicidin D. The structural unit common to ABC transporters includes one membrane-associated region and one nucleotide-binding domain (NBD) of the Walker type. The system characterizes a large series of Mdr3 mutants showing alterations in TMDs and NBDs. The P . pastoris system is superior in several aspects to the available expression systems for production of Pgp and perhaps other ABC transporters.

The HsdR subunit of R.EcoR124II: cloning and over-expression of the gene and unexpected properties of the subunit.

Type I restriction endonucleases are composed of three subunits, HsdR, HsdM and HsdS. The HsdR subunit is absolutely required for restriction activity; while an independent methylase is composed of HsdM and HsdS subunits. DNA cleavage is associated with a powerful ATPase activity during which DNA is translocated by the enzyme prior to cleavage. The presence of a Walker type I ATP-binding site within the HsdR subunit suggested that the subunit may be capable of independent enzymatic activity. Therefore, we have, for the first time, cloned and over-expressed the hsdRgene of the type IC restriction endonuclease EcoR124II. The purified HsdR subunit was found to be a soluble monomeric protein capable of DNA- and Mg2+-dependent ATP hydrolysis. The subunit was found to have a weak nuclease activity both in vivo and in vitro, and to bind plasmid DNA; although was not capable of binding a DNA oligoduplex. We were also able to reconstitute the fully active endonuclease from purified M. EcoR124I and HsdR. This is the first clear demonstration that the HsdR subunit of a type I restriction endonuclease is capable of independent enzyme activity, and suggests a mechanism for the evolution of the endonuclease from the independent methylase.

Cloning and Characterization of Two K+ Inward Rectifier (Kir) 1.1 Potassium Channel Homologs from Human Kidney (Kir1.2 and Kir1.3)

The DNA sequence encoding the rat brain inward rectifier-10 K+ channel was amplified from rat brain RNA using reverse transcription-polymerase chain reaction and used to clone the human homolog. Low stringency screening of a human kidney cDNA library and subsequent DNA sequence analysis identified two related K+ inward rectifier cDNAs, referred to as Kir1.2 and Kir1.3, which were derived from transcription of distinct human genes. Kir1.2 represents the human homolog of the rat BIRK-10 sequence, whereas Kir1.3 was unique compared with all available sequence data bases. The genes that encode Kir1.2 and Kir1.3 were mapped to human chromosomes 1 and 21, respectively. Both genes showed tissue-specific expression when analyzed by Northern blots. Kir1.2 was only detected in brain >> kidney and was detected at high levels in all brain regions examined. Kir1.3 was most readily detected in kidney and was also expressed in pancreas > lung. Comparative analysis of the predicted amino acid sequences for Kir1.2 and Kir1.3 revealed they were 62% identical. The most remarkable difference between the two polypeptides is that the Walker Type A consensus binding motif present in both Kir1.1 and Kir1.2 was not conserved in the Kir1.3 sequence. Expression of the Kir1.2 polypeptide in Xenopus oocytes resulted in the synthesis of a K+-selective channel that exhibited an inwardly rectifying current-voltage relationship and was inhibited by external Ba2+ and Cs+. Kir1.2 current amplitude was reduced by >85% when the pH was decreased from pH 7.4 to 5.9 using the membrane-permeant buffer acetate but was relatively unaffected when pH was similarly lowered using membrane-impermeant biphthalate. The inhibition by intracellular protons was voltage-independent with an IC50 of pH 6.2 and a Hill coefficient of 1.9, suggesting the cooperative binding of 2 protons to the intracellular face of the channel. In contrast, Kir1.3 expression in Xenopus oocytes was not detectable despite the fact that the cRNA efficiently directed the synthesis of a polypeptide of the expected Mr in an in vitro translation system. Co-expression of Kir1.3 with either Kir1.1 or Kir1.2 reduced currents resulting from expression of these inward-rectifier subunits alone, consistent with a dominant negative influence on Kir1.1 and Kir1.2 expression.

ESR Observations in Small Particles of Palladium and Their Origins

The ESR signal observed in small particles of palladium with the passivated surface was investigated in various temperatures and sizes. We assigned the signal to the overlap of the spin wave and conduction electron spin resonance (CESR) of palladium. The spin wave was attributed to conduction electrons with the strong many-body effect in palladium and could be analyzed qualitatively by the theory of Platzman and Wolff. It seems that the mode analogous to Walker's type is also excited in a metallic particle of palladium.

A novel neuronal P2x ATP receptor ion channel with widespread distribution in the brain

There is strong evidence that ATP acts as an excitatory neurotransmitter in the periphery, yet little is known about fast central ATP-mediated transmission. We report here the molecular cloning of a novel neuronal ionotropic ATP receptor of the P2x subtype (P2x3) isolated from rat brain. This central P2x channel subunit has significant amino acid homology with two recently cloned ATP-gated channels from rat smooth muscle (47%) and pheochromocytoma PC12 cells (37%). P2x3 receptor contains the characteristic 10 conserved cysteines of ATP-gated channels, a putative extracellular region homologous to the Walker type A motif found in various nucleotide-binding proteins, and two potential sites for phosphorylation by protein kinase C. Homomeric receptor P2x3 channels expressed in Xenopus oocytes produce rapid cation-selective purinergic currents that are potentiated by zinc ions and reversibly blocked by the P2x antagonists suramin, Reactive Blue 2, and pyridoxalphosphate-6-axophenyl-2U,4U-disulfonic acid. P2x3-receptor subunit mRNA is found in the Purkinje cells and the granule cells of the cerebellum as well as in CA3 pyramidal cells of the hippocampus that are innervated by zinc-rich axon terminals of mossy fibers. Our results suggest that fast excitatory synaptic transmission mediated by zinc-sensitive ATP-gated channels is widespread in mammalian brain.

Injuries Associated With Infant Walkers

Infant walkers, or baby walkers, generally consist of a wheeled base supporting a rigid frame that holds a fabric seat with leg openings and usually a plastic feeding/play tray. The two basic types of walkers include the X frame, in which the steel support bars form an X, and the circular frame, in which the support bars rise vertically from the circular base to the tray. The device is designed to support a preambulatory infant, with feet on the floor, and allow mobility while the infant is learning to walk. Some walkers are equipped with bouncing mechanisms, activity toys, or locking devices that keep them from moving, and some fold flat for storage. Estimated annual sales of walkers are over 3 million.1(pp72-86) Studies have found that between 55% and 92% of infants between 5 and 15 months of age use walkers.2-6 Parents give various reasons for using walkers-to keep the infant quiet and happy, to encourage mobility and promote walking, to provide exercise, and to hold the infant during feeding.4,5,7 One third of parents in one study used walkers because they believed that walkers would keep their infant safe.5 According to the National Electronic Injury Surveillance System (NEISS) of the United States Consumer Products Safety Commission (CPSC), 25 000 children, almost all between the ages of 5 and 15 months, were treated in hospital emergency departments in 1993 for injuries associated with the use of infant walkers, at an estimated cost of $90 000 000 annually.1(pp72-86),8 Eleven deaths occurred during the years 1989 through 1993.8

A chromosomally encoded two-component sensory transduction system is required for virulence of Agrobacterium tumefaciens

TnphoA mutagenesis of Agrobacterium tumefaciens identified new extracytoplasmic protein-encoding virulence loci. Mutations in these loci conferred increased sensitivity to detergents and several antibiotics. Clones carrying these loci were isolated from an A. tumefaciens cosmid library by complementation of the detergent sensitivities of the mutants. The locus on one complementing clone was delineated by Tn5 and TnphoA mutagenesis. DNA sequence analysis of the delineated region revealed that this locus is made up of two transcriptional units, chvG and chvI, which were predicted, on the basis of amino acid sequence homology, to encode the members of a two-component sensory transduction system. The membrane-spanning sensor, a histidine protein kinase, was designated ChvG, and the response regulator, presumably a transcriptional activator, was designated ChvI. Surprisingly, ChvG was also predicted to contain a Walker type A consensus nucleotide binding site, which is unusual for sensor histidine protein kinases. Site-specific insertion mutations in either chvG or chvI abolished tumor formation ability, as well as the ability to grow on complex media. Neither the genes which are regulated nor the inducing signal is known yet for this system.