Review of lattice results concerning low-energy particle physics: Flavour Lattice Averaging Group (FLAG).

We review lattice results related to pion, kaon, D- and B-meson physics with the aim of making them easily accessible to the particle-physics community. More specifically, we report on the determination of the light-quark masses, the form factor [Formula: see text], arising in the semileptonic [Formula: see text] transition at zero momentum transfer, as well as the decay constant ratio [Formula: see text] and its consequences for the CKM matrix elements [Formula: see text] and [Formula: see text]. Furthermore, we describe the results obtained on the lattice for some of the low-energy constants of [Formula: see text] and [Formula: see text] Chiral Perturbation Theory. We review the determination of the [Formula: see text] parameter of neutral kaon mixing as well as the additional four B parameters that arise in theories of physics beyond the Standard Model. The latter quantities are an addition compared to the previous review. For the heavy-quark sector, we provide results for [Formula: see text] and [Formula: see text] (also new compared to the previous review), as well as those for D- and B-meson-decay constants, form factors, and mixing parameters. These are the heavy-quark quantities most relevant for the determination of CKM matrix elements and the global CKM unitarity-triangle fit. Finally, we review the status of lattice determinations of the strong coupling constant [Formula: see text].

Review of lattice results concerning low-energy particle physics.

We review lattice results related to pion, kaon, [Formula: see text]- and [Formula: see text]-meson physics with the aim of making them easily accessible to the particle-physics community. More specifically, we report on the determination of the light-quark masses, the form factor [Formula: see text], arising in semileptonic [Formula: see text] transition at zero momentum transfer, as well as the decay-constant ratio [Formula: see text] of decay constants and its consequences for the CKM matrix elements [Formula: see text] and [Formula: see text]. Furthermore, we describe the results obtained on the lattice for some of the low-energy constants of [Formula: see text] and [Formula: see text] Chiral Perturbation Theory and review the determination of the [Formula: see text] parameter of neutral kaon mixing. The inclusion of heavy-quark quantities significantly expands the FLAG scope with respect to the previous review. Therefore, we focus here on [Formula: see text]- and [Formula: see text]-meson decay constants, form factors, and mixing parameters, since these are most relevant for the determination of CKM matrix elements and the global CKM unitarity-triangle fit. In addition we review the status of lattice determinations of the strong coupling constant [Formula: see text].

Determination of the chiral condensate from (2+1)-flavor lattice QCD.

We perform a precise calculation of the chiral condensate in QCD using lattice QCD with 2+1 flavors of dynamical overlap quarks. Up and down quark masses cover a range between 3 and 100 MeV on a 16{3}x48 lattice at a lattice spacing approximately 0.11 fm. At the lightest sea quark mass, the finite volume system on the lattice is in the regime. By matching the low-lying eigenvalue spectrum of the Dirac operator with the prediction of chiral perturbation theory at the next-to-leading order, we determine the chiral condensate in (2+1)-flavor QCD with strange quark mass fixed at its physical value as Sigma;{MS[over ]}(2 GeV)=[242(04)(+19/-18) MeV]{3} where the errors are statistical and systematic, respectively.

Convergence of the chiral expansion in two-flavor lattice QCD.

We test the convergence property of the chiral perturbation theory using a lattice QCD calculation of pion mass and decay constant with two dynamical quark flavors. The lattice calculation is performed using the overlap fermion formulation, which realizes exact chiral symmetry at finite lattice spacing. By comparing various expansion prescriptions, we find that the chiral expansion is well saturated at the next-to-leading order for pions lighter than approximately 450 MeV. Better convergence behavior is found, in particular, for a resummed expansion parameter xi, with which the lattice data in the pion mass region 290-750 MeV can be fitted well with the next-to-next-to-leading order formulas. We obtain the results in two-flavor QCD for the low energy constants l[over ]_{3} and l[over ]_{4} as well as the pion decay constant, the chiral condensate, and the average up and down quark mass.

S parameter and pseudo Nambu-Goldstone boson mass from lattice QCD.

We present a lattice calculation of L10, one of the low-energy constants in chiral perturbation theory, and the charged-neutral pion squared-mass splitting, using dynamical overlap fermion. The exact chiral symmetry of the overlap fermion allows us to reliably extract these quantities from the difference of the vacuum polarization functions for vector and axial-vector currents. In the context of the technicolor models, these two quantities are read as the S parameter and the pseudo Nambu-Goldstone boson mass, respectively, and play an important role in discriminating the models from others. This calculation can serve as a feasibility study of the lattice techniques for more general technicolor gauge theories.

B(0)-B(0) mixing in unquenched lattice QCD.

We present an unquenched lattice calculation for the B(0)-B(0) transition amplitude. The calculation, carried out at an inverse lattice spacing 1/a=2.22(4) GeV, incorporates two flavors of dynamical quarks described by the O(a)-improved Wilson fermion action and heavy quarks described by nonrelativistic QCD. Particular attention is paid to the uncertainty that arises from the chiral extrapolation, especially the effect of pion loops, for light quarks, which we find could be sizable for the leptonic decay constant, whereas it is small for the B parameters. We obtain f(B(d))=191(10)(+12-22) MeV, f(B(s))/f(B(d))=1.13(3)(+13-2), B(B(d))(m(b))=0.836(27)(+56-62), B(B(s))/B(B(d))=1.017(16)(+56-17), and xi=1.14(3)(+13-2), where the first error is statistical, and the second is systematic, including uncertainties due to chiral extrapolation, finite lattice spacing, heavy quark expansion, and perturbative operator matching.

Dopant-pair structures segregated on a hydrogen-terminated Si(100) surface.

Novel atomic structures on a H-terminated Si(100)-(2x1)-H surface were found using scanning tunneling microscopy (STM). The structures are distinguishable only from Si dimers in empty-state STM images. They were observed on arsenic- and phosphorus-doped substrates, but not on boron-doped substrates. Surface density of these structures was found to be proportional to the dopant density in the substrate. First-principles calculations clarify that they are consisting of dopant pairs that are segregated from the bulk material. Hydrogen atoms attached to the dopant pair are found to flip between two positions on the surface due to a quantum effect.

Sister chromosome cohesion of Escherichia coli.

We analysed Escherichia coli cells synchronized for initiation of chromosomal DNA replication by fluorescence in situ hybridization (FISH) using fluorescent DNA probes corresponding to various chromosomal regions. Sister copies of regions in an approximately oriC-proximal half of the chromosome are cohesive with each other after replication until the late period of chromosome replication. Sister copies of regions relatively close to the terminus are also separated from each other in the same late period of replication. It is important that sister copies in all the tested regions are thus separated from each other nearly all at once in the late period of chromosome replication. These results are consistent with results obtained by FISH in randomly growing cultures. Cohesion of sister copies in an oriC-close region is observed in a dam null mutant lacking DNA adenine methyltransferase the same as in the parental isogenic dam+ strain, indicating that the cohesion is independent of DNA adenine methyltransferase. This further implies that hemimethylated DNA-binding proteins, such as SeqA, are not involved in the cohesion. On the other hand, the cohesion of sister copies of the oriC-close region was not observed in mukB null mutant cells, suggesting that MukB might be involved in the chromosome cohesion.

Null mutation of the dam or seqA gene suppresses temperature-sensitive lethality but not hypersensitivity to novobiocin of muk null mutants.

Escherichia coli mukF, mukE, and mukB null mutants have common phenotypes such as temperature-dependent colony formation, anucleate cell production, chromosome cutting by septum closure, and abnormal localization of SeqA-DNA clusters. We show here that the associated muk null mutations cause hypersensitivity to novobiocin. Null mutation of either dam or seqA suppressed partially the temperature-sensitive lethality but failed to suppress the anucleate cell production and the hypersensitivity to novobiocin caused by muk null mutations.

Bidirectional migration of SeqA-bound hemimethylated DNA clusters and pairing of oriC copies in Escherichia coli.

BACKGROUND: We previously found that SeqA protein, which binds preferentially to newly replicated hemimethylated DNA, is localized as discrete fluorescent foci in Escherichia coli cells. A single SeqA focus, localized at midcell, separates into two foci and these foci migrate abruptly in opposite directions. RESULTS: The present study shows that (i) appearance of SeqA foci depends on continuous DNA replication, suggesting that the SeqA foci represent clusters consisting of SeqA and newly replicated hemimethylated DNA, (ii) in a synchronous round of replication, a single SeqA focus at midcell separates into two foci and these foci abruptly migrate in opposite directions midway through replication from oriC to the terminus, and (iii) oriC is replicated at midcell but replicated oriC copies remain linked with each other at midcell for 40 min after replication at 30 degrees C. Subsequently, the linked oriC copies separate and migrate gradually towards both borders of the nucleoid before cell division. CONCLUSIONS: A single cluster of SeqA-bound hemimethylated DNA segment separates into two clusters and these clusters migrate abruptly in a bipolar fashion during progress of replication and prior to separation of linked sister oriC copies.

Complex formation of MukB, MukE and MukF proteins involved in chromosome partitioning in Escherichia coli.

mukF, mukE and mukB genes are essential for the process of chromosome partitioning in Escherichia coli. We have studied protein-protein interactions among MukB, MukE and MukF proteins by co-immunoprecipitation and sucrose gradient sedimentation experiments, using mukFEB null cells harboring plasmids carrying the wild-type or mutant-type mukFEB operon. MukB forms a complex with MukF and MukE. Analysis of mutant MukB proteins suggested that MukF and MukE bind the C-terminal globular domain of MukB. MukF is indispensable for an interaction between MukB and MukE; however, MukF itself is able to associate with MukB even in the absence of MukE. We have also found that MukF has a Ca(2+)-binding activity. Although purified MukF was able to make a complex either with MukE or MukB, a complex consisting of the three Muk proteins was barely detected in vitro. However, increasing the Ca(2+) or Mg(2+) concentration in the reaction partially restored complex formation. This suggests that Ca(2+) or Mg(2+) may be required for the formation of a complex consisting of the three Muk proteins, and thus may participate in a particular step during chromosome partitioning.

The assembly and migration of SeqA-Gfp fusion in living cells of Escherichia coli.

SeqA protein, which binds to hemi-methylated GATC sequences of DNA, is localized to discrete fluorescent foci in wild-type Escherichia coli cells. In this work, we observed cellular localization of the SeqA-Gfp fusion in living cells. SeqA-Gfp was localized to a discrete focus or foci in wild-type and seqA null mutant cells, but the fusion was dispersed in the whole cell in dam null mutant cells lacking Dam methyltransferase. These results were consistent with the previous description of the localization of SeqA by immunofluorescence microscopy. Time-lapse experiments revealed that duplicated SeqA-Gfp foci migrated rapidly in opposite directions. Flow cytometry demonstrated that the fusion restored synchronous replication of chromosomal DNA from multiple origins in seqA null mutant cells, indicating that SeqA-Gfp is biologically active. Immunoprecipitation of the fusion from cell extracts using anti-Gfp antibody indicated that the fusion was assembled with the wild-type SeqA protein.

Autoregulation of the partition genes of the mini-F plasmid and the intracellular localization of their products in Escherichia coli.

The sopAB operon and the sopC sequence, which acts as a centromere, are essential for stable maintenance of the mini-F plasmid. Immunoprecipitation experiments with purified SopA and SopB proteins have demonstrated that these proteins interact in vitro. Expression studies using the lacZ gene as a reporter revealed that the sopAB operon is repressed by the cooperative action of SopA and SopB. Using immunofluorescence microscopy, we found discrete fluorescent foci of SopA and SopB in cells that produce both SopA and SopB in the presence of the sopC DNA segment, but not in the absence of sopC, suggesting the SopA-SopB complex binds to sopC segments. SopA was exclusively found to colocalize with nucleoids in cells that produced only SopA, while, in the absence of SopA, SopB was distributed in the cytosolic spaces.

A single residue, Lys108, of the delta-opioid receptor prevents the mu-opioid-selective ligand [D-Ala2,N-MePhe4,Gly-ol5]enkephalin from binding to the delta-opioid receptor.

Previously, we found that replacement of the region around the first extracellular loop of the delta-opioid receptor (OPR) with the corresponding region of the mu-OPR gives the high affinity for [D-Ala2,N-MePhe4,Gly-ol5]enkephalin (DAMGO), a mu-opioid-selective ligand, to the resultant chimeric receptor, DMDD, suggesting that the difference in the amino acid sequence within this region between the mu- and delta-OPRs is critical for the discrimination between these receptors by DAMGO. In the current study, we carried out systematic replacements of seven non-conserved residues in this region of the delta-OPR with the corresponding amino acid found in the mu-OPR. Among the seven mutant receptors, only one mutant receptor, delta K108N, showed high affinity (Ki = 18.68 +/- 5.27 nM) for DAMGO, which was comparable to that of the DMDD receptor (Ki = 23.77 +/- 4.27 nM) and 75-fold higher than that of the wild-type delta-OPR (Ki = 1405 +/- 161 nM). Lys108 in the delta-OPR was systematically replaced with 19 kinds of amino acids other than lysine. Among the resultant mutant receptors, 14 mutants bound DAMGO with Ki values comparable to those of the DMDD receptor, ranging from 4.20 to 43.38 nM. These findings suggest that Lys108 of the delta-OPR prevents DAMGO from binding to the delta-OPR rather than that the asparagine residue at the corresponding position in the mu-OPR is necessary for DAMGO binding. In addition, the replacement of Lys108 of the delta-OPR with asparagine dramatically increased the affinity for other peptidic mu receptor-selective ligands, such as dermorphin and D-Pen-Cys-Tyr-D-Trp-Orn-Thr-Pen-Thr-NH2.

DAMGO, a mu-opioid receptor selective ligand, distinguishes between mu-and kappa-opioid receptors at a different region from that for the distinction between mu- and delta-opioid receptors.

The structural basis of opioid receptors (OPRs) for the subtype-selective binding of DAMGO, a mu-opioid receptor selective ligand, was investigated using chimeric mu/kappa-OPRs. Replacement of the region from the middle of the fifth transmembrane domain to the C-terminal of mu-OPR with the corresponding region of mu-OPR remarkably decreased the binding affinity to DAMGO, while the reciprocal chimera revealed the high affinity to DAMGO. These results indicate that DAMGO distinguishes between mu- and mu-OPRs at the region around the third extracellular loop, different from the case of the distinction between mu-and delta-OPRs in which the region around the first extracellular loop is important. Furthermore, displacement studies revealed that the region around the third extracellular loop is involved in the discrimination between mu- and kappa-OPRs not only by peptidic mu- selective ligands but also by non-peptidic ligands, such as morphine and naloxone.

DAMGO, a mu-opioid receptor selective agonist, distinguishes between mu- and delta-opioid receptors around their first extracellular loops.

The structural basis of mu-opioid receptor (OPR) for the specificity in its ligand binding was investigated using chimeric mu/delta-OPRs. Replacement of the region around the first extracellular loop of delta-OPR with the corresponding region of mu-OPR gave the resultant chimeric receptor the similar affinity to DAMGO compared with the native mu-OPR. The reciprocal replacement deprived the high affinity to DAMGO from mu-OPR. These results indicate that the difference(s) in the structure around the first extracellular loop is critical for DAMGO to distinguish between mu- and delta-OPRs. Furthermore, displacement studies revealed that this region is partly involved in the discrimination between mu- and delta-OPRs by other peptidic mu-selective ligands, such as dermorphin, morphiceptin and CTOP, but not by non-peptidic ligands, such as morphine and naloxone.

Intrathecal neuromedin C enhances mechanical nociception: possible involvement of NMDA receptors.

Intrathecal administration of neuromedin C (3, 10 nmol/rat) significantly decreased the nociceptive threshold of rats in the paw-pressure test. This effect was abolished by co-administration of [Leu13 psi(CH2NH)-Leu14]bombesin (10 nmol/rat), a bombesin receptor antagonist. Co-administration of 2-amino-5-phosphonovaleric acid (APV) at a dose (10 nmol/rat) which did not affect the nociceptive threshold by itself significantly inhibited the effect of neuromedin C. 6-Cyano-7-nitroquinoxaline-2,3-dione (CNQX) (10 nmol/rat) did not significantly inhibit the neuromedin C-induced hyperalgesia. These results indicate that neuromedin C could modulate mechanical nociception through bombesin receptors at the spinal level, where glutamate is involved through NMDA receptors.