Search

Abstract We report a determination of the CKM angle ϕ 3, also known as γ, from a combination of measurements using samples of up to 711 fb −1 from the Belle experiment and up to 362 fb −1 from the Belle II experiment. We combine results from analyses of B + → DK +, B + → Dπ +, and B + → D * K + decays, where D is an admixture of D 0 and D ¯ 0 $$ {\overline{D}}^0 $$ mesons, in a likelihood fit to obtain ϕ 3 = (75.2 ± 7.6) ° . We also briefly discuss the interpretation of this result.

Abstract We report measurements of the e + e − → B B ¯ $$ B\overline{B} $$ , B B ¯ ∗ $$ B{\overline{B}}^{\ast } $$ , and B ∗ B ¯ ∗ $$ {B}^{\ast }{\overline{B}}^{\ast } $$ cross sections at four energies, 10653, 10701, 10746 and 10805 MeV, using data collected by the Belle II experiment. We reconstruct one B meson in a large number of hadronic final states and use its momentum to identify the production process. In the first 2 – 5 MeV above B ∗ B ¯ ∗ $$ {B}^{\ast }{\overline{B}}^{\ast } $$ threshold, the e + e − → B ∗ B ¯ ∗ $$ {B}^{\ast }{\overline{B}}^{\ast } $$ cross section increases rapidly. This may indicate the presence of a pole close to the threshold.

Abstract We present a study of Ξ c 0 → Ξ 0 π 0 $$ {\Xi}_c^0\to {\Xi}^0{\pi}^0 $$ , Ξ c 0 → Ξ 0 η $$ {\Xi}_c^0\to {\Xi}^0\eta $$ , and Ξ c 0 → Ξ 0 η ′ $$ {\Xi}_c^0\to {\Xi}^0{\eta}^{\prime } $$ decays using the Belle and Belle II data samples, which have integrated luminosities of 980 fb −1 and 426 fb −1, respectively. We measure the following relative branching fractions B Ξ c 0 → Ξ 0 π 0 / B Ξ c 0 → Ξ − π + = 0.48 ± 0.02 stat ± 0.03 syst , B Ξ c 0 → Ξ 0 η / B Ξ c 0 → Ξ − π + = 0.11 ± 0.01 stat ± 0.01 syst , B Ξ c 0 → Ξ 0 η ′ / B Ξ c 0 → Ξ − π + = 0.08 ± 0.02 stat ± 0.01 syst $$ {\displaystyle \begin{array}{c}\mathcal{B}\left({\Xi}_c^0\to {\Xi}^0{\pi}^0\right)/\mathcal{B}\left({\Xi}_c^0\to {\Xi}^{-}{\pi}^{+}\right)=0.48\pm 0.02\left(\textrm{stat}\right)\pm 0.03\left(\textrm{syst}\right),\\ {}\mathcal{B}\left({\Xi}_c^0\to {\Xi}^0\eta \right)/\mathcal{B}\left({\Xi}_c^0\to {\Xi}^{-}{\pi}^{+}\right)=0.11\pm 0.01\left(\textrm{stat}\right)\pm 0.01\left(\textrm{syst}\right),\\ {}\mathcal{B}\left({\Xi}_c^0\to {\Xi}^0{\eta}^{\prime}\right)/\mathcal{B}\left({\Xi}_c^0\to {\Xi}^{-}{\pi}^{+}\right)=0.08\pm 0.02\left(\textrm{stat}\right)\pm 0.01\left(\textrm{syst}\right)\end{array}} $$ for the first time, where the uncertainties are statistical (stat) and systematic (syst). By multiplying by the branching fraction of the normalization mode, B Ξ c 0 → Ξ − π + $$ \mathcal{B}\left({\Xi}_c^0\to {\Xi}^{-}{\pi}^{+}\right) $$ , we obtain the following absolute branching fraction results B Ξ c 0 → Ξ 0 π 0 = 6.9 ± 0.3 stat ± 0.5 syst ± 1.3 norm × 10 − 3 , B Ξ c 0 → Ξ 0 η = 1.6 ± 0.2 stat ± 0.2 syst ± 0.3 norm × 10 − 3 , B Ξ c 0 → Ξ 0 η ′ = 1.2 ± 0.3 stat ± 0.1 syst ± 0.2 norm × 10 − 3 , $$ {\displaystyle \begin{array}{c}\mathcal{B}\left({\Xi}_c^0\to {\Xi}^0{\pi}^0\right)=\left(6.9\pm 0.3\left(\textrm{stat}\right)\pm 0.5\left(\textrm{syst}\right)\pm 1.3\left(\operatorname{norm}\right)\right)\times {10}^{-3},\\ {}\mathcal{B}\left({\Xi}_c^0\to {\Xi}^0\eta \right)=\left(1.6\pm 0.2\left(\textrm{stat}\right)\pm 0.2\left(\textrm{syst}\right)\pm 0.3\left(\operatorname{norm}\right)\right)\times {10}^{-3},\\ {}\mathcal{B}\left({\varXi}_c^0\to {\Xi}^0{\eta}^{\prime}\right)=\left(1.2\pm 0.3\left(\textrm{stat}\right)\pm 0.1\left(\textrm{syst}\right)\pm 0.2\left(\operatorname{norm}\right)\right)\times {10}^{-3},\end{array}} $$ where the third uncertainties are from B Ξ c 0 → Ξ − π + $$ \mathcal{B}\left({\Xi}_c^0\to {\Xi}^{-}{\pi}^{+}\right) $$ . The asymmetry parameter for Ξ c 0 → Ξ 0 π 0 $$ {\Xi}_c^0\to {\Xi}^0{\pi}^0 $$ is measured to be α Ξ c 0 → Ξ 0 π 0 = − 0.90 ± 0.15 stat ± 0.23 syst $$ \alpha \left({\Xi}_c^0\to {\Xi}^0{\pi}^0\right)=-0.90\pm 0.15\left(\textrm{stat}\right)\pm 0.23\left(\textrm{syst}\right) $$ .

Abstract We present the result of a search for the charged-lepton-flavor violating decay τ − → μ − μ + μ − using a 424 fb −1 sample of data recorded by the Belle II experiment at the SuperKEKB e + e − collider. The selection of e + e − → τ + τ − events is based on an inclusive reconstruction of the non-signal tau decay, and on a boosted decision tree to suppress background. We observe one signal candidate, which is compatible with the expectation from background processes. We set a 90% confidence level upper limit of 1.9 × 10 −8 on the branching fraction of the τ − → μ − μ + μ − decay, which is the most stringent bound to date.

Abstract We present a measurement of the ratio R μ = B τ − → μ − ν ¯ μ ν τ / B τ − → e − ν ¯ e ν τ $$ {R}_{\mu }=\mathcal{B}\left({\tau}^{-}\to {\mu}^{-}{\overline{\nu}}_{\mu }{\nu}_{\tau}\right)/\mathcal{B}\left({\tau}^{-}\to {e}^{-}{\overline{\nu}}_e{\nu}_{\tau}\right) $$ of branching fractions B $$ \mathcal{B} $$ of the τ lepton decaying to muons or electrons using data collected with the Belle II detector at the SuperKEKB e + e − collider. The sample has an integrated luminosity of 362 ± 2 fb −1 at a centre-of-mass energy of 10.58 GeV. Using an optimised event selection, a binned maximum likelihood fit is performed using the momentum spectra of the electron and muon candidates. The result, R μ = 0.9675 ± 0.0007 ± 0.0036, where the first uncertainty is statistical and the second is systematic, is the most precise to date. It provides a stringent test of the light-lepton universality, translating to a ratio of the couplings of the muon and electron to the W boson in τ decays of 0.9974 ± 0.0019, in agreement with the standard model expectation of unity.

Abstract We present measurements of the branching fractions of eight B ¯ 0 $$ {\overline{B}}^0 $$ → D (*)+ K − K S ∗ 0 $$ {K}_{(S)}^{\left(\ast \right)0} $$ , B − → D (*)0 K − K S ∗ 0 $$ {K}_{(S)}^{\left(\ast \right)0} $$ decay channels. The results are based on data from SuperKEKB electron-positron collisions at the Υ(4S) resonance collected with the Belle II detector, corresponding to an integrated luminosity of 362 fb −1. The event yields are extracted from fits to the distributions of the difference between expected and observed B meson energy, and are efficiency-corrected as a function of m(K − K S ∗ 0 $$ {K}_{(S)}^{\left(\ast \right)0} $$ ) and m(D (*) K S ∗ 0 $$ {K}_{(S)}^{\left(\ast \right)0} $$ ) in order to avoid dependence on the decay model. These results include the first observation of B ¯ 0 $$ {\overline{B}}^0 $$ → D + K − K S 0 $$ {K}_S^0 $$ , B − → D* 0 K − K S 0 $$ {K}_S^0 $$ , and B ¯ 0 $$ {\overline{B}}^0 $$ → D* + K − K S 0 $$ {K}_S^0 $$ decays and a significant improvement in the precision of the other channels compared to previous measurements. The helicity-angle distributions and the invariant mass distributions of the K − K S ∗ 0 $$ {K}_{(S)}^{\left(\ast \right)0} $$ systems are compatible with quasi-two-body decays via a resonant transition with spin-parity J P = 1− for the K − K S 0 $$ {K}_S^0 $$ systems and J P = 1+ for the K − K* 0 systems. We also present measurements of the branching fractions of four B ¯ 0 $$ {\overline{B}}^0 $$ → D (*)+ D s − $$ {D}_s^{-} $$ , B − → D (*)0 D s − $$ {D}_s^{-} $$ decay channels with a precision compatible to the current world averages.

Abstract We present an analysis of the process e + e − → π + π − Υ(nS) (where n = 1, 2, or 3) reconstructed in 19.6 fb −1 of Belle II data during a special run of the SuperKEKB collider at four energy points near the peak of the Υ(10753) resonance. By analyzing the mass distribution of the π + π − Υ(nS) system and the Born cross sections of the e + e − → π + π − Υ(nS) process, we report the first observation of Υ(10753) decays to the π + π − Υ(1S) and π + π − Υ(2S) final states, and find no evidence for decays to π + π − Υ(3S). Possible intermediate states in the π + π − Υ(1S, 2S) transitions are also investigated, and no evidence for decays proceeding via the π ∓ Z b ± $$ {\pi}^{\mp }{Z}_b^{\pm } $$ or f 0(980)Υ(nS) intermediate states is found. We measure Born cross sections for the e + e − → π + π − Υ(nS) process that, combined with results from Belle, obtain the mass and width of Υ(10753) to be (10756.6 ± 2.7 ± 0.9) MeV/c 2 and (29.0 ± 8.8 ± 1.2) MeV, respectively. The relative ratios of the Born cross sections at the Υ(10753) resonance peak are also reported for the first time.

Abstract We report results from a study of B ± → DK ± decays followed by D decaying to the CP-even final state K + K − and CP-odd final state K S 0 π 0 $$ {K}_S^0{\pi}^0 $$ , where D is an admixture of D 0 and D ¯ 0 $$ {\overline{D}}^0 $$ states. These decays are sensitive to the Cabibbo-Kobayashi-Maskawa unitarity-triangle angle ϕ 3. The results are based on a combined analysis of the final data set of 772 × 106 B B ¯ $$ B\overline{B} $$ pairs collected by the Belle experiment and a data set of 198 × 106 B B ¯ $$ B\overline{B} $$ pairs collected by the Belle II experiment, both in electron-positron collisions at the Υ(4S) resonance. We measure the CP asymmetries to be A $$ \mathcal{A} $$ CP+ = (+12.5 ± 5.8 ± 1.4)% and A $$ \mathcal{A} $$ CP− = (−16.7 ± 5.7 ± 0.6)%, and the ratios of branching fractions to be R $$ \mathcal{R} $$ CP+ = 1.164 ± 0.081 ± 0.036 and R $$ \mathcal{R} $$ CP− = 1.151 ± 0.074 ± 0.019. The first contribution to the uncertainties is statistical, and the second is systematic. The asymmetries A $$ \mathcal{A} $$ CP+ and A $$ \mathcal{A} $$ CP− have similar magnitudes and opposite signs; their difference corresponds to 3.5 standard deviations. From these values we calculate 68.3% confidence intervals of (8.5 ° < ϕ 3 < 16.5 ° ) or (84.5 ° < ϕ 3 < 95.5 ° ) or (163.3 ° < ϕ 3 < 171.5 ° ) and 0.321 < r B < 0.465.

Abstract We measure CP asymmetries and branching-fraction ratios for B ± → DK ± and Dπ ± decays with D → K S 0 $$ {K}_{\textrm{S}}^0 $$ K ± π ∓, where D is a superposition of D 0 and D ¯ $$ \overline{D} $$ 0. We use the full data set of the Belle experiment, containing 772 × 106 B B ¯ $$ B\overline{B} $$ pairs, and data from the Belle II experiment, containing 387 × 106 B B ¯ $$ B\overline{B} $$ pairs, both collected in electron-positron collisions at the Υ(4S) resonance. Our results provide model-independent information on the unitarity triangle angle ϕ 3.

The collective behavior of an ion cloud confined in a linear Paul trap is physically almost equivalent to that of a relativistic beam traveling in a particle accelerator. This fact provides a new possibility for experimental beam-dynamics studies that can be done without relying on large-scale machines. We have constructed a compact ion trap to explore various accelerator-physics issues in a local tabletop environment. The present trap system is designed particularly for the study of high-intensity short hadron bunches typical in linear accelerators. Resonance-induced ion losses are measured and plotted as a function of the betatron and synchrotron phase advances over a wide range, which offers a piece of indisputable experimental evidence for the presence of various betatron and synchrobetatron resonance stop bands. We confirm that these instability bands shift in the stability map depending on the ion density. The recently proposed stop-band diagram, free from the conventional concept of incoherent tune spread, is employed to explain the experimental observations.

The space-charge-induced resonance band just above the betatron phase advance of 90° per cell is of great practical importance. The instability is closely related to the linear collective mode and can thus give rise to severe emittance growth at high beam density. In a circular machine, this type of second-order resonance occurs not only at half-integer tunes but also near quarter-integer tunes, depending on the lattice superperiodicity. Self-consistent numerical simulations are carried out to elucidate the resonance feature above the 90° cell tune. The present results suggest the existence of three different resonance mechanisms working there; namely, the fourth-order incoherent resonance in the beam tail, the second-order and fourth-order coherent resonances in the beam core. It is reconfirmed that no serious emittance growth occurs even if particles deep inside the core satisfy the incoherent resonance condition. The recently proposed stop-band diagram, free from the concept of incoherent tune spread, appears to be consistent with the numerical observations.

The space-charge potential can be a source of various resonances in high-intensity hadron bunches traveling in linear accelerators at relatively low energy. Those natural resonances, which may occur even without external driving fields, have to be avoided carefully to minimize undesired beam loss. We perform self-consistent multiparticle simulations systematically to locate major resonance stop bands in the tune diagram, starting from equipartitioned and nonequipartitioned beams. Serious excitation of synchrobetatron resonances is confirmed, depending on the emittance condition at injection. It is demonstrated that a synchrobetatron difference resonance of any order can be suppressed strongly by controlling the ratio of the transverse and longitudinal projected emittances. The equipartitioned linac design is shown to broaden the usable operating area in the tune space, though that has almost nothing to do with thermodynamic effects.

The internal quantum efficiency (IQE) of radiation for bulk CH3NH3PbBr3 crystals was quantified by using omnidirectional photoluminescence spectroscopy. The angle-resolved photoluminescence revealed that the emission with photon energies higher than the absorption-edge shows a Lambertian distribution and that the light extraction efficiency is determined by the escaping cone. The IQE value strongly depends on the photo-excitation density (P), and a CH3NH3PbBr3 crystal fabricated under the methylammonium-rich conditions gave the maximum IQE of 62.5% under P = 28 W/cm2. A further increase in P gave rise to the decrease in IQE due to the Auger effects.

In the Comment on our paper [Phys. Rev. Accel. Beams 22, 074201 (2019)PRABCJ2469-988810.1103/PhysRevAccelBeams.22.074201], Hofmann claims that our conclusions are based on a questionable interpretation of Vlasov’s equation and an over-interpretation of our multiparticle simulations. This assertion, however, comes largely from his misinterpretations of the essence of our work and proposed resonance condition. His criticism based on experimental data from some operating machines has also missed the point; we see no essential conflict between our arguments and experimental observations. While most of the questions raised by Hofmann have already been answered in our original paper above and previous publications, we take this opportunity to provide more information and explanation for clarity.

This paper addresses the generalization of the single-particle betatron resonance condition derived by Courant and Snyder more than a half century ago. A two-dimensional resonance condition including the effect of space-charge interaction was recently conjectured from one-dimensional Vlasov predictions made by Sacherer, Okamoto, and Yokoya [K. Ito et al., Phys. Rev. Accel. Beams 20, 064201 (2017)PRABCJ2469-988810.1103/PhysRevAccelBeams.20.064201]. The condition is remarkably simple which only contains a few measurable quantities and indicates the possibility that twice as many resonance stop bands as expected from the conventional incoherent picture may exist at high beam density. Self-consistent multiparticle simulations are performed systematically to locate low-order stop bands in the tune diagram. The proposed betatron resonance formula is shown to explain the basic feature of numerical observations, which suggests that no serious incoherent resonance is activated inside the phase-space core of a dense beam matched to the external linear focusing potential. It is confirmed that the coherent tune-shift factor of any collective mode is less than unity and practically considered as a constant over the whole tune space in a typical high-intensity storage ring. The procedure for finding the optimum operating point of the ring is discussed on the basis of the coherent picture instead of the commonly used picture relying on the concept of incoherent tune spread. Despite years of theoretical efforts by many researchers, the coherent resonance concept is still not being employed for the construction of a stability tune diagram. We here provide a simple prescription to draw the diagram quickly. The present study also indicates the possibility of complete suppression of emittance exchange on particular difference resonances by choosing a proper emittance ratio.

At the Bacho peatland in southern Thailand, peat subsidence was measured at four locations on abandoned agricultural land (degraded peat swamp forest) and at one location in a conservation zone, at monthly intervals over a period of more than 20 years. Average peat subsidence rates during the observation period were 3.1–5.2 cm y−1 on the degraded peatland, reducing to 1.8–2.6 cm y−1 when peat loss due to field fires was discounted, and 1.0 cm y−1 reducing to 0.7 cm y-1 in the conservation zone. Due to martial law restrictions on access to the Bacho site, measurements of the peat soil respiration rate under various water table conditions were made mostly at other sites in Thailand with similar climate. During these measurements the position of the water table ranged from 0.92 m above the peat surface to more than one metre below it, and daily mean respiration rates ranged from 0.57 to 8.20 μmol CO2 m−2 s−1. The CO2 efflux attributed to peat respiration was 13.7–18.9 Mg ha−1 y−1 on the degraded peatland but only 7.5 Mg ha−1 y−1 in the conservation zone. To simulate the CO2 efflux resulting from soil respiration at Bacho on the basis of data collected elsewhere, we developed an empirical three-stage model (NAIS Peat Model) that treats the position of the water table as a proxy variable. The observed values of peat subsidence were in good agreement with simulated values of CO2 efflux in two tests. The implications for peatland management are considered.

Background SINE- VNTR- Alu (SVA) retrotransposons move from one genomic location to another in a 'copyand- paste' manner. They continue to move actively and cause monogenic diseases through various mechanisms. Currently, disease- causing SVA retrotransposons are classified into human- specific young SVA_E or SVA_F subfamilies. In this study, we identified an evolutionarily old SVA_D retrotransposon as a novel cause of occipital horn syndrome (OHS). OHS is an X- linked, copper metabolism disorder caused by dysfunction of the copper transporter, ATP7A. Methods We investigated a 16- year- old boy with OHS whose pathogenic variant could not be detected via routine molecular genetic analyses. Results A 2.8 kb insertion was detected deep within the intron of the patient's ATP7A gene. This insertion caused aberrant mRNA splicing activated by a new donor splice site located within it. Long- read circular consensus sequencing enabled us to accurately read the entire insertion sequence, which contained highly repetitive and GC- rich segments. Consequently, the insertion was identified as an SVA_D retrotransposon. Antisense oligonucleotides (AOs) targeting the new splice site restored the expression of normal transcripts and functional ATP7A proteins. AO treatment alleviated excessive accumulation of copper in patient fibroblasts in a dose- dependent manner. Pedigree analysis revealed that the retrotransposon had moved into the OHScausing position two generations ago. Conclusion This is the first report of a human monogenic disease caused by the SVA_D retrotransposon. The fact that the evolutionarily old SVA_D is still actively transposed, leading to increased copy numbers may make a notable impact on rare genetic disease research. [ABSTRACT FROM AUTHOR]

Most non-long terminal repeat (non-LTR) retrotransposons encoding a restriction-like endonuclease show target-specific integration into repetitive sequences such as ribosomal RNA genes and microsatellites. However, only a few target-specific lineages of non-LTR retrotransposons are distributed widely and no lineage is found across the eukaryotic kingdoms. Here we report the most widely distributed lineage of target sequence-specific non-LTR retrotransposons, designated Utopia. Utopia is found in three supergroups of eukaryotes: Amoebozoa, SAR, and Opisthokonta. Utopia is inserted into a specific site of U2 small nuclear RNA genes with different strength of specificity for each family. Utopia families from oomycetes and wasps show strong target specificity while only a small number of Utopia copies from reptiles are flanked with U2 snRNA genes. Oomycete Utopia families contain an "archaeal" RNase H domain upstream of reverse transcriptase (RT), which likely originated from a plant RNase H gene. Analysis of Utopia from oomycetes indicates that multiple lineages of Utopia have been maintained inside of U2 genes with few copy numbers. Phylogenetic analysis of RT suggests the monophyly of Utopia, and it likely dates back to the early evolution of eukaryotes.

Abstract  A reporter gene assay revealed that promoters derived from Synechococcus PCC7942 (S.7942) psbAI and Synechocystis PCC6803 (S.6803) psbAII were suitable for the expression of foreign ribulose-bisphosphate carboxylase (RuBisCO; EC 4.1.1.39) in S.7942 cells. Transformational vectors with a promoter and a foreign RuBisCO gene, cvrbc originated from Allochromatium vinosum, were constructed on a binary vector, pUC303, and introduced to S.7942 cells. When the cvrbc was expressed with the S.7942 psbAI promoter, the total RuBisCO activity increased 2.5- to 4-fold than that of the wild type cell. The S.6803 psbAII promoter increased the activity of the transformant 1.5–2 times of that of wild type cell. There was a significant increase in the rate of photosynthesis depending on the increase of RuBisCO activity. The maximum rate of photosynthesis of the transformant cell was 1.63 times higher than that of the wild type under the illumination of 400 μmol m−2 s−1, at 20 mM bicarbonate and at 30 °C. Although the photosynthesis of the higher plant is limited by the ability of photosystems under high irradiance and the high CO2 concentration, that of the S.7942 cell is limited by the RuBisCO activity, even at high CO2 concentrations and under high irradiance. [ABSTRACT FROM AUTHOR]

Abstract Most insects have telomeres that consist of pentanucleotide (TTAGG) telomeric repeats, which are synthesized by telomerase. However, all species in Diptera so far examined and several species in other orders of insect have lost the (TTAGG)n repeats, suggesting that some of them recruit telomerase-independent telomere maintenance. The silkworm, Bombyx mori, retains the TTAGG motifs in the chromosomal ends but expresses quite a low level of telomerase activity in all stages of various tissues. Just proximal to a 6–8-kb stretch of the TTAGG repeats in B. mori, more than 1000 copies of non-LTR retrotransposons, designated TRAS and SART families, occur among the telomeric repeats and accumulate. TRAS and SART are abundantly transcribed and actively retrotransposed into TTAGG telomeric repeats in a highly sequence-specific manner. They have three possible mechanisms to ensure specific integration into the telomeric repeats. This article focuses on the telomere structure and telomere-specific non-LTR retrotransposons in B. mori and discusses the mechanisms for telomere maintenance in this insect. [ABSTRACT FROM AUTHOR]

Summary. Long electropherotype with Subgroup I specificity is a common feature of animal rotaviruses. In an epidemic of infantile gastroenteritis in Manipur, India, long but SG I strains predominated in the outbreak in the year 1987?88. One such strain isolated from that region, following the outbreak had G9P [19] specificity. As this is a rare combination, the gene sequences encoding VP4, VP6, VP7, NSP1, NSP2, NSP3, NSP4 and NSP5 of this strain were analyzed. All these genes except VP7 were closely related to porcine rotaviruses (95?99% identity at amino acid level) and clustered with the porcine strains in phylogenetic analysis. In addition, it had subgroup I nature and belonged to NSP4 genotype B which is characteristic of animal rotaviruses. This is the first report of a rotavirus with VP6 and NSP4, two crucial proteins thought to be involved in host range restriction and pathogenicity, were of porcine origin and caused diarrhoea in a human host. Among the genes of this strain sequenced so far, only VP7 had highest identity to human strains at amino acid level. This study suggests reassortment may be occurring between human and other animal strains and some of the reassortant viruses may be virulent to humans. [ABSTRACT FROM AUTHOR]

Abstract??Seedlings planted on degraded lands experience high leaf temperature in daytime because of the lack of vegetation shading. The effect of high temperature on the photosynthetic capacity was investigated inDipterocarpus obtusifoliusTeijsm.exMiq. andD. chartaceusSym. seedlings planted on degraded sandy soils in southern Thailand. Neither species showed decrease in photosynthetic capacity at leaf temperature over 38 ?C as compared to that at 28 ?C.D. obtusifoliusshowed higher photosynthetic capacity at high temperatures. Enhanced photosynthetic capacity at high temperatures would be a key for high photosynthetic performance ofD. obtusifoliusplanted on degraded sandy soils. [ABSTRACT FROM AUTHOR]

We report the investigation of the performance of an interleaved Reed-Solomon forward error correction code in the presence of optical power transients in a DWDM transmission system for the first time. These transients were generated by adding-dropping channels in an erbium-doped fiber amplifier or Raman amplified systems. [ABSTRACT FROM PUBLISHER]

We describe dense wavelength-division-multiplexing (DWDM) operation of a reconfigurable optical add-drop multiplexer subsystem module employing silica waveguide technology that is suitable for use with both fixed-wavelength and wavelength-selectable add-drop transceivers. We illustrate its use in providing modular growth in high channel-count DWDM systems. [ABSTRACT FROM PUBLISHER]

We investigate the cascadability and transient effects of an micro-electromechanical-systems-based 64-channel blocker. We observe no transient effect due to the blocker. We limited our study to ten cascades and observe negligible optical power penalty with or without the 7-dB maximum allowable equalization for both nonreturn-to-zero and return-to-zero pulses. [ABSTRACT FROM PUBLISHER]

Abstract Background DNA transposons are ubiquitous components of eukaryotic genomes. A major group of them encode a DDD/E transposase and contain terminal inverted repeats (TIRs) of varying lengths. The Kolobok superfamily of DNA transposons has been found in a wide spectrum of organisms. Results Here we report a new Kolobok lineage, designated KolobokP. They were identified in 7 animal phyla (Mollusca, Phoronida, Annelida, Nemertea, Bryozoa, Chordata, and Echinodermata), and are especially rich in bivalves. Unlike other Kolobok families, KolobokP adopts a composite-like architecture: an internal region (INT) flanked by two long terminal direct repeats (LTDRs), which exhibit their own short terminal inverted repeats ranging up to 18 bps. The excision of LTDRs was strongly suggested. The LTDR lengths seem to be constrained to be either around 450-bp or around 660-bp. The internal region encodes a DDD/E transposase and a small His-Me finger nuclease, which likely originated from the homing endonuclease encoded by a group I intron from a eukaryotic species. The architecture of KolobokP resembles composite DNA transposons, usually observed in bacterial genomes, and long terminal repeat (LTR) retrotransposons. In addition to this monomeric LTDR-INT-LTDR structure, plenty of solo LTDRs and multimers represented as (LTDR-INT)n-LTDR are also observed. Our structural and phylogenetic analysis supported the birth of KolobokP in the late stage of the Kolobok evolution. We propose KolobokP families propagate themselves in two ways: the canonical transposition catalyzed by their transposase and the sequence-specific cleavage by their endonuclease followed by the multimerization through the unequal crossover. Conclusions The presence of homing endonuclease and long terminal direct repeats of KolobokP families suggest their unique dual replication mechanisms: transposition and induced unequal crossover.

Terminal repeat retrotransposons in miniature (TRIMs) are short non-autonomous long terminal repeat (LTR) retrotransposons found from various eukaryotes. Cassandra is a unique TRIM lineage which contains a 5S rRNA-derived sequence in its LTRs. Here, two new groups of TRIMs, designated Helenus and Ajax, are reported based on bioinformatics analysis and the usage of Repbase. Helenus is found from fungi, animals, and plants, and its LTRs contain a tRNA-like sequence. It includes two LTRs and between them, a primer-binding site (PBS) and polypurine tract (PPT) exist. Fungal and plant Helenus generate 5 bp target site duplications (TSDs) upon integration, while animal Helenus generates 4 bp TSDs. Ajax includes a 5S rRNA-derived sequence in its LTR and is found from two nemertean genomes. Ajax generates 5 bp TSDs upon integration. These results suggest that despite their unique promoters, Helenus and Ajax are TRIMs whose transposition is dependent on autonomous LTR retrotransposon. These TRIMs can originate through an insertion of SINE in an LTR of TRIM. The discovery of Helenus and Ajax suggests the presence of TRIMs with a promoter for RNA polymerase III derived from a small RNA gene, which is here collectively termed TRIMp3.

Mechanical properties of high quality tetragonal hen egg-white lysozyme single crystals which are one type of protein crystal were investigated by the indentation method. The indentation marks were clearly observed on the crystal surface and no elastic recovery of them occurred. The value of the micro-Vickers hardness in the wet condition was estimated to be about 20 MPa at room temperature. The hardness greatly depended on the amount of intracrystalline water (mobile water) contained in the crystals. The hardness increased with increasing evaporation time to air at room temperature. It reached the maximum at about 260 MPa, which is 13 times as much as that in the wet condition. The origin of such a change in hardness was explained in terms of the dislocation mechanisms in lysozyme single crystals. [ABSTRACT FROM AUTHOR]

We investigated dislocation motions in C60 crystals after indentation, by x-ray topography and etching method. A rosette pattern was observed around an indentation after etching. The dislocations in the rosette were moved by thermal annealing and the positions in the dislocations were measured before and after annealing by the double etching method. The annealing temperature dependence of dislocation motions was measured in the temperature range 490-610 K. The characteristics of dislocation motion showed dislocation locking due to impurity atmosphere. It was concluded that oxygen and oxide of C60 molecules could lock the dislocations. Moreover, a pair of pits in the rosette pattern were observed after annealing. It corresponded to a pair of Shockley's partial dislocations. [ABSTRACT FROM AUTHOR]

Abstract Background Short interspersed elements (SINEs) are ubiquitous components of eukaryotic genomes. SINEs are composite transposable elements that are mobilized by non-long terminal repeat (non-LTR) retrotransposons, also called long interspersed elements (LINEs). The 3′ part of SINEs usually originated from that of counterpart non-LTR retrotransposons. The 5′ part of SINEs mostly originated from small RNA genes. SINE1 is a group of SINEs whose 5′ part originated from 7SL RNA, and is represented by primate Alu and murine B1. Well-defined SINE1 has been found only from Euarchontoglires, a group of mammals, in contrast to the wide distribution of SINE2, which has a tRNA-derived sequence, from animals to plants to protists. Both Alu and B1 are mobilized by L1-type non-LTR retrotransposons, which are the only lineage of autonomous non-LTR retrotransposons active in these mammalian lineages. Results Here a new lineage of SINE1 is characterized from the seashore hagfish Eptatretus burgeri genome. This SINE1 family, designated SINE1-1_EBu, is young, and is transposed by RTE-type non-LTR retrotransposon, not L1-type. Comparison with other SINE families from hagfish indicated the birth of SINE1-1_EBu through chimera formation of a 7SL RNA-derived sequence and an older tRNA-derived SINE family. It reveals parallel evolution of SINE1 in two vertebrate lineages with different autonomous non-LTR retrotransposon partners. The comparison between two SINE1 lineages supports that the RNA secondary structure of the Alu domain of 7SL RNA is required for the efficient retrotransposition. Conclusions The hagfish SINE1 is the first evident SINE1 family found outside of Euarchontoglires. Independent evolution of SINE1 with similar RNA secondary structure originated in 7SL RNA indicates the functional importance of 7SL RNA-derived sequence in the proliferation of SINEs.

Abstract Background DNA transposons are ubiquitous components of eukaryotic genomes. Academ superfamily of DNA transposons is one of the least characterized DNA transposon superfamilies in eukaryotes. DNA transposons belonging to the Academ superfamily have been reported from various animals, one red algal species Chondrus crispus, and one fungal species Puccinia graminis. Six Academ families from P. graminis encode a helicase in addition to putative transposase, while some other families encode a single protein which contains a putative transposase and an XPG nuclease. Results Systematic searches on Repbase and BLAST searches against publicly available genome sequences revealed that several species of fungi and animals contain multiple Academ transposon families encoding a helicase. These AcademH families generate 9 or 10-bp target site duplications (TSDs) while Academ families lacking helicase generate 3 or 4-bp TSDs. Phylogenetic analysis clearly shows two lineages inside of Academ, designated here as AcademH and AcademX for encoding helicase or XPG nuclease, respectively. One sublineage of AcademH in animals encodes plant homeodomain (PHD) finger in its transposase, and its remnants are found in several fish genomes. Conclusions The AcademH lineage of TEs is widely distributed in animals and fungi, and originated early in the evolution of Academ DNA transposons. This analysis highlights the structural diversity in one less studied superfamily of eukaryotic DNA transposons.

DDD/E transposase gene is the most abundant gene in nature and many DNA transposons in all three domains of life use it for their transposition. A substantial number of eukaryotic DNA transposons show similarity to prokaryotic insertion sequences (ISs). The presence of IS481-like DNA transposons was indicated in the genome of Trichomonas vaginalis. Here, we surveyed IS481-like eukaryotic sequences using a bioinformatics approach and report a group of eukaryotic IS481-like DNA transposons, designated IS481EU, from parabasalids including T. vaginalis. The lengths of target site duplications (TSDs) of IS481EU are around 4 bps, around 15 bps, or around 25 bps, and strikingly, these discrete lengths of TSDs can be observed even in a single IS481EU family. Phylogenetic analysis indicated the close relationships of IS481EU with some of the prokaryotic IS481 family members. IS481EU was not well separated from IS3EU/GingerRoot in the phylogenetic analysis, but was distinct from other eukaryotic DNA transposons including Ginger1 and Ginger2. The unique characteristics of IS481EU in protein sequences and the distribution of TSD lengths support its placement as a new superfamily of eukaryotic DNA transposons.

Dada is a unique superfamily of DNA transposons, inserted specifically in multicopy RNA genes. The zebrafish genome harbors five families of Dada transposons, whose targets are U6 and U1 snRNA genes, and tRNA-Ala and tRNA-Leu genes. Dada-U6, which is inserted specifically in U6 snRNA genes, is found in four animal phyla, but other target-specific lineages have been reported only from one or two species. Here, vertebrate genomes and transcriptomes were surveyed to characterize Dada families with new target specificities, and over 120 Dada families were characterized from the genomes of actinopterygian fish. They were classified into 12 groups with confirmed target specificities. Newly characterized Dada families target tRNA genes for Asp, Asn, Arg, Gly, Lys, Ser, Tyr, and Val, and 5S rRNA genes. Targeted positions inside of tRNA genes are concentrated in two regions: around the anticodon and the A box of RNA polymerase III promoter. Phylogenetic analysis revealed the relationships among actinopterygian Dada families, and one domestication event in the common ancestor of carps and minnows belonging to Cyprinoidei, Cypriniformes. Sequences targeted by phylogenetically related Dada families show sequence similarities, indicating that the target specificity of Dada is accomplished through the recognition of primary nucleotide sequences.

Abstract Repbase is a comprehensive database of eukaryotic transposable elements (TEs) and repeat sequences, containing over 1300 human repeat sequences. Recent analyses of these repeat sequences have accumulated evidences for their contribution to human evolution through becoming functional elements, such as protein-coding regions or binding sites of transcriptional regulators. However, resolving the origins of repeat sequences is a challenge, due to their age, divergence, and degradation. Ancient repeats have been continuously classified as TEs by finding similar TEs from other organisms. Here, the most comprehensive picture of human repeat sequences is presented. The human genome contains traces of 10 clades (L1, CR1, L2, Crack, RTE, RTEX, R4, Vingi, Tx1 and Penelope) of non-long terminal repeat (non-LTR) retrotransposons (long interspersed elements, LINEs), 3 types (SINE1/7SL, SINE2/tRNA, and SINE3/5S) of short interspersed elements (SINEs), 1 composite retrotransposon (SVA) family, 5 classes (ERV1, ERV2, ERV3, Gypsy and DIRS) of LTR retrotransposons, and 12 superfamilies (Crypton, Ginger1, Harbinger, hAT, Helitron, Kolobok, Mariner, Merlin, MuDR, P, piggyBac and Transib) of DNA transposons. These TE footprints demonstrate an evolutionary continuum of the human genome.

A bacterial insertion sequence (IS) is a mobile DNA sequence carrying only the transposase gene (tnp) that acts as a mutator to disrupt genes, alter gene expressions, and cause genomic rearrangements. "Canonical" ISs have historically been characterized by their terminal inverted repeats (IRs), which may form a stem-loop structure, and duplications of a short (non-IR) target sequence at both ends, called target site duplications (TSDs). The IS distributions and virulence potentials of Staphylococcus aureus genomes in familial infection cases are unclear. Here, we determined the complete circular genome sequences of familial strains from a Panton-Valentine leukocidin (PVL)-positive ST50/agr4 S. aureus (GN) infection of a 4-year old boy with skin abscesses. The genomes of the patient strain (GN1) and parent strain (GN3) were rich for "canonical" IS1272 with terminal IRs, both having 13 commonly-existing copies (ce-IS1272). Moreover, GN1 had a newly-inserted IS1272 (ni-IS1272) on the PVL-converting prophage, while GN3 had two copies of ni-IS1272 within the DNA helicase gene and near rot. The GN3 genome also had a small deletion. The targets of ni-IS1272 transposition were IR structures, in contrast with previous "canonical" ISs. There were no TSDs. Based on a database search, the targets for ce-IS1272 were IRs or "non-IRs". IS1272 included a larger structure with tandem duplications of the left (IRL) side sequence; tnp included minor cases of a long fusion form and truncated form. One ce-IS1272 was associated with the segments responsible for immune evasion and drug resistance. Regarding virulence, GN1 expressed cytolytic peptides (phenol-soluble modulin α and δ-hemolysin) and PVL more strongly than some other familial strains. These results suggest that IS1272 transposes through an IR-replacing mechanism, with an irreversible process unlike that of "canonical" transpositions, resulting in genomic variations, and that, among the familial strains, the patient strain has strong virulence potential based on community-associated virulence factors.

In the terrestrial ciliate Colpoda cucullus, an elevation of the intracellular cAMP concentration was reported to be involved in environment-resistant resting cyst formation. In the present study, cAMP-dependently phosphorylated proteins of encystment-induced C. cucullus were isolated with Phos-tag agarose phosphate-affinity beads and subsequent SDS-PAGE. In a liquid chromatography/tandem mass spectrometry analysis of these phosphoproteins, 27-, 37- and 43-kDa proteins (p27, p37 and p43) were identified as Rieske iron-sulfur protein, histone H4 (hyperacetylated form), and actin, respectively.

Genomes of a given bacterial species can show great variation in gene content and thus systematic analysis of the entire gene repertoire, termed the pan-genome, is important for understanding bacterial intra-species diversity, population genetics, and evolution. Here, we analyzed the pan-genome from 30 completely sequenced strains of the human gastric pathogen Helicobacter pylori belonging to various phylogeographic groups, focusing on 991 accessory (not fully conserved) orthologous groups (OGs). We developed a method to evaluate the mobility of genes within a genome, using the gene order in the syntenically conserved regions as a reference, and classified the 991 accessory OGs into five classes: Core, Stable, Intermediate, Mobile, and Unique. Phylogenetic networks based on the gene content of Core and Stable classes are highly congruent with that created from the concatenated alignment of fully conserved core genes, in contrast to those of Intermediate and Mobile classes, which show quite different topologies. By clustering the accessory OGs on the basis of phylogenetic pattern similarity and chromosomal proximity, we identified 60 co-occurring gene clusters (CGCs). In addition to known genomic islands, including cag pathogenicity island, bacteriophages, and integrating conjugative elements, we identified some novel ones. One island encodes TerY-phosphorylation triad, which includes the eukaryote-type protein kinase/phosphatase gene pair, and components of type VII secretion system. Another one contains a reverse-transcriptase homolog, which may be involved in the defense against phage infection through altruistic suicide. Many of the CGCs contained restriction-modification (RM) genes. Different RM systems sometimes occupied the same (orthologous) locus in the strains. We anticipate that our method will facilitate pan-genome studies in general and help identify novel genomic islands in various bacterial species.

Transposons, or transposable elements, are the major components of genomes in most eukaryotes. Some groups of transposons have developed target specificity that limits the integration sites to a specific nonessential sequence or a genomic region to avoid gene disruption caused by insertion into an essential gene. R2 is one of the most intensively investigated groups of sequence-specific non-LTR retrotransposons and is inserted at a specific site inside of 28S ribosomal RNA (rRNA) genes. R2 is known to be distributed among at least six animal phyla even though its occurrence is reported to be patchy. Here, in order to obtain a more detailed picture of the distribution of R2, we surveyed R2 using both in silico screening and degenerate PCR, particularly focusing on actinopterygian fish. We found two families of the R2C lineage from vertebrates, although it has previously only been found in platyhelminthes. We also revealed the apparent movement of insertion sites of a lineage of actinopterygian R2, which was likely concurrent with the acquisition of a 28S rRNA-derived sequence in their 3' UTR. Outside of actinopterygian fish, we revealed the maintenance of a single R2 lineage in birds; the co-existence of four lineages of R2 in the leafcutter bee Megachile rotundata; the first examples of R2 in Ctenophora, Mollusca, and Hemichordata; and two families of R2 showing no target specificity. These findings indicate that R2 is relatively stable and universal, while differences in the distribution and maintenance of R2 lineages probably reflect characteristics of some combination of both R2 lineages and host organisms.

Target-specific integration of transposable elements for multicopy genes, such as ribosomal RNA and small nuclear RNA (snRNA) genes, is of great interest because of the relatively harmless nature, stable inheritance and possible application for targeted gene delivery of target-specific transposable elements. To date, such strict target specificity has been observed only among non-LTR retrotransposons. We here report a new superfamily of sequence-specific DNA transposons, designated Dada. Dada encodes a DDE-type transposase that shows a distant similarity to transposases encoded by eukaryotic MuDR, hAT, P and Kolobok transposons, as well as the prokaryotic IS256 insertion element. Dada generates 6-7 bp target site duplications upon insertion. One family of Dada DNA transposons targets a specific site inside the U6 snRNA genes and are found in various fish species, water flea, oyster and polycheate worm. Other target sequences of the Dada transposons are U1 snRNA genes and different tRNA genes. The targets are well conserved in multicopy genes, indicating that copy number and sequence conservation are the primary constraints on the target choice of Dada transposons. Dada also opens a new frontier for target-specific gene delivery application.

BackgroundThe wheat stripe rust fungus (Puccinia striiformis f. sp. tritici, PST) is responsible for significant yield losses in wheat production worldwide. In spite of its economic importance, the PST genomic sequence is not currently available. Fortunately Next Generation Sequencing (NGS) has radically improved sequencing speed and efficiency with a great reduction in costs compared to traditional sequencing technologies. We used Illumina sequencing to rapidly access the genomic sequence of the highly virulent PST race 130 (PST-130).Methodology/principal findingsWe obtained nearly 80 million high quality paired-end reads (>50x coverage) that were assembled into 29,178 contigs (64.8 Mb), which provide an estimated coverage of at least 88% of the PST genes and are available through GenBank. Extensive micro-synteny with the Puccinia graminis f. sp. tritici (PGTG) genome and high sequence similarity with annotated PGTG genes support the quality of the PST-130 contigs. We characterized the transposable elements present in the PST-130 contigs and using an ab initio gene prediction program we identified and tentatively annotated 22,815 putative coding sequences. We provide examples on the use of comparative approaches to improve gene annotation for both PST and PGTG and to identify candidate effectors. Finally, the assembled contigs provided an inventory of PST repetitive elements, which were annotated and deposited in Repbase.Conclusions/significanceThe assembly of the PST-130 genome and the predicted proteins provide useful resources to rapidly identify and clone PST genes and their regulatory regions. Although the automatic gene prediction has limitations, we show that a comparative genomics approach using multiple rust species can greatly improve the quality of gene annotation in these species. The PST-130 sequence will also be useful for comparative studies within PST as more races are sequenced. This study illustrates the power of NGS for rapid and efficient access to genomic sequence in non-model organisms.