A possible way that φC31 integrase regulates the recombination direction

φC31 integrase encoded by Streptomyces phage can mediate site-specific recombination between phage and host genomes. The recombination direction is generally considered to be accurately regulated, but the regulatory mechanisms involved are still unclear. Recently, some hyperactive mutants of φC31 integrase that can bypass the regulatory steps have been isolated and extensively studied. A putative coiled-coil region is found to play a critical role in controlling recombination direction. Further analysis led us to the speculation that at least two regions in the N-terminal domain of φC31 integrase are involved in the tetrameric interfaces and that the putative coiled coil interacts with one of the regions to regulate the recombination direction.

In situ Si doping of heteroepitaxially grown c-BN thin films at different temperatures

Phase pure cubic boron nitride (c-BN) films have been epitaxially grown on (001) diamond substrates at 420 °C, 600 °C and 900 °C.

Gradientless temperature-driven rotating motor from a double-walled carbon nanotube

Rotation of the inner tube in a double-walled carbon nanotube (DWCNT) system with a fixed outer tube is investigated and found to be inducible by a relatively high uniform temperature (say, 300 K). We also found the mechanism of a gradientless temperature-driven rotating motor lies in the inner tube losing its geometric symmetry in a high-temperature field. This mechanism can be taken as a guide for designing a motor from such a bi-tube system. Using a computational molecular dynamics (CMD) approach and the adaptive intermolecular reactive empirical bond order (AIREBO) potential, the dynamic behavior of a bi-tube system subjected to uniformly distributed temperature is studied. In particular, the effects of environmental temperature, boundary conditions of the outer tube, and intertube gap on the dynamic behavior of the bi-tube system are investigated. Numerical examples show that a bi-tube system with the inner tube having 0.335 nm of interlayer gap produces the highest rotational speed.

Systems and synthetic biology approaches to alter plant cell walls and reduce biomass recalcitrance

Fine-tuning plant cell wall properties to render plant biomass more amenable to biofuel conversion is a colossal challenge. A deep knowledge of the biosynthesis and regulation of plant cell wall and a high-precision genome engineering toolset are the two essential pillars of efforts to alter plant cell walls and reduce biomass recalcitrance. The past decade has seen a meteoric rise in use of transcriptomics and high-resolution imaging methods resulting in fresh insights into composition, structure, formation and deconstruction of plant cell walls. Subsequent gene manipulation approaches, however, commonly include ubiquitous mis-expression of a single candidate gene in a host that carries an intact copy of the native gene. The challenges posed by pleiotropic and unintended changes resulting from such an approach are moving the field towards synthetic biology approaches. Synthetic biology builds on a systems biology knowledge base and leverages high-precision tools for high-throughput assembly of multigene constructs and pathways, precision genome editing and site-specific gene stacking, silencing and/or removal. Here, we summarize the recent breakthroughs in biosynthesis and remodelling of major secondary cell wall components, assess the impediments in obtaining a systems-level understanding and explore the potential opportunities in leveraging synthetic biology approaches to reduce biomass recalcitrance.

Distinct double flower varieties in Camellia japonica exhibit both expansion and contraction of C-class gene expression

BACKGROUND

Double flower domestication is of great value in ornamental plants and presents an excellent system to study the mechanism of morphological alterations by human selection. The classic ABC model provides a genetic framework underlying the control of floral organ identity and organogenesis from which key regulators have been identified and evaluated in many plant species. Recent molecular studies have underscored the importance of C-class homeotic genes, whose functional attenuation contributed to the floral diversity in various species. Cultivated Camellia japonica L. possesses several types of double flowers, however the molecular mechanism underlying their floral morphological diversification remains unclear.

RESULTS

In this study, we cloned the C-class orthologous gene CjAG in C. japonica. We analyzed the expression patterns of CjAG in wild C. japonica, and performed ectopic expression in Arabidopsis. These results revealed that CjAG shared conserved C-class function that controls stamen and carpel development. Further we analyzed the expression pattern of CjAG in two different C. japonica double-flower varieties, 'Shibaxueshi' and 'Jinpanlizhi', and showed that expression of CjAG was highly contracted in 'Shibaxueshi' but expanded in inner petals of 'Jinpanlizhi'. Moreover, detailed expression analyses of B- and C-class genes have uncovered differential patterns of B-class genes in the inner organs of 'Jinpanlizhi'.

CONCLUSIONS

These results demonstrated that the contraction and expansion of CjAG expression were associated with the formation of different types of double flowers. Our studies have manifested two different trajectories of double flower domestication regarding the C-class gene expression in C. japonica.

Constraints on models for the Higgs boson with exotic spin and parity in VH → Vbb final states

We present constraints on models containing non-standard-model values for the spin J and parity P of the Higgs boson H in up to 9.7 fb(-1) of pp collisions at sqrt[s] = 1.96 TeV collected with the D0 detector at the Fermilab Tevatron Collider. These are the first studies of Higgs boson J(P) with fermions in the final state. In the ZH → ℓℓbb, WH → ℓνbb, and ZH → ννbb final states, we compare the standard model (SM) Higgs boson prediction, J(P) = 0(+), with two alternative hypotheses, J(P) = 0(-) and J(P) = 2(+). We use a likelihood ratio to quantify the degree to which our data are incompatible with non-SM J(P) predictions for a range of possible production rates. Assuming that the production rate in the signal models considered is equal to the SM prediction, we reject the J(P) = 0(-) and J(P) = 2(+) hypotheses at the 97.6% CL and at the 99.0% CL, respectively. The expected exclusion sensitivity for a J(P) = 0(-) (J(P) = 2(+)) state is at the 99.86% (99.94%) CL. Under the hypothesis that our data are the result of a combination of the SM-like Higgs boson and either a J(P) = 0(-) or a J(P) = 2(+) signal, we exclude a J(P) = 0(-) fraction above 0.80 and a J(P) = 2(+) fraction above 0.67 at the 95% CL. The expected exclusion covers J(P) = 0(-) (J(P) = 2(+)) fractions above 0.54 (0.47).

Metabotropic glutamate receptor 5 modulates calcium oscillation and innate immune response induced by lipopolysaccharide in microglial cell

Microglia, the primary immune cells in the brain, have been implicated as the predominant cells governing inflammation-mediated neuronal damage. In response to immunological challenges such as lipopolysaccharide (LPS), microglia are activated and subsequently inflammatory process is initiated as evidenced by the release of pro-inflammatory chemokines and cytokines. Here we show that Group I metabotropic glutamate receptor 5 (mGluR5) is involved in LPS-induced microglia activation. LPS triggered a similar pattern of [Ca2+]i oscillation in N9, Toll-like receptor 4 (TLR4)-mutant EOC 20, TLR4-wild-type and TLR4-deficient primary mouse microglia, suggesting that LPS-induced [Ca2+]i oscillation is independent of TLR4. The characteristics of [Ca2+]i oscillation induced by LPS are consistent with those observed in mGluR5 activation. In addition, mGluR5 antagonist 3-[(2-methyl-1,3-thiazol-4-yl)ethynyl]pyridine (MTEP) abolished LPS-induced [Ca2+]i oscillation. Immunocytochemistry demonstrated that LPS colocalizes with mGluR5 in microglia and the direct binding of LPS and mGluR5 was further validated by antibody-based fluorescence resonance energy transfer (FRET) technology. Activation of mGluR5 using a selective agonist (RS)-2-chloro-5-hydroxyphenylglycine (CHPG) significantly expanded LPS-induced nuclear factor-kappa B (NF-κB) activity and CHPG alone increased NF-κB activity as well. But, mGluR5 antagonist MTEP attenuated the actions of LPS, CHPG and the additive effect of LPS and CHPG in microglia. LPS induced tumor necrosis factor-α (TNF-α) secretion in N9 microglia, but not in TLR4-mutant EOC 20 and TLR4-deficient primary mouse microglia. CHPG reduced LPS-caused TNF-α production, but MTEP increased LPS-induced TNF-α production and blocked the effect of CHPG in N9 microglia. These data demonstrate that mGluR5 and TLR4 are two critical receptors that mediate microglia activation in response to LPS, suggesting that mGluR5 may represent a novel target for modulating microglia-dependent neuroinflammation.

Precision measurement of the top quark mass in lepton + jets final States

We measure the mass of the top quark in lepton+jets final states using the full sample of pp collision data collected by the D0 experiment in Run II of the Fermilab Tevatron Collider at sqrt[s] = 1.96 TeV, corresponding to 9.7 fb(-1) of integrated luminosity. We use a matrix element technique that calculates the probabilities for each event to result from tt production or background. The overall jet energy scale is constrained in situ by the mass of the W boson. We measure m(t) = 174.98 ± 0.76 GeV. This constitutes the most precise single measurement of the top-quark mass.

Observation of s-channel production of single top quarks at the Tevatron

We report the first observation of single-top-quark production in the s channel through the combination of the CDF and D0 measurements of the cross section in proton-antiproton collisions at a center-of-mass energy of 1.96 TeV. The data correspond to total integrated luminosities of up to 9.7 fb(-1) per experiment. The measured cross section is σ(s) = 1.29(-0.24)(+0.26) pb. The probability of observing a statistical fluctuation of the background to a cross section of the observed size or larger is 1.8 × 10(-10), corresponding to a significance of 6.3 standard deviations for the presence of an s-channel contribution to the production of single-top quarks.

Measurement of the W boson production charge asymmetry in pp̄→W+X→eν+X events at √s=1.96 TeV

We present a measurement of the W boson production charge asymmetry in pp̄→W+X→eν+X events at a center of mass energy of 1.96 TeV, using 9.7  fb-1 of integrated luminosity collected with the D0 detector at the Fermilab Tevatron Collider. The neutrino longitudinal momentum is determined by using a neutrino weighting method, and the asymmetry is measured as a function of the W boson rapidity. The measurement extends over wider electron pseudorapidity region than previous results and is the most precise to date, allowing for precise determination of proton parton distribution functions in global fits.

Measurement of the direct CP-violating charge asymmetry in Ds ± → ϕ π ± decays

We present a measurement of the direct CP-violating charge asymmetry in Ds+ → ϕ π(±) decays where the ϕ meson decays to K(+)K(-), using the full Run II data set with an integrated luminosity of 10.4  fb-1 of proton-antiproton collisions collected using the D0 detector at the Fermilab Tevatron Collider. The normalized difference A(CP) in the yield of D(s)(+) and D(s)(-) mesons in these decays is measured by fitting the difference between their reconstructed invariant mass distributions. This results in an asymmetry of A(CP) = [-0.38 ± 0.27]%, which is the most precise measurement of this quantity to date. The result is consistent with the standard model prediction of zero CP asymmetry in this decay.

Measurement of associated production of z bosons with charm quark jets in pp collisions at √s=1.96 TeV

We present the first measurements of the ratios of cross sections σ(pp → Z+c jet)/σ(pp → Z+jet) and σ(pp → Z+c jet)/σ(pp → Z+b jet) for the associated production of a Z boson with at least one charm or bottom quark jet. Jets have transverse momentum ​pT(jet)​>20  GeV and pseudorapidity |​η(jet)​|<2.5. These cross section ratios are measured differentially as a function of jet and Z boson transverse momenta, based on 9.7  fb(-1) of pp collisions collected with the D0 detector at the Fermilab Tevatron Collider at √s=1.96  TeV. The measurements show significant deviations from perturbative QCD calculations and predictions from various event generators.