Modeling pion physics in the ϵ\epsilon-regime of two-flavor QCD using strong coupling lattice QED

In order to model pions of two-flavor QCD we consider a lattice field theory involving two flavors of staggered quarks interacting strongly with U(1) gauge fields. For massless quarks, this theory has an $SU_L(2)\times SU_R(2) \times U_A(1)$ symmetry. By adding a four-fermion term we can break the U_A(1) symmetry and thus incorporate the physics of the QCD anomaly. We can also tune the pion decay constant F, to be small compared to the lattice cutoff by starting with an extra fictitious dimension, thus allowing us to model low energy pion physics in a setting similar to lattice QCD from first principles. However, unlike lattice QCD, a major advantage of our model is that we can easily design efficient algorithms to compute a variety of quantities in the chiral limit. Here we show that the model reproduces the predictions of chiral perturbation theory in the $\epsilon$-regime.Comment: 24 pages, 7 figure

Absence of vortex condensation in a two dimensional fermionic XY model

Motivated by a puzzle in the study of two dimensional lattice Quantum Electrodynamics with staggered fermions, we construct a two dimensional fermionic model with a global U(1) symmetry. Our model can be mapped into a model of closed packed dimers and plaquettes. Although the model has the same symmetries as the XY model, we show numerically that the model lacks the well known Kosterlitz-Thouless phase transition. The model is always in the gapless phase showing the absence of a phase with vortex condensation. In other words the low energy physics is described by a non-compact U(1) field theory. We show that by introducing an even number of layers one can introduce vortex condensation within the model and thus also induce a KT transition.Comment: 5 pages, 5 figure

Role of the σ\sigma-resonance in determining the convergence of chiral perturbation theory

The dimensionless parameter $\xi = M_\pi^2/(16 \pi^2 F_\pi^2)$, where $F_\pi$ is the pion decay constant and $M_\pi$ is the pion mass, is expected to control the convergence of chiral perturbation theory applicable to QCD. Here we demonstrate that a strongly coupled lattice gauge theory model with the same symmetries as two-flavor QCD but with a much lighter $\sigma$-resonance is different. Our model allows us to study efficiently the convergence of chiral perturbation theory as a function of $\xi$. We first confirm that the leading low energy constants appearing in the chiral Lagrangian are the same when calculated from the $p$-regime and the $\epsilon$-regime as expected. However, $\xi \lesssim 0.002$ is necessary before 1-loop chiral perturbation theory predicts the data within 1%. For $\xi > 0.0035$ the data begin to deviate dramatically from 1-loop chiral perturbation theory predictions. We argue that this qualitative change is due to the presence of a light $\sigma$-resonance in our model. Our findings may be useful for lattice QCD studies.Comment: 5 pages, 6 figures, revtex forma

Alanine scanning mutagenesis of a high-affinity nitrate transporter highlights the requirement for glycine and asparagine residues in the two nitrate signature motifs

Common to all of the nitrate nitrite porter family are two conserved motifs in transmembrane helices 5 and 11 termed NS (nitrate signature) 1 and NS2. Although perfectly conserved substrate-interacting arginine residues have been described in transmembrane helices 2 and 8, the role of NSs has not been investigated. In the present study, a combination of structural modelling of NrtA (nitrate transporter from Aspergillus nidulans) with alanine scanning mutagenesis of residues within and around the NSs has been used to shed light on the probable role of conserved residues in the NSs. Models show that Asn 168 in NS1 and Asn 459 in NS2 are positioned approximately midway within the protein at the central pivot point in close proximity to the substrate-binding residues Arg 368 and Arg 87 respectively, which lie offset from the pivot point towards the cytoplasmic face. The Asn 168 /Arg 368 and Asn 459 /Arg 87 residue pairs are relatively widely separated on opposite sides of the probable substrate translocation pore. The results of the present study demonstrate the critical structural contribution of several glycine residues in each NS at sites of close helix packing. Given the relative locations of Asn 168 /Arg 368 and Asn 459 /Arg 87 pairs, the validity of the models and possible role of the NSs together with the substrate-binding arginine residues are discusse

Soil carbon dioxide venting through rice roots

The growth of rice in submerged soils depends on its ability to form continuous gas channels—aerenchyma—through which oxygen (O2) diffuses from the shoots to aerate the roots. Less well understood is the extent to which aerenchyma permits venting of respiratory carbon dioxide (CO2) in the opposite direction. Large, potentially toxic concentrations of dissolved CO2 develop in submerged rice soils. We show using X‐ray computed tomography and image‐based mathematical modelling that CO2 venting through rice roots is far greater than thought hitherto. We found rates of venting equivalent to a third of the daily CO2 fixation in photosynthesis. Without this venting through the roots, the concentrations of CO2 and associated bicarbonate (HCO3−) in root cells would have been well above levels known to be toxic to roots. Removal of CO2 and hence carbonic acid (H2CO3) from the soil was sufficient to increase the pH in the rhizosphere close to the roots by 0.7 units, which is sufficient to solubilize or immobilize various nutrients and toxicants. A sensitivity analysis of the model showed that such changes are expected for a wide range of plant and soil conditions

Soil CO2 venting as one of the mechanisms for tolerance of Zn deficiency by rice in flooded soils

We sought to explain rice (Oryza sativa) genotype differences in tolerance of zinc (Zn) deficiency in flooded paddy soils and the counter-intuitive observation, made in earlier field experiments, that Zn uptake per plant increases with increasing planting density. We grew tolerant and intolerant genotypes in a Zn-deficient flooded soil at high and low planting densities, and found (a) plant Zn concentrations and growth increased with planting density and more so in the tolerant genotype, whereas the concentrations of other nutrients decreased, indicating a specific effect on Zn uptake; (b) the effects of planting density and genotype on Zn uptake could only be explained if the plants induced changes in the soil to make Zn more soluble; and (c) the genotype and planting density effects were both associated with decreases in dissolved CO2 in the rhizosphere soil solution and resulting increases in pH. We suggest the increases in pH caused solubilisation of soil Zn by dissolution of alkali-soluble, Zn-complexing organic ligands from soil organic matter. We conclude that differences in venting of soil CO2 through root aerenchyma were responsible for the genotype and planting density effects

Characterisation of microbial communities of drill cuttings piles from offshore oil and gas installations

Acknowledgements The authors would like to acknowledge the support of the Maxwell computer cluster funded by the University of Aberdeen. Dr. Axel Aigle is acknowledged for guidance and assistance in molecular analysis. Hedda Weitz and Heather Richmond are thanked for technical support. This work was supported by the Natural Environment Research Council [NE/L00982X/1 to UW, JA and EG]. CGR was supported by a University Research Fellowship from the Royal Society [UF150571]. DC samples, environmental analysis and all geochemical datasets were kindly provided by Marathon Oil UK LLC (referred to as Marathon Oil).Peer reviewedPublisher PD

A simple vector system to improve performance and utilisation of recombinant antibodies

BACKGROUND: Isolation of recombinant antibody fragments from antibody libraries is well established using technologies such as phage display. Phage display vectors are ideal for efficient display of antibody fragments on the surface of bacteriophage particles. However, they are often inefficient for expression of soluble antibody fragments, and sub-cloning of selected antibody populations into dedicated soluble antibody fragment expression vectors can enhance expression. RESULTS: We have developed a simple vector system for expression, dimerisation and detection of recombinant antibody fragments in the form of single chain Fvs (scFvs). Expression is driven by the T7 RNA polymerase promoter in conjunction with the inducible lysogen strain BL21 (DE3). The system is compatible with a simple auto-induction culture system for scFv production. As an alternative to periplasmic expression, expression directly in the cytoplasm of a mutant strain with a more oxidising cytoplasmic environment (Origami 2™ (DE3)) was investigated and found to be inferior to periplasmic expression in BL21 (DE3) cells. The effect on yield and binding activity of fusing scFvs to the N terminus of maltose binding protein (a solubility enhancing partner), bacterial alkaline phosphatase (a naturally dimeric enzymatic reporter molecule), or the addition of a free C-terminal cysteine was determined. Fusion of scFvs to the N-terminus of maltose binding protein increased scFv yield but binding activity of the scFv was compromised. In contrast, fusion to the N-terminus of bacterial alkaline phosphatase led to an improved performance. Alkaline phosphatase provides a convenient tag allowing direct enzymatic detection of scFv fusions within crude extracts without the need for secondary reagents. Alkaline phosphatase also drives dimerisation of the scFv leading to an improvement in performance compared to monovalent constructs. This is illustrated by ELISA, western blot and immunohistochemistry. CONCLUSION: Nine scFv expression vectors have been generated and tested. Three vectors showed utility for expression of functional scFv fragments. One vector, pSANG14-3F, produces scFv-alkaline phosphatase fusion molecules which offers a simple, convenient and sensitive way of determining the reactivity of recombinant antibody fragments in a variety of common assay systems