Perturbative expansions from Monte Carlo simulations at weak coupling: Wilson loops and the static-quark self-energy

Perturbative coefficients for Wilson loops and the static-quark self-energy are extracted from Monte Carlo simulations at weak coupling. The lattice volumes and couplings are chosen to ensure that the lattice momenta are all perturbative. Twisted boundary conditions are used to eliminate the effects of lattice zero modes and to suppress nonperturbative finite-volume effects due to Z(3) phases. Simulations of the Wilson gluon action are done with both periodic and twisted boundary conditions, and over a wide range of lattice volumes (from $3^4$ to $16^4$) and couplings (from $\beta \approx 9$ to $\beta \approx 60$). A high precision comparison is made between the simulation data and results from finite-volume lattice perturbation theory. The Monte Carlo results are shown to be in excellent agreement with perturbation theory through second order. New results for third-order coefficients for a number of Wilson loops and the static-quark self-energy are reported.Comment: 36 pages, 15 figures, REVTEX documen

Resonant acousto-optics in the terahertz range: TO-phonon polaritons driven by an ultrasonic wave

The resonant acousto-optic effect is studied both analytically and numerically in the terahertz range where the transverse-optical (TO) phonons play the role of a mediator which strongly couples the ultrasound and light fields. A propagating acoustic wave interacts with the TO phonons via anharmonic channels and opens band gaps in the TO-phonon polariton energy dispersion that results in pronounced Bragg scattering and reflection of the incoming light. The separation in frequency of different Bragg replicas, which is at the heart of acousto-optics, allows us to study the resonant acousto-optic effect in the most simple and efficient geometry of collinear propagation of electromagnetic and ultrasonic waves. The acoustically induced energy gaps, Bragg reflection spectra, and the spatial distribution of the electric field and polarization are calculated for CuCl parameters, in a wide range of frequencies and intensities of the pumping acoustic wave. Our results show drastic changes in terahertz spectra of semiconductor crystals that opens the way for efficient and accessible manipulation of their infrared properties, by tuning the parameters of the acoustic wave.Comment: 20 pages, 14 figure

Energetics and mechanism of drug transport mediated by the lactococcal multidrug transporter LmrP

The gene encoding the secondary multidrug transporter LmrP of Lactococcus lactis was heterologously expressed in Escherichia coli. The energetics and mechanism of drug extrusion mediated by LmrP were studied in membrane vesicles of E. coli, LmrP-mediated extrusion of tetraphenyl phosphonium (TPP+) from right-side-out membrane vesicles and uptake of the fluorescent membrane probe 1-[4-(trimethylamino)phenyl]-6-phenylhexa-1,3,5-triene (TMA-DPH) into inside-out membrane vesicles are driven by the membrane potential (Delta psi) and the transmembrane proton gradient (Delta pH), pointing to an electrogenic drug/proton antiport mechanism, Ethidium bromide, a substrate for LmrP, inhibited the LmrP-mediated TPP+ extrusion from right-side-out membrane vesicles, showing that LmrP is capable of transporting structurally unrelated drugs. Kinetic analysis of LmrP-mediated TMA-DPH transport revealed a direct relation between the transport rate and the amount of TMA-DPH associated with the cytoplasmic leaflet of the lipid bilayer. This observation indicates that drugs are extruded from the inner leaflet of the cytoplasmic membrane into the external medium. This is the first report that shows that drug extrusion by a secondary multidrug resistance (MDR) transporter occurs by a ''hydrophobic vacuum cleaner'' mechanism in a similar way as was proposed for the primary lactococcal MDR transporter, LmrA

In vitro reassembly of the malolactic fermentation pathway of Leuconostoc oenos (Oenococcus oeni)

The mechanism of metabolic energy generation by malolactic fermentation was studied with artificial membrane vesicles of Leuconostoc oenos (Oenococcus oeni), (Note that although L. oenos was recently reclassified as O. oeni [L. M. T. Dicks, F. Dellaglio, and M. D. Collins, Int. J. Syst. Bacteriol. 45:395-397, 1995], the old designation was kept in the present work,) Purified malolactic enzyme was entrapped in artificial membrane vesicles prepared from L. oenos cells able to transport L-malate. We show that the in vitro reconstituted system, including an electrogenic L-malate carrier and the decarboxylating malolactic enzyme, generated a proton motive force that was able to drive intravesicular accumulation of leucine

Purification and Reconstitution of the Glutamate Carrier GltT of the Thermophilic Bacterium Bacillus stearothermophilus

An affinity tag consisting of six adjacent histidine residues followed by an enterokinase cleavage site was genetically engineered at the N-terminus of the glutamate transport protein GltT of the thermophilic bacterium Bacillus stearothermophilus. The fusion protein was expressed in Escherichia coli and shown to transport glutamate. The highest levels of expression were observed in E. coli strain DH5α grown on rich medium. The protein could be purified in a single step by Ni2+-NTA affinity chromatography after solubilization of the cytoplasmic membranes with the detergent Triton X100. Purified GltT was reconstituted in an active state in liposomes prepared from E. coli phospholipids. The protein was reconstituted in detergent-treated preformed liposomes, followed by removal of the detergent with polystyrene beads. Active reconstitution was realized with a wide range of Triton X100 concentrations. Neither the presence of glycerol, phospholipids, nor substrates of the transporter was necessary during the purification and reconstitution procedure to keep the enzyme in an active state. In B. stearothermophilus, GltT translocates glutamate in symport with protons or sodium ions. In membrane vesicles derived from E. coli cells expressing GltT, the Na+ ion dependency seems to be lost, suggesting a role for the lipid environment in the cation specificity. In agreement with the last observation, glutamate transport catalyzed by purified GltT reconstituted in E. coli phospholipid is driven by an electrochemical gradient of H+ but not of Na+.

Computer modelling applied to the Calvin Cycle

This thesis developes computer modelling techniques, and their use in the investigation of biochemical systems, principally the photosynthetic Calvin cycle. A set of metabolic modelling software tools, "Scampi", constructed as part of this project is presented. A unique feature of Scampi is that it allows the user to make a particular model the subject of arbitrary algorithms. This provides a much greater flexibility than is available with other metabolic modelling software, and is necessary for work on models of (or approaching) realistic complexity. A detailed model of the Calvin cycle is introduced. It differs from previously published models of this system in that all reactions are assigned explicit rate equations (no equilibrium assumptions are made), and it includes the degradation, as well as the synthesis, of starch. The model is later extended to include aspects of the thioredoxin system, and oxidative pentose phosphate pathway. Much of the observed behaviour is consistent with experimental observation. In particular, Metabolic Control Analysis of the model shows that control of assimilation flux is likely to be shared between two enzymes, rubisco and sedoheptulose bisphosphotase (SBPase), and can readily be transferred between them. This appears to offer an explanation of experimental evidence, obtained by genetic manipulation, that both of these enzymes can exert high control over assimilation. A further finding is that the output fluxes from the cycle (to starch and the cytosol), show markedly different patterns of control from assimilation, and from each other. An novel observation in behaviour of the Calvin cycle model is that, under certain circumstances, particularly at low light levels, the model has two steady-states and can be induced to switch between them. Although this exact behaviour has not been described experimentally, published results show charecteristics suggesting the potential is there in vivo. An explanation of all the observed behaviour is proposed, based upon the topology of the model. If this is correct then it may be concluded that the qualitative behaviour observed in the model is to be expected in vivo, although the quantitative detail may vary considerably

Tensor Analyzing Powers for Quasi-Elastic Electron Scattering from Deuterium

We report on a first measurement of tensor analyzing powers in quasi-elastic electron-deuteron scattering at an average three-momentum transfer of 1.7 fm$^{-1}$. Data sensitive to the spin-dependent nucleon density in the deuteron were obtained for missing momenta up to 150 MeV/$c$ with a tensor polarized $^2$H target internal to an electron storage ring. The data are well described by a calculation that includes the effects of final-state interaction, meson-exchange and isobar currents, and leading-order relativistic contributions.Comment: 4 pages, 3 figure

Return to Sports and Physical Activity After Total and Unicondylar Knee Arthroplasty: A Systematic Review and Meta-Analysis

People today are living longer and want to remain active. While obesity is becoming an epidemic, the number of patients suffering from osteoarthritis (OA) is expected to grow exponentially in the coming decades. Patients with OA of the knee are progressively being restricted in their activities. Since a knee arthroplasty (KA) is a well accepted, cost-effective intervention to relieve pain, restore function and improve health-related quality of life, indications are expanding to younger and more active patients. However, evidence concerning return to sports (RTS) and physical activity (PA) after KA is sparse. Our aim was to systematically summarise the available literature concerning the extent to which patients can RTS and be physically active after total (TKA) and unicondylar knee arthroplasty (UKA), as well as the time it takes. PRISMA guidelines were followed and our study protocol was published online at PROSPERO under registration number CRD42014009370. Based on the keywords (and synonyms of) 'arthroplasty', 'sports' and 'recovery of function', the databases MEDLINE, Embase and SPORTDiscus up to January 5, 2015 were searched. Articles concerning TKA or UKA patients who recovered their sporting capacity, or intended to, were included and were rated by outcomes of our interest. Methodological quality was assessed using Quality in Prognosis Studies (QUIPS) and data extraction was performed using a standardised extraction form, both conducted by two independent investigators. Out of 1115 hits, 18 original studies were included. According to QUIPS, three studies had a low risk of bias. Overall RTS varied from 36 to 89% after TKA and from 75 to >100% after UKA. The meta-analysis revealed that participation in sports seems more likely after UKA than after TKA, with mean numbers of sports per patient postoperatively of 1.1-4.6 after UKA and 0.2-1.0 after TKA. PA level was higher after UKA than after TKA, but a trend towards lower-impact sports was shown after both TKA and UKA. Mean time to RTS after TKA and UKA was 13 and 12 weeks, respectively, concerning low-impact types of sports in more than 90 % of cases. Low- and higher-impact sports after both TKA and UKA are possible, but it is clear that more patients RTS (including higher-impact types of sports) after UKA than after TKA. However, the overall quality of included studies was limited, mainly because confounding factors were inadequately taken into account in most studie

Is there evidence for accelerated polyethylene wear in uncemented compared to cemented acetabular components? A systematic review of the literature

Joint arthroplasty registries show an increased rate of aseptic loosening in uncemented acetabular components as compared to cemented acetabular components. Since loosening is associated with particulate wear debris, we postulated that uncemented acetabular components demonstrate a higher polyethylene wear rate than cemented acetabular components in total hip arthroplasty. We performed a systematic review of the peer-reviewed literature, comparing the wear rate in uncemented and cemented acetabular components in total hip arthroplasty. Studies were identified using MEDLINE (PubMed), EMBASE and the Cochrane Central Register of Controlled Trials. Study quality was assessed using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach. The search resulted in 425 papers. After excluding duplicates and selection based on title and abstracts, nine studies were found eligible for further analysis: two randomised controlled trials, and seven observational studies. One randomised controlled trial found a higher polyethylene wear rate in uncemented acetabular components, while the other found no differences. Three out of seven observational studies showed a higher polyethylene wear in uncemented acetabular component fixation; the other four studies did not show any differences in wear rates. The available evidence suggests that a higher annual wear rate may be encountered in uncemented acetabular components as compared to cemented components

High-throughput cloning and expression in recalcitrant bacteria

We developed a generic method for high-throughput cloning in bacteria that are less amenable to conventional DNA manipulations. The method involves ligation-independent cloning in an intermediary Escherichia coli vector, which is rapidly converted via vector-backbone exchange (VBEx) into an organism-specific plasmid ready for high-efficiency transformation. We demonstrated VBEx proof of principle for Lactococcus lactis, but the method can be adapted to all organisms for which plasmids are available