1,411 research outputs found
Quasi-circular Orbits for Spinning Binary Black Holes
Using an effective potential method we examine binary black holes where the
individual holes carry spin. We trace out sequences of quasi-circular orbits
and locate the innermost stable circular orbit as a function of spin. At large
separations, the sequences of quasi-circular orbits match well with
post-Newtonian expansions, although a clear signature of the simplifying
assumption of conformal flatness is seen. The position of the ISCO is found to
be strongly dependent on the magnitude of the spin on each black hole. At close
separations of the holes, the effective potential method breaks down. In all
cases where an ISCO could be determined, we found that an apparent horizon
encompassing both holes forms for separations well inside the ISCO.
Nevertheless, we argue that the formation of a common horizon is still
associated with the breakdown of the effective potential method.Comment: 13 pages, 10 figures, submitted to PR
Step size of the rotary proton motor in single FoF1-ATP synthase from a thermoalkaliphilic bacterium by DCO-ALEX FRET
Thermophilic enzymes can operate at higher temperatures but show reduced
activities at room temperature. They are in general more stable during
preparation and, accordingly, are considered to be more rigid in structure.
Crystallization is often easier compared to proteins from bacteria growing at
ambient temperatures, especially for membrane proteins. The ATP-producing
enzyme FoF1-ATP synthase from thermoalkaliphilic Caldalkalibacillus thermarum
strain TA2.A1 is driven by a Fo motor consisting of a ring of 13 c-subunits. We
applied a single-molecule F\"orster resonance energy transfer (FRET) approach
using duty cycle-optimized alternating laser excitation (DCO-ALEX) to monitor
the expected 13-stepped rotary Fo motor at work. New FRET transition histograms
were developed to identify the smaller step sizes compared to the 10-stepped Fo
motor of the Escherichia coli enzyme. Dwell time analysis revealed the
temperature and the LDAO dependence of the Fo motor activity on the single
molecule level. Back-and-forth stepping of the Fo motor occurs fast indicating
a high flexibility in the membrane part of this thermophilic enzyme.Comment: 14 pages, 7 figure
Assessment of the effectiveness of head only and back-of-the-head electrical stunning of chickens
The study assesses the effectiveness of reversible head-only and back-of-the-head electrical stunning of chickens using 130–950 mA per bird at 50 Hz AC
Collisions of boosted black holes: perturbation theory prediction of gravitational radiation
We consider general relativistic Cauchy data representing two nonspinning,
equal-mass black holes boosted toward each other. When the black holes are
close enough to each other and their momentum is sufficiently high, an
encompassing apparent horizon is present so the system can be viewed as a
single, perturbed black hole. We employ gauge-invariant perturbation theory,
and integrate the Zerilli equation to analyze these time-asymmetric data sets
and compute gravitational wave forms and emitted energies. When coupled with a
simple Newtonian analysis of the infall trajectory, we find striking agreement
between the perturbation calculation of emitted energies and the results of
fully general relativistic numerical simulations of time-symmetric initial
data.Comment: 5 pages (RevTex 3.0 with 3 uuencoded figures), CRSR-107
CydDC-mediated reductant export in Escherichia coli controls the transcriptional wiring of energy metabolism and combats nitrosative stress
The glutathione/cysteine exporter CydDC maintains redox balance in Escherichia coli. A cydD mutant strain was used to probe the influence of CydDC upon reduced thiol export, gene expression, metabolic perturbations, intracellular pH homeostasis, and tolerance to nitric oxide (NO). Loss of CydDC was found to decrease extracytoplasmic thiol levels, whereas overexpression diminished the cytoplasmic thiol content. Transcriptomic analysis revealed a dramatic up-regulation of protein chaperones, protein degradation (via phenylpropionate/phenylacetate catabolism), ?-oxidation of fatty acids, and genes involved in nitrate/nitrite reduction. 1H NMR metabolomics revealed elevated methionine and betaine and diminished acetate and NAD+ in cydD cells, which was consistent with the transcriptomics-based metabolic model. The growth rate and ?pH, however, were unaffected, although the cydD strain did exhibit sensitivity to the NO-releasing compound NOC-12. These observations are consistent with the hypothesis that the loss of CydDC-mediated reductant export promotes protein misfolding, adaptations to energy metabolism, and sensitivity to NO. The addition of both glutathione and cysteine to the medium was found to complement the loss of bd -type cytochrome synthesis in a cydD strain (a key component of the pleiotropic cydDC phenotype), providing the first direct evidence that CydDC substrates are able to restore the correct assembly of this respiratory oxidase. These data provide an insight into the metabolic flexibility of E. coli , highlight the importance of bacterial redox homeostasis during nitrosative stress, and report for the first time the ability of periplasmic low molecular weight thiols to restore haem incorporation into a cytochrome complex
Functional characterization of BcrR:a one-component transmembrane signal transduction system for bacitracin resistance
Bacitracin is a cell wall targeting antimicrobial with clinical and agricultural applications. With the growing mismatch between antimicrobial resistance and development, it is essential we understand the molecular mechanisms of resistance in order to prioritize and generate new effective antimicrobials. BcrR is a unique membrane-bound one-component system that regulates high-level bacitracin resistance in Enterococcus faecalis. In the presence of bacitracin, BcrR activates transcription of the bcrABD operon conferring resistance through a putative ATP-binding cassette (ABC) transporter (BcrAB). BcrR has three putative functional domains, an N-terminal helix-turn-helix DNA-binding domain, an intermediate oligomerization domain and a C-terminal transmembrane domain. However, the molecular mechanisms of signal transduction remain unknown. Random mutagenesis of bcrR was performed to generate loss- and gain-of-function mutants using transcriptional reporters fused to the target promoter PbcrA. Fifteen unique mutants were isolated across all three proposed functional domains, comprising 14 loss-of-function and one gain-of-function mutant. The gain-of-function variant (G64D) mapped to the putative dimerization domain of BcrR, and functional analyses indicated that the G64D mutant constitutively expresses the PbcrA-luxABCDE reporter. DNA-binding and membrane insertion were not affected in the five mutants chosen for further characterization. Homology modelling revealed putative roles for two key residues (R11 and S33) in BcrR activation. Here we present a new model of BcrR activation and signal transduction, providing valuable insight into the functional characterization of membrane-bound one-component systems and how they can coordinate critical bacterial responses, such as antimicrobial resistance.</p
Functional characterization of BcrR:a one-component transmembrane signal transduction system for bacitracin resistance
Bacitracin is a cell wall targeting antimicrobial with clinical and agricultural applications. With the growing mismatch between antimicrobial resistance and development, it is essential we understand the molecular mechanisms of resistance in order to prioritize and generate new effective antimicrobials. BcrR is a unique membrane-bound one-component system that regulates high-level bacitracin resistance in Enterococcus faecalis. In the presence of bacitracin, BcrR activates transcription of the bcrABD operon conferring resistance through a putative ATP-binding cassette (ABC) transporter (BcrAB). BcrR has three putative functional domains, an N-terminal helix-turn-helix DNA-binding domain, an intermediate oligomerization domain and a C-terminal transmembrane domain. However, the molecular mechanisms of signal transduction remain unknown. Random mutagenesis of bcrR was performed to generate loss- and gain-of-function mutants using transcriptional reporters fused to the target promoter PbcrA. Fifteen unique mutants were isolated across all three proposed functional domains, comprising 14 loss-of-function and one gain-of-function mutant. The gain-of-function variant (G64D) mapped to the putative dimerization domain of BcrR, and functional analyses indicated that the G64D mutant constitutively expresses the PbcrA-luxABCDE reporter. DNA-binding and membrane insertion were not affected in the five mutants chosen for further characterization. Homology modelling revealed putative roles for two key residues (R11 and S33) in BcrR activation. Here we present a new model of BcrR activation and signal transduction, providing valuable insight into the functional characterization of membrane-bound one-component systems and how they can coordinate critical bacterial responses, such as antimicrobial resistance.</p
A new type of Na+-driven ATP synthase membrane rotor with a two-carboxylate ion-coupling motif
Abstract: The anaerobic bacterium Fusobacterium nucleatum uses glutamate decarboxylation to generate a transmembrane gradient of Na+. Here, we demonstrate that this ion-motive force is directly coupled to ATP synthesis, via an F1Fo-ATP synthase with a novel Na+ recognition motif, shared by other human pathogens. Molecular modeling and free-energy simulations of the rotary element of the enzyme, the c-ring, indicate Na+ specificity in physiological settings. Consistently, activity measurements showed Na+ stimulation of the enzyme, either membrane-embedded or isolated, and ATP synthesis was sensitive to the Na+ ionophore monensin. Furthermore, Na+ has a protective effect against inhibitors targeting the ion-binding sites, both in the complete ATP synthase and the isolated c-ring. Definitive evidence of Na+ coupling is provided by two identical crystal structures of the c11 ring, solved by X-ray crystallography at 2.2 and 2.6 Ã… resolution, at pH 5.3 and 8.7, respectively. Na+ ions occupy all binding sites, each coordinated by four amino acids and a water molecule. Intriguingly, two carboxylates instead of one mediate ion binding. Simulations and experiments demonstrate that this motif implies that a proton is concurrently bound to all sites, although Na+ alone drives the rotary mechanism. The structure thus reveals a new mode of ion coupling in ATP synthases and provides a basis for drug-design efforts against this opportunistic pathogen.
Author Summary: Essential cellular processes such as biosynthesis, transport, and motility are sustained by the energy released in the hydrolysis of ATP, the universal energy carrier in living cells. Most ATP in the cell is produced by a membrane-bound enzyme, the ATP synthase, through a rotary mechanism that is coupled to the translocation of ions across the membrane. The majority of ATP synthases are energized by transmembrane electrochemical gradients of protons (proton-motive force), but a number of organisms, including some important human pathogens, use gradients of sodium ions instead (sodium-motive force). The ion specificity of ATP synthases is determined by a membrane-embedded sub-complex, the c-ring, which is the smallest known biological rotor. The functional mechanism of the rotor ring and its variations among different organisms are of wide interest, because of this enzyme's impact on metabolism and disease, and because of its potential for nanotechnology applications. Here, we characterize a previously unrecognized type of Na+-driven ATP synthase from the opportunistic human pathogen Fusobacterium nucleatum, which is implicated in periodontal diseases. We analyzed this ATP synthase and its rotor ring through a multi-disciplinary approach, combining cell-growth and biochemical assays, X-ray crystallography and computer-simulation methods. Two crystal structures of the membrane rotor were solved, at low and high pH, revealing an atypical ion-recognition motif mediated by two carboxylate side-chains. This motif is shared by other human pathogens, such as Mycobacterium tuberculosis or Streptococcus pneumonia, whose ATP synthases are targets of novel antibiotic drugs. The implications of this ion-recognition mode on the mechanism of the ATP synthase and the cellular bioenergetics of F. nucleatum were thus examined. Our results provide the basis for future pharmacological efforts against this important pathogen
Solving Einstein's equations for rotating spacetimes: Evolution of relativistic star clusters
A numerical relativity code designed to evolve rotating axisymmetric spacetimes is constructed. Both polarization states of gravitational radiation can be tracked. The source of the gravitational field is chosen to be a configuration of collisionless particles. The code is used to evaluate the stability of polytropic and toroidal star clusters. The formation of Kerr black holes by the collapse of unstable clusters is demonstrated. Unstable clusters with J/(M^2) 1 collapse to new equilibrium configurations
Excision boundary conditions for black hole initial data
We define and extensively test a set of boundary conditions that can be
applied at black hole excision surfaces when the Hamiltonian and momentum
constraints of general relativity are solved within the conformal thin-sandwich
formalism. These boundary conditions have been designed to result in black
holes that are in quasiequilibrium and are completely general in the sense that
they can be applied with any conformal three-geometry and slicing condition.
Furthermore, we show that they retain precisely the freedom to specify an
arbitrary spin on each black hole. Interestingly, we have been unable to find a
boundary condition on the lapse that can be derived from a quasiequilibrium
condition. Rather, we find evidence that the lapse boundary condition is part
of the initial temporal gauge choice. To test these boundary conditions, we
have extensively explored the case of a single black hole and the case of a
binary system of equal-mass black holes, including the computation of
quasi-circular orbits and the determination of the inner-most stable circular
orbit. Our tests show that the boundary conditions work well.Comment: 23 pages, 23 figures, revtex4, corrected typos, added reference,
minor content changes including additional post-Newtonian comparison. Version
accepted by PR
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