Potential Energy Surface for H_2 Dissociation over Pd(100)

The potential energy surface (PES) of dissociative adsorption of H_2 on Pd(100) is investigated using density functional theory and the full-potential linear augmented plane wave (FP-LAPW) method. Several dissociation pathways are identified which have a vanishing energy barrier. A pronounced dependence of the potential energy on ``cartwheel'' rotations of the molecular axis is found. The calculated PES shows no indication of the presence of a precursor state in front of the surface. Both results indicate that steering effects determine the observed decrease of the sticking coefficient at low energies of the H_2 molecules. We show that the topology of the PES is related to the dependence of the covalent H(s)-Pd(d) interactions on the orientation of the H_2 molecule.Comment: RevTeX, 8 pages, 5 figures in uufiles forma

High-dimensional quantum dynamics of adsorption and desorption of H2_2 at Cu(111)

We performed high-dimensional quantum dynamical calculations of the dissociative adsorption and associative desorption of hydrogen on Cu(111). The potential energy surface (PES) is obtained from density functional theory calculations. Two regimes of dynamics are found, at low energies sticking is determined by the minimum energy barrier, at high energies by the distribution of barrier heights. Experimental results are well-reproduced qualitatively, but some quantitative discrepancies are identified as well.Comment: 4 two column pages, revtex, 4 figures, to appear in Phys. Rev. Let

Predatory Bacteria: A Potential Ally against Multidrug-Resistant Gram-Negative Pathogens

Multidrug-resistant (MDR) Gram-negative bacteria have emerged as a serious threat to human and animal health. Bdellovibrio spp. and Micavibrio spp. are Gram-negative bacteria that prey on other Gram-negative bacteria. In this study, the ability of Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus to prey on MDR Gram-negative clinical strains was examined. Although the potential use of predatory bacteria to attack MDR pathogens has been suggested, the data supporting these claims is lacking. By conducting predation experiments we have established that predatory bacteria have the capacity to attack clinical strains of a variety of ß-lactamase-producing, MDR Gram-negative bacteria. Our observations indicate that predatory bacteria maintained their ability to prey on MDR bacteria regardless of their antimicrobial resistance, hence, might be used as therapeutic agents where other antimicrobial drugs fail. © 2013 Kadouri et al

Ab initio Quantum and ab initio Molecular Dynamics of the Dissociative Adsorption of Hydrogen on Pd(100)

The dissociative adsorption of hydrogen on Pd(100) has been studied by ab initio quantum dynamics and ab initio molecular dynamics calculations. Treating all hydrogen degrees of freedom as dynamical coordinates implies a high dimensionality and requires statistical averages over thousands of trajectories. An efficient and accurate treatment of such extensive statistics is achieved in two steps: In a first step we evaluate the ab initio potential energy surface (PES) and determine an analytical representation. Then, in an independent second step dynamical calculations are performed on the analytical representation of the PES. Thus the dissociation dynamics is investigated without any crucial assumption except for the Born-Oppenheimer approximation which is anyhow employed when density-functional theory calculations are performed. The ab initio molecular dynamics is compared to detailed quantum dynamical calculations on exactly the same ab initio PES. The occurence of quantum oscillations in the sticking probability as a function of kinetic energy is addressed. They turn out to be very sensitive to the symmetry of the initial conditions. At low kinetic energies sticking is dominated by the steering effect which is illustrated using classical trajectories. The steering effects depends on the kinetic energy, but not on the mass of the molecules. Zero-point effects lead to strong differences between quantum and classical calculations of the sticking probability. The dependence of the sticking probability on the angle of incidence is analysed; it is found to be in good agreement with experimental data. The results show that the determination of the potential energy surface combined with high-dimensional dynamical calculations, in which all relevant degrees of freedon are taken into account, leads to a detailed understanding of the dissociation dynamics of hydrogen at a transition metal surface.Comment: 15 pages, 9 figures, subm. to Phys. Rev.

Applying laboratory thermal desorption data in an interstellar context: sublimation of methanol thin films

Methods by which experimental measurements of thermal desorption can be applied in astrophysical environments have been developed, using the sublimation of solid methanol as an example. The temperature programmed desorption of methanol from graphitic, amorphous silica and polycrystalline gold substrates was compared, with the kinetic parameters of desorption extracted by either a leading edge analysis or by fitting using a stochastic integration method. At low coverages, the desorption shows a substrate-dependent fractional order. However, at higher coverages methanol desorption is zeroth order with kinetic parameters independent of substrate. Using a kinetic model based on the stochastic integration analyses, desorption under astrophysically relevant conditions can be simulated. We find that the chemical and morphological nature of the substrate has relatively little impact on the desorption temperature of solid methanol, and that the substrate independent zeroth-order kinetics can provide a satisfactory model for desorption in astrophysical environments. Uncertainties in the heating rate and the distribution of grain sizes will have the largest influence on the range of desorption temperature. These conclusions are likely to be generally applicable to all species in dust grain ice mantles

Comparison of the complete genome sequencesof Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04

Bifidobacteria are important members of the human gut flora, especially in infants. Comparative genomic analysis of two Bifidobacterium animalis subsp. lactis strains revealed evolution by internal deletion of consecutive spacer-repeat units within a novel clustered regularly interspaced short palindromic repeat locus, which represented the largest differential content between the two genomes. Additionally, 47 single nucleotide polymorphisms were identified, consisting primarily of nonsynonymous mutations, indicating positive selection and/or recent divergence. A particular nonsynonymous mutation in a putative glucose transporter was linked to a negative phenotypic effect on the ability of the variant to catabolize glucose, consistent with a modification in the predicted protein transmembrane topology. Comparative genome sequence analysis of three Bifidobacterium species provided a core genome set of 1,117 orthologs complemented by a pan-genome of 2,445 genes. The genome sequences of the intestinal bacterium B. animalis subsp. lactis provide insights into rapid genome evolution and the genetic basis for adaptation to the human gut environment, notably with regard to catabolism of dietary carbohydrates, resistance to bile and acid, and interaction with the intestinal epithelium. The high degree of genome conservation observed between the two strains in terms of size, organization, and sequence is indicative of a genomically monomorphic subspecies and explains the inability to differentiate the strains by standard techniques such as pulsed-field gel electrophoresis

Assessment of the Mobilizable Vector Plasmids pSUP202 and pSUP404.2 as Genetic Tools for the Predatory Bacterium Bdellovibrio bacteriovorus

Bdellovibrio and like organisms (BALOs) form the group of predatory bacteria which require Gram-negative bacteria as prey. Genetic studies with Bdellovibrio bacteriovorus can be performed with vectors which are introduced into the predator via conjugation. The usefulness of the two vectors pSUP202 and pSUP404.2 as genetic tools were assessed. Both vectors were transferable into B. bacteriovorus by conjugative matings with an Escherichia coli K12 strain as donor. The transfer frequency was higher for vector pSUP404.2 (approx. 10−1–10−4) as for pSUP202 (approx. 10−5–10−6). Vector pSUP202 with a pMB1 origin is unstable in the predatory bacterium, whereas pSUP404.2 is stably maintained in the absence of selective antibiotics. pSUP404.2 harbors two plasmid replicons, the p15A ori and the RSF1010 replication region The copy number of pSUP404.2 was determined by quantitative PCR in B. bacteriovorus and averages seven copies per genome. pSUP404.2 harbors two resistance genes (chloramphenicol and kanamycin) which can be used for cloning either by selection for transconjugants or by insertional inactivation

Mutation Detection with Next-Generation Resequencing through a Mediator Genome

The affordability of next generation sequencing (NGS) is transforming the field of mutation analysis in bacteria. The genetic basis for phenotype alteration can be identified directly by sequencing the entire genome of the mutant and comparing it to the wild-type (WT) genome, thus identifying acquired mutations. A major limitation for this approach is the need for an a-priori sequenced reference genome for the WT organism, as the short reads of most current NGS approaches usually prohibit de-novo genome assembly. To overcome this limitation we propose a general framework that utilizes the genome of relative organisms as mediators for comparing WT and mutant bacteria. Under this framework, both mutant and WT genomes are sequenced with NGS, and the short sequencing reads are mapped to the mediator genome. Variations between the mutant and the mediator that recur in the WT are ignored, thus pinpointing the differences between the mutant and the WT. To validate this approach we sequenced the genome of Bdellovibrio bacteriovorus 109J, an obligatory bacterial predator, and its prey-independent mutant, and compared both to the mediator species Bdellovibrio bacteriovorus HD100. Although the mutant and the mediator sequences differed in more than 28,000 nucleotide positions, our approach enabled pinpointing the single causative mutation. Experimental validation in 53 additional mutants further established the implicated gene. Our approach extends the applicability of NGS-based mutant analyses beyond the domain of available reference genomes

Ankyrin-mediated self-protection during cell invasion by the bacterial predator Bdellovibrio bacteriovorus

Predatory Bdellovibrio bacteriovorus are natural antimicrobial organisms, killing other bacteria by whole-cell invasion. Self-protection against prey-metabolizing enzymes is important for the evolution of predation. Initial prey entry involves the predator’s peptidoglycan DD-endopeptidases, which decrosslink cell walls and prevent wasteful entry by a second predator. Here we identify and characterize a self-protection protein from B. bacteriovorus, Bd3460, which displays an ankyrin-based fold common to intracellular pathogens of eukaryotes. Co-crystal structures reveal Bd3460 complexation of dual targets, binding a conserved epitope of each of the Bd3459 and Bd0816 endopeptidases. Complexation inhibits endopeptidase activity and cell wall decrosslinking in vitro. Self-protection is vital — DBd3460 Bdellovibrio deleteriously decrosslink self-peptidoglycan upon invasion, adopt a round morpholog, and lose predatory capacity and cellular integrity. Our analysis provides the first mechanistic examination of self-protection in Bdellovibrio, documents protection-multiplicity for products of two different genomic loci, and reveals an important evolutionary adaptation to an invasive predatory bacterial lifestyle