Bioengineered Nisin A Derivatives with Enhanced Activity against Both Gram Positive and Gram Negative Pathogens

peer-reviewedNisin is a bacteriocin widely utilized in more than 50 countries as a safe and natural antibacterial food preservative. It is the most extensively studied bacteriocin, having undergone decades of bioengineering with a view to improving function and physicochemical properties. The discovery of novel nisin variants with enhanced activity against clinical and foodborne pathogens has recently been described. We screened a randomized bank of nisin A producers and identified a variant with a serine to glycine change at position 29 (S29G), with enhanced efficacy against S. aureus SA113. Using a site-saturation mutagenesis approach we generated three more derivatives (S29A, S29D and S29E) with enhanced activity against a range of Gram positive drug resistant clinical, veterinary and food pathogens. In addition, a number of the nisin S29 derivatives displayed superior antimicrobial activity to nisin A when assessed against a range of Gram negative food-associated pathogens, including E. coli, Salmonella enterica serovar Typhimurium and Cronobacter sakazakii. This is the first report of derivatives of nisin, or indeed any lantibiotic, with enhanced antimicrobial activity against both Gram positive and Gram negative bacteria.This work was supported by the Irish Government under the National Development Plan, through Science Foundation Ireland Investigator awards (10/IN.1/B3027) and (06/IN.1/B98) (http://www.sfi.ie)

Effect of the bound nucleon form factors on charged-current neutrino-nucleus scattering

We study the effect of bound nucleon form factors on charged-current neutrino-nucleus scattering. The bound nucleon form factors of the vector and axial-vector currents are calculated in the quark-meson coupling model. We compute the inclusive $^{12}$C($\nu_\mu,\mu^-$)$X$ cross sections using a relativistic Fermi gas model with the calculated bound nucleon form factors. The effect of the bound nucleon form factors for this reaction is a reduction of $\sim$8% for the total cross section, relative to that calculated with the free nucleon form factors.Comment: Latex, 11 pages, 3 figures, version to appear in Phys. Rev. C (Brief Report

Electron transport chains of lactic acid bacteria - walking on crutches is part of their lifestyle

A variety of lactic acid bacteria contain rudimentary electron transport chains that can be reconstituted by the addition of heme and menaquinone to the growth medium. These activated electron transport chains lead to higher biomass production and increased robustness, which is beneficial for industrial applications, but a major concern when dealing with pathogenic lactic acid bacteria

An extension of the coupled-cluster method: A variational formalism

A general quantum many-body theory in configuration space is developed by extending the traditional coupled cluter method (CCM) to a variational formalism. Two independent sets of distribution functions are introduced to evaluate the Hamiltonian expectation. An algebraic technique for calculating these distribution functions via two self-consistent sets of equations is given. By comparing with the traditional CCM and with Arponen's extension, it is shown that the former is equivalent to a linear approximation to one set of distribution functions and the later is equivalent to a random-phase approximation to it. In additional to these two approximations, other higher-order approximation schemes within the new formalism are also discussed. As a demonstration, we apply this technique to a quantum antiferromagnetic spin model.Comment: 15 pages. Submitted to Phys. Rev.

Conservation of connectivity of model-space effective interactions under a class of similarity transformation

Effective interaction operators usually act on a restricted model space and give the same energies (for Hamiltonian) and matrix elements (for transition operators etc.) as those of the original operators between the corresponding true eigenstates. Various types of effective operators are possible. Those well defined effective operators have been shown being related to each other by similarity transformation. Some of the effective operators have been shown to have connected-diagram expansions. It is shown in this paper that under a class of very general similarity transformations, the connectivity is conserved. The similarity transformation between hermitian and non-hermitian Rayleigh-Schr\"{o}dinger perturbative effective operators is one of such transformation and hence the connectivity can be deducted from each other.Comment: 12 preprint page

On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria

The origin of oxygenic photosynthesis in Cyanobacteria led to the rise of oxygen on Earth ~2.3 billion years ago, profoundly altering the course of evolution by facilitating the development of aerobic respiration and complex multicellular life. Here we report the genomes of 41 uncultured organisms related to the photosynthetic Cyanobacteria (class Oxyphotobacteria), including members of the class Melainabacteria and a new class of Cyanobacteria (class Sericytochromatia) that is basal to the Melainabacteria and Oxyphotobacteria. All members of the Melainabacteria and Sericytochromatia lack photosynthetic machinery, indicating that phototrophy was not an ancestral feature of the Cyanobacteria and that Oxyphotobacteria acquired the genes for photosynthesis relatively late in cyanobacterial evolution. We show that all three classes independently acquired aerobic respiratory complexes, supporting the hypothesis that aerobic respiration evolved after oxygenic photosynthesis

Intestinal microbiome landscaping : insight in community assemblage and implications for microbial modulation strategies

High individuality, large complexity and limited understanding of the mechanisms underlying human intestinal microbiome function remain the major challenges for designing beneficial modulation strategies. Exemplified by the analysis of intestinal bacteria in a thousand Western adults, we discuss key concepts of the human intestinal microbiome landscape, i.e. the compositional and functional 'core', the presence of community types and the existence of alternative stable states. Genomic investigation of core taxa revealed functional redundancy, which is expected to stabilize the ecosystem, as well as taxa with specialized functions that have the potential to shape the microbiome landscape. The contrast between Prevotella-and Bacteroides-dominated systems has been well described. However, less known is the effect of not so abundant bacteria, for example, Dialister spp. that have been proposed to exhibit distinct bistable dynamics. Studies employing time-series analysis have highlighted the dynamical variation in the microbiome landscape with and without the effect of defined perturbations, such as the use of antibiotics or dietary changes. We incorporate ecosystem-level observations of the human intestinal microbiota and its keystone species to suggest avenues for designing microbiome modulation strategies to improve host health.Peer reviewe

Conserving Gapless Mean-Field Theory for Bose-Einstein Condensates

We formulate a conserving gapless mean-field theory for Bose-Einstein condensates on the basis of a Luttinger-Ward thermodynamic functional. It is applied to a weakly interacting uniform gas with density $n$ and s-wave scattering length $a$ to clarify its fundamental thermodynamic properties. It is found that the condensation here occurs as a first-order transition. The shift of the transition temperature $\Delta T_c$ from the ideal-gas result $T_{0}$ is positive and given to the leading order by $\Delta T_c = 2.33a n^{1/3}T_0$, in agreement with a couple of previous estimates. The theory is expected to form a new theoretical basis for trapped Bose-Einstein condensates at finite temperatures.Comment: Minor errors remove