Discovery and characterization of a putrescine oxidase from Rhodococcus erythropolis NCIMB 11540

A gene encoding a putrescine oxidase (PuO(Rh), EC 1.4.3.10) was identified from the genome of Rhodococcus erythropolis NCIMB 11540. The gene was cloned in the pBAD vector and overexpressed at high levels in Escherichia coli. The purified enzyme was shown to be a soluble dimeric flavoprotein consisting of subunits of 50 kDa and contains non-covalently bound flavin adenine dinucleotide as a cofactor. From all substrates, the highest catalytic efficiency was found with putrescine (K(M) = 8.2 μM, k(cat) = 26 s(−1)). PuO(Rh) accepts longer polyamines, while short diamines and monoamines strongly inhibit activity. PuO(Rh) is a reasonably thermostable enzyme with t(1/2) at 50°C of 2 h. Based on the crystal structure of human monoamine oxidase B, we constructed a model structure of PuO(Rh), which hinted to a crucial role of Glu324 for substrate binding. Mutation of this residue resulted in a drastic drop (five orders of magnitude) in catalytic efficiency. Interestingly, the mutant enzyme showed activity with monoamines, which are not accepted by wt-PuO(Rh). ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00253-007-1310-4) contains supplementary material, which is available to authorized users

Improving membrane based multiplex immunoassays for semi-quantitative detection of multiple cytokines in a single sample

BACKGROUND: Inflammatory mediators can serve as biomarkers for the monitoring of the disease progression or prognosis in many conditions. In the present study we introduce an adaptation of a membrane-based technique in which the level of up to 40 cytokines and chemokines can be determined in both human and rodent blood in a semi-quantitative way. The planar assay was modified using the LI-COR (R) detection system (fluorescence based) rather than chemiluminescence and semi-quantitative outcomes were achieved by normalizing the outcomes using the automated exposure settings of the Odyssey readout device. The results were compared to the gold standard assay, namely ELISA. RESULTS: The improved planar assay allowed the detection of a considerably higher number of analytes (n = 30 and n = 5 for fluorescent and chemiluminescent detection, respectively). The improved planar method showed high sensitivity up to 17 pg/ml and a linear correlation of the normalized fluorescence intensity with the results from the ELISA (r = 0.91). CONCLUSIONS: The results show that the membrane-based technique is a semi-quantitative assay that correlates satisfactorily to the gold standard when enhanced by the use of fluorescence and subsequent semi-quantitative analysis. This promising technique can be used to investigate inflammatory profiles in multiple conditions, particularly in studies with constraints in sample sizes and/or budget

Persistent anti-brane singularities

Anti-D-branes inserted in warped throat geometries (supported by fluxes that carry D-brane charges) develop unphysical singularities. It has been argued that these singularities could be resolved when one goes beyond the linearized approximation or includes the effects of brane polarization. In this paper we consider anti-D6 branes, whose singularities have been shown to exist at the full non-linear level, and demonstrate that there is no D8 brane polarization that can resolve the singularity. We comment on the potential implications of this result for the resolution of anti-D3 brane singularities in the Klebanov-Strassler geometry.Comment: 16 pages; v2: comments added, version to appear in JHE

Smeared versus localised sources in flux compactifications

We investigate whether vacuum solutions in flux compactifications that are obtained with smeared sources (orientifolds or D-branes) still survive when the sources are localised. This seems to rely on whether the solutions are BPS or not. First we consider two sets of BPS solutions that both relate to the GKP solution through T-dualities: (p+1)-dimensional solutions from spacetime-filling Op-planes with a conformally Ricci-flat internal space, and p-dimensional solutions with Op-planes that wrap a 1-cycle inside an everywhere negatively curved twisted torus. The relation between the solution with smeared orientifolds and the localised version is worked out in detail. We then demonstrate that a class of non-BPS AdS_4 solutions that exist for IASD fluxes and with smeared D3-branes (or analogously for ISD fluxes with anti-D3-branes) does not survive the localisation of the (anti) D3-branes. This casts doubts on the stringy consistency of non-BPS solutions that are obtained in the limit of smeared sources.Comment: 23 pages; v2: minor corrections, added references, version published in JHE

The non-equilibrium response of the critical Ising model: Universal scaling properties and Local Scale Invariance

Motivated by recent numerical findings [M. Henkel, T. Enss, and M. Pleimling, J. Phys. A: Math. Gen. 39 (2006) L589] we re-examine via Monte Carlo simulations the linear response function of the two-dimensional Ising model with Glauber dynamics quenched to the critical point. At variance with the results of Henkel et al., we detect discrepancies between the actual scaling behavior of the response function and the prediction of Local Scale Invariance. Such differences are clearly visible in the impulse autoresponse function, whereas they are drastically reduced in integrated response functions. Accordingly, the scaling form predicted on the basis of Local Scale Invariance simply provides an accurate fitting form for some quantities but cannot be considered to be exact.Comment: 25 pages, 4 figure

Eight grand challenges in socio-environmental systems modeling

Modeling is essential to characterize and explore complex societal and environmental issues in systematic and collaborative ways. Socio-environmental systems (SES) modeling integrates knowledge and perspectives into conceptual and computational tools that explicitly recognize how human decisions affect the environment. Depending on the modeling purpose, many SES modelers also realize that involvement of stakeholders and experts is fundamental to support social learning and decision-making processes for achieving improved environmental and social outcomes. The contribution of this paper lies in identifying and formulating grand challenges that need to be overcome to accelerate the development and adaptation of SES modeling. Eight challenges are delineated: bridging epistemologies across disciplines; multi-dimensional uncertainty assessment and management; scales and scaling issues; combining qualitative and quantitative methods and data; furthering the adoption and impacts of SES modeling on policy; capturing structural changes; representing human dimensions in SES; and leveraging new data types and sources. These challenges limit our ability to effectively use SES modeling to provide the knowledge and information essential for supporting decision making. Whereas some of these challenges are not unique to SES modeling and may be pervasive in other scientific fields, they still act as barriers as well as research opportunities for the SES modeling community. For each challenge, we outline basic steps that can be taken to surmount the underpinning barriers. Thus, the paper identifies priority research areas in SES modeling, chiefly related to progressing modeling products, processes and practices

The problematic backreaction of SUSY-breaking branes

In this paper we investigate the localisation of SUSY-breaking branes which, in the smeared approximation, support specific non-BPS vacua. We show, for a wide class of boundary conditions, that there is no flux vacuum when the branes are described by a genuine delta-function. Even more, we find that the smeared solution is the unique solution with a regular brane profile. Our setup consists of a non-BPS AdS_7 solution in massive IIA supergravity with smeared anti-D6-branes and fluxes T-dual to ISD fluxes in IIB supergravity.Comment: 27 pages, Latex2e, 5 figure