A novel and robust method for counting components within bio-molecular complexes using fluorescence microscopy and statistical modelling

Cellular biology occurs through myriad interactions between diverse molecular components, many of which assemble in to specific complexes. Various techniques can provide a qualitative survey of which components are found in a given complex. However, quantitative analysis of the absolute number of molecules within a complex (known as stoichiometry) remains challenging. Here we provide a novel method that combines fluorescence microscopy and statistical modelling to derive accurate molecular counts. We have devised a system in which batches of a given biomolecule are differentially labelled with spectrally distinct fluorescent dyes (label A or B), and mixed such that B-labelled molecules are vastly outnumbered by those with label A. Complexes, containing this component, are then simply scored as either being positive or negative for label B. The frequency of positive complexes is directly related to the stoichiometry of interaction and molecular counts can be inferred by statistical modelling. We demonstrate this method using complexes of Adenovirus particles and monoclonal antibodies, achieving counts that are in excellent agreement with previous estimates. Beyond virology, this approach is readily transferable to other experimental systems and, therefore, provides a powerful tool for quantitative molecular biology

Using landscape topology to compare continuous metaheuristics: a framework and case study on EDAs and ridge structure

In this paper we extend a previously proposed randomized landscape generator in combination with a comparative experimental methodology to study the behavior of continuous metaheuristic optimization algorithms. In particular, we generate twodimensional landscapes with parameterized, linear ridge structure, and perform pairwise comparisons of algorithms to gain insight into what kind of problems are easy and difficult for one algorithm instance relative to another.We apply thismethodology to investigate the specific issue of explicit dependency modeling in simple continuous estimation of distribution algorithms. Experimental results reveal specific examples of landscapes (with certain identifiable features) where dependency modeling is useful, harmful, or has little impact on mean algorithm performance. Heat maps are used to compare algorithm performance over a large number of landscape instances and algorithm trials. Finally, we perform ameta-search in the landscape parameter space to find landscapes which maximize the performance between algorithms. The results are related to some previous intuition about the behavior of these algorithms, but at the same time lead to new insights into the relationship between dependency modeling in EDAs and the structure of the problem landscape. The landscape generator and overall methodology are quite general and extendable and can be used to examine specific features of other algorithms

Uremic cardiomyopathy is characterised by loss of the cardioprotective effects of insulin

Chronic kidney disease is associated with a unique cardiomyopathy, characterised by a combination of structural and cellular remodelling, and an enhanced susceptibility to ischaemia-reperfusion injury. This may represent dysfunction of the reperfusion injury salvage kinase pathway, due to insulin resistance. Aims: The susceptibility of the uraemic heart to ischaemia-reperfusion injury and the cardioprotective effects of insulin and rosiglitazone were investigated. Methods and Results: Uraemia was induced in Sprague-Dawley rats by subtotal nephrectomy. Functional recovery from ischaemia was investigated in vitro in control and uraemic hearts ±insulin ±rosiglitazone. The response of myocardial oxidative metabolism to insulin was determined by 13C NMR spectroscopy. Activation of reperfusion injury salvage kinase pathway intermediates (Akt and GSK3β) were assessed by SDS-PAGE and immuno-precipitation. Insulin improved post-ischaemic rate pressure product in control but not uraemic hearts, (recovered rate pressure product (%), control 59.6±10.7 vs 88.9±8.5, p<0.05; uraemic 19.3±4.6 vs 28.5±10.4, p=ns). Rosiglitazone resensitised uraemic hearts to insulin-mediated cardio-protection (recovered rate pressure product (%) 12.7±7.0 vs. 61.8±15.9, p<0.05). Myocardial carbohydrate metabolism remained responsive to insulin in uraemic hearts. Uraemia was associated with increased phosphorylation of Akt (1.00±0.08 vs. 1.31±0.11, p<0.05) in normoxia, but no change in post-ischaemic phosphorylation of Akt or GSK3β. Akt2 isoform expression was decreased post-ischaemia in uraemic hearts (p<0.05). Conclusion: Uraemia is associated with enhanced susceptibility to ischaemia-reperfusion injury and a loss of insulin-mediated cardio-protection, which can be restored by administration of rosiglitazone. Altered Akt2 expression in uraemic hearts post ischaemia-reperfusion and impaired activation of reperfusion injury salvage kinase pathway may underlie these findings

Near threshold eta meson production in the d+d->alpha+eta reaction

The d+d->alpha+eta reaction has been investigated near threshold using the ANKE facility at COSY-Juelich. Both total and differential cross sections have been measured at two excess energies, Q=2.6 MeV and 7.7 MeV, with a subthreshold measurement being undertaken at Q=-2.6 MeV to study the physical background. While consistent with isotropy at the lower energy, the angular distribution reveals a pronounced anisotropy at the higher one, indicating the presence of higher partial waves. Options for the decomposition into partial amplitudes and their consequences for determination of the s-wave eta-alpha scattering length are discussed.Comment: 8pp, fig.3 added, normalisation in eq.4.1 correcte

The Near-Threshold Production of Phi Mesons in pp Collisions

The pp->pp phi reaction has been studied at the Cooler Synchrotron COSY-Juelich, using the internal beam and ANKE facility. Total cross sections have been determined at three excess energies epsilon near the production threshold. The differential cross section closest to threshold at epsilon=18.5 MeV exhibits a clear S-wave dominance as well as a noticeable effect due to the proton-proton final state interaction. Taken together with data for pp omega-production, a significant enhancement of the phi/omega ratio of a factor 8 is found compared to predictions based on the Okubo-Zweig-Iizuka rule.Comment: 4 Pages, 3 Figures, 1 Table, submitted to Phys. Rev. Let

TVB-EduPack: An interactive learning and scripting platform for The Virtual Brain

The Virtual Brain (TVB; thevirtualbrain.org) is a neuroinformatics platform for full brain network simulation based on individual anatomical connectivity data. The framework addresses clinical and neuroscientific questions by simulating multi-scale neural dynamics that range from local population activity to large-scale brain function and related macroscopic signals like electroencephalography and functional magnetic resonance imaging. TVB is equipped with a graphical and a command-line interface to create models that capture the characteristic biological variability to predict the brain activity of individual subjects. To enable researchers from various backgrounds a quick start into TVB and brain network modeling in general, we developed an educational module: TVB-EduPack. EduPack offers two educational functionalities that seamlessly integrate into TVB's graphical user interface (GUI): (i) interactive tutorials introduce GUI elements, guide through the basic mechanics of software usage and develop complex use-case scenarios; animations, videos and textual descriptions transport essential principles of computational neuroscience and brain modeling; (ii) an automatic script generator records model parameters and produces input files for TVB's Python programming interface; thereby, simulation configurations can be exported as scripts that allow flexible customization of the modeling process and self-defined batch- and post-processing applications while benefitting from the full power of the Python language and its toolboxes. This article covers the implementation of TVB-EduPack and its integration into TVB architecture. Like TVB, EduPack is an open source community project that lives from the participation and contribution of its users. TVB-EduPack can be obtained as part of TVB from thevirtualbrain.org

Kaon Pair Production in Proton--Proton Collisions

The differential and total cross sections for kaon pair production in the pp->ppK+K- reaction have been measured at three beam energies of 2.65, 2.70, and 2.83 GeV using the ANKE magnetic spectrometer at the COSY-Juelich accelerator. These near-threshold data are separated into pairs arising from the decay of the phi-meson and the remainder. For the non-phi selection, the ratio of the differential cross sections in terms of the K-p and K+p invariant masses is strongly peaked towards low masses. This effect can be described quantitatively by using a simple ansatz for the K-p final state interaction, where it is seen that the data are sensitive to the magnitude of an effective K-p scattering length. When allowance is made for a small number of phi events where the K- rescatters from the proton, the phi region is equally well described at all three energies. A very similar phenomenon is discovered in the ratio of the cross sections as functions of the K-pp and K+pp invariant masses and the identical final state interaction model is also very successful here. The world data on the energy dependence of the non-phi total cross section is also reproduced, except possibly for the results closest to threshold.Comment: 12 two-column pages, 12 figures, 1 tabl

The production of K+K- pairs in proton-proton collisions at 2.83 GeV

Differential and total cross sections for the pp -> ppK+K- reaction have been measured at a proton beam energy of 2.83 GeV using the COSY-ANKE magnetic spectrometer. Detailed model descriptions fitted to a variety of one-dimensional distributions permit the separation of the pp -> pp phi cross section from that of non-phi production. The differential spectra show that higher partial waves represent the majority of the pp -> pp phi total cross section at an excess energy of 76 MeV, whose energy dependence would then seem to require some s-wave phi-p enhancement near threshold. The non-phi data can be described in terms of the combined effects of two-body final state interactions using the same effective scattering parameters determined from lower energy data.Comment: 12 pages, 12 figures, 3 table