Ubiquitin-based probes prepared by total synthesis to profile the activity of deubiquitinating enzymes

Epitope-tagged active-site-directed probes are widely used to visualize the activity of deubiquitinases (DUBs) in cell extracts, to investigate the specificity and potency of small-molecule DUB inhibitors, and to isolate and identify DUBs by mass spectrometry. With DUBs arising as novel potential drug targets, probes are required that can be produced in sufficient amounts and to meet the specific needs of a given experiment. The established method for the generation of DUB probes makes use of labor-intensive intein-based methods that have inherent limitations concerning the incorporation of unnatural amino acids and the amount of material that can be obtained. Here, we describe the total chemical synthesis of active-site-directed probes and their application to activity-based profiling and identification of functional DUBs. This synthetic methodology allowed the easy incorporation of desired tags for specific applications, for example, fluorescent reporters, handles for immunoprecipitation or affinity pull-down, and cleavable linkers. Additionally, the synthetic method can be scaled up to provide significant amounts of probe. Fluorescent ubiquitin probes allowed faster, in-gel detection of active DUBs, as compared to (immuno)blotting procedures. A biotinylated probe holding a photocleavable linker enabled the affinity pull-down and subsequent mild, photorelease of DUBs. Also, DUB activity levels were monitored in response to overexpression or knockdown, and to inhibition by small molecules. Furthermore, fluorescent probes revealed differential DUB activity profiles in a panel of lung and prostate cancer cells

Glauber Critical Dynamics: Exact Solution of the Kinetic Gaussian Model

In this paper, we have exactly solved Glauber critical dynamics of the Gaussian model on three dimensions. Of course, it is much easy to apply to low dimensional case. The key steps are that we generalize the spin change mechanism from Glauber's single-spin flipping to single-spin transition and give a normalized version of the transition probability . We have also investigated the dynamical critical exponent and found surprisingly that the dynamical critical exponent is highly universal which refer to that for one- two- and three-dimensions they have same value independent of spatial dimensionality in contrast to static (equilibrium) critical exponents.Comment: 9 page

Solvable Kinetic Gaussian Model in External Field

In this paper, the single-spin transition dynamics is used to investigate the kinetic Gaussian model in a periodic external field. We first derive the fundamental dynamic equations, and then treat an isotropic d-dimensional hypercubic lattice Gaussian spin system with Fourier's transformation method. We obtain exactly the local magnetization and the equal-time pair correlation function. The critical characteristics of the dynamical, the complex susceptibility, and the dynamical response are discussed. The results show that the time evolution of the dynamical quantities and the dynamical responses of the system strongly depend on the frequency and the wave vector of the external field.Comment: 11 page

'A habitual disposition to the good': on reason, virtue and realism

Amidst the crisis of instrumental reason, a number of contemporary political philosophers including Jürgen Habermas have sought to rescue the project of a reasonable humanism from the twin threats of religious fundamentalism and secular naturalism. In his recent work, Habermas defends a post-metaphysical politics that aims to protect rationality against encroachment while also accommodating religious faith within the public sphere. This paper contends that Habermas’ post-metaphysical project fails to provide a robust alternative either to the double challenge of secular naturalism and religious fundamentalism or to the ruthless instrumentalism that underpins capitalism. By contrast with Habermas and also with the ‘new realism’ of contemporary political philosophers such as Raymond Geuss or Bernard Williams, realism in the tradition of Plato and Aristotle can defend reason against instrumental rationality and blind belief by integrating it with habit, feeling and even faith. Such metaphysical–political realism can help develop a politics of virtue that goes beyond communitarian thinking by emphasising plural modes of association (not merely ‘community’), substantive ties of sympathy and the importance of pursuing goodness and mutual flourishing

Barking up the same tree: a comparison of ethnomedicine and canine ethnoveterinary medicine among the Aguaruna

<p>Abstract</p> <p>Background</p> <p>This work focuses on plant-based preparations that the Aguaruna Jivaro of Peru give to hunting dogs. Many plants are considered to improve dogs' sense of smell or stimulate them to hunt better, while others treat common illnesses that prevent dogs from hunting. This work places canine ethnoveterinary medicine within the larger context of Aguaruna ethnomedicine, by testing the following hypotheses: H1 -- Plants that the Aguaruna use to treat dogs will be the same plants that they use to treat people and H2 -- Plants that are used to treat both people and dogs will be used for the same illnesses in both cases.</p> <p>Methods</p> <p>Structured interviews with nine key informants were carried out in 2007, in Aguaruna communities in the Peruvian department of Amazonas. Informants provided freelists of plants given to dogs and explained the purpose, preparation and route of administration used. For each plant, informants also described any uses for treating people. Botanical voucher specimens were collected and additional informal observations were made, accompanying people on hunting trips.</p> <p>Results</p> <p>Out of 35 plant species given to dogs, 29 (83%) are also given to humans for some medicinal purpose, while five are used only for dogs. However, the same plant is used to treat the same illness in both humans and dogs in only 53% of the cases. Forty-three percent of plants used to treat a particular illness for both dogs and people are administered in the same manner for both.</p> <p>Conclusion</p> <p>Results suggest that Aguaruna canine ethnoveterinary medicine is, at least partly, an independent cognitive domain. Some of the difference in plant use between dogs and people can be explained by the fact that certain diseases mentioned only apply to dogs. Although reports of canine ethnoveterinary medicine are very sparse in the literature, Aguaruna practices show some similarities with a few trends reported for other Amazonian societies, particularly, in the prevalence of the nasal route of administration, the use of plant-based psychoactives and in the importance of ants and wasps, in some form, for training dogs.</p

Watchfully checking rapport with the Primary Child Health Care nurses - a theoretical model from the perspective of parents of foreign origin

<p>Abstract</p> <p>Background</p> <p>Worldwide, multicultural interaction within health care seems to be challenging and problematic. This is also true among Primary Child Health Care nurses (PCHC nurses) in the Swedish Primary Child Health Care services (PCHC services). Therefore, there was a need to investigate the parents' perspective in-depth.</p> <p>Aim</p> <p>The aim of the study was to construct a theoretical model that could promote further understanding of the variety of experiences of parents of foreign origin regarding their interaction with the PCHC nurses at PCHC services.</p> <p>Method</p> <p>The study used Grounded Theory Methodology. Twenty-one parents of foreign origin in contact with PCHC servicies were interviewed.</p> <p>Results</p> <p>In our study parents were watchfully checking rapport, i.e. if they could perceive sympathy and understanding from the PCHC nurses. This was done by checking the nurse's demeanour and signs of judgement. From these interviews we created a theoretical model illustrating the interactive process between parents and PCHC nurses.</p> <p>Conclusion</p> <p>We found it to be of utmost importance for parents to be certain that it was possible to establish rapport with the PCHC nurse. If not, disruptions in the child's attendance at PCHC services could result. PCHC nurses can use the theoretical model resulting from this study as a basis for understanding parents, avoiding a demeanour and judgements that may cause misunderstandings thus promoting high-quality interaction in PCHC services.</p

Tight-binding parameters for charge transfer along DNA

We systematically examine all the tight-binding parameters pertinent to charge transfer along DNA. The $\pi$ molecular structure of the four DNA bases (adenine, thymine, cytosine, and guanine) is investigated by using the linear combination of atomic orbitals method with a recently introduced parametrization. The HOMO and LUMO wavefunctions and energies of DNA bases are discussed and then used for calculating the corresponding wavefunctions of the two B-DNA base-pairs (adenine-thymine and guanine-cytosine). The obtained HOMO and LUMO energies of the bases are in good agreement with available experimental values. Our results are then used for estimating the complete set of charge transfer parameters between neighboring bases and also between successive base-pairs, considering all possible combinations between them, for both electrons and holes. The calculated microscopic quantities can be used in mesoscopic theoretical models of electron or hole transfer along the DNA double helix, as they provide the necessary parameters for a tight-binding phenomenological description based on the $\pi$ molecular overlap. We find that usually the hopping parameters for holes are higher in magnitude compared to the ones for electrons, which probably indicates that hole transport along DNA is more favorable than electron transport. Our findings are also compared with existing calculations from first principles.Comment: 15 pages, 3 figures, 7 table

Reinventing grounded theory: some questions about theory, ground and discovery

Grounded theory’s popularity persists after three decades of broad-ranging critique. In this article three problematic notions are discussed—‘theory,’ ‘ground’ and ‘discovery’—which linger in the continuing use and development of grounded theory procedures. It is argued that far from providing the epistemic security promised by grounded theory, these notions—embodied in continuing reinventions of grounded theory—constrain and distort qualitative inquiry, and that what is contrived is not in fact theory in any meaningful sense, that ‘ground’ is a misnomer when talking about interpretation and that what ultimately materializes following grounded theory procedures is less like discovery and more akin to invention. The procedures admittedly provide signposts for qualitative inquirers, but educational researchers should be wary, for the significance of interpretation, narrative and reflection can be undermined in the procedures of grounded theory

Thermodynamic characteristics of the classical n-vector magnetic model in three dimensions

The method of calculating the free energy and thermodynamic characteristics of the classical n-vector three-dimensional (3D) magnetic model at the microscopic level without any adjustable parameters is proposed. Mathematical description is perfomed using the collective variables (CV) method in the framework of the $\rho^4$ model approximation. The exponentially decreasing function of the distance between the particles situated at the N sites of a simple cubic lattice is used as the interaction potential. Explicit and rigorous analytical expressions for entropy,internal energy, specific heat near the phase transition point as functions of the temperature are obtained. The dependence of the amplitudes of the thermodynamic characteristics of the system for $T>T_c$ and $T<T_c$ on the microscopic parameters of the interaction potential are studied for the cases $n=1,2,3$ and $n\to\infty$. The obtained results provide the basis for accurate analysis of the critical behaviour in three dimensions including the nonuniversal characteristics of the system.Comment: 25 pages, 5 figure