Analysis of transient phosphorylation-dependent protein-protein interactions in living mammalian cells using split-TEV

Abstract Background Regulated protein-protein interactions (PPIs) are pivotal molecular switches that are important for the regulation of signaling processes within eukaryotic cells. Cellular signaling is altered in various disease conditions and offers interesting options for pharmacological interventions. Constitutive PPIs are usually mediated by large interaction domains. In contrast, stimulus-regulated PPIs often depend on small post-translational modifications and are thus better suited targets for drug development. However, the detection of modification-dependent PPIs with biochemical methods still remains a labour- and material-intensive task, and many pivotal PPIs that are potentially suited for pharmacological intervention most likely remain to be identified. The availability of methods to easily identify and quantify stimulus-dependent, potentially also transient interaction events, is therefore essential. The assays should be applicable to intact mammalian cells, optimally also to primary cells in culture. Results In this study, we adapted the split-TEV system to quantify phosphorylation-dependent and transient PPIs that occur at the membrane and in the cytosol of living mammalian cells. Split-TEV is based on a PPI-induced functional complementation of two inactive TEV protease fragments fused to interaction partners of choice. Genetically encoded transcription-coupled and proteolysis-only TEV reporter systems were used to convert the TEV activity into an easily quantifiable readout. We measured the phosphorylation-dependent interaction between the pro-apoptotic protein Bad and the adapter proteins 14-3-3ε and ζ in NIH-3T3 fibroblasts and in primary cultured neurons. Using split-TEV assays, we show that Bad specifically interacts with 14-3-3 isoforms when phosphorylated by protein kinase Akt-1/PKB at Ser136. We also measured the phosphorylation-dependent Bad/14-3-3 interactions mediated by endogenous and transient Akt-1 activity. We furthermore applied split-TEV assays to measure the phosphorylation-dependent interactions of Neuregulin-1-stimulated ErbB4 receptors with several adapter proteins. Conclusion Split-TEV assays are well suited to measure phosphorylation-dependent and transient PPIs that occur specifically at the membrane and in the cytosol of heterologous and primary cultured mammalian cells. Given the high sensitivity of the split-TEV system, all assays were performed in multi-plate formats and could be adapted for higher throughput to screen for pharmacologically active substances.</p

Linearity of cortical receptive fields measured with natural sounds

How do cortical neurons represent the acoustic environment? This question is often addressed by probing with simple stimuli such as clicks or tone pips. Such stimuli have the advantage of yielding easily interpreted answers, but have the disadvantage that they may fail to uncover complex or higher-order neuronal response properties. Here, we adopt an alternative approach, probing neuronal responses with complex acoustic stimuli, including animal vocalizations. We used in vivo whole-cell methods in the rat auditory cortex to record subthreshold membrane potential fluctuations elicited by these stimuli. Most neurons responded robustly and reliably to the complex stimuli in our ensemble. Using regularization techniques, we estimated the linear component, the spectrotemporal receptive field (STRF), of the transformation from the sound (as represented by its time-varying spectrogram) to the membrane potential of the neuron. We find that the STRF has a rich dynamical structure, including excitatory regions positioned in general accord with the prediction of the classical tuning curve. However, whereas the STRF successfully predicts the responses to some of the natural stimuli, it surprisingly fails completely to predict the responses to others; on average, only 11% of the response power could be predicted by the STRF. Therefore, most of the response of the neuron cannot be predicted by the linear component, although the response is deterministically related to the stimulus. Analysis of the systematic errors of the STRF model shows that this failure cannot be attributed to simple nonlinearities such as adaptation to mean intensity, rectification, or saturation. Rather, the highly nonlinear response properties of auditory cortical neurons must be attributable to nonlinear interactions between sound frequencies and time-varying properties of the neural encoder

Primary gas thermometry by means of laser-absorption spectroscopy: Determination of the Boltzmann constant

We report on a new optical implementation of primary gas thermometry based on laser absorption spectrometry in the near infrared. The method consists in retrieving the Doppler broadening from highly accurate observations of the line shape of the R(12) $\nu_{1} + 2 \nu_{2}^{\phantom{1}0} + \nu_{3}$ transition in CO$_{2}$ gas at thermodynamic equilibrium. Doppler width measurements as a function of gas temperature, ranging between the triple point of water and the gallium melting point, allowed for a spectroscopic determination of the Boltzmann constant with a relative accuracy of $\sim1.6\times10^{-4}$.Comment: Submitted to Physical Review Letter

Epistemic Uncertainty: A Problematic Component of Justifications for the Continued Use of Drone Strikes

The purpose of this paper is to present an objection to justifications for the continued use of drone strikes. This objection requires an examination of the fundamental aspects of the drone strike process. Considerations of strike authorization, outcome assessment, and intelligence gathering reveal deficiencies that contribute to the problematic status of the act. Arguments intended to justify the use of drone strikes rely on an analysis of outcomes that is impossible to satisfactorily apply to an evaluation of the tactic. These justifications are wholly insufficient on the grounds that we do not truly understand the nature of the use of drone strikes. The problematic nature of these justifications is fostered by a disabling epistemic uncertainty concerning the true nature of the act. In order to satisfactorily evaluate an act, the essential features of the act must be understood. Without a sufficient understanding of these features, it is impossible to produce a satisfactory justification of the act. The epistemic uncertainty inherent to the practice of employing drone strikes implies that a satisfactory determination of their status is impossible to achieve, and that the act is entirely unjustifiable

Ground State Energy of the One-Dimensional Discrete Random Schr\"{o}dinger Operator with Bernoulli Potential

In this paper, we show the that the ground state energy of the one dimensional Discrete Random Schroedinger Operator with Bernoulli Potential is controlled asymptotically as the system size N goes to infinity by the random variable \ell_N, the length the longest consecutive sequence of sites on the lattice with potential equal to zero. Specifically, we will show that for almost every realization of the potential the ground state energy behaves asymptotically as $\frac{\pi^2}{\ell_N+1)^2}$ in the sense that the ratio of the quantities goes to one