882 research outputs found

    Rapid degradation of FAD following lysis of Neurospora crassa cells: Consequences for evaluation of flavin composition in vivo.

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    Rapid degradation of FAD following lysis of Neurospora crassa cells: Consequences for evaluation of flavin composition in vivo

    A computational framework to emulate the human perspective in flow cytometric data analysis

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    Background: In recent years, intense research efforts have focused on developing methods for automated flow cytometric data analysis. However, while designing such applications, little or no attention has been paid to the human perspective that is absolutely central to the manual gating process of identifying and characterizing cell populations. In particular, the assumption of many common techniques that cell populations could be modeled reliably with pre-specified distributions may not hold true in real-life samples, which can have populations of arbitrary shapes and considerable inter-sample variation. <p/>Results: To address this, we developed a new framework flowScape for emulating certain key aspects of the human perspective in analyzing flow data, which we implemented in multiple steps. First, flowScape begins with creating a mathematically rigorous map of the high-dimensional flow data landscape based on dense and sparse regions defined by relative concentrations of events around modes. In the second step, these modal clusters are connected with a global hierarchical structure. This representation allows flowScape to perform ridgeline analysis for both traversing the landscape and isolating cell populations at different levels of resolution. Finally, we extended manual gating with a new capacity for constructing templates that can identify target populations in terms of their relative parameters, as opposed to the more commonly used absolute or physical parameters. This allows flowScape to apply such templates in batch mode for detecting the corresponding populations in a flexible, sample-specific manner. We also demonstrated different applications of our framework to flow data analysis and show its superiority over other analytical methods. <p/>Conclusions: The human perspective, built on top of intuition and experience, is a very important component of flow cytometric data analysis. By emulating some of its approaches and extending these with automation and rigor, flowScape provides a flexible and robust framework for computational cytomics

    PIP3-dependent macropinocytosis is incompatible with chemotaxis

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    In eukaryotic chemotaxis, the mechanisms connecting external signals to the motile apparatus remain unclear. The role of the lipid phosphatidylinositol 3,4,5-trisphosphate (PIP3) has been particularly controversial. PIP3 has many cellular roles, notably in growth control and macropinocytosis as well as cell motility. Here we show that PIP3 is not only unnecessary for Dictyostelium discoideum to migrate toward folate, but actively inhibits chemotaxis. We find that macropinosomes, but not pseudopods, in growing cells are dependent on PIP3. PIP3 patches in these cells show no directional bias, and overall only PIP3-free pseudopods orient up-gradient. The pseudopod driver suppressor of cAR mutations (SCAR)/WASP and verprolin homologue (WAVE) is not recruited to the center of PIP3 patches, just the edges, where it causes macropinosome formation. Wild-type cells, unlike the widely used axenic mutants, show little macropinocytosis and few large PIP3 patches, but migrate more efficiently toward folate. Tellingly, folate chemotaxis in axenic cells is rescued by knocking out phosphatidylinositide 3-kinases (PI 3-kinases). Thus PIP3 promotes macropinocytosis and interferes with pseudopod orientation during chemotaxis of growing cells

    Time as an operator/observable in nonrelativistic quantum mechanics

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    The nonrelativistic Schroedinger equation for motion of a structureless particle in four-dimensional space-time entails a well-known expression for the conserved four-vector field of local probability density and current that are associated with a quantum state solution to the equation. Under the physical assumption that each spatial, as well as the temporal, component of this current is observable, the position in time becomes an operator and an observable in that the weighted average value of the time of the particle's crossing of a complete hyperplane can be simply defined: ... When the space-time coordinates are (t,x,y,z), the paper analyzes in detail the case that the hyperplane is of the type z=constant. Particles can cross such a hyperplane in either direction, so it proves convenient to introduce an indefinite metric, and correspondingly a sesquilinear inner product with non-Hilbert space structure, for the space of quantum states on such a surface. >... A detailed formalism for computing average crossing times on a z=constant hyperplane, and average dwell times and delay times for a zone of interaction between a pair of z=constant hyperplanes, is presented.Comment: 31 pages, no figures. Differs from published version by minor corrections and additions, and two citation
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