Active site voltage clamp fluorometry of the sodium glucose cotransporter hSGLT1.

In the human sodium glucose cotransporter (hSGLT1) cycle, the protein undergoes conformational changes where the sugar-binding site alternatively faces the external and internal surfaces. Functional site-directed fluorometry was used to probe the conformational changes at the sugar-binding site. Residues (Y290, T287, H83, and N78) were mutated to cysteines. The mutants were expressed in Xenopus laevis oocytes and tagged with environmentally sensitive fluorescent rhodamines [e.g., tetramethylrhodamine (TMR)-thiols]. The fluorescence intensity was recorded as the mutants were driven into different conformations using voltage jumps. Sugar binding and transport by the fluorophore-tagged mutants were blocked, but Na+ binding and the voltage-dependent conformational transitions were unaffected. Structural models indicated that external Na+ binding opened a large aqueous vestibule (600 Å3) leading to the sugar-binding site. The fluorescence of TMR covalently linked to Y290C, T287C, and H83C decreased as the mutant proteins were driven from the inward to the outward open Na+-bound conformation. The time courses of fluorescence changes (milliseconds) were close to the SGLT1 capacitive charge movements. The quench in rhodamine fluorescence indicated that the environment of the chromophores became more polar with opening of the external gates as the protein transitioned from the inward to outward facing state. Structural analyses showed an increase in polar side chains and a decrease in hydrophobic side chains lining the vestibule, and this was reflected in solvation of the chromophore. The results demonstrate the opening and closing of external gates in real time, with the accompanying changes of polarity of the sugar vestibule

Analisis Bentuk Kecemasan Tokoh Utama dalam Novel “Le Dernier Jour D\u27un Condamné À Mort” Karya Victor Hugo

Les mots clés : Le Roman “La Dernier Jour d\u27un Condamné à Mort”, La psychologie littéraire, L\u27anxiété, Le mécanisme de la défense et du conflit. Le roman est un exemple d\u27un oeuvre littéraire qui est une expression d\u27âme d\u27humain dans laquelle existe un sens psychologique. Il possède des expressionspsychologiques qui sont representées par des personnages avec lesquelles on trouvele conflit. La majorité du conflit spirituel est décrit à travers le personnage principal.Elle existe à cause d\u27une lutte qui n\u27est pas en accord avec les désirs des personnages principaux, si bien qu\u27il cause de l\u27anxiété. Ce conflit spirituel est présent avec le personnage principal dans le roman ”Le Dernier Jour d\u27un Condamné à Mort” par Victor Hugo. Il dévoile des problèmes sur “comment est la forme d\u27anxiété du héros principal et sa manière de surpasser son anxiété”. L\u27approche psychologique littéraire est utilisée pour analyser les problèmes. C\u27est la théorie d\u27anxiété de Sigmund Freud qui distingue l\u27anxiété sous trois types ; l\u27anxiété réaliste, morale et neurotique. De plus, on utilise de même le mécanisme de la défense et du conflit pour surmonter les anxiétés. Ce mécanisme de la défense et duconflit est divisé comme le rejet, la répression, l\u27introjection, la sublimation, la rationalitation, la réaction et la fantaisie. Le résultat de cette analyse montre que l\u27anxiété neurotique domine la psychologie du personnage principal. Elle est liée avec la nervosité et la perte du contrôle de son propre corps et sa pensée. Ce personnage pratique de même sept types du mécanisme de la défense et du conflit pour surmonter des anxiétés; le rejet, la répression, l\u27interjection, la sublimation, la rationalitation, la réaction et la fantaisie. Enfin, nous conseillons aux autres chercheurs de prendre les differentes idées comme la sociologie littéraire du fait que l\u27histoire qui se déroule au 19ème siècle dans le roman “Le Dernier Jour d\u27un Condamné à Mort” est interessante à analyser

Evaluating the accuracy of diffusion MRI models in white matter

Models of diffusion MRI within a voxel are useful for making inferences about the properties of the tissue and inferring fiber orientation distribution used by tractography algorithms. A useful model must fit the data accurately. However, evaluations of model-accuracy of some of the models that are commonly used in analyzing human white matter have not been published before. Here, we evaluate model-accuracy of the two main classes of diffusion MRI models. The diffusion tensor model (DTM) summarizes diffusion as a 3-dimensional Gaussian distribution. Sparse fascicle models (SFM) summarize the signal as a linear sum of signals originating from a collection of fascicles oriented in different directions. We use cross-validation to assess model-accuracy at different gradient amplitudes (b-values) throughout the white matter. Specifically, we fit each model to all the white matter voxels in one data set and then use the model to predict a second, independent data set. This is the first evaluation of model-accuracy of these models. In most of the white matter the DTM predicts the data more accurately than test-retest reliability; SFM model-accuracy is higher than test-retest reliability and also higher than the DTM, particularly for measurements with (a) a b-value above 1000 in locations containing fiber crossings, and (b) in the regions of the brain surrounding the optic radiations. The SFM also has better parameter-validity: it more accurately estimates the fiber orientation distribution function (fODF) in each voxel, which is useful for fiber tracking

Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer

Comprehensive analyses of cancer genomes promise to inform prognoses and precise cancer treatments. A major barrier, however, is inaccessibility of metastatic tissue. A potential solution is to characterize circulating tumor cells (CTCs), but this requires overcoming the challenges of isolating rare cells and sequencing low-input material. Here we report an integrated process to isolate, qualify and sequence whole exomes of CTCs with high fidelity using a census-based sequencing strategy. Power calculations suggest that mapping of >99.995% of the standard exome is possible in CTCs. We validated our process in two patients with prostate cancer, including one for whom we sequenced CTCs, a lymph node metastasis and nine cores of the primary tumor. Fifty-one of 73 CTC mutations (70%) were present in matched tissue. Moreover, we identified 10 early trunk and 56 metastatic trunk mutations in the non-CTC tumor samples and found 90% and 73% of these mutations, respectively, in CTC exomes. This study establishes a foundation for CTC genomics in the clinic.National Science Foundation (U.S.). Graduate Research FellowshipNational Cancer Institute (U.S.) (Koch Institute Support (Core) Grant P30-CA14051)Janssen Pharmaceutical Ltd.Klarman Family Foundatio

Effective field theory

I give a brief review of effective field theory, disscussing the contribution of Feza G\"ursey in particular and focusing on the literature I am most familiar with.Comment: 17 pages, no figs, macros appended, plain te

Stochastic Simulation of Process Calculi for Biology

Biological systems typically involve large numbers of components with complex, highly parallel interactions and intrinsic stochasticity. To model this complexity, numerous programming languages based on process calculi have been developed, many of which are expressive enough to generate unbounded numbers of molecular species and reactions. As a result of this expressiveness, such calculi cannot rely on standard reaction-based simulation methods, which require fixed numbers of species and reactions. Rather than implementing custom stochastic simulation algorithms for each process calculus, we propose to use a generic abstract machine that can be instantiated to a range of process calculi and a range of reaction-based simulation algorithms. The abstract machine functions as a just-in-time compiler, which dynamically updates the set of possible reactions and chooses the next reaction in an iterative cycle. In this short paper we give a brief summary of the generic abstract machine, and show how it can be instantiated with the stochastic simulation algorithm known as Gillespie's Direct Method. We also discuss the wider implications of such an abstract machine, and outline how it can be used to simulate multiple calculi simultaneously within a common framework.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

Tensor interaction constraints from beta decay recoil spin asymmetry of trapped atoms

We have measured the angular distribution of recoiling daughter nuclei emitted from the Gamow-Teller $\beta$ decay of spin-polarized $^{80}$Rb. The asymmetry of this distribution vanishes to lowest order in the Standard Model (SM) in pure Gamow-Teller decays, producing an observable very sensitive to new interactions. We measure the non-SM contribution to the asymmetry to be $A_{T}$= 0.015 $\pm$ 0.029 (stat) $\pm$ 0.019 (syst), consistent with the SM prediction. We constrain higher-order SM corrections using the measured momentum dependence of the asymmetry, and their remaining uncertainty dominates the systematic error. Future progress in determining the weak magnetism term theoretically or experimentally would reduce the final errors. We describe the resulting constraints on fundamental 4-Fermi tensor interactions.Comment: 11 pages, 13 figures; v2 published in Phys. Rev. C, with referee clarifications and figures improved for black-and-whit

Dynamical Generation of Extended Objects in a 1+11+1 Dimensional Chiral Field Theory: Non-Perturbative Dirac Operator Resolvent Analysis

We analyze the $1+1$ dimensional Nambu-Jona-Lasinio model non-perturbatively. In addition to its simple ground state saddle points, the effective action of this model has a rich collection of non-trivial saddle points in which the composite fields \sigx=\lag\bar\psi\psi\rag and \pix=\lag\bar\psi i\gam_5\psi\rag form static space dependent configurations because of non-trivial dynamics. These configurations may be viewed as one dimensional chiral bags that trap the original fermions (``quarks") into stable extended entities (``hadrons"). We provide explicit expressions for the profiles of these objects and calculate their masses. Our analysis of these saddle points is based on an explicit representation we find for the diagonal resolvent of the Dirac operator in a \{\sigx, \pix\} background which produces a prescribed number of bound states. We analyse in detail the cases of a single as well as two bound states. We find that bags that trap $N$ fermions are the most stable ones, because they release all the fermion rest mass as binding energy and become massless. Our explicit construction of the diagonal resolvent is based on elementary Sturm-Liouville theory and simple dimensional analysis and does not depend on the large $N$ approximation. These facts make it, in our view, simpler and more direct than the calculations previously done by Shei, using the inverse scattering method following Dashen, Hasslacher, and Neveu. Our method of finding such non-trivial static configurations may be applied to other $1+1$ dimensional field theories

Conformational transitions of the sodium-dependent sugar transporter, vSGLT.

Sodium-dependent transporters couple the flow of Na+ ions down their electrochemical potential gradient to the uphill transport of various ligands. Many of these transporters share a common core structure composed of a five-helix inverted repeat and deliver their cargo utilizing an alternating-access mechanism. A detailed characterization of inward-facing conformations of the Na+-dependent sugar transporter from Vibrio parahaemolyticus (vSGLT) has previously been reported, but structural details on additional conformations and on how Na+ and ligand influence the equilibrium between other states remains unknown. Here, double electron-electron resonance spectroscopy, structural modeling, and molecular dynamics are utilized to deduce ligand-dependent equilibria shifts of vSGLT in micelles. In the absence and presence of saturating amounts of Na+, vSGLT favors an inward-facing conformation. Upon binding both Na+ and sugar, the equilibrium shifts toward either an outward-facing or occluded conformation. While Na+ alone does not stabilize the outward-facing state, gating charge calculations together with a kinetic model of transport suggest that the resting negative membrane potential of the cell, absent in detergent-solubilized samples, may stabilize vSGLT in an outward-open conformation where it is poised for binding external sugars. In total, these findings provide insights into ligand-induced conformational selection and delineate the transport cycle of vSGLT