A fluorophore attached to nicotinic acetylcholine receptor beta M2 detects productive binding of agonist to the alpha delta site

To study conformational transitions at the muscle nicotinic acetylcholine (ACh) receptor (nAChR), a rhodamine fluorophore was tethered to a Cys side chain introduced at the beta-19' position in the M2 region of the nAChR expressed in Xenopus oocytes. This procedure led to only minor changes in receptor function. During agonist application, fluorescence increased by (Delta-F/F) approximate to 10%, and the emission peak shifted to lower wavelengths, indicating a more hydrophobic environment for the fluorophore. The dose-response relations for Delta-F agreed well with those for epibatidine-induced currents, but were shifted approximate to 100-fold to the left of those for ACh-induced currents. Because (i) epibatidine binds more tightly to the alpha-gamma-binding site than to the alpha-delta site and (ii) ACh binds with reverse-site selectivity, these data suggest that Delta-F monitors an event linked to binding specifically at the alpha-delta-subunit interface. In experiments with flash-applied agonists, the earliest detectable Delta-F occurs within milliseconds, i.e., during activation. At low [ACh] (less than or equal to 10 muM), a phase of Delta-F occurs with the same time constant as desensitization, presumably monitoring an increased population of agonist-bound receptors. However, recovery from Delta-F is complete before the slowest phase of recovery from desensitization (time constant approximate to 250 s), showing that one or more desensitized states have fluorescence like that of the resting channel. That conformational transitions at the alpha-delta-binding site are not tightly coupled to channel activation suggests that sequential rather than fully concerted transitions occur during receptor gating. Thus, time-resolved fluorescence changes provide a powerful probe of nAChR conformational changes

Noise sensitivity of an atomic velocity sensor

We use Bloch oscillations to accelerate coherently Rubidium atoms. The variation of the velocity induced by this acceleration is an integer number times the recoil velocity due to the absorption of one photon. The measurement of the velocity variation is achieved using two velocity selective Raman pi-pulses: the first pulse transfers atoms from the hyperfine state 5S1/2 |F=2, mF=0> to 5S1/2, |F=1, mF = 0> into a narrow velocity class. After the acceleration of this selected atomic slice, we apply the second Raman pulse to bring the resonant atoms back to the initial state 5S1/2, |F=2, mF = 0>. The populations in (F=1 and F=2) are measured separately by using a one-dimensional time-of-flight technique. To plot the final velocity distribution we repeat this procedure by scanning the Raman beam frequency of the second pulse. This two pi-pulses system constitutes then a velocity sensor. Any noise in the relative phase shift of the Raman beams induces an error in the measured velocity. In this paper we present a theoretical and an experimental analysis of this velocity sensor, which take into account the phase fluctuations during the Raman pulses

Dipole and Bloch oscillations of cold atoms in a parabolic lattice

The paper studies the dynamics of a Bose-Einstein condensate loaded into a 1D parabolic optical lattice, and excited by a sudden shift of the lattice center. Depending on the magnitude of the initial shift, the condensate undergoes either dipole or Bloch oscillations. The effects of dephasing and of atom-atom interactions on these oscillations are discussed.Comment: 3 pages, to appear in proceeding of LPHYS'05 conference (July 4-8, 2005, Kyoto, Japan

Microstructured blood vessel surrogates reveal structural tropism of motile malaria parasites

Plasmodium sporozoites, the highly motile forms of the malaria parasite, are transmitted naturally by mosquitoes and traverse the skin to find, associate with, and enter blood capillaries. Research aimed at understanding how sporozoites select blood vessels is hampered by the lack of a suitable experimental system. Arrays of uniform cylindrical pillars can be used to study small cells moving in controlled environments. Here, an array system displaying a variety of pillars with different diameters and shapes is developed in order to investigate how Plasmodium sporozoites associate to the pillars as blood vessel surrogates. Investigating the association of sporozoites to pillars in arrays displaying pillars of different diameters reveals that the crescent-shaped parasites prefer to associate with and migrate around pillars with a similar curvature. This suggests that after transmission by a mosquito, malaria parasites may use a structural tropism to recognize blood capillaries in the dermis in order to gain access to the blood stream

An optical lattice on an atom chip

Optical dipole traps and atom chips are two very powerful tools for the quantum manipulation of neutral atoms. We demonstrate that both methods can be combined by creating an optical lattice potential on an atom chip. A red-detuned laser beam is retro-reflected using the atom chip surface as a high-quality mirror, generating a vertical array of purely optical oblate traps. We load thermal atoms from the chip into the lattice and observe cooling into the two-dimensional regime where the thermal energy is smaller than a quantum of transverse excitation. Using a chip-generated Bose-Einstein condensate, we demonstrate coherent Bloch oscillations in the lattice.Comment: 3 pages, 2 figure

Mapping adaptation of barley to droughted environments

Identifying barley genomic regions influencing the response of yield and its components to water deficits will aid in our understanding of the genetics of drought tolerance and the development of more drought tolerant cultivars. We assembled a population of 192 genotypes that represented landraces, old, and contemporary cultivars sampling key regions around the Mediterranean basin and the rest of Europe. The population was genotyped with a stratified set of 50 genomic and EST derived molecular markers, 49 of which were Simple Sequence Repeats (SSRs), which revealed an underlying population sub-structure that corresponded closely to the geographic regions in which the genotypes were grown. A more dense whole genome scan was generated by using Diversity Array Technology (DArT®) to generate 1130 biallelic markers for the population. The population was grown at two contrasting sites in each of seven Mediterranean countries for harvest 2004 and 2005 and grain yield data collected. Mean yield levels ranged from 0.3 to 6.2 t/ha, with highly significant genetic variation in low-yielding environments. Associations of yield with barley genomic regions were then detected by combining the DArT marker data with the yield data in mixed model analyses for the individual trials, followed by multiple regression of yield on markers to identify a multi-locus subset of significant markers/QTLs. QTLs exhibiting a pre-defined consistency across environments were detected in bins 4, 6, 6 and 7 on barley chromosomes 3H, 4H, 5H and 7H respectivel

Forecasting in the light of Big Data

Predicting the future state of a system has always been a natural motivation for science and practical applications. Such a topic, beyond its obvious technical and societal relevance, is also interesting from a conceptual point of view. This owes to the fact that forecasting lends itself to two equally radical, yet opposite methodologies. A reductionist one, based on the first principles, and the naive inductivist one, based only on data. This latter view has recently gained some attention in response to the availability of unprecedented amounts of data and increasingly sophisticated algorithmic analytic techniques. The purpose of this note is to assess critically the role of big data in reshaping the key aspects of forecasting and in particular the claim that bigger data leads to better predictions. Drawing on the representative example of weather forecasts we argue that this is not generally the case. We conclude by suggesting that a clever and context-dependent compromise between modelling and quantitative analysis stands out as the best forecasting strategy, as anticipated nearly a century ago by Richardson and von Neumann

Superfluid Dynamics of a Bose-Einstein Condensate in a Periodic Potential

We investigate the superfluid properties of a Bose-Einstein condensate (BEC) trapped in a one dimensional periodic potential. We study, both analytically (in the tight binding limit) and numerically, the Bloch chemical potential, the Bloch energy and the Bogoliubov dispersion relation, and we introduce {\it two} different, density dependent, effective masses and group velocities. The Bogoliubov spectrum predicts the existence of sound waves, and the arising of energetic and dynamical instabilities at critical values of the BEC quasi-momentum which dramatically affect its coherence properties. We investigate the dependence of the dipole and Bloch oscillation frequencies in terms of an effective mass averaged over the density of the condensate. We illustrate our results with several animations obtained solving numerically the time-dependent Gross-Pitaevskii equation.Comment: 13 pages, 7 figures, movies and published paper available at http://www.iop.org/EJ/abstract/1367-2630/5/1/11

Theoretical Analysis of a Large Momentum Beamsplitter using Bloch Oscillations

In this paper, we present the implementation of Bloch oscillations in an atomic interferometer to increase the separation of the two interfering paths. A numerical model, in very good agreement with the experiment, is developed. The contrast of the interferometer and its sensitivity to phase fluctuations and to intensity fluctuations are also calculated. We demonstrate that the sensitivity to phase fluctuations can be significantly reduced by using a suitable arrangement of Bloch oscillations pulses