Evolution of phototaxis

Phototaxis in the broadest sense means positive or negative displacement along a light gradient or vector. Prokaryotes most often use a biased random walk strategy, employing type I sensory rhodopsin photoreceptors and two-component signalling to regulate flagellar reversal. This strategy only allows phototaxis along steep light gradients, as found in microbial mats or sediments. Some filamentous cyanobacteria evolved the ability to steer towards a light vector. Even these cyanobacteria, however, can only navigate in two dimensions, gliding on a surface. In contrast, eukaryotes evolved the capacity to follow a light vector in three dimensions in open water. This strategy requires a polarized organism with a stable form, helical swimming with cilia and a shading or focusing body adjacent to a light sensor to allow for discrimination of light direction. Such arrangement and the ability of three-dimensional phototactic navigation evolved at least eight times independently in eukaryotes. The origin of three-dimensional phototaxis often followed a transition from a benthic to a pelagic lifestyle and the acquisition of chloroplasts either via primary or secondary endosymbiosis. Based on our understanding of the mechanism of phototaxis in single-celled eukaryotes and animal larvae, it is possible to define a series of elementary evolutionary steps, each of potential selective advantage, which can lead to pelagic phototactic navigation. We can conclude that it is relatively easy to evolve phototaxis once cell polarity, ciliary swimming and a stable cell shape are present

Intricacies and inter-relationships between HIV disclosure and HAART: A qualitative study

This study aimed to understand whether and how highly active antiretroviral treatment (HAART) affects views and patterns of disclosure and how disclosure interacts with treatment decisions. One hundred and fifty-two HIV-positive adults (52 MSM, 56 women and 44 IDU men) from four US cities participated in two to three-hour, semi-structured interviews in 1998–99. Results indicate that HAART interacts with and shapes HIV disclosure issues in several ways. Medications may ‘out’ people living with HIV. Thus, in different settings (e.g. work, prisons, drug rehabs and public situations), some try to hide medications or modify dosing schedules, which can contribute to non-adherence, and affect sexual behaviours. Disclosure of HIV and/or HAART may also result in antagonism from others who hold negative attitudes and beliefs about HAART, potentially impeding adherence. Observable side effects of medications can also ‘out’ individuals. Conversely, medications may improve appearance, delaying or impeding disclosure. Some wait until they are on HAART and look ‘well’ before disclosing; some who look healthy as a result of medication deny being HIV-positive. Alternatively, HIV disclosure can lead to support that facilitates initiation of, and adherence to, treatment. HIV disclosure and adherence can shape one another in critical ways. Yet these interactions have been under-studied and need to be further examined. Interventions and studies concerning each of these domains have generally been separate, but need to be integrated, and the importance of relationships between these two areas needs to be recognized

Nonlinear Lattice Waves in Random Potentials

Localization of waves by disorder is a fundamental physical problem encompassing a diverse spectrum of theoretical, experimental and numerical studies in the context of metal-insulator transition, quantum Hall effect, light propagation in photonic crystals, and dynamics of ultra-cold atoms in optical arrays. Large intensity light can induce nonlinear response, ultracold atomic gases can be tuned into an interacting regime, which leads again to nonlinear wave equations on a mean field level. The interplay between disorder and nonlinearity, their localizing and delocalizing effects is currently an intriguing and challenging issue in the field. We will discuss recent advances in the dynamics of nonlinear lattice waves in random potentials. In the absence of nonlinear terms in the wave equations, Anderson localization is leading to a halt of wave packet spreading. Nonlinearity couples localized eigenstates and, potentially, enables spreading and destruction of Anderson localization due to nonintegrability, chaos and decoherence. The spreading process is characterized by universal subdiffusive laws due to nonlinear diffusion. We review extensive computational studies for one- and two-dimensional systems with tunable nonlinearity power. We also briefly discuss extensions to other cases where the linear wave equation features localization: Aubry-Andre localization with quasiperiodic potentials, Wannier-Stark localization with dc fields, and dynamical localization in momentum space with kicked rotors.Comment: 45 pages, 19 figure

Optical investigation on the electronic structures of Y_{2}Ru_{2}O_{7}, CaRuO_{3}, SrRuO_{3}, and Bi_{2}Ru_{2}O_{7}

We investigated the electronic structures of the bandwidth-controlled ruthenates, Y$_{2}$Ru$_{2}$O$_{7}$, CaRuO$_{3}$, SrRuO$_{3}$, and Bi$_{2}$Ru$_{2}$O$_{7}$, by optical conductivity analysis in a wide energy region of 5 meV $\sim$ 12 eV. We could assign optical transitions from the systematic changes of the spectra and by comparison with the O 1$s$ x-ray absorption data. We estimated some physical parameters, such as the on-site Coulomb repulsion energy and the crystal-field splitting energy. These parameters show that the 4$d$ orbitals should be more extended than 3$d$ ones. These results are also discussed in terms of the Mott-Hubbard model.Comment: 12 pages (1 table), 3 figure

Consequences of converting graded to action potentials upon neural information coding and energy efficiency

Information is encoded in neural circuits using both graded and action potentials, converting between them within single neurons and successive processing layers. This conversion is accompanied by information loss and a drop in energy efficiency. We investigate the biophysical causes of this loss of information and efficiency by comparing spiking neuron models, containing stochastic voltage-gated Na+ and K+ channels, with generator potential and graded potential models lacking voltage-gated Na+ channels. We identify three causes of information loss in the generator potential that are the by-product of action potential generation: (1) the voltage-gated Na+ channels necessary for action potential generation increase intrinsic noise and (2) introduce non-linearities, and (3) the finite duration of the action potential creates a ‘footprint’ in the generator potential that obscures incoming signals. These three processes reduce information rates by ~50% in generator potentials, to ~3 times that of spike trains. Both generator potentials and graded potentials consume almost an order of magnitude less energy per second than spike trains. Because of the lower information rates of generator potentials they are substantially less energy efficient than graded potentials. However, both are an order of magnitude more efficient than spike trains due to the higher energy costs and low information content of spikes, emphasizing that there is a two-fold cost of converting analogue to digital; information loss and cost inflation

Protemic identification of Germline Proteins in Caenorhabditis elegans

Sexual reproduction involves fusion of 2 haploid gametes to form diploid offspring with genetic contributions from both parents. Gamete formation represents a unique developmental program involving the action of numerous germline-specific proteins. In an attempt to identify novel proteins involved in reproduction and embryonic development, we have carried out a proteomic characterization of the process in Caenorhabditis elegans. To identify candidate proteins, we used 2D gel electrophoresis (2DGE) to compare protein abundance in nucleus-enriched extracts from wild-type C. elegans, and in extracts from mutant worms with greatly reduced gonads (glp-4(bn2) worms reared at 25°C); 84 proteins whose abundance correlated with germline presence were identified. To validate candidates, we used feeding RNAi to deplete candidate proteins, and looked for reduction in fertility and/or germline cytological defects. Of 20 candidates so screened for involvement in fertility, depletion of 13 (65%) caused a significant reduction in fertility, and 6 (30%) resulted in sterility (\u3c5 % of wild-type fertility). Five of the 13 proteins with demonstrated roles in fertility have not previously been implicated in germline function. The high frequency of defects observed after RNAi depletion of candidate proteins suggests that this approach is effective at identifying germline proteins, thus contributing to our understanding of this complex organ

Search for Θ+(1540)\Theta^+(1540) pentaquark in high statistics measurement of γp→Kˉ0K+n\gamma p \to \bar K^0 K^+ n at CLAS

The exclusive reaction $\gamma p \to \bar K^0 K^+ n$ was studied in the photon energy range between 1.6-3.8 GeV searching for evidence of the exotic baryon $\Theta^+(1540)\to nK^+$. The decay to $nK^+$ requires the assignment of strangeness $S=+1$ to any observed resonance. Data were collected with the CLAS detector at the Thomas Jefferson National Accelerator Facility corresponding to an integrated luminosity of 70 $pb^{-1}$. No evidence for the $\Theta^+$ pentaquark was found. Upper limits were set on the production cross section as function of center-of-mass angle and $nK^+$ mass. The 95% CL upper limit on the total cross section for a narrow resonance at 1540 MeV was found to be 0.8 nb.Comment: Submitted to Physical Review Letter

Light Vector Mesons in the Nuclear Medium

The light vector mesons ($\rho$, $\omega$, and $\phi$) were produced in deuterium, carbon, titanium, and iron targets in a search for possible in-medium modifications to the properties of the $\rho$ meson at normal nuclear densities and zero temperature. The vector mesons were detected with the CEBAF Large Acceptance Spectrometer (CLAS) via their decays to $e^{+}e^{-}$. The rare leptonic decay was chosen to reduce final-state interactions. A combinatorial background was subtracted from the invariant mass spectra using a well-established event-mixing technique. The $\rho$ meson mass spectrum was extracted after the $\omega$ and $\phi$ signals were removed in a nearly model-independent way. Comparisons were made between the $\rho$ mass spectra from the heavy targets ($A > 2$) with the mass spectrum extracted from the deuterium target. With respect to the $\rho$-meson mass, we obtain a small shift compatible with zero. Also, we measure widths consistent with standard nuclear many-body effects such as collisional broadening and Fermi motion.Comment: 15 pages, 18 figures, 3 table

Photoproduction of phi(1020) mesons on the proton at large momentum transfer

The cross section for $\phi$ meson photoproduction on the proton has been measured for the first time up to a four-momentum transfer -t = 4 GeV^2, using the CLAS detector at the Thomas Jefferson National Accelerator Facility. At low four-momentum transfer, the differential cross section is well described by Pomeron exchange. At large four-momentum transfer, above -t = 1.8 GeV^2, the data support a model where the Pomeron is resolved into its simplest component, two gluons, which may couple to any quark in the proton and in the $\phi$.Comment: 5 pages; 7 figure

Deeply virtual and exclusive electroproduction of omega mesons

The exclusive omega electroproduction off the proton was studied in a large kinematical domain above the nucleon resonance region and for the highest possible photon virtuality (Q2) with the 5.75 GeV beam at CEBAF and the CLAS spectrometer. Cross sections were measured up to large values of the four-momentum transfer (-t < 2.7 GeV2) to the proton. The contributions of the interference terms sigma_TT and sigma_TL to the cross sections, as well as an analysis of the omega spin density matrix, indicate that helicity is not conserved in this process. The t-channel pi0 exchange, or more generally the exchange of the associated Regge trajectory, seems to dominate the reaction gamma* p -> omega p, even for Q2 as large as 5 GeV2. Contributions of handbag diagrams, related to Generalized Parton Distributions in the nucleon, are therefore difficult to extract for this process. Remarkably, the high-t behaviour of the cross sections is nearly Q2-independent, which may be interpreted as a coupling of the photon to a point-like object in this kinematical limit.Comment: 15 pages,19 figure