Covalent Modification of Mutant Rat P2X2 Receptors with a Thiol-Reactive Fluorophore Allows Channel Activation by Zinc or Acidic pH without ATP

Rat P2X2 receptors open at an undetectably low rate in the absence of ATP. Furthermore, two allosteric modulators, zinc and acidic pH, cannot by themselves open these channels. We describe here the properties of a mutant receptor, K69C, before and after treatment with the thiol-reactive fluorophore Alexa Fluor 546 C₅-maleimide (AM546). Xenopus oocytes expressing unmodified K69C were not activated under basal conditions nor by 1,000 µM ATP. AM546 treatment caused a small increase in the inward holding current which persisted on washout and control experiments demonstrated this current was due to ATP independent opening of the channels. Following AM546 treatment, zinc (100 µM) or acidic external solution (pH 6.5) elicited inward currents when applied without any exogenous ATP. In the double mutant K69C/H319K, zinc elicited much larger inward currents, while acidic pH generated outward currents. Suramin, which is an antagonist of wild type receptors, behaved as an agonist at AM546-treated K69C receptors. Several other cysteine-reactive fluorophores tested on K69C did not cause these changes. These modified receptors show promise as a tool for studying the mechanisms of P2X receptor activation.     

Stochastic errors vs. modeling errors in distance based phylogenetic reconstructions

ABSTRACT: BACKGROUND: Distance-based phylogenetic reconstruction methods use evolutionary distances between species in order to reconstruct the phylogenetic tree spanning them. There are many different methods for estimating distances from sequence data. These methods assume different substitution models and have different statistical properties. Since the true substitution model is typically unknown, it is important to consider the effect of model misspecification on the performance of a distance estimation method. RESULTS: This paper continues the line of research which attempts to adjust to each given set of input sequences a distance function which maximizes the expected topological accuracy of the reconstructed tree. We focus here on the effect of systematic error caused by assuming an inadequate model, but consider also the stochastic error caused by using short sequences. We introduce a theoretical framework for analyzing both sources of error based on the notion of deviation from additivity, which quantifies the contribution of model misspecification to the estimation error. We demonstrate this framework by studying the behavior of the Jukes-Cantor distance function when applied to data generated according to Kimura's two-parameter model with a transition-transversion bias. We provide both a theoretical derivation for this case, and a detailed simulation study on quartet trees. CONCLUSIONS: We demonstrate both analytically and experimentally that by deliberately assuming an oversimplified evolutionary model, it is possible to increase the topological accuracy of reconstruction. Our theoretical framework provides new insights into the mechanisms that enables statistically inconsistent reconstruction methods to outperform consistent methods.     

The surgical management of fibrous dysplasia of bone

The surgical management of Polyostotic Fibrous Dysplasia (FD) of bone is technically demanding. The most effective methods to manage the associated bone deformity remain unclear. The marked variation in the degree and pattern of bone involvement has made it difficult to acquire data to guide the surgeon's approach to these patients. In light of the paucity of data, but need for guidance, recognized experts in the management of these patients came together at the National Institutes of Health in Bethesda, Maryland as part of an International meeting to address issues related to fibrous dysplasia of bone to discuss and refine their recommendations regarding the surgical indications and preferred methods for the management of these challenging patients. The specific challenges, recommended approaches, and "lessons learned" are presented in hopes that surgeons faced with typical deformities can be guided in the surgical reconstruction of both children and adults with FD.     

Unperturbing a non-helically perturbed bacterial flagellar filament: Salmonella typhimurium SJW23

Salmonella typhimurium SJW23 has a right-handed, non-helically perturbed filament of serotype gt with a unique surface pattern. Non-helical perturbations involve symmetry reduction along the five-start helical lines resulting in layer lines of fractional Bessel orders and a consequent seam. The flagellin gene, fliC₂₃, which we sequenced, differs from the sequence of the canonic, plain SJW1655 flagellin, fliC₁₆₅₅. We modified discrete components of fliC₂₃ in order to localize, in the expressed filament, the submolecular site responsible for the non-helical perturbation. These modifications include (i) deleting the outermost domain  D3₂₃, (ii) replacing D3₂₃ with D3₁₆₅₅, (iii) substituting a hydrophilic α-helix at the interface between the neighboring domains D1 and D2 with a hydrophobic one from fliC₁₆₅₅, and (iv) substituting a serine/glycine pair in the loop connecting the modified α-helix to its neighbor; these modifications were made in the presence and absence of D3₂₃. We used S. typhimurium SJW1655 both as a reference and as a source for ‘spare parts’. The symmetry of the constructs was assessed from the power spectra through changes in the layer lines at a height of 〈1/105〉 and 〈1/35〉 Å^? 1 , unique to the non-helical perturbation. Deleting D3₂₃, either alone or in combination with various substitutions, or replacing it with D3₁₆₅₅ transforms the non-helically perturbed filament into a plain one as judged by the disappearance of the typical layer lines from the power spectra. We conclude that the non-helical perturbation is a product of unique interactions in the D3₂₃ density shell. Whereas other minor structural changes may occur at the filaments interior, they are all helically symmetric.     

Visualizing neuromodulation in vivo: TANGO-mapping of dopamine signaling reveals appetite control of sugar sensing

Behavior cannot be predicted from a "connectome" because the brain contains a chemical "map" of neuromodulation superimposed upon its synaptic connectivity map. Neuromodulation changes how neural circuits process information in different states, such as hunger or arousal. Here we describe a genetically based method to map, in an unbiased and brain-wide manner, sites of neuromodulation under different conditions in the Drosophila brain. This method, and genetic perturbations, reveal that the well-known effect of hunger to enhance behavioral sensitivity to sugar is mediated, at least in part, by the release of dopamine onto primary gustatory sensory neurons, which enhances sugar-evoked calcium influx. These data reinforce the concept that sensory neurons constitute an important locus for state-dependent gain control of behavior and introduce a methodology that can be extended to other neuromodulators and model organisms.     

Invasiveness,chimerism and genetic diversity

Adaptation for invasiveness should comprise the capability to exploit and prosper in a wide range of ecological conditions and is therefore expected to be associated with a certain level of genetic diversity. Paradoxically, however, invasive populations are established by only a few founders, resulting in low genetic diversity. As a conceivable way of attaining high genetic diversity and high variance of gene expression even when a small number of founders is involved in invasiveness, I suggest here chimerism, a fusion between different individuals—a common phenomenon found in numerous phyla. The composite entity offers the chimeric organism genetic flexibility and higher inclusive fitness that depends on the joint genomic fitness of the original partners. The ability to form a chimeric entity is also applied to subsequent generations, and consequently, the level of genetic diversity does not decline over generations of population establishment following invasion.     

Isolation of Mycoplasma Membranes by Digitonin

The cell membrane of Mycoplasma hominis was isolated by lysing the cells with digitonin. Electron microscopy and chemical, density gradient, and electrophoretic analyses of the membrane proteins showed the membranes so obtained, like those isolated by osmotic lysis, to be relatively free of cytoplasmic contaminants. Sensitivity to digitonin lysis depended on temperature but was not affected by Mg(2+) ions and was only slightly affected by the age of the culture. Accordingly, it seems that digitonin may be used for the isolation of cell membranes from sterol-requiring mycoplasmas that tend to be fairly resistant to osmotic lysis.     

Factors Affecting the Design of Slow Release Formulations of Herbicides Based on Clay-Surfactant Systems. A Methodological Approach

A search for clay-surfactant based formulations with high percentage of the active ingredient, which can yield slow release of active molecules is described. The active ingredients were the herbicides metribuzin (MZ), mesotrione (MS) and flurtamone (FL), whose solubilities were examined in the presence of four commercial surfactants; (i) neutral: two berols (B048, B266) and an alkylpolyglucoside (AG6202); (ii) cationic: an ethoxylated amine (ET/15). Significant percent of active ingredient (a.i.) in the clay/surfactant/herbicide formulations could be achieved only when most of the surfactant was added as micelles. MZ and FL were well solubilized by berols, whereas MS by ET/15. Sorption of surfactants on the clay mineral sepiolite occurred mostly by sorption of micelles, and the loadings exceeded the CEC. Higher loadings were determined for B266 and ET/15. The sorption of surfactants was modeled by using the Langmuir-Scatchard equation which permitted the determination of binding coefficients that could be used for further predictions of the sorbed amounts of surfactants under a wide range of clay/surfactant ratios. A possibility was tested of designing clay-surfactant based formulations of certain herbicides by assuming the same ratio between herbicides and surfactants in the formulations as for herbicides incorporated in micelles in solution. Calculations indicated that satisfactory FL formulations could not be synthesized. The experimental fractions of herbicides in the formulations were in agreement with the predicted ones for MS and MZ. The validity of this approach was confirmed in in vitro release tests that showed a slowing down of the release of a.i. from the designed formulations relative to the technical products. Soil dissipation studies with MS formulations also showed improved bioactivity of the clay-surfactant formulation relative to the commercial one. This methodological approach can be extended to other clay-surfactant systems for encapsulation and slow release of target molecules of interest.