Cystic Fibrosis Transmembrane Conductance Regulator: Using Differential Reactivity toward Channel-Permeant and Channel-Impermeant Thiol-Reactive Probes To Test a Molecular Model for the Pore†

ABSTRACT: The sixth transmembrane segment (TM6) of the CFTR chloride channel has been intensively investigated. The effects of amino acid substitutions and chemical modification of engineered cysteines (cysteine scanning) on channel properties strongly suggest that TM6 is a key component of the anion-conducting pore, but previous cysteine-scanning studies of TM6 have produced conflicting results. Our aim was to resolve these conflicts by combining a screening strategy based on multiple, thiol-directed probes with molecular modeling of the pore. CFTR constructs were screened for reactivity toward both channel-permeant and channel-impermeant thiol-directed reagents, and patterns of reactivity in TM6 were mapped onto two new, molecular models of the CFTR pore: one based on homology modeling using Sav1866 as the template and a second derived from the first by molecular dynamics simulation. Comparison of the pattern of cysteine reactivity with model predictions suggests that nonreactive sites are those where the TM6 side chains are occluded by other TMs. Reactive sites, in contrast, are generally situated such that the respective amino acid side chains either project into the predicted pore or lie within a predicted extracellular loop. Sites wher

Stationary Distribution and Eigenvalues for a de Bruijn Process

We define a de Bruijn process with parameters n and L as a certain continuous-time Markov chain on the de Bruijn graph with words of length L over an n-letter alphabet as vertices. We determine explicitly its steady state distribution and its characteristic polynomial, which turns out to decompose into linear factors. In addition, we examine the stationary state of two specializations in detail. In the first one, the de Bruijn-Bernoulli process, this is a product measure. In the second one, the Skin-deep de Bruin process, the distribution has constant density but nontrivial correlation functions. The two point correlation function is determined using generating function techniques.Comment: Dedicated to Herb Wilf on the occasion of his 80th birthda

Nonperturbative improvement and tree-level correction of the quark propagator

We extend an earlier study of the Landau gauge quark propagator in quenched QCD where we used two forms of the O(a)-improved propagator with the Sheikholeslami-Wohlert quark action. In the present study we use the nonperturbative value for the clover coefficient c_sw and mean-field improvement coefficients in our improved quark propagators. We compare this to our earlier results which used the mean-field c_sw and tree-level improvement coefficients for the propagator. We also compare three different implementations of tree-level correction: additive, multiplicative, and hybrid. We show that the hybrid approach is the most robust and reliable and can successfully deal even with strong ultraviolet behavior and zero-crossing of the lattice tree-level expression. We find good agreement between our improved quark propagators when using the appropriate nonperturbative improvement coefficients and hybrid tree-level correction. We also present a simple extrapolation of the quark mass function to the chiral limit.Comment: 12 pages, 18 figures, RevTeX4. Some clarifications and corrections. Final version, to appear in Phys.Rev.

Complete Genome Sequence of Curtobacterium sp. Strain MR_MD2014, Isolated from Topsoil in Woods Hole, Massachusetts

Here, we present the 3,443,800-bp complete genome sequence of Curtobacterium sp. strain MR_MD2014 (phylum Actinobacteria). This strain was isolated from soil in Woods Hole, MA, as part of the 2014 Microbial Diversity Summer Program at the Marine Biological Laboratory in Woods Hole, MA

Coherent averaging of pseudorandom binary stimuli: is the dynamic cerebral autoregulatory response symmetrical?

Objective: Previous studies on cerebral autoregulation have shown the existence of hemispheric symmetry, which may be altered in stroke and traumatic brain injury. There is a paucity of data however on whether the response is symmetrical between those disturbances that cause cerebral hyperperfusion, to those that cause hypoperfusion. Our aim was to investigate whether the responses of cerebral autoregulation to haemodynamic stimuli of different directions are symmetrical. 
 Approach: Using a previously described assessment method, we employed coherent averaging of the cerebral blood flow velocity (CBFV) responses to thigh cuff inflation and deflation, as driven by pseudorandom binary sequences, whilst simultaneously altering the inspired CO2. The symmetry of the autoregulatory response was assessed with regards to two parameters, its speed and gain. Using the first harmonic method, critical closing pressure (CrCP) and resistance area product (RAP) were estimated, and the gain of the autoregulatory response was calculated by performing linear regression between the coherent averages of arterial blood pressure (ABP) and CBFV, ABP and CrCP and finally ABP and RAP. A two-way repeated measures ANOVA was used to assess for the effect of the direction of change in ABP and the method of CO2 administration. 
 Main results: Our results suggest that whilst the direction of ABP change does not have a significant effect, the effect of CO2 administration method is highly significant (p<10-4). 
 Significance: This is the first report to report to demonstrate the symmetry of the autoregulatory response to stimuli of different directions as well as the short term dynamics of RAP and CrCP under intermittent and constant hypercapnia. As haemodynamic stimulus direction does not appear to have an influence, our findings validate previous work done using different assessment methods

Studies of the transmissibility of the agent of bovine spongiform encephalopathy to the domestic chicken

<p>Abstract</p> <p>Background</p> <p>Transmission of the prion disease bovine spongiform encephalopathy (BSE) occurred accidentally to cattle and several other mammalian species via feed supplemented with meat and bone meal contaminated with infected bovine tissue. Prior to United Kingdom controls in 1996 on the feeding of mammalian meat and bone meal to farmed animals, the domestic chicken was potentially exposed to feed contaminated with the causal agent of BSE. Although confirmed prion diseases are unrecorded in avian species a study was undertaken to transmit BSE to the domestic chicken by parenteral and oral inoculations. Transmissibility was assessed by clinical monitoring, histopathological examinations, detection of a putative disease form of an avian prion protein (PrP) in recipient tissues and by mouse bioassay of tissues. Occurrence of a progressive neurological syndrome in the primary transmission study was investigated by sub-passage experiments.</p> <p>Results</p> <p>No clinical, pathological or bioassay evidence of transmission of BSE to the chicken was obtained in the primary or sub-passage experiments. Survival data showed no significant differences between control and treatment groups. Neurological signs observed, not previously described in the domestic chicken, were not associated with significant pathology. The diagnostic techniques applied failed to detect a disease associated form of PrP.</p> <p>Conclusion</p> <p>Important from a risk assessment perspective, the present study has established that the domestic chicken does not develop a prion disease after large parenteral exposures to the BSE agent or after oral exposures equivalent to previous exposures via commercial diets. Future investigations into the potential susceptibility of avian species to mammalian prion diseases require species-specific immunochemical techniques and more refined experimental models.</p

The intestinal expulsion of the roundworm Ascaris suum is associated with eosinophils, intra-epithelial T cells and decreased intestinal transit time

Ascaris lumbricoides remains the most common endoparasite in humans, yet there is still very little information available about the immunological principles of protection, especially those directed against larval stages. Due to the natural host-parasite relationship, pigs infected with A. suum make an excellent model to study the mechanisms of protection against this nematode. In pigs, a self-cure reaction eliminates most larvae from the small intestine between 14 and 21 days post infection. In this study, we investigated the mucosal immune response leading to the expulsion of A. suum and the contribution of the hepato-tracheal migration. Self-cure was independent of previous passage through the liver or lungs, as infection with lung stage larvae did not impair self-cure. When animals were infected with 14-day-old intestinal larvae, the larvae were being driven distally in the small intestine around 7 days post infection but by 18 days post infection they re-inhabited the proximal part of the small intestine, indicating that more developed larvae can counter the expulsion mechanism. Self-cure was consistently associated with eosinophilia and intra-epithelial T cells in the jejunum. Furthermore, we identified increased gut movement as a possible mechanism of self-cure as the small intestinal transit time was markedly decreased at the time of expulsion of the worms. Taken together, these results shed new light on the mechanisms of self-cure that occur during A. suum infections

Assembly of the Red Sequence in Infrared-Selected Galaxy Clusters from the IRAC Shallow Cluster Survey

We present results for the assembly and star formation histories of massive (~L*) red sequence galaxies in 11 spectroscopically confirmed, infrared-selected galaxy clusters at 1.0 < z < 1.5, the precursors to present-day massive clusters with M ~ 10^15 M_sun. Using rest-frame optical photometry, we investigate evolution in the color and scatter of the red sequence galaxy population, comparing with models of possible star formation histories. In contrast to studies of central cluster galaxies at lower redshift (z < 1), these data are clearly inconsistent with the continued evolution of stars formed and assembled primarily at a single, much-earlier time. Specifically, we find that the colors of massive cluster galaxies at z = 1.5 imply that the bulk of star formation occurred at z ~ 3, whereas by z = 1 their colors imply formation at z ~ 2; therefore these galaxies exhibit approximately the same luminosity-weighted stellar age at 1 < z < 1.5. This likely reflects star formation that occurs over an extended period, the effects of significant progenitor bias, or both. Our results generally indicate that massive cluster galaxy populations began forming a significant mass of stars at z >~ 4, contained some red spheroids by z ~ 1.5, and were actively assembling much of their final mass during 1 < z < 2 in the form of younger stars. Qualitatively, the slopes of the cluster color-magnitude relations are consistent with no significant evolution relative to local clusters.Comment: 24 pages, 9 figures, accepted to Ap