Quantitative trait locus analysis of tolerance to temperature fluctuations in winter,fruit characteristics,flower color,and prickle-free canes in raspberry

Despite the interest in growing raspberries (Rubus idaeus) in the southeastern USA, production is limited by the lack of cultivars adapted to the climate. One of these major climate adaptations is the ability to tolerate fluctuating winter temperatures. Perennial plants have adapted to these conditions by having high chilling requirements. Breeding efforts are underway for developing adapted cultivars, but breeding improvements in Rubus is a time-consuming process. In order to expedite the breeding process, molecular breeding tools are being developed. In this work, the cross (Rubus parvifolius × Tulameen) × Qualicum was used for the construction of a genetic linkage map and for quantitative trait locus (QTL) analyses of chilling requirement, prickle density, fruit color, fruit shape, fruit size, and flower color. Chilling requirements were determined by measuring bud break in chilled cuttings; all other traits were scored visually. Seven linkage groups were constructed and compared to an established Rubus map. Four regions were associated with chilling requirement, and were mostly consistent across 3 years of evaluation. For the fruit and flower color traits, significant regions were consistent across 2 years, and either one or two QTL were found. Two QTL linked to prickle density were detected; one coincided with previous studies, while the second QTL was found in linkage group 4 and co-localized with the marker for lack of prickles. This region is proposed to contain gene s for the prickle-free trait.     

The mechanism for RNA recognition by ANTAR regulators of gene expression

ANTAR proteins are widespread bacterial regulatory proteins that have RNA-binding output domains and utilize antitermination to control gene expression at the post-initiation level. An ANTAR protein, EutV, regulates the ethanolamine-utilization genes (eut) in Enterococcus faecalis. Using this system, we present genetic and biochemical evidence of a general mechanism of antitermination used by ANTARs, including details of the antiterminator structure. The novel antiterminator structure consists of two small hairpins with highly conserved terminal loop residues, both features being essential for successful antitermination. The ANTAR protein dimerizes and associates with its substrate RNA in response to signal-induced phosphorylation. Furthermore, bioinformatic searches using this conserved antiterminator motif identified many new ANTAR target RNAs in phylogenetically diverse bacterial species, some comprising complex regulons. Despite the unrelatedness of the species in which they are found, the majority of the ANTAR-associated genes are thematically related to nitrogen management. These data suggest that the central tenets for gene regulation by ANTAR antitermination occur widely in nature to specifically control nitrogen metabolism.     

Home Videophones Improve Direct Observation in Tuberculosis Treatment: A Mixed Methods Evaluation

Background

The use of direct observation to monitor tuberculosis treatment is controversial: cost, practical difficulties, and lack of patient acceptability limit effectiveness. Telehealth is a promising alternative delivery method for improving implementation. This study aimed to evaluate the clinical and cost-effectiveness of a telehealth service delivering direct observation, compared to an in-person drive-around service.

Methodology/Principal Findings

The study was conducted within a community nursing service in South Australia. Telehealth patients received daily video calls at home on a desktop videophone provided by the nursing call center. A retrospective cohort study assessed the effectiveness of the telehealth and traditional forms of observation, defined by the proportion of missed observations recorded in case notes. This data was inputted to a model, estimating the incremental cost-effectiveness ratio (ICER) of telehealth. Semi-structured interviews were conducted with current patients, community nursing and Chest Clinic staff, concerning service acceptability, usability and sustainability. The percentage of missed observations for the telehealth service was 12.1 (n = 58), compared to 31.1 for the in-person service (n = 70). Most of the difference of 18.9% (95% CI: 12.2 – 25.4) was due to fewer pre-arranged absences. The economic analysis calculated the ICER to be AUD$1.32 (95% CI: $0.51 – $2.26) per extra day of successful observation. The video service used less staff time, and became dominant if implemented on a larger scale and/or with decreased technology costs. Qualitative analysis found enabling factors of flexible timing, high patient acceptance, staff efficiency, and Chest Clinic support. Substantial technical problems were manageable, and improved liaison between the nursing service and Chest Clinic was an unexpected side-benefit.

Conclusions/Significance

Home video observation is a patient-centered, resource efficient way of delivering direct observation for TB, and is cost-effective when compared with a drive-around service. Future research is recommended to determine applicability and effectiveness in other settings.     

Are There Neurophenotypes for Asthma? Functional Brain Imaging of the Interaction between Emotion and Inflammation in Asthma

Background

Asthma is a chronic inflammatory disease noteworthy for its vulnerability to stress and emotion-induced symptom intensification. The fact that psychological stress and mood and anxiety disorders appear to increase expression of asthma symptoms suggests that neural signaling between the brain and lung at least partially modulates the inflammatory response and lung function. However, the precise nature of the neural pathways implicated in modulating asthma symptoms is unknown. Moreover, the extent to which variations in neural signaling predict different phenotypes of disease expression has not been studied.

Methods and Results

We used functional magnetic resonance imaging to measure neural signals in response to asthma-specific emotional cues, following allergen exposure, in asthmatics with a dual response to allergen challenge (significant inflammation), asthmatics with only an immediate response (minimal inflammation), and healthy controls. The anterior insular cortex was differentially activated by asthma-relevant cues, compared to general negative cues, during the development of the late phase of the dual response in asthmatics. Moreover, the degree of this differential activation predicted changes in airway inflammation.

Conclusions

These findings indicate that neurophenotypes for asthma may be identifiable by neural reactivity of brain circuits known to be involved in processing emotional information. Those with greater activation in the anterior insula, in response to asthma-relevant psychological stimuli, exhibit greater inflammatory signals in the lung and increased severity of disease and may reflect a subset of asthmatics most vulnerable to the development of psychopathology. This approach offers an entirely new target for potential therapeutic intervention in asthma.     

The repeated replacement method: a pure lagrangian meshfree method for computational fluid dynamics

In this paper we describe the repeated replacement method (RRM), a new meshfree method for computational fluid dynamics (CFD). RRM simulates fluid flow by modeling compressible fluids' tendency to evolve towards a state of constant density, velocity, and pressure. To evolve a fluid flow simulation forward in time, RRM repeatedly "chops out" fluid from active areas and replaces it with new "flattened" fluid cells with the same mass, momentum, and energy. We call the new cells "flattened" because we give them constant density, velocity, and pressure, even though the chopped-out fluid may have had gradients in these primitive variables. RRM adaptively chooses the sizes and locations of the areas it chops out and replaces. It creates more and smaller new cells in areas of high gradient, and fewer and larger new cells in areas of lower gradient. This naturally leads to an adaptive level of accuracy, where more computational effort is spent on active areas of the fluid, and less effort is spent on inactive areas. We show that for common test problems, RRM produces results similar to other high-resolution CFD methods, while using a very different mathematical framework. RRM does not use Riemann solvers, flux or slope limiters, a mesh, or a stencil, and it operates in a purely Lagrangian mode. RRM also does not evaluate numerical derivatives, does not integrate equations of motion, and does not solve systems of equations.     

Ozone effects in a drier climate: implications for stomatal fluxes of reduced stomatal sensitivity to soil drying in a typical grassland species

The widely distributed temperate grassland species Dactylis glomerata was grown in competition with Ranunculus acris at two different watering regimes and exposed for 20 weeks to eight ozone treatments with mean concentrations ranging from 16.2 to 89.5 ppb, representing pre‐industrial to predicted post‐2100 ozone climates. Measurements of stomatal conductance were used to parameterize ozone flux models for D. glomerata. For the first time, a modification was made to the standard flux model to account for the observed decrease in sensitivity of stomatal conductance to reduced water availability with increasing ozone. Comparison of calculated cumulative ozone flux between the two versions of the model demonstrated that exclusion of the ozone effect on stomatal conductance in the standard flux model led to a large underestimation of ozone fluxes at mid‐ to high‐ozone concentrations. For example, at a mean ozone concentration of 55 ppb (as predicted for many temperate areas in the next few decades), the standard flux model underestimated ozone fluxes in D. glomerata by 30–40% under reduced water availability. Although the modified flux model does not markedly change the flux‐based critical level for D. glomerata, this study indicates that use of the standard flux model to quantify the risk of ozone damage to a widely distributed grassland species such as D. glomerata in areas where high ozone concentrations and reduced soil moisture coincide could lead to an underestimation of effects. Thus, this study has shown that under predicted future climate change and ozone scenarios, ozone effects on vegetation may be even greater than previously predicted in the drier areas of the world.     

Electrostatic Ratchet in the Protective Antigen Channel Promotes Anthrax Toxin Translocation

Central to the power-stroke and Brownian-ratchet mechanisms of protein translocation is the process through which nonequilibrium fluctuations are rectified or ratcheted by the molecular motor to transport substrate proteins along a specific axis. We investigated the ratchet mechanism using anthrax toxin as a model. Anthrax toxin is a tripartite toxin comprised of the protective antigen (PA) component, a homooligomeric transmembrane translocase, which translocates two other enzyme components, lethal factor (LF) and edema factor (EF), into the cytosol of the host cell under the proton motive force (PMF). The PA-binding domains of LF and EF (LF_N and EF_N) possess identical folds and similar solution stabilities; however, EF_N translocates ∼10–200-fold slower than LF_N, depending on the electrical potential (Δψ) and chemical potential (ΔpH) compositions of the PMF. From an analysis of LF_N/EF_N chimera proteins, we identified two 10-residue cassettes comprised of charged sequence that were responsible for the impaired translocation kinetics of EF_N. These cassettes have nonspecific electrostatic requirements: one surprisingly prefers acidic residues when driven by either a Δψ or a ΔpH; the second requires basic residues only when driven by a Δψ. Through modeling and experiment, we identified a charged surface in the PA channel responsible for charge selectivity. The charged surface latches the substrate and promotes PMF-driven transport. We propose an electrostatic ratchet in the channel, comprised of opposing rings of charged residues, enforces directionality by interacting with charged cassettes in the substrate, thereby generating forces sufficient to drive unfolding.     

Free-ranging black howler monkeys, Alouatta pigra, in southern Belize are not parasitized by Controrchis biliophilus

Several coprological studies of Alouatta pigra, the black howler monkey, inhabiting Belize and Mexico have been published in the past several years. Trematodes, specifically Controrchis biliophilus (Dicrocoeliidae), have been detected in A. pigra from all locations in Belize and Mexico examined in those studies. A routine coprological survey of A. pigra was conducted in May and June 2010 as part of baseline data collection for an A. pigra population in Punta Gorda, Toledo District, southern Belize. The 51 fecal samples collected in this area were all negative for C. biliophilus. Subsequently, two additional fecal samples were collected from another population of A. pigra in Toledo District and 25 additional fecal samples were collected from six other areas of Belize during December 2010 and January 2011 and were examined for parasites. To date, C. biliophilus eggs have been detected in fecal samples from A. pigra inhabiting every district of Belize except Toledo District in southern Belize. This finding is notable, for no other population of A. pigra completely free of C. biliophilus infection had been located prior to this study.     

Prevalence,Characteristics, and Correlates of Teasing Experiences among Overweight Children vs. Non‐overweight Peers

Objective: Information regarding the prevalence, nature, sources, and psychosocial correlates of teasing was obtained for overweight (OV) children (10 to 14 years of age) vs. non‐overweight (non‐OV) peers. It was hypothesized that weight‐related teasing would be negatively correlated with self‐esteem in specific domains and with enjoyment of physical/social activities and positively correlated with loneliness, bulimic behaviors, body dissatisfaction, and enjoyment of sedentary/isolative activities. Research Methods and Procedures: Teasing experiences and psychosocial correlates were assessed among OV children from a fitness camp and a demographically similar school sample of non‐OV children. Results: Among the OV children, appearance‐related teasing was more prevalent, frequent, and upsetting, involved disparaging nicknames focusing more on weight rather than less stigmatized aspects of appearance, and more often perpetrated by peers in general rather than a specific peer. Degree of teasing within the full sample was significantly associated with higher weight concerns, more loneliness, poorer self‐perception of one's physical appearance, higher preference for sedentary/isolative activities, and lower preference for active/social activities, all but the latter association holding up above and beyond actual weight status and demographics. Among OV children, teasing was associated with bulimic behaviors. Associations with type of teasing showed specificity, with weight‐related teasing predicting weight and appearance variables and competency‐related teasing related to social domain factors. Discussion: When frequency, intensity, emotional impact, and stigmatized content are examined, findings indicate that teasing is more severe for OV children. Effective interventions are needed to help victims cope with and prevent further weight‐related teasing, which may improve peer functioning, enhance weight control efforts, and reduce risk for future eating disturbance.