Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function

To determine which of seven library design algorithms best introduces new protein function without destroying it altogether, seven combinatorial libraries of green fluorescent protein variants were designed and synthesized. Each was evaluated by distributions of emission intensity and color compiled from measurements made in vivo. Additional comparisons were made with a library constructed by error-prone PCR. Among the designed libraries, fluorescent function was preserved for the greatest fraction of samples in a library designed by using a structure-based computational method developed and described here. A trend was observed toward greater diversity of color in designed libraries that better preserved fluorescence. Contrary to trends observed among libraries constructed by error-prone PCR, preservation of function was observed to increase with a library's average mutation level among the four libraries designed with structure-based computational methods

Mechanism of the Very Efficient Quenching of Tryptophan Fluorescence in Human γD- and γS-Crystallins: The γ-Crystallin Fold May Have Evolved To Protect Tryptophan Residues from Ultraviolet Photodamage†

Proteins exposed to UV radiation are subject to irreversible photodamage through covalent modification of tryptophans (Trps) and other UV-absorbing amino acids. Crystallins, the major protein components of the vertebrate eye lens that maintain lens transparency, are exposed to ambient UV radiation throughout life. The duplicated β-sheet Greek key domains of β- and γ-crystallins in humans and all other vertebrates each have two conserved buried Trps. Experiments and computation showed that the fluorescence of these Trps in human γD-crystallin is very efficiently quenched in the native state by electrostatically enabled electron transfer to a backbone amide [Chen et al. (2006) Biochemistry 45, 11552−11563]. This dispersal of the excited state energy would be expected to minimize protein damage from covalent scission of the excited Trp ring. We report here both experiments and computation showing that the same fast electron transfer mechanism is operating in a different crystallin, human γS-crystallin. Examination of solved structures of other crystallins reveals that the Trp conformation, as well as favorably oriented bound waters, and the proximity of the backbone carbonyl oxygen of the n − 3 residues before the quenched Trps (residue n), are conserved in most crystallins. These results indicate that fast charge transfer quenching is an evolved property of this protein fold, probably protecting it from UV-induced photodamage. This UV resistance may have contributed to the selection of the Greek key fold as the major lens protein in all vertebrates.National Eye Institute (Grant EY 015834

Staying well after depression: trial design and protocol

<p>Abstract</p> <p>Background</p> <p>Depression is often a chronic relapsing condition, with relapse rates of 50-80% in those who have been depressed before. This is particularly problematic for those who become suicidal when depressed since habitual recurrence of suicidal thoughts increases likelihood of further acute suicidal episodes. Therefore the question how to prevent relapse is of particular urgency in this group.</p> <p>Methods/Design</p> <p>This trial compares Mindfulness-Based Cognitive Therapy (MBCT), a novel form of treatment combining mindfulness meditation and cognitive therapy for depression, with both Cognitive Psycho-Education (CPE), an equally plausible cognitive treatment but without meditation, and treatment as usual (TAU). It will test whether MBCT reduces the risk of relapse in recurrently depressed patients and the incidence of suicidal symptoms in those with a history of suicidality who do relapse. It recruits participants, screens them by telephone for main inclusion and exclusion criteria and, if they are eligible, invites them to a pre-treatment session to assess eligibility in more detail. This trial allocates eligible participants at random between MBCT and TAU, CPE and TAU, and TAU alone in a ratio of 2:2:1, stratified by presence of suicidal ideation or behaviour and current anti-depressant use. We aim to recruit sufficient participants to allow for retention of 300 following attrition. We deliver both active treatments in groups meeting for two hours every week for eight weeks. We shall estimate effects on rates of relapse and suicidal symptoms over 12 months following treatment and assess clinical status immediately after treatment, and three, six, nine and twelve months thereafter.</p> <p>Discussion</p> <p>This will be the first trial of MBCT to investigate whether MCBT is effective in preventing relapse to depression when compared with a control psychological treatment of equal plausibility; and to explore the use of MBCT for the most severe recurrent depression - that in people who become suicidal when depressed.</p> <p>Trial Registration</p> <p>Current Controlled Trials: ISRCTN97185214.</p

Decision-making of English Netball Superleague umpires: Contextual and dispositional influences

Objectives. The decisions made by officials have a direct bearing on the outcomes of competitive sport contests. In an exploratory study, we examine the interrelationships between the decisions made by elite netball umpires, the potential contextual and environmental influences (e.g., crowd size), and the umpires’ dispositional tendencies – specifically, their propensity to deliberate and ruminate on their decisions. Design/Method. Filmed footage from 60 England Netball Superleague matches was coded using performance analysis software. We measured the number of decisions made overall, and for home and away teams; league position; competition round; match quarter; and crowd size. Additionally, 10 umpires who officiated in the matches completed the Decision-Specific Reinvestment Scale (DSRS). Results. Regression analyses predicted that as home teams’ league position improved the number of decisions against away teams increased. A model comprising competition round and average league position of both teams predicted the number of decisions made in matches, but neither variable emerged as a significant predictor. The umpire analyses revealed that greater crowd size was associated with an increase in decisions against away teams. The Decision Rumination factor was strongly negatively related to the number of decisions in Quarters 1 and 3, this relationship was driven by fewer decisions against home teams by umpires who exhibited higher Rumination subscale scores. Conclusions. These findings strengthen our understanding of contextual, environmental, and dispositional influences on umpires’ decision-making behaviour. The tendency to ruminate upon decisions may explain the changes in decision behaviour in relation to the home team advantage effect

Do Worry and Brooding Predict Health Behaviors? A Daily Diary Investigation

Background Meta-analyses have reported associations between perseverative cognition (both worry and brooding) and increased engagement in health-risk behaviors, poorer sleep, and poorer physiological health outcomes. Method Using a daily diary design, this study investigated the within- and between-person relationships between state and trait perseverative cognition and health behaviors (eating behavior, physical activity, alcohol consumption, and sleep) both crosssectionally and prospectively. Participants (n = 273, 93% students, Mage = 20.2, SD = 4.11, 93% female) completed morning and evening diaries across 7 consecutive days. Results Multilevel modeling analyses revealed that, cross-sectionally, higher levels of state worry were associated with more time spent sitting and higher levels of state brooding predicted less daily walking. Conclusion Worry and brooding may represent useful intervention targets for improving inactivity and walking levels, respectively

Common Versus Unique Variance Across Measures of Worry and Rumination: Predictive Utility and Mediational Models for Anxiety and Depression

Repetitive negative thinking (RNT) has been identified as a transdiagnostic construct. However, diagnosis- specific questionnaires have traditionally been used to measure RNT across emotional disorders, and thus the degree to which they assess shared versus unique aspects of RNT is unclear. Furthermore, the degree to which shared versus unique variance across these measures contributes to the prediction of anxiety and depression symptoms is yet to be fully understood. This study had three aims. First, confirmatory factor analysis was used to test the degree to which two common, diagnosis-specific questionnaires assess common versus unique variance in RNT. One questionnaire measured worry whereas the other measured two aspects of rumination (brooding, reflection). Second, the contribution of the shared and unique variance in predicting symptoms of anxiety and depression was determined. Third, the role of shared and unique variance in mediating the relationships between the vulnerability factor of negative affectivity and symptoms of anxiety and depression was assessed

Redirecting research efforts on the diversification-performance linkage: The search for synergy

We review the literature on the diversification-performance (D-P) relationship to a) propose that the time is ripe for a renewed attack on understanding the relationship between diversification and firm performance, and b) outline a new approach to attacking the question. Our paper makes four main contributions. First, through a review of the literature we establish the inherent complexities in the D-P relationship and the methodological challenges confronted by the literature in reaching its current conclusion of a non-linear relationship between diversification and performance. Second, we argue that to better guide managers the literature needs to develop along a complementary path – whereas past research has often focused on answering the big question of does diversification affect firm performance, this second path would focus more on identifying the precise micro-mechanisms through which diversification adds or subtracts value. Third, we outline a new approach to the investigation of this topic, based on (a) identifying the precise underlying mechanisms through which diversification affects performance; (b) identifying performance outcomes that are “proximate” to the mechanism that the researcher is studying, and (c) identifying an appropriate research design that can enable a causal claim. Finally, we outline a set of directions for future research