Fission yeast 26S proteasome mutants are multi-drug resistant due to stabilization of the pap1 transcription factor

Here we report the result of a genetic screen for mutants resistant to the microtubule poison methyl benzimidazol-2-yl carbamate (MBC) that were also temperature sensitive for growth. In total the isolated mutants were distributed in ten complementation groups. Cloning experiments revealed that most of the mutants were in essential genes encoding various 26S proteasome subunits. We found that the proteasome mutants are multi-drug resistant due to stabilization of the stress-activated transcription factor Pap1. We show that the ubiquitylation and ultimately the degradation of Pap1 depend on the Rhp6/Ubc2 E2 ubiquitin conjugating enzyme and the Ubr1 E3 ubiquitin-protein ligase. Accordingly, mutants lacking Rhp6 or Ubr1 display drug-resistant phenotypes

Wave Intensity Analysis Provides Novel Insights Into Pulmonary Arterial Hypertension and Chronic Thromboembolic Pulmonary Hypertension.

BACKGROUND: In contrast to systemic hypertension, the significance of arterial waves in pulmonary hypertension (PH) is not well understood. We hypothesized that arterial wave energy and wave reflection are augmented in PH and that wave behavior differs between patients with pulmonary arterial hypertension (PAH) and chronic thromboembolic pulmonary hypertension (CTEPH). METHODS AND RESULTS: Right heart catheterization was performed using a pressure and Doppler flow sensor-tipped catheter to obtain simultaneous pressure and flow velocity measurements in the pulmonary artery. Wave intensity analysis was subsequently applied to the acquired data. Ten control participants, 11 patients with PAH, and 10 patients with CTEPH were studied. Wave speed and wave power were significantly greater in PH patients compared with controls, indicating increased arterial stiffness and right ventricular work, respectively. The ratio of wave power to mean right ventricular power was lower in PAH patients than CTEPH patients and controls. Wave reflection index in PH patients (PAH: ≈25%; CTEPH: ≈30%) was significantly greater compared with controls (≈4%), indicating downstream vascular impedance mismatch. Although wave speed was significantly correlated to disease severity, wave reflection indexes of patients with mildly and severely elevated pulmonary pressures were similar. CONCLUSIONS: Wave reflection in the pulmonary artery increased in PH and was unrelated to severity, suggesting that vascular impedance mismatch occurs early in the development of pulmonary vascular disease. The lower wave power fraction in PAH compared with CTEPH indicates differences in the intrinsic and/or extrinsic ventricular load between the 2 diseases

Communicating effectiveness of intervention for chronic diseases: what single format can replace comprehensive information?

<p>Abstract</p> <p>Background</p> <p>There is uncertainty about how GPs should convey information about treatment effectiveness to their patients in the context of cardiovascular disease. Hence we study the concordance of decisions based on one of four single information formats for treatment effectiveness with subsequent decisions based on all four formats combined with a pictorial representation.</p> <p>Methods</p> <p>A randomized study comprising 1,169 subjects aged 40–59 in Odense, Denmark. Subjects were randomized to receive information in terms of absolute risk reduction (ARR), relative risk reduction (RRR), number needed to treat (NNT), or prolongation of life (POL) without heart attack, and were asked whether they would consent to treatment. Subsequently the same information was conveyed with all four formats jointly accompanied by a pictorial presentation of treatment effectiveness. Again, subjects should consider consent to treatment.</p> <p>Results</p> <p>After being informed about all four formats, 52%–79% of the respondents consented to treatment, depending on level of effectiveness and initial information format. Overall, ARR gave highest concordance, 94% (95% confidence interval (91%; 97%)) between initial and final decision, but ARR was not statistically superior to the other formats.</p> <p>Conclusion</p> <p>Decisions based on ARR had the best concordance with decisions based on all four formats and pictorial representation, but the difference in concordance between the four formats was small, and it is unclear whether respondents fully understood the information they received.</p

Waterborne Electrospinning of α-Lactalbumin Generates Tunable and Biocompatible Nanofibers for Drug Delivery

This is the author accepted manuscript. The final version is available from the American Chemical Society via the DOI in this recordProtein-based drug carriers are an interesting alternative to traditional polymeric drug delivery systems due to their intrinsic biocompatibility and biodegradability. Electrospinning of neat proteins holds advantages over electrospinning of protein mixtures, e.g., whey isolates, such as better control of the physicochemical and biological function of the resulting nanofiber-based system. In this study, we explore electrospinning of the isolated milk protein α-lactalbumin (ALA), which is a whey protein with important nutritional and pharmacological properties. Via waterborne electrospinning of ALA with a minimum amount of poly(ethylene oxide) (PEO) as a cospininng polymer, nanofibers of high protein content were successfully produced (up to 84% (w/w)). We demonstrate the ability to produce ALA-based nanofibers with a high degree of tunability in terms of size, stability in water, and mechanical properties. The nanofibers displayed excellent biocompatibility in vitro as the viability of cultured TR146 human buccal epithelium and NIH 3T3 murine fibroblast cells was not influenced by exposure to ALA-based nanofibers. ALA-based nanofibers were loaded with up to 6% (w/w) ampicilin, and the nanofibers were capable of maintaining the activity of the antibiotic after electrospinning and cross-linking. Using such a property of the material, we demonstrate that ampicillin-loaded nanofibers successfully inhibit the growth of Gram-negative bacteria in vitro. Importantly, after treatment with ampicillin-loaded nanofibers, no bacterial regrowth was observed, which indicates that this treatment may clear eventual persisters to ampicillin. Finally, the structural properties of the native functional protein were maintained after release of ALA from the nanofibers. This promotes our platform, not only as a sustainable protein-based drug delivery system, but also as an innovative solid form of ALA for food and pharmaceutical applications.Villum FoundationDanish Council for Independent Research; Technology and ProductionRoyal SocietyMedical Research Council (MRC)Wellcome Trus

A frequentist framework of inductive reasoning

Reacting against the limitation of statistics to decision procedures, R. A. Fisher proposed for inductive reasoning the use of the fiducial distribution, a parameter-space distribution of epistemological probability transferred directly from limiting relative frequencies rather than computed according to the Bayes update rule. The proposal is developed as follows using the confidence measure of a scalar parameter of interest. (With the restriction to one-dimensional parameter space, a confidence measure is essentially a fiducial probability distribution free of complications involving ancillary statistics.) A betting game establishes a sense in which confidence measures are the only reliable inferential probability distributions. The equality between the probabilities encoded in a confidence measure and the coverage rates of the corresponding confidence intervals ensures that the measure's rule for assigning confidence levels to hypotheses is uniquely minimax in the game. Although a confidence measure can be computed without any prior distribution, previous knowledge can be incorporated into confidence-based reasoning. To adjust a p-value or confidence interval for prior information, the confidence measure from the observed data can be combined with one or more independent confidence measures representing previous agent opinion. (The former confidence measure may correspond to a posterior distribution with frequentist matching of coverage probabilities.) The representation of subjective knowledge in terms of confidence measures rather than prior probability distributions preserves approximate frequentist validity.Comment: major revisio

Can postponement of an adverse outcome be used to present risk reductions to a lay audience? A population survey

BACKGROUND: For shared decision making doctors need to communicate the effectiveness of therapies such that patients can understand it and discriminate between small and large effects. Previous research indicates that patients have difficulties in understanding risk measures. This study aimed to test the hypothesis that lay people may be able to discriminate between therapies when their effectiveness is expressed in terms of postponement of an adverse disease event. METHODS: In 2004 a random sample of 1,367 non-institutionalized Danes aged 40+ was interviewed in person. The participants were asked for demographic information and asked to consider a hypothetical preventive drug treatment. The respondents were randomized to the magnitude of treatment effectiveness (heart attack postponement of 1 month, 6 months, 12 months, 2 years, 4 years and 8 years) and subsequently asked whether they would take such a therapy. They were also asked whether they had hypercholesterolemia or had experienced a heart attack. RESULTS: In total 58% of the respondents consented to the hypothetical treatment. The proportions accepting treatment were 39%, 52%, 56%, 64%, 67% and 73% when postponement was 1 month, 6 months, 12 months, 2 years, 4 years and 8 years respectively. Participants who thought that the effectiveness information was difficult to understand, were less likely to consent to therapy (p = 0.004). CONCLUSION: Lay people can discriminate between levels of treatment effectiveness when they are presented in terms of postponement of an adverse event. The results indicate that such postponement is a comprehensible measure of effectiveness

Species diversity of Trichoderma in Poland

In the present study, we reinvestigate the diversity of Trichoderma in Poland utilizing a combination of morphological and molecular/phylogenetic methods. A total of 170 isolates were collected from six different substrata at 49 sites in Poland. These were divided among 14 taxa as follows: 110 of 170 Trichoderma isolates were identified to the species level by the analysis of their ITS1, ITS2 rDNA sequences as: T. harzianum (43 isolates), T. aggressivum (35), T. citrinoviride (11), T. hamatum (9), T. virens (6), T. longibrachiatum (4), T. polysporum (1), and T. tomentosum (1); 60 isolates belonging to the Viride clade were identified based on a fragment of the translation-elongation factor 1-alpha (tef1) gene as: T. atroviride (20 isolates), T. gamsii (2), T. koningii (17), T. viridescens (13), T. viride (7), and T. koningiopsis (1). Identifications were made using the BLAST interface in TrichOKEY and TrichoBLAST (http://www.isth.info). The most diverse substrata were soil (nine species per 22 isolates) and decaying wood (nine species per 75 isolates). The most abundant species (25%) isolated from all substrata was T. harzianum

Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules

Successful predictions of peptide MHC binding typically require a large set of binding data for the specific MHC molecule that is examined. Structure based prediction methods promise to circumvent this requirement by evaluating the physical contacts a peptide can make with an MHC molecule based on the highly conserved 3D structure of peptide:MHC complexes. While several such methods have been described before, most are not publicly available and have not been independently tested for their performance. We here implemented and evaluated three prediction methods for MHC class II molecules: statistical potentials derived from the analysis of known protein structures; energetic evaluation of different peptide snapshots in a molecular dynamics simulation; and direct analysis of contacts made in known 3D structures of peptide:MHC complexes. These methods are ab initio in that they require structural data of the MHC molecule examined, but no specific peptide:MHC binding data. Moreover, these methods retain the ability to make predictions in a sufficiently short time scale to be useful in a real world application, such as screening a whole proteome for candidate binding peptides. A rigorous evaluation of each methods prediction performance showed that these are significantly better than random, but still substantially lower than the best performing sequence based class II prediction methods available. While the approaches presented here were developed independently, we have chosen to present our results together in order to support the notion that generating structure based predictions of peptide:MHC binding without using binding data is unlikely to give satisfactory results

Laypersons' understanding of relative risk reductions: Randomised cross-sectional study

<p>Abstract</p> <p>Background</p> <p>Despite increasing recognition of the importance of involving patients in decisions on preventive healthcare interventions, little is known about how well patients understand and utilise information provided on the relative benefits from these interventions. The aim of this study was to explore whether lay people can discriminate between preventive interventions when effectiveness is presented in terms of relative risk reduction (RRR), and whether such discrimination is influenced by presentation of baseline risk.</p> <p>Methods</p> <p>The study was a randomised cross-sectional interview survey of a representative sample (n = 1,519) of lay people with mean age 59 (range 40–98) years in Denmark. In addition to demographic information, respondents were asked to consider a hypothetical drug treatment to prevent heart attack. Its effectiveness was randomly presented as RRR of 10, 20, 30, 40, 50 or 60 percent, and half of the respondents were presented with quantitative information on the baseline risk of heart attack. The respondents had also been asked whether they were diagnosed with hypercholesterolemia or had experienced a heart attack.</p> <p>Results</p> <p>In total, 873 (58%) of the respondents consented to the hypothetical treatment. While 49% accepted the treatment when RRR = 10%, the acceptance rate was 58–60% for RRR>10. There was no significant difference in acceptance rates across respondents irrespective of whether they had been presented with quantitative information on baseline risk or not.</p> <p>Conclusion</p> <p>In this study, lay people's decisions about therapy were only slightly influenced by the magnitude of the effect when it was presented in terms of RRR. The results may indicate that lay people have difficulties in discriminating between levels of effectiveness when they are presented in terms of RRR.</p