The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy

Conformational fluctuations of single-stranded DNA (ssDNA) oligonucleotides were studied in aqueous solution by monitoring contact-induced fluorescence quenching of the oxazine fluorophore MR121 by intrinsic guanosine residues (dG). We applied fluorescence correlation spectroscopy as well as steady-state and time-resolved fluorescence spectroscopy to analyze kinetics of DNA hairpin folding. We first characterized the reporter system by investigating bimolecular quenching interactions between MR121 and guanosine monophosphate in aqueous solution estimating rate constants, efficiency and stability for formation of quenched complexes. We then studied the kinetics of complex formation between MR121 and dG residues site-specifically incorporated in DNA hairpins. To uncover the initial steps of DNA hairpin folding we investigated complex formation in ssDNA carrying one or two complementary base pairs (dC–dG pairs) that could hybridize to form a short stem. Our data show that incorporation of a single dC–dG pair leads to non-exponential decays for opening and closing kinetics and reduces rate constants by one to two orders of magnitude. We found positive activation enthalpies independent of the number of dC–dG pairs. These results imply that the rate limiting step of DNA hairpin folding is not determined by loop dynamics, or by mismatches in the stem, but rather by interactions between stem and loop nucleotides

An exploratory cluster randomised trial of a university halls of residence based social norms intervention in Wales, UK

Background: Excessive alcohol consumption amongst university students has received increasing attention. A social norms approach to reducing drinking behaviours has met with some success in the USA. Such an approach is based on the assumption that student's perceptions of the norms of their peers are highly influential, but that these perceptions are often incorrect. Social norms interventions therefore aim to correct these inaccurate perceptions, and in turn, to change behaviours. However, UK studies are scarce and it is increasingly recognised that social norm interventions need to be supported by socio ecological approaches that address the wider determinants of behaviour. Objectives: To describe the research design for an exploratory trial examining the acceptability, hypothesised process of change and implementation of a social norm marketing campaign designed to correct misperceptions of normative alcohol use and reduce levels of misuse, implemented alongside a university wide alcohol harm reduction toolkit. It also assesses the feasibility of a potential large scale effectiveness trial by providing key trial design parameters including randomisation, recruitment and retention, contamination, data collection methods, outcome measures and intracluster correlations. Methods/design: The study adopts an exploratory cluster randomised controlled trial design with halls of residence as the unit of allocation, and a nested mixed methods process evaluation. Four Welsh (UK) universities participated in the study, with residence hall managers consenting to implementation of the trial in 50 university owned campus based halls of residence. Consenting halls were randomised to either a phased multi channel social norm marketing campaign addressing normative discrepancies (n = 25 intervention) or normal practice (n = 25 control). The primary outcome is alcohol consumption (units per week) measured using the Daily Drinking Questionnaire. Secondary outcomes assess frequency of alcohol consumption, higher risk drinking, alcohol related problems and change in perceptions of alcohol-related descriptive and injunctive norms. Data will be collected for all 50 halls at 4 months follow up through a cross-sectional on line and postal survey of approximately 4000 first year students. The process evaluation will explore the acceptability and implementation of the social norms intervention and toolkit and hypothesised process of change including awareness, receptivity and normative changes. Discussion: Exploratory trials such as this are essential to inform future definitive trials by providing crucial methodological parameters and guidance on designing and implementing optimum interventions

Primary and malignant cholangiocytes undergo CD40 mediated Fas dependent Apoptosis, but are insensitive to direct activation with exogenous fas ligand

Introduction Cholangiocarcinoma is a rare malignancy of the biliary tract, the incidence of which is rising, but the pathogenesis of which remains uncertain. No common genetic defects have been described but it is accepted that chronic inflammation is an important contributing factor. We have shown that primary human cholangiocyte and hepatocyte survival is tightly regulated via co-operative interactions between two tumour necrosis family (TNF) receptor family members; CD40 and Fas (CD95). Functional deficiency of CD154, the ligand for CD40, leads to a failure of clearance of biliary tract infections and a predisposition to cholangiocarcinoma implying a direct link between TNF receptor-mediated apoptosis and the development of cholangiocarcinoma. Aims To determine whether malignant cholangiocytes display defects in CD40 mediated apoptosis. By comparing CD40 and Fas-mediated apoptosis and intracellular signalling in primary human cholangiocytes and three cholangiocyte cell lines. Results Primary cholangiocytes and cholangiocyte cell lines were relatively insensitive to direct Fas-mediated killing with exogenous FasL when compared with Jurkat cells, which readily underwent Fas-mediated apoptosis, but were extremely sensitive to CD154 stimulation. The sensitivity of cells to CD40 activation was similar in magnitude in both primary and malignant cells and was STAT-3 and AP-1 dependent in both. Conclusions 1) Both primary and malignant cholangiocytes are relatively resistant to Fas–mediated killing but show exquisite sensitivity to CD154, suggesting that the CD40 pathway is intact and fully functional in both primary and malignant cholangiocytes 2) The relative insensitivity of cholangiocytes to Fas activation demonstrates the importance of CD40 augmentation of Fas dependent death in these cells. Agonistic therapies which target CD40 and associated intracellular signalling pathways may be effective in promoting apoptosis of malignant cholangiocytes

Mean ergodicity and spectrum of the Cesàro operator on weighted c0 spaces

[EN] A detailed investigation is made of the continuity, the compactness and the spectrum of the Cesàro operator C acting on the weighted Banach sequence space c0(w) for a bounded, strictly positive weight w. New features arise in the weighted setting (e.g. existence of eigenvalues, compactness, mean ergodicity) which are not present in the classical setting of c0.The research of the first two authors was partially supported by the Projects MTM2013-43540-P, GVA Prometeo II/2013/013 and ACOMP/2015/186 (Spain).Albanese, AA.; Bonet Solves, JA.; Ricker, WJ. (2016). Mean ergodicity and spectrum of the Cesàro operator on weighted c0 spaces. Positivity. 20:761-803. https://doi.org/10.1007/s11117-015-0385-xS76180320Akhmedov, A.M., Başar, F.: On the fine spectrum of the Cesàro operator in $$c_0$$ c 0 . Math. J. Ibaraki Univ. 36, 25–32 (2004)Akhmedov, A.M., Başar, F.: The fine spectrum of the Cesàro operator $$C_1$$ C 1 over the sequence space $$bv_p, (1 \le p < \infty )$$ b v p , ( 1 ≤ p < ∞ ) . Math. J. Okayama Univ. 50, 135–147 (2008)Albanese, A.A., Bonet, J., Ricker, W.J.: Convergence of arithmetic means of operators in Fréchet spaces. J. Math. Anal. Appl. 401, 160–173 (2013)Albanese, A.A., Bonet, J., Ricker, W.J.: Spectrum and compactness of the Cesàro operator on weighted $$\ell _p$$ ℓ p spaces. J. Aust. Math. Soc. 99, 287–314 (2015)Albanese, A.A., Bonet, J., Ricker, W.J.: The Cesàro operator in the Fréchet spaces $$\ell ^{p+}$$ ℓ p + and $$L ^{p-}$$ L p - . Glasg. Math. J (to appear)Ansari, S.I., Bourdon, P.S.: Some properties of cyclic operators. Acta Sci. Math. Szeged 63, 195–207 (1997)Brown, A., Halmos, P.R., Shields, A.L.: Cesàro operators. Acta Sci. Math. Szeged 26, 125–137 (1965)Curbera, G.P., Ricker, W.J.: Spectrum of the Cesàro operator in $$\ell ^p$$ ℓ p . Arch. Math. 100, 267–271 (2013)Curbera, G.P., Ricker, W.J.: Solid extensions of the Cesàro operator on $$\ell ^p$$ ℓ p and $$c_0$$ c 0 . Integr. Equ. Oper. Theory 80, 61–77 (2014)Curbera, G.P., Ricker, W.J.: The Cesàro operator and unconditional Taylor series in Hardy spaces. Integr. Equ. Oper. Theory 83, 179–195 (2015)Diestel, J.: Sequences and Series in Banach Spaces. Springer, New York (1984)Dowson, H.R.: Spectral Theory of Linear Operators. Academic Press, London (1978)Dunford, N., Schwartz, J.T.: Linear Operators I: General Theory, 2nd Printing. Wiley Interscience Publ, New York (1964)Emilion, R.: Mean-bounded operators and mean ergodic theorems. J. Funct. Anal. 61, 1–14 (1985)Goldberg, S.: Unbounded Linear Operators: Theory and Applications. Dover Publ, New York (1985)Hille, E.: Remarks on ergodic theorems. Trans. Am. Math. Soc. 57, 246–269 (1945)Jarchow, H.: Locally Convex Spaces. Teubner, Stuttgart (1981)Krengel, U.: Ergodic Theorems. de Gruyter, Berlin (1985)Leibowitz, G.: Spectra of discrete Cesàro operators. Tamkang J. Math. 3, 123–132 (1972)Lin, M.: On the uniform ergodic theorem. Proc. Am. Math. Soc. 43, 337–340 (1974)Megginson, R.E.: An Introduction to Banach Space Theory. Springer, New York (1998)Mureşan, M.: A Concrete Approach to Classical Analysis. Springer, Berlin (2008)Okutoyi, J.I.: On the spectrum of $$C_1$$ C 1 as an operator on $$bv_0$$ b v 0 . J. Aust. Math. Soc. Ser. A 48, 79–86 (1990)Radjavi, H., Tam, P.-W., Tan, K.-K.: Mean ergodicity for compact operators. Studia Math. 158, 207–217 (2003)Reade, J.B.: On the spectrum of the Cesàro operator. Bull. Lond. Math. Soc. 17, 263–267 (1985)Rhoades, B.E., Yildirim, M.: The spectra and fine spectra of factorable matrices on $$c_0$$ c 0 . Math. Commun. 16, 265–270 (2011)Taylor, A.E.: Introduction to Functional Analysis. Wiley, New York (1958

Food consumption frequency and perceived stress and depressive symptoms among students in three European countries

Mikolajczyk RT, El Ansari W, Maxwell AE. Food consumption frequency and perceived stress and depressive symptoms among students in three European countries. Nutrition Journal. 2009;8(1):31.Background: Certain foods might be more frequently eaten under stress or when higher levels of depressive symptoms are experienced. We examined whether poor nutritional habits are associated with stress and depressive symptoms and whether the relationships differ by country and gender in a sample from three European countries collected as part of a Cross National Student Health Survey. Methods: A cross-sectional survey was conducted among first-year students in Germany (N = 696), Poland (N = 489) and Bulgaria (N = 654). Self-administered questionnaires included a 12-item food frequency questionnaire, Cohen's Perceived Stress Scale, and a modified Beck Depression Index. Linear regression analyses were conducted for two outcomes, perceived stress and depressive symptoms. Results: Food consumption frequencies differed by country and gender, as did depressive symptoms and perceived stress. For male students, none of the food consumption groups were associated with perceived stress or depressive symptoms. In females, perceived stress was associated with more frequent consumption of sweets/fast foods and less frequent consumption of fruits/vegetables. Additionally, depressive symptoms were associated with less frequent consumption of fruits/vegetables and meat. Conclusion: Our data show consistent associations between unhealthy food consumption and depressive symptoms and perceived stress among female students from three European countries, but not among male students. This suggests that efforts to reduce depressive symptoms and stress among female students may also lead to the consumption of healthier foods and/or vice-versa

Identification of Mannose Interacting Residues Using Local Composition

BACKGROUND: Mannose binding proteins (MBPs) play a vital role in several biological functions such as defense mechanisms. These proteins bind to mannose on the surface of a wide range of pathogens and help in eliminating these pathogens from our body. Thus, it is important to identify mannose interacting residues (MIRs) in order to understand mechanism of recognition of pathogens by MBPs. RESULTS: This paper describes modules developed for predicting MIRs in a protein. Support vector machine (SVM) based models have been developed on 120 mannose binding protein chains, where no two chains have more than 25% sequence similarity. SVM models were developed on two types of datasets: 1) main dataset consists of 1029 mannose interacting and 1029 non-interacting residues, 2) realistic dataset consists of 1029 mannose interacting and 10320 non-interacting residues. In this study, firstly, we developed standard modules using binary and PSSM profile of patterns and got maximum MCC around 0.32. Secondly, we developed SVM modules using composition profile of patterns and achieved maximum MCC around 0.74 with accuracy 86.64% on main dataset. Thirdly, we developed a model on a realistic dataset and achieved maximum MCC of 0.62 with accuracy 93.08%. Based on this study, a standalone program and web server have been developed for predicting mannose interacting residues in proteins (http://www.imtech.res.in/raghava/premier/). CONCLUSIONS: Compositional analysis of mannose interacting and non-interacting residues shows that certain types of residues are preferred in mannose interaction. It was also observed that residues around mannose interacting residues have a preference for certain types of residues. Composition of patterns/peptide/segment has been used for predicting MIRs and achieved reasonable high accuracy. It is possible that this novel strategy may be effective to predict other types of interacting residues. This study will be useful in annotating the function of protein as well as in understanding the role of mannose in the immune system

Prediction of conformational B-cell epitopes from 3D structures by random forests with a distance-based feature

<p>Abstract</p> <p>Background</p> <p>Antigen-antibody interactions are key events in immune system, which provide important clues to the immune processes and responses. In Antigen-antibody interactions, the specific sites on the antigens that are directly bound by the B-cell produced antibodies are well known as B-cell epitopes. The identification of epitopes is a hot topic in bioinformatics because of their potential use in the epitope-based drug design. Although most B-cell epitopes are discontinuous (or conformational), insufficient effort has been put into the conformational epitope prediction, and the performance of existing methods is far from satisfaction.</p> <p>Results</p> <p>In order to develop the high-accuracy model, we focus on some possible aspects concerning the prediction performance, including the impact of interior residues, different contributions of adjacent residues, and the imbalanced data which contain much more non-epitope residues than epitope residues. In order to address above issues, we take following strategies. Firstly, a concept of 'thick surface patch' instead of 'surface patch' is introduced to describe the local spatial context of each surface residue, which considers the impact of interior residue. The comparison between the thick surface patch and the surface patch shows that interior residues contribute to the recognition of epitopes. Secondly, statistical significance of the distance distribution difference between non-epitope patches and epitope patches is observed, thus an adjacent residue distance feature is presented, which reflects the unequal contributions of adjacent residues to the location of binding sites. Thirdly, a bootstrapping and voting procedure is adopted to deal with the imbalanced dataset. Based on the above ideas, we propose a new method to identify the B-cell conformational epitopes from 3D structures by combining conventional features and the proposed feature, and the random forest (RF) algorithm is used as the classification engine. The experiments show that our method can predict conformational B-cell epitopes with high accuracy. Evaluated by leave-one-out cross validation (LOOCV), our method achieves the mean AUC value of 0.633 for the benchmark bound dataset, and the mean AUC value of 0.654 for the benchmark unbound dataset. When compared with the state-of-the-art prediction models in the independent test, our method demonstrates comparable or better performance.</p> <p>Conclusions</p> <p>Our method is demonstrated to be effective for the prediction of conformational epitopes. Based on the study, we develop a tool to predict the conformational epitopes from 3D structures, available at <url>http://code.google.com/p/my-project-bpredictor/downloads/list</url>.</p

HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information

<p>Abstract</p> <p>Background</p> <p>Accurate prediction of binding residues involved in the interactions between proteins and small ligands is one of the major challenges in structural bioinformatics. Heme is an essential and commonly used ligand that plays critical roles in electron transfer, catalysis, signal transduction and gene expression. Although much effort has been devoted to the development of various generic algorithms for ligand binding site prediction over the last decade, no algorithm has been specifically designed to complement experimental techniques for identification of heme binding residues. Consequently, an urgent need is to develop a computational method for recognizing these important residues.</p> <p>Results</p> <p>Here we introduced an efficient algorithm HemeBIND for predicting heme binding residues by integrating structural and sequence information. We systematically investigated the characteristics of binding interfaces based on a non-redundant dataset of heme-protein complexes. It was found that several sequence and structural attributes such as evolutionary conservation, solvent accessibility, depth and protrusion clearly illustrate the differences between heme binding and non-binding residues. These features can then be separately used or combined to build the structure-based classifiers using support vector machine (SVM). The results showed that the information contained in these features is largely complementary and their combination achieved the best performance. To further improve the performance, an attempt has been made to develop a post-processing procedure to reduce the number of false positives. In addition, we built a sequence-based classifier based on SVM and sequence profile as an alternative when only sequence information can be used. Finally, we employed a voting method to combine the outputs of structure-based and sequence-based classifiers, which demonstrated remarkably better performance than the individual classifier alone.</p> <p>Conclusions</p> <p>HemeBIND is the first specialized algorithm used to predict binding residues in protein structures for heme ligands. Extensive experiments indicated that both the structure-based and sequence-based methods have effectively identified heme binding residues while the complementary relationship between them can result in a significant improvement in prediction performance. The value of our method is highlighted through the development of HemeBIND web server that is freely accessible at <url>http://mleg.cse.sc.edu/hemeBIND/</url>.</p