Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces

PubMed Central

Chen, Ching-Tai; Peng, Hung-Pin; Jian, Jhih-Wei; Tsai, Keng-Chang; Chang, Jeng-Yih; Yang, Ei-Wen; Chen, Jun-Bo; Ho, Shinn-Ying; Hsu, Wen-Lian; Yang, An-Suei

2012-01-01

Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI) sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins) and were tested on an independent dataset (consisting of 142 proteins). The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted correctly with the physicochemical complementarity features based on the non-covalent interaction data derived from protein interiors. PMID:22701576

Prediction of cassava protein interactome based on interolog method.

PubMed

Thanasomboon, Ratana; Kalapanulak, Saowalak; Netrphan, Supatcharee; Saithong, Treenut

2017-12-08

Cassava is a starchy root crop whose role in food security becomes more significant nowadays. Together with the industrial uses for versatile purposes, demand for cassava starch is continuously growing. However, in-depth study to uncover the mystery of cellular regulation, especially the interaction between proteins, is lacking. To reduce the knowledge gap in protein-protein interaction (PPI), genome-scale PPI network of cassava was constructed using interolog-based method (MePPI-In, available at http://bml.sbi.kmutt.ac.th/ppi ). The network was constructed from the information of seven template plants. The MePPI-In included 90,173 interactions from 7,209 proteins. At least, 39 percent of the total predictions were found with supports from gene/protein expression data, while further co-expression analysis yielded 16 highly promising PPIs. In addition, domain-domain interaction information was employed to increase reliability of the network and guide the search for more groups of promising PPIs. Moreover, the topology and functional content of MePPI-In was similar to the networks of Arabidopsis and rice. The potential contribution of MePPI-In for various applications, such as protein-complex formation and prediction of protein function, was discussed and exemplified. The insights provided by our MePPI-In would hopefully enable us to pursue precise trait improvement in cassava.

Genome-wide protein-protein interactions and protein function exploration in cyanobacteria

PubMed Central

Lv, Qi; Ma, Weimin; Liu, Hui; Li, Jiang; Wang, Huan; Lu, Fang; Zhao, Chen; Shi, Tieliu

2015-01-01

Genome-wide network analysis is well implemented to study proteins of unknown function. Here, we effectively explored protein functions and the biological mechanism based on inferred high confident protein-protein interaction (PPI) network in cyanobacteria. We integrated data from seven different sources and predicted 1,997 PPIs, which were evaluated by experiments in molecular mechanism, text mining of literatures in proved direct/indirect evidences, and “interologs” in conservation. Combined the predicted PPIs with known PPIs, we obtained 4,715 no-redundant PPIs (involving 3,231 proteins covering over 90% of genome) to generate the PPI network. Based on the PPI network, terms in Gene ontology (GO) were assigned to function-unknown proteins. Functional modules were identified by dissecting the PPI network into sub-networks and analyzing pathway enrichment, with which we investigated novel function of underlying proteins in protein complexes and pathways. Examples of photosynthesis and DNA repair indicate that the network approach is a powerful tool in protein function analysis. Overall, this systems biology approach provides a new insight into posterior functional analysis of PPIs in cyanobacteria. PMID:26490033

Do cancer proteins really interact strongly in the human protein-protein interaction network?

PubMed

Xia, Junfeng; Sun, Jingchun; Jia, Peilin; Zhao, Zhongming

2011-06-01

Protein-protein interaction (PPI) network analysis has been widely applied in the investigation of the mechanisms of diseases, especially cancer. Recent studies revealed that cancer proteins tend to interact more strongly than other categories of proteins, even essential proteins, in the human interactome. However, it remains unclear whether this observation was introduced by the bias towards more cancer studies in humans. Here, we examined this important issue by uniquely comparing network characteristics of cancer proteins with three other sets of proteins in four organisms, three of which (fly, worm, and yeast) whose interactomes are essentially not biased towards cancer or other diseases. We confirmed that cancer proteins had stronger connectivity, shorter distance, and larger betweenness centrality than non-cancer disease proteins, essential proteins, and control proteins. Our statistical evaluation indicated that such observations were overall unlikely attributed to random events. Considering the large size and high quality of the PPI data in the four organisms, the conclusion that cancer proteins interact strongly in the PPI networks is reliable and robust. This conclusion suggests that perturbation of cancer proteins might cause major changes of cellular systems and result in abnormal cell function leading to cancer. © 2011 Elsevier Ltd. All rights reserved.

Do cancer proteins really interact strongly in the human protein-protein interaction network?

PubMed Central

Xia, Junfeng; Sun, Jingchun; Jia, Peilin; Zhao, Zhongming

2011-01-01

Protein-protein interaction (PPI) network analysis has been widely applied in the investigation of the mechanisms of diseases, especially cancer. Recent studies revealed that cancer proteins tend to interact more strongly than other categories of proteins, even essential proteins, in the human interactome. However, it remains unclear whether this observation was introduced by the bias towards more cancer studies in humans. Here, we examined this important issue by uniquely comparing network characteristics of cancer proteins with three other sets of proteins in four organisms, three of which (fly, worm, and yeast) whose interactomes are essentially not biased towards cancer or other diseases. We confirmed that cancer proteins had stronger connectivity, shorter distance, and larger betweenness centrality than non-cancer disease proteins, essential proteins, and control proteins. Our statistical evaluation indicated that such observations were overall unlikely attributed to random events. Considering the large size and high quality of the PPI data in the four organisms, the conclusion that cancer proteins interact strongly in the PPI networks is reliable and robust. This conclusion suggests that perturbation of cancer proteins might cause major changes of cellular systems and result in abnormal cell function leading to cancer. PMID:21666777

Intermolecular interactions and aggregation of fac-tris(2-phenylpyridinato-C2,N)iridium(III) in nonpolar solvents.

PubMed

Takayasu, Satoshi; Suzuki, Takayoshi; Shinozaki, Kazuteru

2013-08-15

The intermolecular interaction and aggregation of the neutral complex fac-tris(2-phenylpyridinato-C(2),N)iridium(III) (fac-Ir(ppy)3) in solution was investigated. Intermolecular interactions were found to effectively decrease the luminescence lifetime via self-quenching with increasing fac-Ir(ppy)3 concentrations. A Stern-Volmer plot for quenching in acetonitrile was linear, due to bimolecular self-quenching, but curved in toluene as the result of excimer formation. (1)H NMR spectra demonstrated a monomer-aggregate equilibrium which resulted in spectral shifts depending on solvent polarity. X-ray crystallography provided structural information concerning the aggregate, which is based on a tetramer consisting of two Δ-fac-Ir(ppy)3-Λ-fac-Ir(ppy)3 pairs. Offset π-π stacking of ppy ligands and electrostatic dipole-dipole interactions between complex molecules play an important role in the formation of these molecular pairs.

Identification of infection- and defense-related genes via a dynamic host-pathogen interaction network using a Candida albicans-zebrafish infection model.

PubMed

Kuo, Zong-Yu; Chuang, Yung-Jen; Chao, Chun-Cheih; Liu, Fu-Chen; Lan, Chung-Yu; Chen, Bor-Sen

2013-01-01

Candida albicans infections and candidiasis are difficult to treat and create very serious therapeutic challenges. In this study, based on interactive time profile microarray data of C. albicans and zebrafish during infection, the infection-related protein-protein interaction (PPI) networks of the two species and the intercellular PPI network between host and pathogen were simultaneously constructed by a dynamic interaction model, modeled as an integrated network consisting of intercellular invasion and cellular defense processes during infection. The signal transduction pathways in regulating morphogenesis and hyphal growth of C. albicans were further investigated based on significant interactions found in the intercellular PPI network. Two cellular networks were also developed corresponding to the different infection stages (adhesion and invasion), and then compared with each other to identify proteins from which we can gain more insight into the pathogenic role of hyphal development in the C. albicans infection process. Important defense-related proteins in zebrafish were predicted using the same approach. The hyphal growth PPI network, zebrafish PPI network and host-pathogen intercellular PPI network were combined to form an integrated infectious PPI network that helps us understand the systematic mechanisms underlying the pathogenicity of C. albicans and the immune response of the host, and may help improve medical therapies and facilitate the development of new antifungal drugs. Copyright © 2013 S. Karger AG, Basel.

Natural products used as a chemical library for protein-protein interaction targeted drug discovery.

PubMed

Jin, Xuemei; Lee, Kyungro; Kim, Nam Hee; Kim, Hyun Sil; Yook, Jong In; Choi, Jiwon; No, Kyoung Tai

2018-01-01

Protein-protein interactions (PPIs), which are essential for cellular processes, have been recognized as attractive therapeutic targets. Therefore, the construction of a PPI-focused chemical library is an inevitable necessity for future drug discovery. Natural products have been used as traditional medicines to treat human diseases for millennia; in addition, their molecular scaffolds have been used in diverse approved drugs and drug candidates. The recent discovery of the ability of natural products to inhibit PPIs led us to use natural products as a chemical library for PPI-targeted drug discovery. In this study, we collected natural products (NPDB) from non-commercial and in-house databases to analyze their similarities to small-molecule PPI inhibitors (iPPIs) and FDA-approved drugs by using eight molecular descriptors. Then, we evaluated the distribution of NPDB and iPPIs in the chemical space, represented by the molecular fingerprint and molecular scaffolds, to identify the promising scaffolds, which could interfere with PPIs. To investigate the ability of natural products to inhibit PPI targets, molecular docking was used. Then, we predicted a set of high-potency natural products by using the iPPI-likeness score based on a docking score-weighted model. These selected natural products showed high binding affinities to the PPI target, namely XIAP, which were validated in an in vitro experiment. In addition, the natural products with novel scaffolds might provide a promising starting point for further medicinal chemistry developments. Overall, our study shows the potency of natural products in targeting PPIs, which might help in the design of a PPI-focused chemical library for future drug discovery. Copyright © 2017 Elsevier Inc. All rights reserved.

Comparative analysis and assessment of M. tuberculosis H37Rv protein-protein interaction datasets

PubMed Central

2011-01-01

Background M. tuberculosis is a formidable bacterial pathogen. There is thus an increasing demand on understanding the function and relationship of proteins in various strains of M. tuberculosis. Protein-protein interactions (PPIs) data are crucial for this kind of knowledge. However, the quality of the main available M. tuberculosis PPI datasets is unclear. This hampers the effectiveness of research works that rely on these PPI datasets. Here, we analyze the two main available M. tuberculosis H37Rv PPI datasets. The first dataset is the high-throughput B2H PPI dataset from Wang et al’s recent paper in Journal of Proteome Research. The second dataset is from STRING database, version 8.3, comprising entirely of H37Rv PPIs predicted using various methods. We find that these two datasets have a surprisingly low level of agreement. We postulate the following causes for this low level of agreement: (i) the H37Rv B2H PPI dataset is of low quality; (ii) the H37Rv STRING PPI dataset is of low quality; and/or (iii) the H37Rv STRING PPIs are predictions of other forms of functional associations rather than direct physical interactions. Results To test the quality of these two datasets, we evaluate them based on correlated gene expression profiles, coherent informative GO term annotations, and conservation in other organisms. We observe a significantly greater portion of PPIs in the H37Rv STRING PPI dataset (with score ≥ 770) having correlated gene expression profiles and coherent informative GO term annotations in both interaction partners than that in the H37Rv B2H PPI dataset. Predicted H37Rv interologs derived from non-M. tuberculosis experimental PPIs are much more similar to the H37Rv STRING functional associations dataset (with score ≥ 770) than the H37Rv B2H PPI dataset. H37Rv predicted physical interologs from IntAct also show extremely low similarity with the H37Rv B2H PPI dataset; and this similarity level is much lower than that between the S. aureus MRSA252 predicted physical interologs from IntAct and S. aureus MRSA252 pull-down PPIs. Comparative analysis with several representative two-hybrid PPI datasets in other species further confirms that the H37Rv B2H PPI dataset is of low quality. Next, to test the possibility that the H37Rv STRING PPIs are not purely direct physical interactions, we compare M. tuberculosis H37Rv protein pairs that catalyze adjacent steps in enzymatic reactions to B2H PPIs and predicted PPIs in STRING, which shows it has much lower similarities with the B2H PPIs than with STRING PPIs. This result strongly suggests that the H37Rv STRING PPIs more likely correspond to indirect relationships between protein pairs than to B2H PPIs. For more precise support, we turn to S. cerevisiae for its comprehensively studied interactome. We compare S. cerevisiae predicted PPIs in STRING to three independent protein relationship datasets which respectively comprise PPIs reported in Y2H assays, protein pairs reported to be in the same protein complexes, and protein pairs that catalyze successive reaction steps in enzymatic reactions. Our analysis reveals that S. cerevisiae predicted STRING PPIs have much higher similarity to the latter two types of protein pairs than to two-hybrid PPIs. As H37Rv STRING PPIs are predicted using similar methods as S. cerevisiae predicted STRING PPIs, this suggests that these H37Rv STRING PPIs are more likely to correspond to the latter two types of protein pairs rather than to two-hybrid PPIs as well. Conclusions The H37Rv B2H PPI dataset has low quality. It should not be used as the gold standard to assess the quality of other (possibly predicted) H37Rv PPI datasets. The H37Rv STRING PPI dataset also has low quality; nevertheless, a subset consisting of STRING PPIs with score ≥770 has satisfactory quality. However, these STRING “PPIs” should be interpreted as functional associations, which include a substantial portion of indirect protein interactions, rather than direct physical interactions. These two factors cause the strikingly low similarity between these two main H37Rv PPI datasets. The results and conclusions from this comparative analysis provide valuable guidance in using these M. tuberculosis H37Rv PPI datasets in subsequent studies for a wide range of purposes. PMID:22369691

Inferring the Brassica rapa Interactome Using Protein–Protein Interaction Data from Arabidopsis thaliana

PubMed Central

Yang, Jianhua; Osman, Kim; Iqbal, Mudassar; Stekel, Dov J.; Luo, Zewei; Armstrong, Susan J.; Franklin, F. Chris H.

2013-01-01

Following successful completion of the Brassica rapa sequencing project, the next step is to investigate functions of individual genes/proteins. For Arabidopsis thaliana, large amounts of protein–protein interaction (PPI) data are available from the major PPI databases (DBs). It is known that Brassica crop species are closely related to A. thaliana. This provides an opportunity to infer the B. rapa interactome using PPI data available from A. thaliana. In this paper, we present an inferred B. rapa interactome that is based on the A. thaliana PPI data from two resources: (i) A. thaliana PPI data from three major DBs, BioGRID, IntAct, and TAIR. (ii) ortholog-based A. thaliana PPI predictions. Linking between B. rapa and A. thaliana was accomplished in three complementary ways: (i) ortholog predictions, (ii) identification of gene duplication based on synteny and collinearity, and (iii) BLAST sequence similarity search. A complementary approach was also applied, which used known/predicted domain–domain interaction data. Specifically, since the two species are closely related, we used PPI data from A. thaliana to predict interacting domains that might be conserved between the two species. The predicted interactome was investigated for the component that contains known A. thaliana meiotic proteins to demonstrate its usability. PMID:23293649

Reporting and appraising the context, process and impact of PPI on contributors, researchers and the trial during a randomised controlled trial - the 3D study.

PubMed

Mann, Cindy; Chilcott, Simon; Plumb, Katrina; Brooks, Edmund; Man, Mei-See

2018-01-01

Including patient and public involvement (PPI) in health research is thought to improve research but it is hard to be clear exactly how it helps. This is because PPI takes many forms, is sometimes only token and is not always reported clearly. This makes it difficult to combine the evidence so that clear conclusions can be reached about the ingredients of successful PPI and what PPI achieves. Previous research that has tried to combine the evidence has led to several guidelines for researchers to use in setting up and reporting PPI.This paper was written jointly by researchers and PPI contributors as a reflection on our experiences. The aim was to add to the evidence, by giving detail about the use of PPI in a large randomised controlled trial and the effect it had. We were guided by published PPI reporting guidelines. The effects on the trial are shown in a table of changes made because of suggestions from the PPI group. A survey was used to ask PPI contributors and researchers about their experience and effects they had noticed. Three themes were noted: impact on the trial, the effect of involvement on individual researchers and group members, and group environment. The PPI work affected the trial in many ways, including changes to documents used in the trial and advice on qualitative data collection methods and analysis. Individuals reported positive effects, including enjoying being in the group, gaining confidence, and learning how to share views. Patient and public involvement (PPI) is believed to enhance health care delivery research, and is widely required in research proposals. Detailed, standardised reporting of PPI is needed so that strategies to implement more than token PPI that achieves impact can be identified, properly evaluated and reproduced. Impact includes effects on the research, PPI contributors and researchers. Using contributor and researcher perspectives and drawing on published guidelines for reporting PPI, we aimed to reflect on our experience and contribute evidence relevant to two important questions: 'What difference does PPI make?' and 'What's the best way to do it?' Fourteen people living with multiple long-term conditions (multimorbidity) were PPI contributors to a randomised controlled trial to improve care for people with multimorbidity. Meetings took place approximately four times a year throughout the trial, beginning at grant application stage. Meeting notes were recorded and a log of PPI involvement was kept. At the end of the trial, seven PPI contributors and four researchers completed free-text questionnaires about their experience of PPI involvement and their perception of PPI impact. The responses were analysed thematically by two PPI contributors and one researcher. The PPI group proposed writing this report, which was co-authored by three PPI contributors and two researchers. Meeting attendance averaged nine PPI contributors and three to four researchers. The involvement log and meeting notes recorded a wide range of activities and impact including changes to participant documentation, advice on qualitative data collection, contribution to data analysis and dissemination advice. Three themes were identified from the questionnaires: impact on the study, including keeping the research grounded in patient experience; impact on individuals, including learning from group diversity and feeling valued; and an environment that facilitated participation. The size of the group influenced impact. Researchers and PPI contributors described a rewarding interaction that benefitted them and the research. PPI was wide-ranging and had impact on the trial, contributors and researchers. The group environment facilitated involvement. Feedback and group interactions benefitted individuals. The insights gained from this study will postitively influence the researchers' and contributors' future involvement with PPI.

MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions.

PubMed

Hayashi, Takanori; Matsuzaki, Yuri; Yanagisawa, Keisuke; Ohue, Masahito; Akiyama, Yutaka

2018-05-08

Protein-protein interactions (PPIs) play several roles in living cells, and computational PPI prediction is a major focus of many researchers. The three-dimensional (3D) structure and binding surface are important for the design of PPI inhibitors. Therefore, rigid body protein-protein docking calculations for two protein structures are expected to allow elucidation of PPIs different from known complexes in terms of 3D structures because known PPI information is not explicitly required. We have developed rapid PPI prediction software based on protein-protein docking, called MEGADOCK. In order to fully utilize the benefits of computational PPI predictions, it is necessary to construct a comprehensive database to gather prediction results and their predicted 3D complex structures and to make them easily accessible. Although several databases exist that provide predicted PPIs, the previous databases do not contain a sufficient number of entries for the purpose of discovering novel PPIs. In this study, we constructed an integrated database of MEGADOCK PPI predictions, named MEGADOCK-Web. MEGADOCK-Web provides more than 10 times the number of PPI predictions than previous databases and enables users to conduct PPI predictions that cannot be found in conventional PPI prediction databases. In MEGADOCK-Web, there are 7528 protein chains and 28,331,628 predicted PPIs from all possible combinations of those proteins. Each protein structure is annotated with PDB ID, chain ID, UniProt AC, related KEGG pathway IDs, and known PPI pairs. Additionally, MEGADOCK-Web provides four powerful functions: 1) searching precalculated PPI predictions, 2) providing annotations for each predicted protein pair with an experimentally known PPI, 3) visualizing candidates that may interact with the query protein on biochemical pathways, and 4) visualizing predicted complex structures through a 3D molecular viewer. MEGADOCK-Web provides a huge amount of comprehensive PPI predictions based on docking calculations with biochemical pathways and enables users to easily and quickly assess PPI feasibilities by archiving PPI predictions. MEGADOCK-Web also promotes the discovery of new PPIs and protein functions and is freely available for use at http://www.bi.cs.titech.ac.jp/megadock-web/ .

[Impact of an evaluation of the professional practices on the relevance of proton pump inhibitors prescriptions pertinence at the hospital].

PubMed

Daumas, A; Garros, E; Mendizabal, H; Gayet, S; Bernard, F; Bagnères, D; Demoux, A-L; Rossi, P; Villani, P; Granel, B

2018-04-05

Proton pump inhibitors (PPI) are widely prescribed for unrecognized indications, at high a dose and for a long duration, in spite of side effects and numerous drug interactions. In 2009, the HAS (French Health Authority) published recommendations of good prescription but the latter are poorly respected. In this context of over prescription and additional cost for the society, we performed a professional practice evaluation of on the model of the Deming wheel. The objective of this work was to optimize the relevance of the prescriptions of the IPP in two services of internal medicine and geriatrics through an evaluation of the professional practices. All PPI prescriptions introduced in outpatient visits or during hospitalization were analyzed. Data collection was prospective, over two periods of 2 months and included 163 (first phase), then 139 patients (second phase). An assessment grid of PPI prescriptions was completed by physicians regarding the active substance, the dose, the duration and the indication of the prescription. The relevance of the prescription corresponded to PPI with a conformed indication and duration and to the prescriptions no recommended stopped. Following the first period of data collection, information was given to medical students and physicians on the relevance of their prescriptions with regard to the current recommendations and informative flyers were offered with the aim of improving the practices before the second period of evaluation (second phase). During the first phase, only 25% of the pre-hospital prescriptions and 33% of the hospital prescriptions respected the HAS recommendations. The main indication of the PPI was the prevention of peptic ulcers in a context of associated drug estimated at risk. An improvement of the global relevance of prescription was observed after awareness of the physicians: 26% relevance during the first phase and 60% in the second one (P<0.012). During the second phase, the part of PPI prescriptions introduced at hospital decreased from 33 to 17% and the discontinuation of the not corresponding prescriptions increased from 6 to 33%, with an additional information given to the general practitioner (P<0.001). However, during the second phase, 33% of the prescriptions introduced in hospitalization were always not corresponding and 61% of the not corresponding prescriptions begun in outpatient visits were always pursued on discharge, probably due to the lack of sufficient information to stop the prescription. Our study underlines the frequent disrespect of the indications in the prescription of PPI. Interestingly, a professional practices evaluation improved the relevance of the prescriptions with a more frequent withdrawal of the not corresponding exposure and a decrease in global not corresponding prescriptions. Our study suggests that it is crucial to regularly inform physicians on the good prescription of PPI. Patient information focused on the indications and the limited duration of PPI prescription, potentially severe side effects of chronic exposure and on the risk of drug interactions also remains necessary in order to facilitate the stop of the exposure and restrict self-medication. Copyright © 2018 Société Nationale Française de Médecine Interne (SNFMI). Published by Elsevier SAS. All rights reserved.

A coproduced patient and public event: An approach to developing and prioritizing ambulance performance measures.

PubMed

Irving, Andy; Turner, Janette; Marsh, Maggie; Broadway-Parkinson, Andrea; Fall, Dan; Coster, Joanne; Siriwardena, A Niroshan

2018-02-01

Patient and public involvement (PPI) is recognized as an important component of high-quality health services research. PPI is integral to the Pre-hospital Outcomes for Evidence Based Evaluation (PhOEBE) programme. The PPI event described in detail in this article focusses on the process of involving patients and public representatives in identifying, prioritizing and refining a set of outcome measures that can be used to support ambulance service performance measurement. To obtain public feedback on little known, complex aspects of ambulance service performance measurement. The event was codesigned and coproduced with the PhOEBE PPI reference group and PhOEBE research team. The event consisted of brief researcher-led presentations, group discussions facilitated by the PPI reference group members and electronic voting. Data were collected from eighteen patient and public representatives who attended an event venue in Yorkshire. The results of the PPI event showed that this interactive format and mode of delivery was an effective method to obtain public feedback and produced a clear indication of which ambulance performance measures were most highly favoured by event participants. The event highlighted valuable contributions the PPI reference group made to the design process, supporting participant recruitment and facilitation of group discussions. In addition, the positive team working experience of the event proved a catalyst for further improvements in PPI within the PhOEBE project. © 2017 The Authors Health Expectations Published by John Wiley & Sons Ltd.

Multichannel Convolutional Neural Network for Biological Relation Extraction.

PubMed

Quan, Chanqin; Hua, Lei; Sun, Xiao; Bai, Wenjun

2016-01-01

The plethora of biomedical relations which are embedded in medical logs (records) demands researchers' attention. Previous theoretical and practical focuses were restricted on traditional machine learning techniques. However, these methods are susceptible to the issues of "vocabulary gap" and data sparseness and the unattainable automation process in feature extraction. To address aforementioned issues, in this work, we propose a multichannel convolutional neural network (MCCNN) for automated biomedical relation extraction. The proposed model has the following two contributions: (1) it enables the fusion of multiple (e.g., five) versions in word embeddings; (2) the need for manual feature engineering can be obviated by automated feature learning with convolutional neural network (CNN). We evaluated our model on two biomedical relation extraction tasks: drug-drug interaction (DDI) extraction and protein-protein interaction (PPI) extraction. For DDI task, our system achieved an overall f -score of 70.2% compared to the standard linear SVM based system (e.g., 67.0%) on DDIExtraction 2013 challenge dataset. And for PPI task, we evaluated our system on Aimed and BioInfer PPI corpus; our system exceeded the state-of-art ensemble SVM system by 2.7% and 5.6% on f -scores.

Impact of Proton Pump Inhibitor Therapy on the Efficacy of Clopidogrel in the CAPRIE and CREDO Trials

PubMed Central

Dunn, Steven P.; Steinhubl, Steven R.; Bauer, Deborah; Charnigo, Richard J.; Berger, Peter B.; Topol, Eric J.

2013-01-01

Background Proton pump inhibitors (PPIs) may interfere with the metabolic activation of clopidogrel via inhibition of cytochrome P450 2C19, but the clinical implications remain unclear. Methods and Results The impact of PPI use on the 1‐year primary end point (ischemic stroke, myocardial infarction [MI], or vascular death) in the Clopidogrel versus Aspirin in Patients at Risk of Ischemic Events (CAPRIE) trial and the 28‐day (all‐cause death, MI, or urgent target vessel revascularization) and 1‐year (all‐cause death, MI, or stroke) primary end points in the Clopidogrel for Reduction of Events During Observation (CREDO) trial were examined. Clopidogrel appeared to elevate risk for the primary end point in CAPRIE among PPI users (estimated hazard ratio [EHR] 2.66, 95% CI 0.94 to 7.50) while lowering it for non‐PPI users (EHR 0.90, 95% CI 0.83 to 0.99, interaction P=0.047). Moreover, PPI use was associated with worse outcomes in patients receiving clopidogrel (EHR 2.39, 95% CI 1.74 to 3.28) but not aspirin (EHR 1.04, 95% CI 0.70 to 1.57, interaction P=0.001). Clopidogrel did not significantly alter risk for the 1‐year primary end point in CREDO among PPI users (EHR 0.82, 95% CI 0.48 to 1.40) while lowering it for non‐PPI users (EHR 0.71, 95% CI 0.52 to 0.98, interaction P=0.682). Also, PPI use was associated with worse outcomes in both patients receiving clopidogrel (EHR 1.67, 95% CI 1.06 to 2.64) and those receiving placebo (EHR 1.56, 95% CI 1.06 to 2.30, interaction P=0.811). Conclusions In CREDO, the efficacy of clopidogrel was not significantly affected by PPI use. However, in CAPRIE, clopidogrel was beneficial to non‐PPI users while apparently harmful to PPI users. Whether this negative interaction is clinically important for patients receiving clopidogrel without aspirin needs further study. PMID:23525436

A knowledge-driven probabilistic framework for the prediction of protein-protein interaction networks.

PubMed

Browne, Fiona; Wang, Haiying; Zheng, Huiru; Azuaje, Francisco

2010-03-01

This study applied a knowledge-driven data integration framework for the inference of protein-protein interactions (PPI). Evidence from diverse genomic features is integrated using a knowledge-driven Bayesian network (KD-BN). Receiver operating characteristic (ROC) curves may not be the optimal assessment method to evaluate a classifier's performance in PPI prediction as the majority of the area under the curve (AUC) may not represent biologically meaningful results. It may be of benefit to interpret the AUC of a partial ROC curve whereby biologically interesting results are represented. Therefore, the novel application of the assessment method referred to as the partial ROC has been employed in this study to assess predictive performance of PPI predictions along with calculating the True positive/false positive rate and true positive/positive rate. By incorporating domain knowledge into the construction of the KD-BN, we demonstrate improvement in predictive performance compared with previous studies based upon the Naive Bayesian approach. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Identifying protein complexes in PPI network using non-cooperative sequential game.

PubMed

Maulik, Ujjwal; Basu, Srinka; Ray, Sumanta

2017-08-21

Identifying protein complexes from protein-protein interaction (PPI) network is an important and challenging task in computational biology as it helps in better understanding of cellular mechanisms in various organisms. In this paper we propose a noncooperative sequential game based model for protein complex detection from PPI network. The key hypothesis is that protein complex formation is driven by mechanism that eventually optimizes the number of interactions within the complex leading to dense subgraph. The hypothesis is drawn from the observed network property named small world. The proposed multi-player game model translates the hypothesis into the game strategies. The Nash equilibrium of the game corresponds to a network partition where each protein either belong to a complex or form a singleton cluster. We further propose an algorithm to find the Nash equilibrium of the sequential game. The exhaustive experiment on synthetic benchmark and real life yeast networks evaluates the structural as well as biological significance of the network partitions.

Linear motif-mediated interactions have contributed to the evolution of modularity in complex protein interaction networks.

PubMed

Kim, Inhae; Lee, Heetak; Han, Seong Kyu; Kim, Sanguk

2014-10-01

The modular architecture of protein-protein interaction (PPI) networks is evident in diverse species with a wide range of complexity. However, the molecular components that lead to the evolution of modularity in PPI networks have not been clearly identified. Here, we show that weak domain-linear motif interactions (DLIs) are more likely to connect different biological modules than strong domain-domain interactions (DDIs). This molecular division of labor is essential for the evolution of modularity in the complex PPI networks of diverse eukaryotic species. In particular, DLIs may compensate for the reduction in module boundaries that originate from increased connections between different modules in complex PPI networks. In addition, we show that the identification of biological modules can be greatly improved by including molecular characteristics of protein interactions. Our findings suggest that transient interactions have played a unique role in shaping the architecture and modularity of biological networks over the course of evolution.

Towards a pedagogy for patient and public involvement in medical education.

PubMed

Regan de Bere, Sam; Nunn, Suzanne

2016-01-01

This paper presents a critique of current knowledge on the engagement of patients and the public, referred to here as patient and public involvement (PPI), and calls for the development of robust and theoretically informed strategies across the continuum of medical education. The study draws on a range of relevant literatures and presents PPI as a response process in relation to patient-centred learning agendas. Through reference to original research it discusses three key priorities for medical educators developing early PPI pedagogies, including: (i) the integration of evidence on PPI relevant to medical education, via a unifying corpus of literature; (ii) conceptual clarity through shared definitions of PPI in medical education, and (iii) an academically rigorous approach to managing complexity in the evaluation of PPI initiatives. As a response to these challenges, the authors demonstrate how activity modelling may be used as an analytical heuristic to provide an understanding of a number of PPI systems that may interact within complex and dynamic educational contexts. The authors highlight the need for a range of patient voices to be evident within such work, from its generation through to dissemination, in order that patients and the public are partners and not merely objects of this endeavour. To this end, this paper has been discussed with and reviewed by our own patient and public research partners throughout the writing process. © 2015 John Wiley & Sons Ltd.

Time-gated detection of protein-protein interactions with transcriptional readout

PubMed Central

Sanchez, Mateo I; Coukos, Robert; von Zastrow, Mark

2017-01-01

Transcriptional assays, such as yeast two-hybrid and TANGO, that convert transient protein-protein interactions (PPIs) into stable expression of transgenes are powerful tools for PPI discovery, screens, and analysis of cell populations. However, such assays often have high background and lose information about PPI dynamics. We have developed SPARK (Specific Protein Association tool giving transcriptional Readout with rapid Kinetics), in which proteolytic release of a membrane-tethered transcription factor (TF) requires both a PPI to deliver a protease proximal to its cleavage peptide and blue light to uncage the cleavage site. SPARK was used to detect 12 different PPIs in mammalian cells, with 5 min temporal resolution and signal ratios up to 37. By shifting the light window, we could reconstruct PPI time-courses. Combined with FACS, SPARK enabled 51 fold enrichment of PPI-positive over PPI-negative cells. Due to its high specificity and sensitivity, SPARK has the potential to advance PPI analysis and discovery. PMID:29189201

Application of the fragment molecular orbital method analysis to fragment-based drug discovery of BET (bromodomain and extra-terminal proteins) inhibitors.

PubMed

Ozawa, Motoyasu; Ozawa, Tomonaga; Ueda, Kazuyoshi

2017-06-01

The molecular interactions of inhibitors of bromodomains (BRDs) were investigated. BRDs are protein interaction modules that recognizing ε-N-acetyl-lysine (εAc-Lys) motifs found in histone tails and are promising protein-protein interaction (PPI) targets. First, we analyzed a peptide ligand containing εAc-Lys to evaluate native PPIs. We then analyzed tetrahydroquinazoline-6-yl-benzensulfonamide derivatives found by fragment-based drug design (FBDD) and examined their interactions with the protein compared with the peptide ligand in terms of the inter-fragment interaction energy. In addition, we analyzed benzodiazepine derivatives that are high-affinity ligands for BRDs and examined differences in the CH/π interactions of the amino acid residues. We further surveyed changes in the charges of the amino acid residues among individual ligands, performed pair interaction energy decomposition analysis and estimated the water profile within the ligand binding site. Thus, useful insights for drug design were provided. Through these analyses and considerations, we show that the FMO method is a useful drug design tool to evaluate the process of FBDD and to explore PPI inhibitors. Copyright © 2017 Elsevier Inc. All rights reserved.

Clopidogrel and proton pump inhibitor (PPI) interaction: separate intake and a non-omeprazole PPI the solution?

PubMed

Kenngott, S; Olze, R; Kollmer, M; Bottheim, H; Laner, A; Holinski-Feder, E; Gross, M

2010-05-18

Dual therapy with aspirin and clopidogrel increases the risk of gastrointestinal bleeding. Therefore, co-therapy with a proton pump inhibitor (PPI) is recommended by most guidelines. However, there are warnings against combining PPIs with clopidogrel because of their interactions with cytochrome P450 isoenzyme 2C19 (CYP2C19). The effects of the combined or separate intake of 20 mg of omeprazole and 75 mg of clopidogrel on the clopidogrel-induced inhibition of platelet aggregation were measured in four healthy subjects whose CYP2C19 exon sequences were determined. The effects of co-therapy with 10 mg of rabeprazole were also examined. Two subjects showed the wild-type CYP2C19 sequence. The concurrent intake of omeprazole had no effect on clopidogrel-induced platelet inhibition in these subjects. Two subjects were heterozygous for the *2 allele, with predicted reduced CYP2C19 activity. One of them was a clopidogrel non-responder. In the second heterozygous subject, omeprazole co-therapy reduced the clopidogrel anti-platelet effect when taken simultaneously or separately. However, the simultaneous intake of rabeprazole did not reduce the clopidogrel effect. The clopidogrel-PPI interaction does not seem to be a PPI class effect. Rabeprazole did not affect the clopidogrel effect in a subject with a clear omeprazole-clopidogrel interaction. The separate intake of PPI and clopidogrel may not be sufficient to prevent their interaction.

Combining active learning and semi-supervised learning techniques to extract protein interaction sentences.

PubMed

Song, Min; Yu, Hwanjo; Han, Wook-Shin

2011-11-24

Protein-protein interaction (PPI) extraction has been a focal point of many biomedical research and database curation tools. Both Active Learning and Semi-supervised SVMs have recently been applied to extract PPI automatically. In this paper, we explore combining the AL with the SSL to improve the performance of the PPI task. We propose a novel PPI extraction technique called PPISpotter by combining Deterministic Annealing-based SSL and an AL technique to extract protein-protein interaction. In addition, we extract a comprehensive set of features from MEDLINE records by Natural Language Processing (NLP) techniques, which further improve the SVM classifiers. In our feature selection technique, syntactic, semantic, and lexical properties of text are incorporated into feature selection that boosts the system performance significantly. By conducting experiments with three different PPI corpuses, we show that PPISpotter is superior to the other techniques incorporated into semi-supervised SVMs such as Random Sampling, Clustering, and Transductive SVMs by precision, recall, and F-measure. Our system is a novel, state-of-the-art technique for efficiently extracting protein-protein interaction pairs.

HomPPI: a class of sequence homology based protein-protein interface prediction methods

PubMed Central

2011-01-01

Background Although homology-based methods are among the most widely used methods for predicting the structure and function of proteins, the question as to whether interface sequence conservation can be effectively exploited in predicting protein-protein interfaces has been a subject of debate. Results We studied more than 300,000 pair-wise alignments of protein sequences from structurally characterized protein complexes, including both obligate and transient complexes. We identified sequence similarity criteria required for accurate homology-based inference of interface residues in a query protein sequence. Based on these analyses, we developed HomPPI, a class of sequence homology-based methods for predicting protein-protein interface residues. We present two variants of HomPPI: (i) NPS-HomPPI (Non partner-specific HomPPI), which can be used to predict interface residues of a query protein in the absence of knowledge of the interaction partner; and (ii) PS-HomPPI (Partner-specific HomPPI), which can be used to predict the interface residues of a query protein with a specific target protein. Our experiments on a benchmark dataset of obligate homodimeric complexes show that NPS-HomPPI can reliably predict protein-protein interface residues in a given protein, with an average correlation coefficient (CC) of 0.76, sensitivity of 0.83, and specificity of 0.78, when sequence homologs of the query protein can be reliably identified. NPS-HomPPI also reliably predicts the interface residues of intrinsically disordered proteins. Our experiments suggest that NPS-HomPPI is competitive with several state-of-the-art interface prediction servers including those that exploit the structure of the query proteins. The partner-specific classifier, PS-HomPPI can, on a large dataset of transient complexes, predict the interface residues of a query protein with a specific target, with a CC of 0.65, sensitivity of 0.69, and specificity of 0.70, when homologs of both the query and the target can be reliably identified. The HomPPI web server is available at http://homppi.cs.iastate.edu/. Conclusions Sequence homology-based methods offer a class of computationally efficient and reliable approaches for predicting the protein-protein interface residues that participate in either obligate or transient interactions. For query proteins involved in transient interactions, the reliability of interface residue prediction can be improved by exploiting knowledge of putative interaction partners. PMID:21682895

Designing focused chemical libraries enriched in protein-protein interaction inhibitors using machine-learning methods.

PubMed

Reynès, Christelle; Host, Hélène; Camproux, Anne-Claude; Laconde, Guillaume; Leroux, Florence; Mazars, Anne; Deprez, Benoit; Fahraeus, Robin; Villoutreix, Bruno O; Sperandio, Olivier

2010-03-05

Protein-protein interactions (PPIs) may represent one of the next major classes of therapeutic targets. So far, only a minute fraction of the estimated 650,000 PPIs that comprise the human interactome are known with a tiny number of complexes being drugged. Such intricate biological systems cannot be cost-efficiently tackled using conventional high-throughput screening methods. Rather, time has come for designing new strategies that will maximize the chance for hit identification through a rationalization of the PPI inhibitor chemical space and the design of PPI-focused compound libraries (global or target-specific). Here, we train machine-learning-based models, mainly decision trees, using a dataset of known PPI inhibitors and of regular drugs in order to determine a global physico-chemical profile for putative PPI inhibitors. This statistical analysis unravels two important molecular descriptors for PPI inhibitors characterizing specific molecular shapes and the presence of a privileged number of aromatic bonds. The best model has been transposed into a computer program, PPI-HitProfiler, that can output from any drug-like compound collection a focused chemical library enriched in putative PPI inhibitors. Our PPI inhibitor profiler is challenged on the experimental screening results of 11 different PPIs among which the p53/MDM2 interaction screened within our own CDithem platform, that in addition to the validation of our concept led to the identification of 4 novel p53/MDM2 inhibitors. Collectively, our tool shows a robust behavior on the 11 experimental datasets by correctly profiling 70% of the experimentally identified hits while removing 52% of the inactive compounds from the initial compound collections. We strongly believe that this new tool can be used as a global PPI inhibitor profiler prior to screening assays to reduce the size of the compound collections to be experimentally screened while keeping most of the true PPI inhibitors. PPI-HitProfiler is freely available on request from our CDithem platform website, www.CDithem.com.

Designing Focused Chemical Libraries Enriched in Protein-Protein Interaction Inhibitors using Machine-Learning Methods

PubMed Central

Reynès, Christelle; Host, Hélène; Camproux, Anne-Claude; Laconde, Guillaume; Leroux, Florence; Mazars, Anne; Deprez, Benoit; Fahraeus, Robin; Villoutreix, Bruno O.; Sperandio, Olivier

2010-01-01

Protein-protein interactions (PPIs) may represent one of the next major classes of therapeutic targets. So far, only a minute fraction of the estimated 650,000 PPIs that comprise the human interactome are known with a tiny number of complexes being drugged. Such intricate biological systems cannot be cost-efficiently tackled using conventional high-throughput screening methods. Rather, time has come for designing new strategies that will maximize the chance for hit identification through a rationalization of the PPI inhibitor chemical space and the design of PPI-focused compound libraries (global or target-specific). Here, we train machine-learning-based models, mainly decision trees, using a dataset of known PPI inhibitors and of regular drugs in order to determine a global physico-chemical profile for putative PPI inhibitors. This statistical analysis unravels two important molecular descriptors for PPI inhibitors characterizing specific molecular shapes and the presence of a privileged number of aromatic bonds. The best model has been transposed into a computer program, PPI-HitProfiler, that can output from any drug-like compound collection a focused chemical library enriched in putative PPI inhibitors. Our PPI inhibitor profiler is challenged on the experimental screening results of 11 different PPIs among which the p53/MDM2 interaction screened within our own CDithem platform, that in addition to the validation of our concept led to the identification of 4 novel p53/MDM2 inhibitors. Collectively, our tool shows a robust behavior on the 11 experimental datasets by correctly profiling 70% of the experimentally identified hits while removing 52% of the inactive compounds from the initial compound collections. We strongly believe that this new tool can be used as a global PPI inhibitor profiler prior to screening assays to reduce the size of the compound collections to be experimentally screened while keeping most of the true PPI inhibitors. PPI-HitProfiler is freely available on request from our CDithem platform website, www.CDithem.com. PMID:20221258

AlphaSpace: Fragment-Centric Topographical Mapping To Target Protein–Protein Interaction Interfaces

PubMed Central

2016-01-01

Inhibition of protein–protein interactions (PPIs) is emerging as a promising therapeutic strategy despite the difficulty in targeting such interfaces with drug-like small molecules. PPIs generally feature large and flat binding surfaces as compared to typical drug targets. These features pose a challenge for structural characterization of the surface using geometry-based pocket-detection methods. An attractive mapping strategy—that builds on the principles of fragment-based drug discovery (FBDD)—is to detect the fragment-centric modularity at the protein surface and then characterize the large PPI interface as a set of localized, fragment-targetable interaction regions. Here, we introduce AlphaSpace, a computational analysis tool designed for fragment-centric topographical mapping (FCTM) of PPI interfaces. Our approach uses the alpha sphere construct, a geometric feature of a protein’s Voronoi diagram, to map out concave interaction space at the protein surface. We introduce two new features—alpha-atom and alpha-space—and the concept of the alpha-atom/alpha-space pair to rank pockets for fragment-targetability and to facilitate the evaluation of pocket/fragment complementarity. The resulting high-resolution interfacial map of targetable pocket space can be used to guide the rational design and optimization of small molecule or biomimetic PPI inhibitors. PMID:26225450

Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns

DOE PAGES

Tian, Wenhong; Samatova, Nagiza F.

2013-01-01

A number of tools for the alignment of protein-protein interaction (PPI) networks have laid the foundation for PPI network analysis. Most of alignment tools focus on finding conserved interaction regions across the PPI networks through either local or global mapping of similar sequences. Researchers are still trying to improve the speed, scalability, and accuracy of network alignment. In view of this, we introduce a connected-components based fast algorithm, HopeMap, for network alignment. Observing that the size of true orthologs across species is small comparing to the total number of proteins in all species, we take a different approach based onmore » a precompiled list of homologs identified by KO terms. Applying this approach to S. cerevisiae (yeast) and D. melanogaster (fly), E. coli K12 and S. typhimurium , E. coli K12 and C. crescenttus , we analyze all clusters identified in the alignment. The results are evaluated through up-to-date known gene annotations, gene ontology (GO), and KEGG ortholog groups (KO). Comparing to existing tools, our approach is fast with linear computational cost, highly accurate in terms of KO and GO terms specificity and sensitivity, and can be extended to multiple alignments easily.« less

Applied Graph-Mining Algorithms to Study Biomolecular Interaction Networks

PubMed Central

2014-01-01

Protein-protein interaction (PPI) networks carry vital information on the organization of molecular interactions in cellular systems. The identification of functionally relevant modules in PPI networks is one of the most important applications of biological network analysis. Computational analysis is becoming an indispensable tool to understand large-scale biomolecular interaction networks. Several types of computational methods have been developed and employed for the analysis of PPI networks. Of these computational methods, graph comparison and module detection are the two most commonly used strategies. This review summarizes current literature on graph kernel and graph alignment methods for graph comparison strategies, as well as module detection approaches including seed-and-extend, hierarchical clustering, optimization-based, probabilistic, and frequent subgraph methods. Herein, we provide a comprehensive review of the major algorithms employed under each theme, including our recently published frequent subgraph method, for detecting functional modules commonly shared across multiple cancer PPI networks. PMID:24800226

PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology

PubMed Central

Gioutlakis, Aris; Klapa, Maria I.

2017-01-01

It has been acknowledged that source databases recording experimentally supported human protein-protein interactions (PPIs) exhibit limited overlap. Thus, the reconstruction of a comprehensive PPI network requires appropriate integration of multiple heterogeneous primary datasets, presenting the PPIs at various genetic reference levels. Existing PPI meta-databases perform integration via normalization; namely, PPIs are merged after converted to a certain target level. Hence, the node set of the integrated network depends each time on the number and type of the combined datasets. Moreover, the irreversible a priori normalization process hinders the identification of normalization artifacts in the integrated network, which originate from the nonlinearity characterizing the genetic information flow. PICKLE (Protein InteraCtion KnowLedgebasE) 2.0 implements a new architecture for this recently introduced human PPI meta-database. Its main novel feature over the existing meta-databases is its approach to primary PPI dataset integration via genetic information ontology. Building upon the PICKLE principles of using the reviewed human complete proteome (RHCP) of UniProtKB/Swiss-Prot as the reference protein interactor set, and filtering out protein interactions with low probability of being direct based on the available evidence, PICKLE 2.0 first assembles the RHCP genetic information ontology network by connecting the corresponding genes, nucleotide sequences (mRNAs) and proteins (UniProt entries) and then integrates PPI datasets by superimposing them on the ontology network without any a priori transformations. Importantly, this process allows the resulting heterogeneous integrated network to be reversibly normalized to any level of genetic reference without loss of the original information, the latter being used for identification of normalization biases, and enables the appraisal of potential false positive interactions through PPI source database cross-checking. The PICKLE web-based interface (www.pickle.gr) allows for the simultaneous query of multiple entities and provides integrated human PPI networks at either the protein (UniProt) or the gene level, at three PPI filtering modes. PMID:29023571

A Method for Predicting Protein Complexes from Dynamic Weighted Protein-Protein Interaction Networks.

PubMed

Liu, Lizhen; Sun, Xiaowu; Song, Wei; Du, Chao

2018-06-01

Predicting protein complexes from protein-protein interaction (PPI) network is of great significance to recognize the structure and function of cells. A protein may interact with different proteins under different time or conditions. Existing approaches only utilize static PPI network data that may lose much temporal biological information. First, this article proposed a novel method that combines gene expression data at different time points with traditional static PPI network to construct different dynamic subnetworks. Second, to further filter out the data noise, the semantic similarity based on gene ontology is regarded as the network weight together with the principal component analysis, which is introduced to deal with the weight computing by three traditional methods. Third, after building a dynamic PPI network, a predicting protein complexes algorithm based on "core-attachment" structural feature is applied to detect complexes from each dynamic subnetworks. Finally, it is revealed from the experimental results that our method proposed in this article performs well on detecting protein complexes from dynamic weighted PPI networks.

Protein-Protein Interaction Network and Gene Ontology

NASA Astrophysics Data System (ADS)

Choi, Yunkyu; Kim, Seok; Yi, Gwan-Su; Park, Jinah

Evolution of computer technologies makes it possible to access a large amount and various kinds of biological data via internet such as DNA sequences, proteomics data and information discovered about them. It is expected that the combination of various data could help researchers find further knowledge about them. Roles of a visualization system are to invoke human abilities to integrate information and to recognize certain patterns in the data. Thus, when the various kinds of data are examined and analyzed manually, an effective visualization system is an essential part. One instance of these integrated visualizations can be combination of protein-protein interaction (PPI) data and Gene Ontology (GO) which could help enhance the analysis of PPI network. We introduce a simple but comprehensive visualization system that integrates GO and PPI data where GO and PPI graphs are visualized side-by-side and supports quick reference functions between them. Furthermore, the proposed system provides several interactive visualization methods for efficiently analyzing the PPI network and GO directedacyclic- graph such as context-based browsing and common ancestors finding.

A scalable double-barcode sequencing platform for characterization of dynamic protein-protein interactions.

PubMed

Schlecht, Ulrich; Liu, Zhimin; Blundell, Jamie R; St Onge, Robert P; Levy, Sasha F

2017-05-25

Several large-scale efforts have systematically catalogued protein-protein interactions (PPIs) of a cell in a single environment. However, little is known about how the protein interactome changes across environmental perturbations. Current technologies, which assay one PPI at a time, are too low throughput to make it practical to study protein interactome dynamics. Here, we develop a highly parallel protein-protein interaction sequencing (PPiSeq) platform that uses a novel double barcoding system in conjunction with the dihydrofolate reductase protein-fragment complementation assay in Saccharomyces cerevisiae. PPiSeq detects PPIs at a rate that is on par with current assays and, in contrast with current methods, quantitatively scores PPIs with enough accuracy and sensitivity to detect changes across environments. Both PPI scoring and the bulk of strain construction can be performed with cell pools, making the assay scalable and easily reproduced across environments. PPiSeq is therefore a powerful new tool for large-scale investigations of dynamic PPIs.

[Chemical libraries dedicated to protein-protein interactions].

PubMed

Sperandio, Olivier; Villoutreix, Bruno O; Morelli, Xavier; Roche, Philippe

2015-03-01

The identification of complete networks of protein-protein interactions (PPI) within a cell has contributed to major breakthroughs in understanding biological pathways, host-pathogen interactions and cancer development. As a consequence, PPI have emerged as a new class of promising therapeutic targets. However, they are still considered as a challenging class of targets for drug discovery programs. Recent successes have allowed the characterization of structural and physicochemical properties of protein-protein interfaces leading to a better understanding of how they can be disrupted with small molecule compounds. In addition, characterization of the profiles of PPI inhibitors has allowed the development of PPI-focused libraries. In this review, we present the current efforts at developing chemical libraries dedicated to these innovative targets. © 2015 médecine/sciences – Inserm.

Clopidogrel and proton pump inhibitor (PPI) interaction: separate intake and a non-omeprazole PPI the solution?

PubMed Central

2010-01-01

Background Dual therapy with aspirin and clopidogrel increases the risk of gastrointestinal bleeding. Therefore, co-therapy with a proton pump inhibitor (PPI) is recommended by most guidelines. However, there are warnings against combining PPIs with clopidogrel because of their interactions with cytochrome P450 isoenzyme 2C19 (CYP2C19). Methods The effects of the combined or separate intake of 20 mg of omeprazole and 75 mg of clopidogrel on the clopidogrel-induced inhibition of platelet aggregation were measured in four healthy subjects whose CYP2C19 exon sequences were determined. The effects of co-therapy with 10 mg of rabeprazole were also examined. Results Two subjects showed the wild-type CYP2C19 sequence. The concurrent intake of omeprazole had no effect on clopidogrel-induced platelet inhibition in these subjects. Two subjects were heterozygous for the *2 allele, with predicted reduced CYP2C19 activity. One of them was a clopidogrel non-responder. In the second heterozygous subject, omeprazole co-therapy reduced the clopidogrel anti-platelet effect when taken simultaneously or separately. However, the simultaneous intake of rabeprazole did not reduce the clopidogrel effect. Conclusion The clopidogrel-PPI interaction does not seem to be a PPI class effect. Rabeprazole did not affect the clopidogrel effect in a subject with a clear omeprazole-clopidogrel interaction. The separate intake of PPI and clopidogrel may not be sufficient to prevent their interaction. PMID:20562062

PROPER: global protein interaction network alignment through percolation matching.

PubMed

Kazemi, Ehsan; Hassani, Hamed; Grossglauser, Matthias; Pezeshgi Modarres, Hassan

2016-12-12

The alignment of protein-protein interaction (PPI) networks enables us to uncover the relationships between different species, which leads to a deeper understanding of biological systems. Network alignment can be used to transfer biological knowledge between species. Although different PPI-network alignment algorithms were introduced during the last decade, developing an accurate and scalable algorithm that can find alignments with high biological and structural similarities among PPI networks is still challenging. In this paper, we introduce a new global network alignment algorithm for PPI networks called PROPER. Compared to other global network alignment methods, our algorithm shows higher accuracy and speed over real PPI datasets and synthetic networks. We show that the PROPER algorithm can detect large portions of conserved biological pathways between species. Also, using a simple parsimonious evolutionary model, we explain why PROPER performs well based on several different comparison criteria. We highlight that PROPER has high potential in further applications such as detecting biological pathways, finding protein complexes and PPI prediction. The PROPER algorithm is available at http://proper.epfl.ch .

Patient and public involvement: how much do we spend and what are the benefits?

PubMed

Pizzo, Elena; Doyle, Cathal; Matthews, Rachel; Barlow, James

2015-12-01

Patient and public involvement (PPI) is seen as a way of helping to shape health policy and ensure a patient-focused health-care system. While evidence indicates that PPI can improve health-care decision making, it also consumes monetary and non-monetary resources. Given the financial climate, it is important to start thinking about the costs and benefits of PPI and how to evaluate it in economic terms. We conducted a literature review to assess the potential benefits and costs of involvement and the challenges in carrying out an economic evaluation of PPI. The benefits of PPI include effects on the design of new projects or services, on NHS governance, on research design and implementation and on citizenship and equity. Economic evaluation of PPI activities is limited. The lack of an appropriate analytical framework, data recording and understanding of the potential costs and benefits of PPI, especially from participants' perspectives, represent serious constraints on the full evaluation of PPI. By recognizing the value of PPI, health-care providers and commissioners can embed it more effectively within their organizations. Better knowledge of costs may prompt organizations to effectively plan, execute, evaluate and target resources. This should increase the likelihood of more meaningful activity, avoid tokenism and enhance organizational efficiency and reputation. © 2014 The Authors Health Expectations Published by John Wiley & Sons Ltd.

Multi-Dimensional Scaling based grouping of known complexes and intelligent protein complex detection.

PubMed

Rehman, Zia Ur; Idris, Adnan; Khan, Asifullah

2018-06-01

Protein-Protein Interactions (PPI) play a vital role in cellular processes and are formed because of thousands of interactions among proteins. Advancements in proteomics technologies have resulted in huge PPI datasets that need to be systematically analyzed. Protein complexes are the locally dense regions in PPI networks, which extend important role in metabolic pathways and gene regulation. In this work, a novel two-phase protein complex detection and grouping mechanism is proposed. In the first phase, topological and biological features are extracted for each complex, and prediction performance is investigated using Bagging based Ensemble classifier (PCD-BEns). Performance evaluation through cross validation shows improvement in comparison to CDIP, MCode, CFinder and PLSMC methods Second phase employs Multi-Dimensional Scaling (MDS) for the grouping of known complexes by exploring inter complex relations. It is experimentally observed that the combination of topological and biological features in the proposed approach has greatly enhanced prediction performance for protein complex detection, which may help to understand various biological processes, whereas application of MDS based exploration may assist in grouping potentially similar complexes. Copyright © 2018 Elsevier Ltd. All rights reserved.

Distributed smoothed tree kernel for protein-protein interaction extraction from the biomedical literature

PubMed Central

Murugesan, Gurusamy; Abdulkadhar, Sabenabanu; Natarajan, Jeyakumar

2017-01-01

Automatic extraction of protein-protein interaction (PPI) pairs from biomedical literature is a widely examined task in biological information extraction. Currently, many kernel based approaches such as linear kernel, tree kernel, graph kernel and combination of multiple kernels has achieved promising results in PPI task. However, most of these kernel methods fail to capture the semantic relation information between two entities. In this paper, we present a special type of tree kernel for PPI extraction which exploits both syntactic (structural) and semantic vectors information known as Distributed Smoothed Tree kernel (DSTK). DSTK comprises of distributed trees with syntactic information along with distributional semantic vectors representing semantic information of the sentences or phrases. To generate robust machine learning model composition of feature based kernel and DSTK were combined using ensemble support vector machine (SVM). Five different corpora (AIMed, BioInfer, HPRD50, IEPA, and LLL) were used for evaluating the performance of our system. Experimental results show that our system achieves better f-score with five different corpora compared to other state-of-the-art systems. PMID:29099838

Distributed smoothed tree kernel for protein-protein interaction extraction from the biomedical literature.

PubMed

Murugesan, Gurusamy; Abdulkadhar, Sabenabanu; Natarajan, Jeyakumar

2017-01-01

Automatic extraction of protein-protein interaction (PPI) pairs from biomedical literature is a widely examined task in biological information extraction. Currently, many kernel based approaches such as linear kernel, tree kernel, graph kernel and combination of multiple kernels has achieved promising results in PPI task. However, most of these kernel methods fail to capture the semantic relation information between two entities. In this paper, we present a special type of tree kernel for PPI extraction which exploits both syntactic (structural) and semantic vectors information known as Distributed Smoothed Tree kernel (DSTK). DSTK comprises of distributed trees with syntactic information along with distributional semantic vectors representing semantic information of the sentences or phrases. To generate robust machine learning model composition of feature based kernel and DSTK were combined using ensemble support vector machine (SVM). Five different corpora (AIMed, BioInfer, HPRD50, IEPA, and LLL) were used for evaluating the performance of our system. Experimental results show that our system achieves better f-score with five different corpora compared to other state-of-the-art systems.

The OncoPPi network of cancer-focused protein-protein interactions to inform biological insights and therapeutic strategies* | Office of Cancer Genomics

Cancer.gov

As genomics advances reveal the cancer gene landscape, a daunting task is to understand how these genes contribute to dysregulated oncogenic pathways. Integration of cancer genes into networks offers opportunities to reveal protein–protein interactions (PPIs) with functional and therapeutic significance. Here, we report the generation of a cancer-focused PPI network, termed OncoPPi, and identification of >260 cancer-associated PPIs not in other large-scale interactomes.

HPIminer: A text mining system for building and visualizing human protein interaction networks and pathways.

PubMed

Subramani, Suresh; Kalpana, Raja; Monickaraj, Pankaj Moses; Natarajan, Jeyakumar

2015-04-01

The knowledge on protein-protein interactions (PPI) and their related pathways are equally important to understand the biological functions of the living cell. Such information on human proteins is highly desirable to understand the mechanism of several diseases such as cancer, diabetes, and Alzheimer's disease. Because much of that information is buried in biomedical literature, an automated text mining system for visualizing human PPI and pathways is highly desirable. In this paper, we present HPIminer, a text mining system for visualizing human protein interactions and pathways from biomedical literature. HPIminer extracts human PPI information and PPI pairs from biomedical literature, and visualize their associated interactions, networks and pathways using two curated databases HPRD and KEGG. To our knowledge, HPIminer is the first system to build interaction networks from literature as well as curated databases. Further, the new interactions mined only from literature and not reported earlier in databases are highlighted as new. A comparative study with other similar tools shows that the resultant network is more informative and provides additional information on interacting proteins and their associated networks. Copyright © 2015 Elsevier Inc. All rights reserved.

LocFuse: human protein-protein interaction prediction via classifier fusion using protein localization information.

PubMed

Zahiri, Javad; Mohammad-Noori, Morteza; Ebrahimpour, Reza; Saadat, Samaneh; Bozorgmehr, Joseph H; Goldberg, Tatyana; Masoudi-Nejad, Ali

2014-12-01

Protein-protein interaction (PPI) detection is one of the central goals of functional genomics and systems biology. Knowledge about the nature of PPIs can help fill the widening gap between sequence information and functional annotations. Although experimental methods have produced valuable PPI data, they also suffer from significant limitations. Computational PPI prediction methods have attracted tremendous attentions. Despite considerable efforts, PPI prediction is still in its infancy in complex multicellular organisms such as humans. Here, we propose a novel ensemble learning method, LocFuse, which is useful in human PPI prediction. This method uses eight different genomic and proteomic features along with four types of different classifiers. The prediction performance of this classifier selection method was found to be considerably better than methods employed hitherto. This confirms the complex nature of the PPI prediction problem and also the necessity of using biological information for classifier fusion. The LocFuse is available at: http://lbb.ut.ac.ir/Download/LBBsoft/LocFuse. The results revealed that if we divide proteome space according to the cellular localization of proteins, then the utility of some classifiers in PPI prediction can be improved. Therefore, to predict the interaction for any given protein pair, we can select the most accurate classifier with regard to the cellular localization information. Based on the results, we can say that the importance of different features for PPI prediction varies between differently localized proteins; however in general, our novel features, which were extracted from position-specific scoring matrices (PSSMs), are the most important ones and the Random Forest (RF) classifier performs best in most cases. LocFuse was developed with a user-friendly graphic interface and it is freely available for Linux, Mac OSX and MS Windows operating systems. Copyright © 2014 Elsevier Inc. All rights reserved.

Assembling of stimuli-responsive tumor targeting polypyrrole nanotubes drug carrier system for controlled release.

PubMed

Chen, Jian; Li, Xiufang; Li, Jiawen; Li, Jianbing; Huang, Ling; Ren, Tao; Yang, Xiao; Zhong, Shian

2018-08-01

A stimuli-responsive polypyrrole (PPy) nanotubes drug carrier system has been designed to deliver anticancer drugs to tumor cells in a targeted and controlled manner. The PPy nanotubes drug carrier was fabricated by a template method. The nanotubes surface was functionalized with cleavable acylhydrazone and disulfide bonds by attaching thiolated β-cyclodextrin (β-CD). The solubilizing poly(ethylene glycol) polymer (PEG), attached with an adamantane (Ad) entity at one end and a folate (FA) entity at the other end, was introduced onto the nanotubes surface via β-cyclodextrin-adamantane interaction. The synthesized FA-PEG-Ad-β-CD-PPy showed excellent biocompatibility and low cytotoxicity for two cell lines. Doxorubicin (Dox) loaded FA-PEG-Ad-β-CD-PPy nanotubes showed a triggered in vitro drug release behavior in the presence of acidic media and reducing agents. The folate-mediated endocytosis and intracellular release of Dox-loaded nanoparticles were confirmed by fluorescence microscopy and cell viability evaluations. In the in vitro study, Dox loaded within the nanoparticles showed enhanced selectivity for cancerous cells and reduced cytotoxicity for normal cells compared to free Dox. The PPy based targeted drug vehicle shows excellent promise for drug delivery. Copyright © 2018 Elsevier B.V. All rights reserved.

Solubility and surface thermodynamics of conducting polymers by inverse gas chromatography. III: polypyrrole chloride.

PubMed

Duaij, Omar K; Alghamdi, Ali; Al-Saigh, Zeki Y

2013-05-24

Inverse gas chromatography, IGC, was applied to characterize conducting polypyrrole chloride (PPyCl) using twenty three solvents. IGC is able to reveal the change in the morphology, the strength of solvent-PPyCl interactions, thermodynamics parameters (χ12, Ω1(∞)), solvent and polymer solubility parameters, and molar heats of sorption, mixing and evaporation (ΔH1(s), ΔH1(∞), ΔH1(v)). The following solvents showed stronger interactions than others; yet, none of these solvents are good solvents for PPyCl: dodecane among the alkane family, tetrahydrofuran and methyl ethyl ketone among the oxy and keto group, dichloromethane among the chlorinated group up to 120°C and chloroform at 180°C, and toluene among the cyclic and aromatic group. Overall, the groups showed higher affinities to PPyCl are: acetates, oxy and cyclic, and chlorinated groups. Comprehensive solvents and PPyCl solubility parameters are obtained. The latter showed that PPyCl is not soluble in any solvent used. Copyright © 2013 Elsevier B.V. All rights reserved.

Improving prediction of heterodimeric protein complexes using combination with pairwise kernel.

PubMed

Ruan, Peiying; Hayashida, Morihiro; Akutsu, Tatsuya; Vert, Jean-Philippe

2018-02-19

Since many proteins become functional only after they interact with their partner proteins and form protein complexes, it is essential to identify the sets of proteins that form complexes. Therefore, several computational methods have been proposed to predict complexes from the topology and structure of experimental protein-protein interaction (PPI) network. These methods work well to predict complexes involving at least three proteins, but generally fail at identifying complexes involving only two different proteins, called heterodimeric complexes or heterodimers. There is however an urgent need for efficient methods to predict heterodimers, since the majority of known protein complexes are precisely heterodimers. In this paper, we use three promising kernel functions, Min kernel and two pairwise kernels, which are Metric Learning Pairwise Kernel (MLPK) and Tensor Product Pairwise Kernel (TPPK). We also consider the normalization forms of Min kernel. Then, we combine Min kernel or its normalization form and one of the pairwise kernels by plugging. We applied kernels based on PPI, domain, phylogenetic profile, and subcellular localization properties to predicting heterodimers. Then, we evaluate our method by employing C-Support Vector Classification (C-SVC), carrying out 10-fold cross-validation, and calculating the average F-measures. The results suggest that the combination of normalized-Min-kernel and MLPK leads to the best F-measure and improved the performance of our previous work, which had been the best existing method so far. We propose new methods to predict heterodimers, using a machine learning-based approach. We train a support vector machine (SVM) to discriminate interacting vs non-interacting protein pairs, based on informations extracted from PPI, domain, phylogenetic profiles and subcellular localization. We evaluate in detail new kernel functions to encode these data, and report prediction performance that outperforms the state-of-the-art.

Large-Scale Validation of Mixed-Solvent Simulations to Assess Hotspots at Protein-Protein Interaction Interfaces.

PubMed

Ghanakota, Phani; van Vlijmen, Herman; Sherman, Woody; Beuming, Thijs

2018-04-23

The ability to target protein-protein interactions (PPIs) with small molecule inhibitors offers great promise in expanding the druggable target space and addressing a broad range of untreated diseases. However, due to their nature and function of interacting with protein partners, PPI interfaces tend to extend over large surfaces without the typical pockets of enzymes and receptors. These features present unique challenges for small molecule inhibitor design. As such, determining whether a particular PPI of interest could be pursued with a small molecule discovery strategy requires an understanding of the characteristics of the PPI interface and whether it has hotspots that can be leveraged by small molecules to achieve desired potency. Here, we assess the ability of mixed-solvent molecular dynamic (MSMD) simulations to detect hotspots at PPI interfaces. MSMD simulations using three cosolvents (acetonitrile, isopropanol, and pyrimidine) were performed on a large test set of 21 PPI targets that have been experimentally validated by small molecule inhibitors. We compare MSMD, which includes explicit solvent and full protein flexibility, to a simpler approach that does not include dynamics or explicit solvent (SiteMap) and find that MSMD simulations reveal additional information about the characteristics of these targets and the ability for small molecules to inhibit the PPI interface. In the few cases were MSMD simulations did not detect hotspots, we explore the shortcomings of this technique and propose future improvements. Finally, using Interleukin-2 as an example, we highlight the advantage of the MSMD approach for detecting transient cryptic druggable pockets that exists at PPI interfaces.

Emory University: Prediction of Protein-Protein Interactions by NanoLuc-Based Protein-Fragment Complementation Assay | Office of Cancer Genomics

Cancer.gov

The CTD2 Center at Emory has developed a new NanoLuc®-based protein-fragment complementation assay (NanoPCA) which allows the detection of novel protein-protein interactions (PPI). NanoPCA allows the study of PPI dynamics with reversible interactions.  Read the abstract. Experimental Approaches Read the detailed Experimetnal Approaches. 

Prediction of Protein-Protein Interactions by NanoLuc-Based Protein-Fragment Complementation Assay | Office of Cancer Genomics

Cancer.gov

The CTD2 Center at Emory has developed a new NanoLuc®-based protein-fragment complementation assay (NanoPCA) which allows the detection of novel protein-protein interactions (PPI). NanoPCA allows the study of PPI dynamics with reversible interactions.  Read the abstract. Experimental Approaches Read the detailed Experimetnal Approaches. 

Revealing protein functions based on relationships of interacting proteins and GO terms.

PubMed

Teng, Zhixia; Guo, Maozu; Liu, Xiaoyan; Tian, Zhen; Che, Kai

2017-09-20

In recent years, numerous computational methods predicted protein function based on the protein-protein interaction (PPI) network. These methods supposed that two proteins share the same function if they interact with each other. However, it is reported by recent studies that the functions of two interacting proteins may be just related. It will mislead the prediction of protein function. Therefore, there is a need for investigating the functional relationship between interacting proteins. In this paper, the functional relationship between interacting proteins is studied and a novel method, called as GoDIN, is advanced to annotate functions of interacting proteins in Gene Ontology (GO) context. It is assumed that the functional difference between interacting proteins can be expressed by semantic difference between GO term and its relatives. Thus, the method uses GO term and its relatives to annotate the interacting proteins separately according to their functional roles in the PPI network. The method is validated by a series of experiments and compared with the concerned method. The experimental results confirm the assumption and suggest that GoDIN is effective on predicting functions of protein. This study demonstrates that: (1) interacting proteins are not equal in the PPI network, and their function may be same or similar, or just related; (2) functional difference between interacting proteins can be measured by their degrees in the PPI network; (3) functional relationship between interacting proteins can be expressed by relationship between GO term and its relatives.

Comparative proteomic analysis provides insight into the biological role of protein phosphatase inhibitor-2 from Arabidopsis.

PubMed

Ahsan, Nagib; Chen, Mingjie; Salvato, Fernanda; Wilson, Rashaun S; Shyama Prasad Rao, R; Thelen, Jay J

2017-08-08

Protein phosphatase inhibitor-2 (PPI-2) is a conserved eukaryotic effector protein that inhibits type one protein phosphatases (TOPP). A transfer-DNA knockdown of AtPPI-2 resulted in stunted growth in both vegetative and reproductive phases of Arabidopsis development. At the cellular level, AtPPI-2 knockdown had 35 to 40% smaller cells in developing roots and leaves. This developmental phenotype was rescued by transgenic expression of the AtPPI-2 cDNA behind a constitutive promoter. Comparative proteomics of developing leaves of wild type (WT) and AtPPI-2 mutant revealed reduced levels of proteins associated with chloroplast development, ribosome biogenesis, transport, and cell cycle regulation processes. Decreased abundance of several ribosomal proteins, a DEAD box RNA helicase family protein (AtRH3), Clp protease (ClpP3) and proteins associated with cell division suggests a bottleneck in chloroplast ribosomal biogenesis and cell cycle regulation in AtPPI-2 mutant plants. In contrast, eight out of nine Arabidopsis TOPP isoforms were increased at the transcript level in AtPPI-2 leaves compared to WT. A protein-protein interaction network revealed that >75% of the differentially accumulated proteins have at least secondary and/or tertiary connections with AtPPI-2. Collectively, these data reveal a potential basis for the growth defects of AtPPI-2 and support the presumed role of AtPPI-2 as a master regulator for TOPPs, which regulate diverse growth and developmental processes. Comparative label-free proteomics was used to characterize an AtPPI-2T-DNA knockdown mutant. The complex, reduced growth phenotype supports the notion that AtPPI-2 is a global regulator of TOPPs, and possibly other proteins. Comparative proteomics revealed a range of differences in protein abundance from various cellular processes such as chloroplast development, ribosome biogenesis, and transporter activity in the AtPPI-2 mutant relative to WT Arabidopsis. Collectively the results of proteomic analysis and the protein-protein network suggest that AtPPI-2 is involved in a wide range of biological processes either directly or indirectly including plastid biogenesis, translational mechanisms, and cell cycle regulation. The proposed protein interaction network comprises a testable model underlying changes in protein abundance in the AtPPI-2 mutant, and provides a better framework for future studies. Copyright © 2017 Elsevier B.V. All rights reserved.

Protein complex prediction in large ontology attributed protein-protein interaction networks.

PubMed

Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian; Li, Yanpeng; Xu, Bo

2013-01-01

Protein complexes are important for unraveling the secrets of cellular organization and function. Many computational approaches have been developed to predict protein complexes in protein-protein interaction (PPI) networks. However, most existing approaches focus mainly on the topological structure of PPI networks, and largely ignore the gene ontology (GO) annotation information. In this paper, we constructed ontology attributed PPI networks with PPI data and GO resource. After constructing ontology attributed networks, we proposed a novel approach called CSO (clustering based on network structure and ontology attribute similarity). Structural information and GO attribute information are complementary in ontology attributed networks. CSO can effectively take advantage of the correlation between frequent GO annotation sets and the dense subgraph for protein complex prediction. Our proposed CSO approach was applied to four different yeast PPI data sets and predicted many well-known protein complexes. The experimental results showed that CSO was valuable in predicting protein complexes and achieved state-of-the-art performance.

Multi-agent-based bio-network for systems biology: protein-protein interaction network as an example.

PubMed

Ren, Li-Hong; Ding, Yong-Sheng; Shen, Yi-Zhen; Zhang, Xiang-Feng

2008-10-01

Recently, a collective effort from multiple research areas has been made to understand biological systems at the system level. This research requires the ability to simulate particular biological systems as cells, organs, organisms, and communities. In this paper, a novel bio-network simulation platform is proposed for system biology studies by combining agent approaches. We consider a biological system as a set of active computational components interacting with each other and with an external environment. Then, we propose a bio-network platform for simulating the behaviors of biological systems and modelling them in terms of bio-entities and society-entities. As a demonstration, we discuss how a protein-protein interaction (PPI) network can be seen as a society of autonomous interactive components. From interactions among small PPI networks, a large PPI network can emerge that has a remarkable ability to accomplish a complex function or task. We also simulate the evolution of the PPI networks by using the bio-operators of the bio-entities. Based on the proposed approach, various simulators with different functions can be embedded in the simulation platform, and further research can be done from design to development, including complexity validation of the biological system.

ChiPPI: a novel method for mapping chimeric protein-protein interactions uncovers selection principles of protein fusion events in cancer.

PubMed

Frenkel-Morgenstern, Milana; Gorohovski, Alessandro; Tagore, Somnath; Sekar, Vaishnovi; Vazquez, Miguel; Valencia, Alfonso

2017-07-07

Fusion proteins, comprising peptides deriving from the translation of two parental genes, are produced in cancer by chromosomal aberrations. The expressed fusion protein incorporates domains of both parental proteins. Using a methodology that treats discrete protein domains as binding sites for specific domains of interacting proteins, we have cataloged the protein interaction networks for 11 528 cancer fusions (ChiTaRS-3.1). Here, we present our novel method, chimeric protein-protein interactions (ChiPPI) that uses the domain-domain co-occurrence scores in order to identify preserved interactors of chimeric proteins. Mapping the influence of fusion proteins on cell metabolism and pathways reveals that ChiPPI networks often lose tumor suppressor proteins and gain oncoproteins. Furthermore, fusions often induce novel connections between non-interactors skewing interaction networks and signaling pathways. We compared fusion protein PPI networks in leukemia/lymphoma, sarcoma and solid tumors finding distinct enrichment patterns for each disease type. While certain pathways are enriched in all three diseases (Wnt, Notch and TGF β), there are distinct patterns for leukemia (EGFR signaling, DNA replication and CCKR signaling), for sarcoma (p53 pathway and CCKR signaling) and solid tumors (FGFR and EGFR signaling). Thus, the ChiPPI method represents a comprehensive tool for studying the anomaly of skewed cellular networks produced by fusion proteins in cancer. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

From plans to actions in patient and public involvement: qualitative study of documented plans and the accounts of researchers and patients sampled from a cohort of clinical trials

PubMed Central

Buck, Deborah; Gamble, Carrol; Dudley, Louise; Preston, Jennifer; Hanley, Bec; Williamson, Paula R; Young, Bridget

2014-01-01

Patient and public involvement (PPI) in research is increasingly required, although evidence to inform its implementation is limited. Objective Inform the evidence base by describing how plans for PPI were implemented within clinical trials and identifying the challenges and lessons learnt by research teams. Methods We compared PPI plans extracted from clinical trial grant applications (funded by the National Institute for Health Research Health Technology Assessment Programme between 2006 and 2010) with researchers’ and PPI contributors’ interview accounts of PPI implementation. Analysis of PPI plans and transcribed qualitative interviews drew on the Framework technique. Results Of 28 trials, 25 documented plans for PPI in funding applications and half described implementing PPI before applying for funding. Plans varied from minimal to extensive, although almost all anticipated multiple modes of PPI. Interview accounts indicated that PPI plans had been fully implemented in 20/25 trials and even expanded in some. Nevertheless, some researchers described PPI within their trials as tokenistic. Researchers and contributors noted that late or minimal PPI engagement diminished its value. Both groups perceived uncertainty about roles in relation to PPI, and noted contributors’ lack of confidence and difficulties attending meetings. PPI contributors experienced problems in interacting with researchers and understanding technical language. Researchers reported difficulties finding ‘the right’ PPI contributors, and advised caution when involving investigators’ current patients. Conclusions Engaging PPI contributors early and ensuring ongoing clarity about their activities, roles and goals, is crucial to PPI's success. Funders, reviewers and regulators should recognise the value of preapplication PPI and allocate further resources to it. They should also consider whether PPI plans in grant applications match a trial's distinct needs. Monitoring and reporting PPI before, during and after trials will help the research community to optimise PPI, although the need for ongoing flexibility in implementing PPI should also be recognised. PMID:25475243

A leap into the chemical space of protein-protein interaction inhibitors.

PubMed

Villoutreix, B O; Labbé, C M; Lagorce, D; Laconde, G; Sperandio, O

2012-01-01

Protein-protein interactions (PPI) are involved in vital cellular processes and are therefore associated to a growing number of diseases. But working with them as therapeutic targets comes with some major hurdles that require substantial mutations from our way to design drugs on historical targets such as enzymes and G-Protein Coupled Receptor (GPCR). Among the numerous ways we could improve our methodologies to maximize the potential of developing new chemical entities on PPI targets, is the fundamental question of what type of compounds should we use to identify the first hits and among which chemical space should we navigate to optimize them to the drug candidate stage. In this review article, we cover different aspects on PPI but with the aim to gain some insights into the specific nature of the chemical space of PPI inhibitors. We describe the work of different groups to highlight such properties and discuss their respective approach. We finally discuss a case study in which we describe the properties of a set of 115 PPI inhibitors that we compare to a reference set of 1730 enzyme inhibitors. This case study highlights interesting properties such as the unfortunate price that still needs to be paid by PPI inhibitors in terms of molecular weight, hydrophobicity, and aromaticity in order to reach a critical level of activity. But it also shows that not all PPI targets are equivalent, and that some PPI targets can demonstrate a better druggability by illustrating the better drug likeness of their associated inhibitors.

Impact of Proton Pump Inhibitor Use on the Comparative Effectiveness and Safety of Prasugrel Versus Clopidogrel: Insights From the Treatment With Adenosine Diphosphate Receptor Inhibitors: Longitudinal Assessment of Treatment Patterns and Events After Acute Coronary Syndrome (TRANSLATE-ACS) Study.

PubMed

Jackson, Larry R; Peterson, Eric D; McCoy, Lisa A; Ju, Christine; Zettler, Marjorie; Baker, Brian A; Messenger, John C; Faries, Douglas E; Effron, Mark B; Cohen, David J; Wang, Tracy Y

2016-10-21

Proton pump inhibitors (PPIs) reduce gastrointestinal bleeding events but may alter clopidogrel metabolism. We sought to understand the comparative effectiveness and safety of prasugrel versus clopidogrel in the context of proton pump inhibitor (PPI) use. Using data on 11 955 acute myocardial infarction (MI) patients treated with percutaneous coronary intervention at 233 hospitals and enrolled in the TRANSLATE-ACS study, we compared whether discharge PPI use altered the association of 1-year adjusted risks of major adverse cardiovascular events (MACE; death, MI, stroke, or unplanned revascularization) and Global Use of Strategies To Open Occluded Arteries (GUSTO) moderate/severe bleeding between prasugrel- and clopidogrel-treated patients. Overall, 17% of prasugrel-treated and 19% of clopidogrel-treated patients received a PPI at hospital discharge. At 1 year, patients discharged on a PPI versus no PPI had higher risks of MACE (adjusted hazard ratio [HR] 1.38, 95% confidence interval [CI] 1.21-1.58) and GUSTO moderate/severe bleeding (adjusted HR 1.55, 95% CI 1.15-2.09). Risk of MACE was similar between prasugrel and clopidogrel regardless of PPI use (adjusted HR 0.88, 95% CI 0.62-1.26 with PPI, adjusted HR 1.07, 95% CI 0.90-1.28 without PPI, interaction P=0.31). Comparative bleeding risk associated with prasugrel versus clopidogrel use differed based on PPI use but did not reach statistical significance (adjusted HR 0.73, 95% CI 0.36-1.48 with PPI, adjusted HR 1.34, 95% CI 0.79-2.27 without PPI, interaction P=0.17). PPIs did not significantly affect the MACE and bleeding risk associated with prasugrel use, relative to clopidogrel. URL: https://www.clinicaltrials.gov. Unique identifier: NCT01088503. © 2016 The Authors and Eli Lilly & Company. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

Efficacy and Safety of Ultrasound-Guided Percutaneous Polidocanol Sclerotherapy in Benign Cystic Thyroid Nodules: Preliminary Results.

PubMed

Gong, Xiaohua; Zhou, Qi; Wang, Fang; Wu, Wenjun; Chen, Xiaojun

2017-01-01

To evaluate the efficacy and safety of percutaneous polidocanol injection (PPI) in treating cystic thyroid nodules. A total of 158 cystic or predominantly cystic thyroid nodules (>80% cystic component) in 143 patients were evaluated. 114 patients with compressive symptoms or aesthetic complaints were offered PPI. 44 individuals without compressive symptoms and aesthetic complaints who were only followed up clinically were used as the control group. The efficacy and safety of PPI were evaluated for 1 month, 3 months, 6 months, 9 months, and 12 months of follow-up. In the PPI group, the mean baseline volume of 15.6 ± 18.9 cm 3 reduced at the 1-month follow-up to 5.1 ± 5.6 cm 3 ( p < 0.001) and 0.6 ± 0.9 ( p < 0.001), and nodules shrunk according to the time after PPI ( p < 0.001). A complete response (if ≥70% decrease) to PPI at the 12-month follow-up occurred in 100% of the cystic or predominant cystic nodules. None of the nodules recurred at the 12-month follow-up after PPI. The side effects were mild. Twenty patients (17.5%) developed mild localized pain, and fourteen cases (12.3%) experienced mild or moderate fever after PPI. PPI is a safe and effective alternative to treat benign cystic or predominant cystic thyroid nodules.

Network topological analysis reveals the functional cohesiveness for the newly discovered links by Yeast 2 Hybrid approach

NASA Astrophysics Data System (ADS)

Ghiassian, Susan; Pevzner, Sam; Rolland, Thomas; Tassan, Murat; Barabasi, Albert Laszlo; Vidal, Mark; CCNR, Northeastern University Collaboration; Dana Farber Cancer Institute Collaboration

2014-03-01

Protein-protein interaction maps and interactomes are the blueprint of Network Medicine and systems biology and are being experimentally studied by different groups. Despite the wide usage of Literature Curated Interactome (LCI), these sources are biased towards different parameters such as highly studied proteins. Yeast two hybrid method is a high throughput experimental setup which screens proteins in an unbiased fashion. Current knowledge of protein interactions is far from complete. In fact the previous offered data from Y2H method (2005), is estimated to offer only 5% of all potential protein interactions. Currently this coverage has increased to 20% of what is known as reference HI In this work we study the topological properties of Y2H protein-protein interactions network with LCI and show although they both agree on some properties, LCI shows a clear unbiased nature of interaction selections. Most importantly, we assess the properties of PPI as it evolves with increasing the coverage. We show that, the newly discovered interactions tend to connect proteins that have been closer than average in the previous PPI release. reinforcing the modular structure of PPI. Furthermore, we show, some unseen effects on PPI (as opposed to LCI) can be explained by its incompleteness.

Kinase Substrate Sensor (KISS), a Mammalian In Situ Protein Interaction Sensor*

PubMed Central

Lievens, Sam; Gerlo, Sarah; Lemmens, Irma; De Clercq, Dries J. H.; Risseeuw, Martijn D. P.; Vanderroost, Nele; De Smet, Anne-Sophie; Ruyssinck, Elien; Chevet, Eric; Van Calenbergh, Serge; Tavernier, Jan

2014-01-01

Probably every cellular process is governed by protein-protein interaction (PPIs), which are often highly dynamic in nature being modulated by in- or external stimuli. Here we present KISS, for KInase Substrate Sensor, a mammalian two-hybrid approach designed to map intracellular PPIs and some of the dynamic features they exhibit. Benchmarking experiments indicate that in terms of sensitivity and specificity KISS is on par with other binary protein interaction technologies while being complementary with regard to the subset of PPIs it is able to detect. We used KISS to evaluate interactions between different types of proteins, including transmembrane proteins, expressed at their native subcellular location. In situ analysis of endoplasmic reticulum stress-induced clustering of the endoplasmic reticulum stress sensor ERN1 and ligand-dependent β-arrestin recruitment to GPCRs illustrated the method's potential to study functional PPI modulation in complex cellular processes. Exploring its use as a tool for in cell evaluation of pharmacological interference with PPIs, we showed that reported effects of known GPCR antagonists and PPI inhibitors are properly recapitulated. In a three-hybrid setup, KISS was able to map interactions between small molecules and proteins. Taken together, we established KISS as a sensitive approach for in situ analysis of protein interactions and their modulation in a changing cellular context or in response to pharmacological challenges. PMID:25154561

Predicting Protein-Protein Interaction Sites with a Novel Membership Based Fuzzy SVM Classifier.

PubMed

Sriwastava, Brijesh K; Basu, Subhadip; Maulik, Ujjwal

2015-01-01

Predicting residues that participate in protein-protein interactions (PPI) helps to identify, which amino acids are located at the interface. In this paper, we show that the performance of the classical support vector machine (SVM) algorithm can further be improved with the use of a custom-designed fuzzy membership function, for the partner-specific PPI interface prediction problem. We evaluated the performances of both classical SVM and fuzzy SVM (F-SVM) on the PPI databases of three different model proteomes of Homo sapiens, Escherichia coli and Saccharomyces Cerevisiae and calculated the statistical significance of the developed F-SVM over classical SVM algorithm. We also compared our performance with the available state-of-the-art fuzzy methods in this domain and observed significant performance improvements. To predict interaction sites in protein complexes, local composition of amino acids together with their physico-chemical characteristics are used, where the F-SVM based prediction method exploits the membership function for each pair of sequence fragments. The average F-SVM performance (area under ROC curve) on the test samples in 10-fold cross validation experiment are measured as 77.07, 78.39, and 74.91 percent for the aforementioned organisms respectively. Performances on independent test sets are obtained as 72.09, 73.24 and 82.74 percent respectively. The software is available for free download from http://code.google.com/p/cmater-bioinfo.

Highly biological active antibiofilm, anticancer and osteoblast adhesion efficacy from MWCNT/PPy/Pd nanocomposite

NASA Astrophysics Data System (ADS)

Murugesan, Balaji; Sonamuthu, Jegatheeswaran; Samayanan, Selvam; Arumugam, Sangili; Mahalingam, Sundrarajan

2018-03-01

Multifunctional biologically active materials have approached for antibiofilm, anticancer and osteoblast adhesion activities with significant biomedical applications, owing to this MWCNT modified with polypyrrole (PPy) matrix with the incorporation of palladium nanoparticles (NPs). The synthesized composite displays a tube-shaped morphology with highly dispersed crystalline Pd NPs, which are established through XRD, SEM, TEM and SAED studies. The pyridinic-N(∼402.7), pyrrolic sbnd N (∼400.8) peak in XPS spectra evidenced the interaction of PPy with Pd and MWCNT. Polymer stretching frequencies in FTIR and Raman spectroscopy proves successful formation of PPy and the Pd-N (1609 cm-1) interaction. In the stability aspect, it is up to 58.73% mass withstood at 800 °C in TGA analysis. The composite exhibits an efficient Anti-biofilm against a set of bacterial stain with planktonic cell growth. In vitro cytotoxicity of Vero and HeLa cell line assess the composites toxicity and anticancer activity up to 100 μg. The outcome of cell adhesions showed that human osteosarcoma cells (HOS) can adhere and to develop on the MWCNT/PPy/Pd composites. Furthermore, the proliferation of cells on MWCNT/PPy/Pd composites was also proved the biocompatibility of the composites against HOS cells. These results suggest that Pd-doped MWCNT/PPy composites are promising materials for biomedical applications.

Hot spot-based design of small-molecule inhibitors for protein-protein interactions.

PubMed

Guo, Wenxing; Wisniewski, John A; Ji, Haitao

2014-06-01

Protein-protein interactions (PPIs) are important targets for the development of chemical probes and therapeutic agents. From the initial discovery of the existence of hot spots at PPI interfaces, it has been proposed that hot spots might provide the key for developing small-molecule PPI inhibitors. However, there has been no review on the ways in which the knowledge of hot spots can be used to achieve inhibitor design, nor critical examination of successful examples. This Digest discusses the characteristics of hot spots and the identification of druggable hot spot pockets. An analysis of four examples of hot spot-based design reveals the importance of this strategy in discovering potent and selective PPI inhibitors. A general procedure for hot spot-based design of PPI inhibitors is outlined. Copyright © 2014 Elsevier Ltd. All rights reserved.

Striking differences in properties of geometric isomers of [Ir(tpy)(ppy)H](+): Experimental and computational studies on their hydricities, interaction with CO 2, and photochemistry

DOE PAGES

Garg, Komal; Fujita, Etsuko; Matsubara, Yasuo; ...

2015-11-16

Here, we prepared two geometric isomers of [Ir(tpy)(ppy)H] +, previously proposed as a key intermediate in the photochemical reduction of CO 2 to CO, and characterized their notably different ground- and excited-state interactions with CO 2 and their hydricities using experimental and computational methods. Only one isomer, C-trans-[Ir(tpy)(ppy)H] +, reacts with CO 2 to generate the formato complex in the ground state, consistent with its calculated hydricity. Under photocatalytic conditions in CH 3CN/TEOA, a common reactive C-trans-[Ir(tpy)(ppy)] 0 species, irrespective of the starting isomer or monodentate ligand (such as hydride or Cl), reacts with CO 2 and produces CO withmore » the same catalytic efficiency.« less

Resonant structure, formation and stability of the planetary system HD155358

NASA Astrophysics Data System (ADS)

Silburt, Ari; Rein, Hanno

2017-08-01

Two Jovian-sized planets are orbiting the star HD155358 near exact mean motion resonance (MMR) commensurability. In this work, we re-analyse the radial velocity (RV) data previously collected by Robertson et al. Using a Bayesian framework, we construct two models - one that includes and the other that excludes gravitational planet-planet interactions (PPIs). We find that the orbital parameters from our PPI and no planet-planet interaction (noPPI) models differ by up to 2σ, with our noPPI model being statistically consistent with previous results. In addition, our new PPI model strongly favours the planets being in MMR, while our noPPI model strongly disfavours MMR. We conduct a stability analysis by drawing samples from our PPI model's posterior distribution and simulating them for 109 yr, finding that our best-fitting values land firmly in a stable region of parameter space. We explore a series of formation models that migrate the planets into their observed MMR. We then use these models to directly fit to the observed RV data, where each model is uniquely parametrized by only three constants describing its migration history. Using a Bayesian framework, we find that a number of migration models fit the RV data surprisingly well, with some migration parameters being ruled out. Our analysis shows that PPIs are important to take into account when modelling observations of multiplanetary systems. The additional information that one can gain from interacting models can help constrain planet migration parameters.

Bioinspired Design of Strong, Tough, and Highly Conductive Polyol-Polypyrrole Composites for Flexible Electronics.

PubMed

Gao, Fengxian; Zhang, Ning; Fang, Xiaodong; Ma, Mingming

2017-02-22

Inspired by the dynamic network structure of animal dermis, we have designed and synthesized a series of polyol-polypyrrole (polyol-PPy) composites. Polyols and polypyrrole are cross-linked by hydrogen bonding and electrostatic interactions to form a dynamic network, which helps to dissipate destructive energy. We have found a clear correlation between the mechanical properties of polyol-PPy composites and the polyols structure. Particularly, the PEE-PPy film shows both high strength and flexibility, leading to a remarkable tensile toughness comparable to cocoon silk. The combination of outstanding strength, ductility, and conductivity enables polyol-PPy composites (especially PEE-PPy) as potential electronic materials for making flexible electronics.

Prioritization of candidate disease genes by combining topological similarity and semantic similarity.

PubMed

Liu, Bin; Jin, Min; Zeng, Pan

2015-10-01

The identification of gene-phenotype relationships is very important for the treatment of human diseases. Studies have shown that genes causing the same or similar phenotypes tend to interact with each other in a protein-protein interaction (PPI) network. Thus, many identification methods based on the PPI network model have achieved good results. However, in the PPI network, some interactions between the proteins encoded by candidate gene and the proteins encoded by known disease genes are very weak. Therefore, some studies have combined the PPI network with other genomic information and reported good predictive performances. However, we believe that the results could be further improved. In this paper, we propose a new method that uses the semantic similarity between the candidate gene and known disease genes to set the initial probability vector of a random walk with a restart algorithm in a human PPI network. The effectiveness of our method was demonstrated by leave-one-out cross-validation, and the experimental results indicated that our method outperformed other methods. Additionally, our method can predict new causative genes of multifactor diseases, including Parkinson's disease, breast cancer and obesity. The top predictions were good and consistent with the findings in the literature, which further illustrates the effectiveness of our method. Copyright © 2015 Elsevier Inc. All rights reserved.

Flexible regenerated cellulose/polypyrrole composite films with enhanced dielectric properties.

PubMed

Raghunathan, Sreejesh Poikavila; Narayanan, Sona; Poulose, Aby Cheruvathur; Joseph, Rani

2017-02-10

Flexible regenerated cellulose/polypyrrole (RC-PPy) conductive composite films were prepared by insitu polymerization of pyrrole on regenerated cellulose (RC) matrix using ammonium persulphate as oxidant. FTIR, XPS and XRD analysis of RC-PPy composite films revealed strong interaction between polypyrrole (PPy) and RC matrix. XRD results indicated that crystalline structure of RC matrix remains intact even after composite formation. SEM micrographs revealed the formation of a continuous conductive network of PPy particles in the RC matrix, leading to significant improvement in electrical and dielectric properties. The electrical conductivity of RC-PPy composites with 12wt% of PPy was 3.2×10 -5 S/cm, which is approximately seven fold higher than that of RC. Composites showed high dielectric constant and low dielectric loss values, which is essential in capacitor application. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evaluation of potential interactions between mycophenolic acid derivatives and proton pump inhibitors.

PubMed

Gabardi, Steven; Olyaei, Ali

2012-01-01

To evaluate the incidence of gastrointestinal (GI) complications in solid organ transplant (SOT) recipients, impact of the complications on transplant outcomes, and the potential interactions between mycophenolic acid (MPA) derivatives and proton pump inhibitors (PPIs). An unrestricted literature search (1980-January 2012) was performed with MEDLINE and EMBASE using the following key words: drug-drug interaction, enteric-coated mycophenolic acid, GI complications, mycophenolate mofetil, solid organ transplant, and proton pump inhibitor, including individual agents within the class. Abstracts from scientific meetings were also evaluated. Additionally, reference citations from identified publications were reviewed. Relevant English-language, original research articles and review articles were evaluated if they focused on any of the topics identified in the search or included substantial content addressing GI complications in SOT recipients or drug interactions. GI complications are frequent among SOT recipients, with some studies showing prevalence rates as high as 70%. Transplant outcomes among renal transplant recipients are significantly impacted by GI complications, especially in patients requiring immunosuppressant dosage reductions or premature discontinuation. To this end, PPI use among patients receiving transplants is common. Recent data demonstrate that PPIs significantly reduce the overall exposure to MPA after oral administration of mycophenolate mofetil. Similar studies show this interaction does not exist between PPIs and enteric-coated mycophenolic acid (EC-MPA). Unfortunately, most of the available data evaluating this interaction are pharmacokinetic analyses that do not investigate the clinical impact of this interaction. A significant interaction exists between PPIs and mycophenolate mofetil secondary to reduced dissolution of mycophenolate mofetil in higher pH environments. EC-MPA is not absorbed in the stomach; therefore, low intragastric acidity does not impact EC-MPA and bioavailability is maintained with this formulation during PPI coadministration. The clinical impact of this interaction is unknown, yet one can theorize that reduced exposure to MPA in SOT recipients can increase the risk of allograft rejection and/or failure.

Efficient prediction of human protein-protein interactions at a global scale.

PubMed

Schoenrock, Andrew; Samanfar, Bahram; Pitre, Sylvain; Hooshyar, Mohsen; Jin, Ke; Phillips, Charles A; Wang, Hui; Phanse, Sadhna; Omidi, Katayoun; Gui, Yuan; Alamgir, Md; Wong, Alex; Barrenäs, Fredrik; Babu, Mohan; Benson, Mikael; Langston, Michael A; Green, James R; Dehne, Frank; Golshani, Ashkan

2014-12-10

Our knowledge of global protein-protein interaction (PPI) networks in complex organisms such as humans is hindered by technical limitations of current methods. On the basis of short co-occurring polypeptide regions, we developed a tool called MP-PIPE capable of predicting a global human PPI network within 3 months. With a recall of 23% at a precision of 82.1%, we predicted 172,132 putative PPIs. We demonstrate the usefulness of these predictions through a range of experiments. The speed and accuracy associated with MP-PIPE can make this a potential tool to study individual human PPI networks (from genomic sequences alone) for personalized medicine.

CellMap visualizes protein-protein interactions and subcellular localization

PubMed Central

Dallago, Christian; Goldberg, Tatyana; Andrade-Navarro, Miguel Angel; Alanis-Lobato, Gregorio; Rost, Burkhard

2018-01-01

Many tools visualize protein-protein interaction (PPI) networks. The tool introduced here, CellMap, adds one crucial novelty by visualizing PPI networks in the context of subcellular localization, i.e. the location in the cell or cellular component in which a PPI happens. Users can upload images of cells and define areas of interest against which PPIs for selected proteins are displayed (by default on a cartoon of a cell). Annotations of localization are provided by the user or through our in-house database. The visualizer and server are written in JavaScript, making CellMap easy to customize and to extend by researchers and developers. PMID:29497493

Large-scale protein-protein interactions detection by integrating big biosensing data with computational model.

PubMed

You, Zhu-Hong; Li, Shuai; Gao, Xin; Luo, Xin; Ji, Zhen

2014-01-01

Protein-protein interactions are the basis of biological functions, and studying these interactions on a molecular level is of crucial importance for understanding the functionality of a living cell. During the past decade, biosensors have emerged as an important tool for the high-throughput identification of proteins and their interactions. However, the high-throughput experimental methods for identifying PPIs are both time-consuming and expensive. On the other hand, high-throughput PPI data are often associated with high false-positive and high false-negative rates. Targeting at these problems, we propose a method for PPI detection by integrating biosensor-based PPI data with a novel computational model. This method was developed based on the algorithm of extreme learning machine combined with a novel representation of protein sequence descriptor. When performed on the large-scale human protein interaction dataset, the proposed method achieved 84.8% prediction accuracy with 84.08% sensitivity at the specificity of 85.53%. We conducted more extensive experiments to compare the proposed method with the state-of-the-art techniques, support vector machine. The achieved results demonstrate that our approach is very promising for detecting new PPIs, and it can be a helpful supplement for biosensor-based PPI data detection.

"Master-Slave" Biological Network Alignment

NASA Astrophysics Data System (ADS)

Ferraro, Nicola; Palopoli, Luigi; Panni, Simona; Rombo, Simona E.

Performing global alignment between protein-protein interaction (PPI) networks of different organisms is important to infer knowledge about conservation across species. Known methods that perform this task operate symmetrically, that is to say, they do not assign a distinct role to the input PPI networks. However, in most cases, the input networks are indeed distinguishable on the basis of how well the corresponding organism is biologically well-characterized. For well-characterized organisms the associated PPI network supposedly encode in a sound manner all the information about their proteins and associated interactions, which is far from being the case for not well characterized ones. Here the new idea is developed to devise a method for global alignment of PPI networks that in fact exploit differences in the characterization of organisms at hand. We assume that the PPI network (called Master) of the best characterized is used as a fingerprint to guide the alignment process to the second input network (called Slave), so that generated results preferably retain the structural characteristics of the Master (and using the Slave) network. We tested our method showing that the results it returns are biologically relevant.

Predicting overlapping protein complexes from weighted protein interaction graphs by gradually expanding dense neighborhoods.

PubMed

Dimitrakopoulos, Christos; Theofilatos, Konstantinos; Pegkas, Andreas; Likothanassis, Spiros; Mavroudi, Seferina

2016-07-01

Proteins are vital biological molecules driving many fundamental cellular processes. They rarely act alone, but form interacting groups called protein complexes. The study of protein complexes is a key goal in systems biology. Recently, large protein-protein interaction (PPI) datasets have been published and a plethora of computational methods that provide new ideas for the prediction of protein complexes have been implemented. However, most of the methods suffer from two major limitations: First, they do not account for proteins participating in multiple functions and second, they are unable to handle weighted PPI graphs. Moreover, the problem remains open as existing algorithms and tools are insufficient in terms of predictive metrics. In the present paper, we propose gradually expanding neighborhoods with adjustment (GENA), a new algorithm that gradually expands neighborhoods in a graph starting from highly informative "seed" nodes. GENA considers proteins as multifunctional molecules allowing them to participate in more than one protein complex. In addition, GENA accepts weighted PPI graphs by using a weighted evaluation function for each cluster. In experiments with datasets from Saccharomyces cerevisiae and human, GENA outperformed Markov clustering, restricted neighborhood search and clustering with overlapping neighborhood expansion, three state-of-the-art methods for computationally predicting protein complexes. Seven PPI networks and seven evaluation datasets were used in total. GENA outperformed existing methods in 16 out of 18 experiments achieving an average improvement of 5.5% when the maximum matching ratio metric was used. Our method was able to discover functionally homogeneous protein clusters and uncover important network modules in a Parkinson expression dataset. When used on the human networks, around 47% of the detected clusters were enriched in gene ontology (GO) terms with depth higher than five in the GO hierarchy. In the present manuscript, we introduce a new method for the computational prediction of protein complexes by making the realistic assumption that proteins participate in multiple protein complexes and cellular functions. Our method can detect accurate and functionally homogeneous clusters. Copyright © 2016 Elsevier B.V. All rights reserved.

Proton Pump Inhibitors and Risk of Rhabdomyolysis.

PubMed

Duncan, Scott J; Howden, Colin W

2017-01-01

Proton pump inhibitors (PPIs) have been associated with a variety of adverse events, although the level of evidence for many of these is weak at best. Recently, one national regulatory authority has mandated a change to the labeling of one PPI based on reports of possible associated rhabdomyolysis. Thus, in this review we summarize the available evidence linking PPI use with rhabdomyolysis. The level of evidence is insufficient to establish a causal relationship and is largely based on sporadic case reports. In general, patients with suspected PPI-associated rhabdomyolysis have not been re-challenged with a PPI after recovery. The mechanism whereby PPIs might have been associated with rhabdomyolysis is unclear but possibly related to interaction with concomitantly administered drugs such as HMG-CoA reductase inhibitors (statins). For patients with rhabdomyolysis, a careful search must be made for possible etiological factors. In patients who recover from an episode of possible PPI-related rhabdomyolysis but do not have a genuine requirement for PPI treatment, the PPI should not be re-introduced. For those with a definite indication for ongoing PPI treatment, the PPI can be re-introduced but should preferably not be administered with a statin.

Using PPI network autocorrelation in hierarchical multi-label classification trees for gene function prediction.

PubMed

Stojanova, Daniela; Ceci, Michelangelo; Malerba, Donato; Dzeroski, Saso

2013-09-26

Ontologies and catalogs of gene functions, such as the Gene Ontology (GO) and MIPS-FUN, assume that functional classes are organized hierarchically, that is, general functions include more specific ones. This has recently motivated the development of several machine learning algorithms for gene function prediction that leverages on this hierarchical organization where instances may belong to multiple classes. In addition, it is possible to exploit relationships among examples, since it is plausible that related genes tend to share functional annotations. Although these relationships have been identified and extensively studied in the area of protein-protein interaction (PPI) networks, they have not received much attention in hierarchical and multi-class gene function prediction. Relations between genes introduce autocorrelation in functional annotations and violate the assumption that instances are independently and identically distributed (i.i.d.), which underlines most machine learning algorithms. Although the explicit consideration of these relations brings additional complexity to the learning process, we expect substantial benefits in predictive accuracy of learned classifiers. This article demonstrates the benefits (in terms of predictive accuracy) of considering autocorrelation in multi-class gene function prediction. We develop a tree-based algorithm for considering network autocorrelation in the setting of Hierarchical Multi-label Classification (HMC). We empirically evaluate the proposed algorithm, called NHMC (Network Hierarchical Multi-label Classification), on 12 yeast datasets using each of the MIPS-FUN and GO annotation schemes and exploiting 2 different PPI networks. The results clearly show that taking autocorrelation into account improves the predictive performance of the learned models for predicting gene function. Our newly developed method for HMC takes into account network information in the learning phase: When used for gene function prediction in the context of PPI networks, the explicit consideration of network autocorrelation increases the predictive performance of the learned models. Overall, we found that this holds for different gene features/ descriptions, functional annotation schemes, and PPI networks: Best results are achieved when the PPI network is dense and contains a large proportion of function-relevant interactions.

Discovering functional interdependence relationship in PPI networks for protein complex identification.

PubMed

Lam, Winnie W M; Chan, Keith C C

2012-04-01

Protein molecules interact with each other in protein complexes to perform many vital functions, and different computational techniques have been developed to identify protein complexes in protein-protein interaction (PPI) networks. These techniques are developed to search for subgraphs of high connectivity in PPI networks under the assumption that the proteins in a protein complex are highly interconnected. While these techniques have been shown to be quite effective, it is also possible that the matching rate between the protein complexes they discover and those that are previously determined experimentally be relatively low and the "false-alarm" rate can be relatively high. This is especially the case when the assumption of proteins in protein complexes being more highly interconnected be relatively invalid. To increase the matching rate and reduce the false-alarm rate, we have developed a technique that can work effectively without having to make this assumption. The name of the technique called protein complex identification by discovering functional interdependence (PCIFI) searches for protein complexes in PPI networks by taking into consideration both the functional interdependence relationship between protein molecules and the network topology of the network. The PCIFI works in several steps. The first step is to construct a multiple-function protein network graph by labeling each vertex with one or more of the molecular functions it performs. The second step is to filter out protein interactions between protein pairs that are not functionally interdependent of each other in the statistical sense. The third step is to make use of an information-theoretic measure to determine the strength of the functional interdependence between all remaining interacting protein pairs. Finally, the last step is to try to form protein complexes based on the measure of the strength of functional interdependence and the connectivity between proteins. For performance evaluation, PCIFI was used to identify protein complexes in real PPI network data and the protein complexes it found were matched against those that were previously known in MIPS. The results show that PCIFI can be an effective technique for the identification of protein complexes. The protein complexes it found can match more known protein complexes with a smaller false-alarm rate and can provide useful insights into the understanding of the functional interdependence relationships between proteins in protein complexes.

Interactions between gastro-oesophageal reflux disease and eosinophilic oesophagitis.

PubMed

Molina-Infante, Javier; van Rhijn, Bram D

2015-10-01

Gastro-oesophageal reflux disease (GORD) is the most common oesophageal disorder, whereas eosinophilic oesophagitis (EoE) is an emerging disease unresponsive to PPI therapy. Updated guidelines in 2011 described proton pump inhibitor-responsive esophageal eosinophilia (PPI-REE), a novel phenotype in EoE patients who were responsive to PPIs. This article aims to update the complex interplay between GORD, EoE and PPIs. Oesophageal mucosal integrity is diffusely impaired in EoE and PPI-REE patients. PPI-REE might occur with either normal or pathological pH monitoring. The genetic hallmark of EoE is overlapped in PPI-REE, but not in GORD. PPIs can partially restore epithelial integrity and reverse allergic inflammation gene expression in PPI-REE. Acid hypersensitivity in EoE patients may explain symptomatic but not histological response on PPIs. Unsolved issues with PPI-REE are whether oesophageal barrier impairment is the cause or the effect of oesophageal eosinophilia and whether PPIs primarily targets barrier integrity or oesophageal inflammation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Gas Sensitivity Study of Polypyrrole Decorated Graphene Oxide Thick Film

NASA Astrophysics Data System (ADS)

Patil, Pritam; Gaikwad, Ganesh; Patil, Devidas Ramrao; Naik, Jitendra

2016-04-01

Polypyrrole (PPy) and graphene oxide (GO) nanocomposites were prepared by in situ polymerization method. The synthesized nanocomposites were characterized for current-voltage characteristic, Fourier transform infrared spectroscopy, X-ray diffraction and field emission scanning electron microscopy, which gave the evidence of the strong interaction between PPy nanofibers and GO nanosheets. The PPy/GO nanocomposites were used for the sensing of H2S, LPG, CO2 and NH3 gases respectively at room temperature. It was observed that PPy/GO nanocomposites with different GO weight ratios (5, 10 and 20 %) had better selectivity and sensitivity towards NH3 at room temperature.

Influence of the Acidic Beverage Cola on the Absorption of Erlotinib in Patients With Non-Small-Cell Lung Cancer.

PubMed

van Leeuwen, Roelof W F; Peric, Robert; Hussaarts, Koen G A M; Kienhuis, Emma; IJzerman, Nikki S; de Bruijn, Peter; van der Leest, Cor; Codrington, Henk; Kloover, Jeroen S; van der Holt, Bronno; Aerts, Joachim G; van Gelder, Teun; Mathijssen, Ron H J

2016-04-20

Erlotinib depends on stomach pH for its bioavailability. When erlotinib is taken concurrently with a proton pump inhibitor (PPI), stomach pH increases, which results in a clinically relevant decrease of erlotinib bioavailability. We hypothesized that this drug-drug interaction is reversed by taking erlotinib with the acidic beverage cola. The effects of cola on erlotinib bioavailability in patients not treated with a PPI were also studied. In this randomized, cross-over, pharmacokinetic study in patients with non-small-cell lung cancer, we studied intrapatient differences in absorption (area under the plasma concentration time curve [AUC0-12h]) after a 7-day period of concomitant treatment with erlotinib, with or without esomeprazole, with either cola or water. At the 7th and 14th day, patients were hospitalized for 1 day for pharmacokinetic sampling. Twenty-eight evaluable patients were included in the analysis. In patients treated with erlotinib and esomeprazole with cola, the mean AUC0-12h increased 39% (range, -12% to 136%; P = .004), whereas in patients not treated with the PPI, the mean AUC0-12h was only slightly higher (9%; range, -10% to +30%; P = .03) after erlotinib intake with cola. Cola intake led to a clinically relevant and statistically significant increase in the bioavailability of erlotinib during esomeprazole treatment. In patients not treated with the PPI, the effects of cola were marginal. These findings can be used to optimize the management of drug-drug interactions between PPIs and erlotinib. © 2016 by American Society of Clinical Oncology.

Docosahexaenoic acid triglyceride-based microemulsions with an added dendrimer - Structural considerations.

PubMed

Lidich, Nina; Francesca Ottaviani, M; Hoffman, Roy E; Aserin, Abraham; Garti, Nissim

2016-12-01

Omega fatty acids, mainly the triglyceride of docosahexaenoic acid (TG-DHA), are considered important nutraceuticals. These compounds are water-insoluble and their transport across membranes depends on their carriers. Dendrimers are known as drug carriers across cell membranes and also as permeation enhancers. The solubilization of TG-DHA and dendrimer into a microemulsion (ME) system serving as a carrier could be used for a targeted delivery in the future. The interactions between TG-DHA and second generation poly(propyleneimine) dendrimers (PPI-G2) and their effect on structural transitions of ME were explored along the water dilution line using electron paramagnetic resonance and pulsed-gradient spin-echo NMR along with other analytical techniques. The microviscosity, order parameter, and micropolarity of all studied systems decrease upon water dilution. Incorporation of TG-DHA reduces the microviscosity, order, and micropolarity, whereas PPI-G2 leads to an increase in these parameters. The effect of PPI-G2 is more pronounced at relative high contents (1 and 5wt%) where PPI-G2 interacts with the hydrophilic headgroups of the surfactants. In the macroscale, the effects of TG-DHA and PPI-G2 differ mostly in the bicontinuous region, where macroviscosity increases upon TG-DHA incorporation and decreases upon solubilization of 5wt% PPI-G2. From DSC measurements it was concluded that in the presence of TG-DHA the PPI-G2 is intercalated easily at the interface. Copyright © 2016 Elsevier Inc. All rights reserved.

A systematic molecular dynamics approach to the study of peptide Keap1-Nrf2 protein-protein interaction inhibitors and its application to p62 peptides.

PubMed

Lu, Meng-Chen; Yuan, Zhen-Wei; Jiang, Yong-Lin; Chen, Zhi-Yun; You, Qi-Dong; Jiang, Zheng-Yu

2016-04-01

Protein-protein interactions (PPIs) as drug targets have been gaining growing interest, though developing drug-like small molecule PPI inhibitors remains challenging. Peptide PPI inhibitors, which can provide informative data on the PPI interface, are good starting points to develop small molecule modulators. Computational methods combining molecular dynamics simulations and binding energy calculations could give both the structural and the energetic perspective of peptide PPI inhibitors. Herein, we set up a computational workflow to investigate Keap1-Nrf2 peptide PPI inhibitors and predict the activity of novel sequences. Furthermore, we applied this method to investigate p62 peptides as PPI inhibitors of Keap1-Nrf2 and explored the activity change induced by the phosphorylation of serine. Our results showed that because of the unfavorable solvation effects, the binding affinity of the phosphorylated p62 peptide is lower than the Nrf2 ETGE peptide. Our research results not only provide a useful method to investigate the Keap1-Nrf2 peptide inhibitors, but also give a good example to show how to incorporate computational methods into the study of peptide PPI inhibitors. Besides, applying this method to p62 peptides provides a detailed explanation for the expression of cytoprotective Nrf2 targets induced by p62 phosphorylation, which may benefit the further study of the crosstalk between the Keap1-Nrf2 pathway and p62-mediated selective autophagy.

In Silico Enhancing M. tuberculosis Protein Interaction Networks in STRING To Predict Drug-Resistance Pathways and Pharmacological Risks.

PubMed

Mei, Suyu

2018-05-04

Bacterial protein-protein interaction (PPI) networks are significant to reveal the machinery of signal transduction and drug resistance within bacterial cells. The database STRING has collected a large number of bacterial pathogen PPI networks, but most of the data are of low quality without being experimentally or computationally validated, thus restricting its further biomedical applications. We exploit the experimental data via four solutions to enhance the quality of M. tuberculosis H37Rv (MTB) PPI networks in STRING. Computational results show that the experimental data derived jointly by two-hybrid and copurification approaches are the most reliable to train an L 2 -regularized logistic regression model for MTB PPI network validation. On the basis of the validated MTB PPI networks, we further study the three problems via breadth-first graph search algorithm: (1) discovery of MTB drug-resistance pathways through searching for the paths between known drug-target genes and drug-resistance genes, (2) choosing potential cotarget genes via searching for the critical genes located on multiple pathways, and (3) choosing essential drug-target genes via analysis of network degree distribution. In addition, we further combine the validated MTB PPI networks with human PPI networks to analyze the potential pharmacological risks of known and candidate drug-target genes from the point of view of system pharmacology. The evidence from protein structure alignment demonstrates that the drugs that act on MTB target genes could also adversely act on human signaling pathways.

Adverse drug reactions due to drug-drug interactions with proton pump inhibitors: assessment of systematic reviews with AMSTAR method.

PubMed

Yucel, Emre; Sancar, Mesut; Yucel, Aylin; Okuyan, Betul

2016-01-01

Many systematic reviews resulted in claims on drug-drug interactions (DDIs) with proton pump inhibitors (PPIs). Such a large number begs for consensus on the clinical significance of findings. We critically evaluated the safety of PPI use with respect to DDIs with a meta-review of systematic reviews published between 1978 and 2015. We assessed the evidence by their reliability, repeatability, transparency, and objectivity according to the Assessment of Multiple Systematic Reviews (AMSTAR) criteria. Clinicians must assess risks for each PPI for certain comorbid conditions. DDIs don't substantiate class effect for PPIs; each PPI could induce unique DDIs. Concomitant use of PPIs with thienopyridines (e.g. clopidogrel) could be justified in patients without strong affinity to cytochrome CYP2C19 and with high risk of bleeding (e.g. patients with prior upper gastrointestinal bleeding, Helicobacter pylori infection, advanced age, steroid treatment, and nonsteroidal anti-inflammatory drug use). DDIs could occur in an AIDS subpopulation treated with highly active antiretroviral therapy (HAART). DDIs exist for cancer patients undergoing targeted therapy. Hypomagnesemia could increase in the setting of advanced age and polypharmacy. Omeprazole poses high risks owing to its pharmacokinetic DDI profile. Future systematic reviews should incorporate these additional risks for better clinical guidance.

Methods for protein complex prediction and their contributions towards understanding the organisation, function and dynamics of complexes.

PubMed

Srihari, Sriganesh; Yong, Chern Han; Patil, Ashwini; Wong, Limsoon

2015-09-14

Complexes of physically interacting proteins constitute fundamental functional units responsible for driving biological processes within cells. A faithful reconstruction of the entire set of complexes is therefore essential to understand the functional organisation of cells. In this review, we discuss the key contributions of computational methods developed till date (approximately between 2003 and 2015) for identifying complexes from the network of interacting proteins (PPI network). We evaluate in depth the performance of these methods on PPI datasets from yeast, and highlight their limitations and challenges, in particular at detecting sparse and small or sub-complexes and discerning overlapping complexes. We describe methods for integrating diverse information including expression profiles and 3D structures of proteins with PPI networks to understand the dynamics of complex formation, for instance, of time-based assembly of complex subunits and formation of fuzzy complexes from intrinsically disordered proteins. Finally, we discuss methods for identifying dysfunctional complexes in human diseases, an application that is proving invaluable to understand disease mechanisms and to discover novel therapeutic targets. We hope this review aptly commemorates a decade of research on computational prediction of complexes and constitutes a valuable reference for further advancements in this exciting area. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Whole-exome sequencing in obsessive-compulsive disorder identifies rare mutations in immunological and neurodevelopmental pathways

PubMed Central

Cappi, C; Brentani, H; Lima, L; Sanders, S J; Zai, G; Diniz, B J; Reis, V N S; Hounie, A G; Conceição do Rosário, M; Mariani, D; Requena, G L; Puga, R; Souza-Duran, F L; Shavitt, R G; Pauls, D L; Miguel, E C; Fernandez, T V

2016-01-01

Studies of rare genetic variation have identified molecular pathways conferring risk for developmental neuropsychiatric disorders. To date, no published whole-exome sequencing studies have been reported in obsessive-compulsive disorder (OCD). We sequenced all the genome coding regions in 20 sporadic OCD cases and their unaffected parents to identify rare de novo (DN) single-nucleotide variants (SNVs). The primary aim of this pilot study was to determine whether DN variation contributes to OCD risk. To this aim, we evaluated whether there is an elevated rate of DN mutations in OCD, which would justify this approach toward gene discovery in larger studies of the disorder. Furthermore, to explore functional molecular correlations among genes with nonsynonymous DN SNVs in OCD probands, a protein–protein interaction (PPI) network was generated based on databases of direct molecular interactions. We applied Degree-Aware Disease Gene Prioritization (DADA) to rank the PPI network genes based on their relatedness to a set of OCD candidate genes from two OCD genome-wide association studies (Stewart et al., 2013; Mattheisen et al., 2014). In addition, we performed a pathway analysis with genes from the PPI network. The rate of DN SNVs in OCD was 2.51 × 10−8 per base per generation, significantly higher than a previous estimated rate in unaffected subjects using the same sequencing platform and analytic pipeline. Several genes harboring DN SNVs in OCD were highly interconnected in the PPI network and ranked high in the DADA analysis. Nearly all the DN SNVs in this study are in genes expressed in the human brain, and a pathway analysis revealed enrichment in immunological and central nervous system functioning and development. The results of this pilot study indicate that further investigation of DN variation in larger OCD cohorts is warranted to identify specific risk genes and to confirm our preliminary finding with regard to PPI network enrichment for particular biological pathways and functions. PMID:27023170

Assessment of drug-drug interaction potential between ceritinib and proton pump inhibitors in healthy subjects and in patients with ALK-positive non-small cell lung cancer.

PubMed

Lau, Yvonne Y; Gu, Wen; Lin, Tiffany; Viraswami-Appanna, Kalyanee; Cai, Can; Scott, Jeffrey W; Shi, Michael

2017-06-01

The impact of proton pump inhibitors (PPIs) on the pharmacokinetics (PK) and efficacy of ceritinib was evaluated. A healthy subject drug-drug interaction (DDI) study was conducted to assess the effect of esomeprazole on the PK of a single 750 mg dose of ceritinib. To further investigate the impact of PPIs on the PK and efficacy of ceritinib in ALK-positive cancer patients, two subgroup analyses were performed. Analysis 1 evaluated ceritinib steady-state trough concentration (C trough,ss ) and overall response rate (ORR) by concomitant use of PPIs in patients from the ASCEND-1, -2, and -3 studies; analysis 2 evaluated ceritinib single-dose and steady-state AUC 0-24h and C max by concomitant PPI use in patients from ASCEND-1 using a definition of PPI usage similar to that used in the healthy subject study. In the healthy subject study, co-administration of a single 750 mg dose of ceritinib with esomeprazole 40 mg for 6 days decreased ceritinib AUC 0-∞ by 76% and C max by 79%. However, based on subgroup analysis 1, patients had similar C trough,ss and ORR regardless of concomitant PPI usage. Based on analysis 2, co-administration of a single 750 mg ceritinib dose with PPIs for 6 days in patients suggested less effect on ceritinib exposure than that observed in healthy subjects as AUC 0-24h decreased by 30% and C max decreased by 25%. No clinically meaningful effect on steady-state exposure was observed after daily dosing. Long-term administration of ceritinib with PPIs does not adversely affect the PK and efficacy of ceritinib in ALK-positive cancer patients.

A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis.

PubMed

Tucker, George; Loh, Po-Ru; Berger, Bonnie

2013-10-04

Comprehensive protein-protein interaction (PPI) maps are a powerful resource for uncovering the molecular basis of genetic interactions and providing mechanistic insights. Over the past decade, high-throughput experimental techniques have been developed to generate PPI maps at proteome scale, first using yeast two-hybrid approaches and more recently via affinity purification combined with mass spectrometry (AP-MS). Unfortunately, data from both protocols are prone to both high false positive and false negative rates. To address these issues, many methods have been developed to post-process raw PPI data. However, with few exceptions, these methods only analyze binary experimental data (in which each potential interaction tested is deemed either observed or unobserved), neglecting quantitative information available from AP-MS such as spectral counts. We propose a novel method for incorporating quantitative information from AP-MS data into existing PPI inference methods that analyze binary interaction data. Our approach introduces a probabilistic framework that models the statistical noise inherent in observations of co-purifications. Using a sampling-based approach, we model the uncertainty of interactions with low spectral counts by generating an ensemble of possible alternative experimental outcomes. We then apply the existing method of choice to each alternative outcome and aggregate results over the ensemble. We validate our approach on three recent AP-MS data sets and demonstrate performance comparable to or better than state-of-the-art methods. Additionally, we provide an in-depth discussion comparing the theoretical bases of existing approaches and identify common aspects that may be key to their performance. Our sampling framework extends the existing body of work on PPI analysis using binary interaction data to apply to the richer quantitative data now commonly available through AP-MS assays. This framework is quite general, and many enhancements are likely possible. Fruitful future directions may include investigating more sophisticated schemes for converting spectral counts to probabilities and applying the framework to direct protein complex prediction methods.

How Structure Defines Affinity in Protein-Protein Interactions

PubMed Central

Erijman, Ariel; Rosenthal, Eran; Shifman, Julia M.

2014-01-01

Protein-protein interactions (PPI) in nature are conveyed by a multitude of binding modes involving various surfaces, secondary structure elements and intermolecular interactions. This diversity results in PPI binding affinities that span more than nine orders of magnitude. Several early studies attempted to correlate PPI binding affinities to various structure-derived features with limited success. The growing number of high-resolution structures, the appearance of more precise methods for measuring binding affinities and the development of new computational algorithms enable more thorough investigations in this direction. Here, we use a large dataset of PPI structures with the documented binding affinities to calculate a number of structure-based features that could potentially define binding energetics. We explore how well each calculated biophysical feature alone correlates with binding affinity and determine the features that could be used to distinguish between high-, medium- and low- affinity PPIs. Furthermore, we test how various combinations of features could be applied to predict binding affinity and observe a slow improvement in correlation as more features are incorporated into the equation. In addition, we observe a considerable improvement in predictions if we exclude from our analysis low-resolution and NMR structures, revealing the importance of capturing exact intermolecular interactions in our calculations. Our analysis should facilitate prediction of new interactions on the genome scale, better characterization of signaling networks and design of novel binding partners for various target proteins. PMID:25329579

The Proton Pump Inhibitor Non-Responder: A Clinical Conundrum

PubMed Central

Hussain, Zilla H; Henderson, Emily E; Maradey-Romerao, Carla; George, Nina; Fass, Ronnie; Lacy, Brian E

2015-01-01

Gastroesophageal reflux disease (GERD) is a highly prevalent chronic condition where in stomach contents reflux into the esophagus causing symptoms, esophageal injury, and subsequent complications. Proton pump inhibitors (PPI) remain the mainstay of therapy for acid suppression. Despite their efficacy, significant proportions of GERD patients are either partial or non-responders to PPI therapy. Patients should be assessed for mechanisms that can lead to PPI failure and may require further evaluation to investigate for alternative causes. This monograph will outline a diagnostic approach to the PPI non-responder, review mechanisms associated with PPI failure, and discuss therapeutic options for those who fail to respond to PPI therapy. PMID:26270485

OncoPPi-informed discovery of mitogen-activated protein kinase kinase 3 as a novel binding partner of c-Myc | Office of Cancer Genomics

Cancer.gov

Mitogen-activated protein kinase kinase 3 (MKK3) is a dual threonine/tyrosine protein kinase that regulates inflammation, proliferation and apoptosis through specific phosphorylation and activation of the p38 mitogen-activated protein kinase. However, the role of MKK3 beyond p38-signaling remains elusive. Recently, we reported a protein-protein interaction (PPI) network of cancer-associated genes, termed OncoPPi, as a resource for the scientific community to generate new biological models. Analysis of the OncoPPi connectivity identified MKK3 as one of the major hub proteins in the network.

Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system.

PubMed

Tudor, Catalina O; Ross, Karen E; Li, Gang; Vijay-Shanker, K; Wu, Cathy H; Arighi, Cecilia N

2015-01-01

Protein phosphorylation is a reversible post-translational modification where a protein kinase adds a phosphate group to a protein, potentially regulating its function, localization and/or activity. Phosphorylation can affect protein-protein interactions (PPIs), abolishing interaction with previous binding partners or enabling new interactions. Extracting phosphorylation information coupled with PPI information from the scientific literature will facilitate the creation of phosphorylation interaction networks of kinases, substrates and interacting partners, toward knowledge discovery of functional outcomes of protein phosphorylation. Increasingly, PPI databases are interested in capturing the phosphorylation state of interacting partners. We have previously developed the eFIP (Extracting Functional Impact of Phosphorylation) text mining system, which identifies phosphorylated proteins and phosphorylation-dependent PPIs. In this work, we present several enhancements for the eFIP system: (i) text mining for full-length articles from the PubMed Central open-access collection; (ii) the integration of the RLIMS-P 2.0 system for the extraction of phosphorylation events with kinase, substrate and site information; (iii) the extension of the PPI module with new trigger words/phrases describing interactions and (iv) the addition of the iSimp tool for sentence simplification to aid in the matching of syntactic patterns. We enhance the website functionality to: (i) support searches based on protein roles (kinases, substrates, interacting partners) or using keywords; (ii) link protein entities to their corresponding UniProt identifiers if mapped and (iii) support visual exploration of phosphorylation interaction networks using Cytoscape. The evaluation of eFIP on full-length articles achieved 92.4% precision, 76.5% recall and 83.7% F-measure on 100 article sections. To demonstrate eFIP for knowledge extraction and discovery, we constructed phosphorylation-dependent interaction networks involving 14-3-3 proteins identified from cancer-related versus diabetes-related articles. Comparison of the phosphorylation interaction network of kinases, phosphoproteins and interactants obtained from eFIP searches, along with enrichment analysis of the protein set, revealed several shared interactions, highlighting common pathways discussed in the context of both diseases. © The Author(s) 2015. Published by Oxford University Press.

Task modulated brain connectivity of the amygdala: a meta-analysis of psychophysiological interactions.

PubMed

Di, Xin; Huang, Jia; Biswal, Bharat B

2017-01-01

Understanding functional connectivity of the amygdala with other brain regions, especially task modulated connectivity, is a critical step toward understanding the role of the amygdala in emotional processes and the interactions between emotion and cognition. The present study performed coordinate-based meta-analysis on studies of task modulated connectivity of the amygdala which used psychophysiological interaction (PPI) analysis. We first analyzed 49 PPI studies on different types of tasks using activation likelihood estimation (ALE) meta-analysis. Widespread cortical and subcortical regions showed consistent task modulated connectivity with the amygdala, including the medial frontal cortex, bilateral insula, anterior cingulate, fusiform gyrus, parahippocampal gyrus, thalamus, and basal ganglia. These regions were in general overlapped with those showed coactivations with the amygdala, suggesting that these regions and amygdala are not only activated together, but also show different levels of interactions during tasks. Further analyses with subsets of PPI studies revealed task specific functional connectivities with the amygdala that were modulated by fear processing, face processing, and emotion regulation. These results suggest a dynamic modulation of connectivity upon task demands, and provide new insights on the functions of the amygdala in different affective and cognitive processes. The meta-analytic approach on PPI studies may offer a framework toward systematical examinations of task modulated connectivity.

FACETS: multi-faceted functional decomposition of protein interaction networks.

PubMed

Seah, Boon-Siew; Bhowmick, Sourav S; Dewey, C Forbes

2012-10-15

The availability of large-scale curated protein interaction datasets has given rise to the opportunity to investigate higher level organization and modularity within the protein-protein interaction (PPI) network using graph theoretic analysis. Despite the recent progress, systems level analysis of high-throughput PPIs remains a daunting task because of the amount of data they present. In this article, we propose a novel PPI network decomposition algorithm called FACETS in order to make sense of the deluge of interaction data using Gene Ontology (GO) annotations. FACETS finds not just a single functional decomposition of the PPI network, but a multi-faceted atlas of functional decompositions that portray alternative perspectives of the functional landscape of the underlying PPI network. Each facet in the atlas represents a distinct interpretation of how the network can be functionally decomposed and organized. Our algorithm maximizes interpretative value of the atlas by optimizing inter-facet orthogonality and intra-facet cluster modularity. We tested our algorithm on the global networks from IntAct, and compared it with gold standard datasets from MIPS and KEGG. We demonstrated the performance of FACETS. We also performed a case study that illustrates the utility of our approach. Supplementary data are available at the Bioinformatics online. Our software is available freely for non-commercial purposes from: http://www.cais.ntu.edu.sg/~assourav/Facets/

Identifying essential proteins based on sub-network partition and prioritization by integrating subcellular localization information.

PubMed

Li, Min; Li, Wenkai; Wu, Fang-Xiang; Pan, Yi; Wang, Jianxin

2018-06-14

Essential proteins are important participants in various life activities and play a vital role in the survival and reproduction of living organisms. Identification of essential proteins from protein-protein interaction (PPI) networks has great significance to facilitate the study of human complex diseases, the design of drugs and the development of bioinformatics and computational science. Studies have shown that highly connected proteins in a PPI network tend to be essential. A series of computational methods have been proposed to identify essential proteins by analyzing topological structures of PPI networks. However, the high noise in the PPI data can degrade the accuracy of essential protein prediction. Moreover, proteins must be located in the appropriate subcellular localization to perform their functions, and only when the proteins are located in the same subcellular localization, it is possible that they can interact with each other. In this paper, we propose a new network-based essential protein discovery method based on sub-network partition and prioritization by integrating subcellular localization information, named SPP. The proposed method SPP was tested on two different yeast PPI networks obtained from DIP database and BioGRID database. The experimental results show that SPP can effectively reduce the effect of false positives in PPI networks and predict essential proteins more accurately compared with other existing computational methods DC, BC, CC, SC, EC, IC, NC. Copyright © 2018 Elsevier Ltd. All rights reserved.

An electrochemical aptasensor based on a TiO2/three-dimensional reduced graphene oxide/PPy nanocomposite for the sensitive detection of lysozyme.

PubMed

Wang, Minghua; Zhai, Shuyong; Ye, Zihan; He, Linghao; Peng, Donglai; Feng, Xiaozhong; Yang, Yanqin; Fang, Shaoming; Zhang, Hongzhong; Zhang, Zhihong

2015-04-14

A sensitive aptasensor based on a nanocomposite of hollow titanium dioxide nanoball, three-dimensional reduced graphene oxide, and polypyrrole (TiO2/3D-rGO/PPy) was developed for lysozyme detection. A lysozyme aptamer was easily immobilized onto the TiO2/3D-rGO/PPy nanocomposite matrix by assembling the aptamer onto graphene through simple π-stacking interactions and electrostatic interactions between PPy molecular chains and aptamer strands. In the presence of lysozyme, the aptamer on the adsorbent layer catches the target on the electrode interface, which generates a barrier for electrons and inhibits electron transfer, subsequently resulting in decreased electrochemically differential pulse voltammetric signals of a gold electrode modified with TiO2/3D-rGO/PPy. Using this strategy, a low limit of detection of 0.085 ng mL(-1) (5.5 pM) for detecting lysozyme was observed within the detection range of 0.1-50 ng mL(-1) (0.007-3.5 nM). The aptasensor also presents high specificity for lysozyme, which is unaffected by the coexistence of other proteins. Such an aptasensor opens a rapid, selective, and sensitive route to lysozyme detection. This finding indicates that the TiO2/3D-rGO/PPy nanocomposite could be used as an electrochemical biosensor for detecting proteins in the biomedical field.

Multiplex detection of protein-protein interactions using a next generation luciferase reporter.

PubMed

Verhoef, Lisette G G C; Mattioli, Michela; Ricci, Fernanda; Li, Yao-Cheng; Wade, Mark

2016-02-01

Cell-based assays of protein-protein interactions (PPIs) using split reporter proteins can be used to identify PPI agonists and antagonists. Generally, such assays measure one PPI at a time, and thus counterscreens for on-target activity must be run in parallel or at a subsequent stage; this increases both the cost and time during screening. Split luciferase systems offer advantages over those that use split fluorescent proteins (FPs). This is since split luciferase offers a greater signal:noise ratio and, unlike split FPs, the PPI can be reversed upon small molecule treatment. While multiplexed PPI assays using luciferase have been reported, they suffer from low signal:noise and require fairly complex spectral deconvolution during analysis. Furthermore, the luciferase enzymes used are large, which limits the range of PPIs that can be interrogated due to steric hindrance from the split luciferase fragments. Here, we report a multiplexed PPI assay based on split luciferases from Photinus pyralis (firefly luciferase, FLUC) and the deep-sea shrimp, Oplophorus gracilirostris (NanoLuc, NLUC). Specifically, we show that the binding of the p53 tumor suppressor to its two major negative regulators, MDM2 and MDM4, can be simultaneously measured within the same sample, without the requirement for complex filters or deconvolution. We provide chemical and genetic validation of this system using MDM2-targeted small molecules and mutagenesis, respectively. Combined with the superior signal:noise and smaller size of split NanoLuc, this multiplexed PPI assay format can be exploited to study the induction or disruption of pairwise interactions that are prominent in many cell signaling pathways. Copyright © 2015 Elsevier B.V. All rights reserved.

Protein-protein interaction site prediction in Homo sapiens and E. coli using an interaction-affinity based membership function in fuzzy SVM.

PubMed

Sriwastava, Brijesh Kumar; Basu, Subhadip; Maulik, Ujjwal

2015-10-01

Protein-protein interaction (PPI) site prediction aids to ascertain the interface residues that participate in interaction processes. Fuzzy support vector machine (F-SVM) is proposed as an effective method to solve this problem, and we have shown that the performance of the classical SVM can be enhanced with the help of an interaction-affinity based fuzzy membership function. The performances of both SVM and F-SVM on the PPI databases of the Homo sapiens and E. coli organisms are evaluated and estimated the statistical significance of the developed method over classical SVM and other fuzzy membership-based SVM methods available in the literature. Our membership function uses the residue-level interaction affinity scores for each pair of positive and negative sequence fragments. The average AUC scores in the 10-fold cross-validation experiments are measured as 79.94% and 80.48% for the Homo sapiens and E. coli organisms respectively. On the independent test datasets, AUC scores are obtained as 76.59% and 80.17% respectively for the two organisms. In almost all cases, the developed F-SVM method improves the performances obtained by the corresponding classical SVM and the other classifiers, available in the literature.

Mining disease genes using integrated protein-protein interaction and gene-gene co-regulation information.

PubMed

Li, Jin; Wang, Limei; Guo, Maozu; Zhang, Ruijie; Dai, Qiguo; Liu, Xiaoyan; Wang, Chunyu; Teng, Zhixia; Xuan, Ping; Zhang, Mingming

2015-01-01

In humans, despite the rapid increase in disease-associated gene discovery, a large proportion of disease-associated genes are still unknown. Many network-based approaches have been used to prioritize disease genes. Many networks, such as the protein-protein interaction (PPI), KEGG, and gene co-expression networks, have been used. Expression quantitative trait loci (eQTLs) have been successfully applied for the determination of genes associated with several diseases. In this study, we constructed an eQTL-based gene-gene co-regulation network (GGCRN) and used it to mine for disease genes. We adopted the random walk with restart (RWR) algorithm to mine for genes associated with Alzheimer disease. Compared to the Human Protein Reference Database (HPRD) PPI network alone, the integrated HPRD PPI and GGCRN networks provided faster convergence and revealed new disease-related genes. Therefore, using the RWR algorithm for integrated PPI and GGCRN is an effective method for disease-associated gene mining.

Facile Synthesis of Conductive Polypyrrole Wrinkle Topographies on Polydimethylsiloxane via a Swelling-Deswelling Process and Their Potential Uses in Tissue Engineering.

PubMed

Aufan, M Rifqi; Sumi, Yang; Kim, Semin; Lee, Jae Young

2015-10-28

Electrically conducting biomaterials have gained great attention in various biomedical studies especially to influence cell and tissue responses. In addition, wrinkling can present a unique topography that can modulate cell-material interactions. In this study, we developed a simple method to create wrinkle topographies of conductive polypyrrole (wPPy) on soft polydimethylsiloxane surfaces via a swelling-deswelling process during and after PPy polymerization and by varying the thickness of the PPy top layers. As a result, various features of wPPy in the range of the nano- and microscales were successfully obtained. In vitro cell culture studies with NIH 3T3 fibroblasts and PC12 neuronal cells indicated that the conductive wrinkle topographies promote cell adhesion and neurite outgrowth of PC12 cells. Our studies help to elucidate the design of the surface coating and patterning of conducting polymers, which will enable us to simultaneously provide topographical and electrical signals to improve cell-surface interactions for potential tissue-engineering applications.

Enhancement of p-Type Dye-Sensitized Solar Cell Performance by Supramolecular Assembly of Electron Donor and Acceptor

PubMed Central

Tian, Haining; Oscarsson, Johan; Gabrielsson, Erik; Eriksson, Susanna K.; Lindblad, Rebecka; Xu, Bo; Hao, Yan; Boschloo, Gerrit; Johansson, Erik M. J.; Gardner, James M.; Hagfeldt, Anders; Rensmo, Håkan; Sun, Licheng

2014-01-01

Supramolecular interactions based on porphyrin and fullerene derivatives were successfully adopted to improve the photovoltaic performance of p-type dye-sensitized solar cells (DSCs). Photoelectron spectroscopy (PES) measurements suggest a change in binding configuration of ZnTCPP after co-sensitization with C60PPy, which could be ascribed to supramolecular interaction between ZnTCPP and C60PPy. The performance of the ZnTCPP/C60PPy-based p-type DSC has been increased by a factor of 4 in comparison with the DSC with the ZnTCPP alone. At 560 nm, the IPCE value of DSCs based on ZnTCPP/C60PPy was a factor of 10 greater than that generated by ZnTCPP-based DSCs. The influence of different electrolytes on charge extraction and electron lifetime was investigated and showed that the enhanced Voc from the Co2+/3+(dtbp)3-based device is due to the positive EF shift of NiO. PMID:24603319

Prediction and functional analysis of the sweet orange protein-protein interaction network.

PubMed

Ding, Yu-Duan; Chang, Ji-Wei; Guo, Jing; Chen, Dijun; Li, Sen; Xu, Qiang; Deng, Xiu-Xin; Cheng, Yun-Jiang; Chen, Ling-Ling

2014-08-05

Sweet orange (Citrus sinensis) is one of the most important fruits world-wide. Because it is a woody plant with a long growth cycle, genetic studies of sweet orange are lagging behind those of other species. In this analysis, we employed ortholog identification and domain combination methods to predict the protein-protein interaction (PPI) network for sweet orange. The K-nearest neighbors (KNN) classification method was used to verify and filter the network. The final predicted PPI network, CitrusNet, contained 8,195 proteins with 124,491 interactions. The quality of CitrusNet was evaluated using gene ontology (GO) and Mapman annotations, which confirmed the reliability of the network. In addition, we calculated the expression difference of interacting genes (EDI) in CitrusNet using RNA-seq data from four sweet orange tissues, and also analyzed the EDI distribution and variation in different sub-networks. Gene expression in CitrusNet has significant modular features. Target of rapamycin (TOR) protein served as the central node of the hormone-signaling sub-network. All evidence supported the idea that TOR can integrate various hormone signals and affect plant growth. CitrusNet provides valuable resources for the study of biological functions in sweet orange.

Reinforce: An Ensemble Approach for Inferring PPI Network from AP-MS Data.

PubMed

Tian, Bo; Duan, Qiong; Zhao, Can; Teng, Ben; He, Zengyou

2017-05-17

Affinity Purification-Mass Spectrometry (AP-MS) is one of the most important technologies for constructing protein-protein interaction (PPI) networks. In this paper, we propose an ensemble method, Reinforce, for inferring PPI network from AP-MS data set. The new algorithm named Reinforce is based on rank aggregation and false discovery rate control. Under the null hypothesis that the interaction scores from different scoring methods are randomly generated, Reinforce follows three steps to integrate multiple ranking results from different algorithms or different data sets. The experimental results show that Reinforce can get more stable and accurate inference results than existing algorithms. The source codes of Reinforce and data sets used in the experiments are available at: https://sourceforge.net/projects/reinforce/.

Guidance of neurite outgrowth on aligned electrospun polypyrrole/poly(styrene-beta-isobutylene-beta-styrene) fiber platforms.

PubMed

Liu, Xiao; Chen, Jun; Gilmore, Kerry J; Higgins, Michael J; Liu, Yong; Wallace, Gordon G

2010-09-15

The purpose of this work was to investigate the potential biomedical application of novel aligned electrospun polypyrrole (PPy)/poly(styrene-beta-isobutylene-beta-styrene) (SIBS) fibers. After successfully aligning the electroactive PPy/SIBS fibers based on our modified electrospinning method, we demonstrated that neurite outgrowth from PC12 cells could be highly orientated parallel to the aligned PPy/SIBS fibers. Physical interactions between the nerve cells and PPy/SIBS fibers through filopodia "sensing" were observed using atomic force microscopy. These observations indicate a role of contact guidance as a mechanism for the observed alignment. This work highlights the capacity for electroactive PPy/SIBS fibers to support and guide nerve cell differentiation through topographic cues, which is a highly desirable characteristic in medical implants for neurological applications. (c) 2010 Wiley Periodicals, Inc.

Clustering PPI data by combining FA and SHC method.

PubMed

Lei, Xiujuan; Ying, Chao; Wu, Fang-Xiang; Xu, Jin

2015-01-01

Clustering is one of main methods to identify functional modules from protein-protein interaction (PPI) data. Nevertheless traditional clustering methods may not be effective for clustering PPI data. In this paper, we proposed a novel method for clustering PPI data by combining firefly algorithm (FA) and synchronization-based hierarchical clustering (SHC) algorithm. Firstly, the PPI data are preprocessed via spectral clustering (SC) which transforms the high-dimensional similarity matrix into a low dimension matrix. Then the SHC algorithm is used to perform clustering. In SHC algorithm, hierarchical clustering is achieved by enlarging the neighborhood radius of synchronized objects continuously, while the hierarchical search is very difficult to find the optimal neighborhood radius of synchronization and the efficiency is not high. So we adopt the firefly algorithm to determine the optimal threshold of the neighborhood radius of synchronization automatically. The proposed algorithm is tested on the MIPS PPI dataset. The results show that our proposed algorithm is better than the traditional algorithms in precision, recall and f-measure value.

Clustering PPI data by combining FA and SHC method

PubMed Central

2015-01-01

Clustering is one of main methods to identify functional modules from protein-protein interaction (PPI) data. Nevertheless traditional clustering methods may not be effective for clustering PPI data. In this paper, we proposed a novel method for clustering PPI data by combining firefly algorithm (FA) and synchronization-based hierarchical clustering (SHC) algorithm. Firstly, the PPI data are preprocessed via spectral clustering (SC) which transforms the high-dimensional similarity matrix into a low dimension matrix. Then the SHC algorithm is used to perform clustering. In SHC algorithm, hierarchical clustering is achieved by enlarging the neighborhood radius of synchronized objects continuously, while the hierarchical search is very difficult to find the optimal neighborhood radius of synchronization and the efficiency is not high. So we adopt the firefly algorithm to determine the optimal threshold of the neighborhood radius of synchronization automatically. The proposed algorithm is tested on the MIPS PPI dataset. The results show that our proposed algorithm is better than the traditional algorithms in precision, recall and f-measure value. PMID:25707632

Synthesis, characterization and antimicrobial activity of biodegradable conducting polypyrrole-graft-chitosan copolymer

NASA Astrophysics Data System (ADS)

Cabuk, Mehmet; Alan, Yusuf; Yavuz, Mustafa; Unal, Halil Ibrahim

2014-11-01

In this study, polypyrrole-graft-chitosan (PPy-g-CS) copolymer was chemically synthesized and its structural and morphological properties characterized by FTIR, UV-vis, SEM, XRD, TGA and zeta-potential techniques. The results revealed that there were strong interactions between PPy and CS chains. The electrical conductivity of CS increased to semiconducting range by grafting. The crystallinity and thermal stability of PPy-g-CS copolymer improved when compared to CS. The copolymer was tested against various bacterial and fungal strains at various concentrations and results obtained were compared with the reference antibiotics. The results indicated that the antibacterial activity of PPy-g-CS copolymer was stronger than CS and PPy alone. The antibacterial activity of the PPy-g-CS copolymer observed to increase with rising concentration, and showed stronger activity against bacteria than Penicillin (10 mg), Rifampicin (5 mg) and Trimethoprim (25 mg), whereas showed equipotent activity with Amikacin (30 mg) and Erythromycin (15 mg) antibiotics.

The OncoPPi Portal: an integrative resource to explore and prioritize protein-protein interactions for cancer target discovery. | Office of Cancer Genomics

Cancer.gov

Motivation: As cancer genomics initiatives move toward comprehensive identification of genetic alterations in cancer, attention is now turning to understanding how interactions among these genes lead to the acquisition of tumor hallmarks. Emerging pharmacological and clinical data suggest a highly promising role of cancer-specific protein-protein interactions (PPIs) as druggable cancer targets. However, large-scale experimental identification of cancer-related PPIs remains challenging, and currently available resources to explore oncogenic PPI networks are limited.

The Functional Networks of Prepulse Inhibition: Neuronal Connectivity Analysis Based on FDG-PET in Awake and Unrestrained Rats.

PubMed

Rohleder, Cathrin; Wiedermann, Dirk; Neumaier, Bernd; Drzezga, Alexander; Timmermann, Lars; Graf, Rudolf; Leweke, F Markus; Endepols, Heike

2016-01-01

Prepulse inhibition (PPI) is a neuropsychological process during which a weak sensory stimulus ("prepulse") attenuates the motor response ("startle reaction") to a subsequent strong startling stimulus. It is measured as a surrogate marker of sensorimotor gating in patients suffering from neuropsychological diseases such as schizophrenia, as well as in corresponding animal models. A variety of studies has shown that PPI of the acoustical startle reaction comprises three brain circuitries for: (i) startle mediation, (ii) PPI mediation, and (iii) modulation of PPI mediation. While anatomical connections and information flow in the startle and PPI mediation pathways are well known, spatial and temporal interactions of the numerous regions involved in PPI modulation are incompletely understood. We therefore combined [(18)F]fluoro-2-deoxyglucose positron-emission-tomography (FDG-PET) with PPI and resting state control paradigms in awake rats. A battery of subtractive, correlative as well as seed-based functional connectivity analyses revealed a default mode-like network (DMN) active during resting state only. Furthermore, two functional networks were observed during PPI: Metabolic activity in the lateral circuitry was positively correlated with PPI effectiveness and involved the auditory system and emotional regions. The medial network was negatively correlated with PPI effectiveness, i.e., associated with startle, and recruited a spatial/cognitive network. Our study provides evidence for two distinct neuronal networks, whose continuous interplay determines PPI effectiveness in rats, probably by either protecting the prepulse or facilitating startle processing. Discovering similar networks affected in neuropsychological disorders may help to better understand mechanisms of sensorimotor gating deficits and provide new perspectives for therapeutic strategies.

Deficient prepulse inhibition in schizophrenia detected by the multi-site COGS.

PubMed

Swerdlow, Neal R; Light, Gregory A; Sprock, Joyce; Calkins, Monica E; Green, Michael F; Greenwood, Tiffany A; Gur, Raquel E; Gur, Ruben C; Lazzeroni, Laura C; Nuechterlein, Keith H; Radant, Allen D; Ray, Amrita; Seidman, Larry J; Siever, Larry J; Silverman, Jeremy M; Stone, William S; Sugar, Catherine A; Tsuang, Debby W; Tsuang, Ming T; Turetsky, Bruce I; Braff, David L

2014-02-01

Startle inhibition by weak prepulses (PPI) is studied to understand the biology of information processing in schizophrenia patients and healthy comparison subjects (HCS). The Consortium on the Genetics of Schizophrenia (COGS) identified associations between PPI and single nucleotide polymorphisms in schizophrenia probands and unaffected relatives, and linkage analyses extended evidence for the genetics of PPI deficits in schizophrenia in the COGS-1 family study. These findings are being extended in a 5-site "COGS-2" study of 1800 patients and 1200 unrelated HCS to facilitate genetic analyses. We describe a planned interim analysis of COGS-2 PPI data. Eyeblink startle was measured in carefully screened HCS and schizophrenia patients (n=1402). Planned analyses of PPI (60 ms intervals) assessed effects of diagnosis, sex and test site, PPI-modifying effects of medications and smoking, and relationships between PPI and neurocognitive measures. 884 subjects met strict inclusion criteria. ANOVA of PPI revealed significant effects of diagnosis (p=0.0005) and sex (p<0.002), and a significant diagnosis×test site interaction. HCS>schizophrenia PPI differences were greatest among patients not taking 2nd generation antipsychotics, and were independent of smoking status. Modest but significant relationships were detected between PPI and performance in specific neurocognitive measures. The COGS-2 multi-site study detects schizophrenia-related PPI deficits reported in single-site studies, including patterns related to diagnosis, prepulse interval, sex, medication and other neurocognitive measures. Site differences were detected and explored. The target COGS-2 schizophrenia "endophenotype" of reduced PPI should prove valuable for identifying and confirming schizophrenia risk genes in future analyses. Copyright © 2013 Elsevier B.V. All rights reserved.

Deficient prepulse inhibition in schizophrenia detected by the multi-site COGS

PubMed Central

Swerdlow, Neal R.; Light, Gregory A.; Sprock, Joyce; Calkins, Monica E.; Green, Michael F.; Greenwood, Tiffany A.; Gur, Raquel E.; Gur, Ruben C.; Lazzeroni, Laura C.; Nuechterlein, Keith H.; Radant, Allen D.; Ray, Amrita; Seidman, Larry J.; Siever, Larry J.; Silverman, Jeremy M.; Stone, William S.; Sugar, Catherine A.; Tsuang, Debby W.; Tsuang, Ming T.; Turetsky, Bruce I.; Braff, David L.

2014-01-01

Background Startle inhibition by weak prepulses (PPI) is studied to understand the biology of information processing in schizophrenia patients and healthy comparison subjects (HCS). The Consortium on the Genetics of Schizophrenia (COGS) identified associations between PPI and single nucleotide polymorphisms in schizophrenia probands and unaffected relatives, and linkage analyses extended evidence for the genetics of PPI deficits in schizophrenia in the COGS-1 family study. These findings are being extended in a 5-site “COGS-2” study of 1800 patients and 1200 unrelated HCS to facilitate genetic analyses. We describe a planned interim analysis of COGS-2 PPI data. Methods Eyeblink startle was measured in carefully screened HCS and schizophrenia patients (n=1402). Planned analyses of PPI (60 ms intervals) assessed effects of diagnosis, sex and test site, PPI-modifying effects of medications and smoking, and relationships between PPI and neurocognitive measures. Results 884 subjects met strict inclusion criteria. ANOVA of PPI revealed significant effects of diagnosis (p=0.0005) and sex (p<0.002), and a significant diagnosis × test site interaction. HCS > schizophrenia PPI differences were greatest among patients not taking 2nd generation antipsychotics, and were independent of smoking status. Modest but significant relationships were detected between PPI and performance in specific neurocognitive measures. Discussion The COGS-2 multi-site study detects schizophrenia-related PPI deficits reported in single-site studies, including patterns related to diagnosis, prepulse interval, sex, medication and other neurocognitive measures. Site differences were detected and explored. The target COGS-2 schizophrenia “endophenotype” of reduced PPI should prove valuable for identifying and confirming schizophrenia risk genes in future analyses. PMID:24405980

Disease gene classification with metagraph representations.

PubMed

Kircali Ata, Sezin; Fang, Yuan; Wu, Min; Li, Xiao-Li; Xiao, Xiaokui

2017-12-01

Protein-protein interaction (PPI) networks play an important role in studying the functional roles of proteins, including their association with diseases. However, protein interaction networks are not sufficient without the support of additional biological knowledge for proteins such as their molecular functions and biological processes. To complement and enrich PPI networks, we propose to exploit biological properties of individual proteins. More specifically, we integrate keywords describing protein properties into the PPI network, and construct a novel PPI-Keywords (PPIK) network consisting of both proteins and keywords as two different types of nodes. As disease proteins tend to have a similar topological characteristics on the PPIK network, we further propose to represent proteins with metagraphs. Different from a traditional network motif or subgraph, a metagraph can capture a particular topological arrangement involving the interactions/associations between both proteins and keywords. Based on the novel metagraph representations for proteins, we further build classifiers for disease protein classification through supervised learning. Our experiments on three different PPI databases demonstrate that the proposed method consistently improves disease protein prediction across various classifiers, by 15.3% in AUC on average. It outperforms the baselines including the diffusion-based methods (e.g., RWR) and the module-based methods by 13.8-32.9% for overall disease protein prediction. For predicting breast cancer genes, it outperforms RWR, PRINCE and the module-based baselines by 6.6-14.2%. Finally, our predictions also turn out to have better correlations with literature findings from PubMed. Copyright © 2017 Elsevier Inc. All rights reserved.

It's not just 'What' you do, it's also the 'Way' that you do it: Patient and Public Involvement in the Development of Health Research.

PubMed

Devonport, Tracey J; Nicholls, Wendy; Johnston, Lynne H; Gutteridge, Robin; Watt, Angela

2018-03-01

This article presents a reflective account of Patient and Public Involvement (PPI) in the development of obesity and binge eating research. We established Patient Advisory Groups (PAGs) at two English regional National Health Service (NHS) weight management services. PPI was evaluated as follows: (i) PAG members completed a Post Participation Evaluation Questionnaire, (ii) PAG meetings captured group discussion on PPI involvement, (iii) practitioner and researchers produced written reflections on PPI and (iv) sources one to three were consolidated during reflections that took place via e-mail and telephone correspondence between researchers and practitioners, culminating in a summary SKYPE meeting between one practitioner and one researcher involved in the PAGs. Results in the form of reflections suggest guidelines on undertaking PPI were helpful with regard 'what to do', but less helpful on 'how'. For example, suggestions for the management of interpersonal factors such as eliciting self-disclosure and managing power differentials are insufficiently addressed in existing guidelines. The present case study illustrated how interpersonal considerations can help or hinder the optimal use of PPI. Recommendations for practitioners and researchers planning PPI are offered.

Review of proton pump inhibitors for the initial treatment of heartburn: is there a dose ceiling effect?

PubMed

Kushner, Pamela R; Peura, David A

2011-05-01

Proton pump inhibitors (PPIs) are widely used in clinical practice. However, concerns have been expressed about their long-term use, particularly with regard to bone health, Clostridium difficile infections, and drug interactions with platelet aggregation inhibitors. There has been limited guidance for clinicians concerning appropriate dose selection of PPIs for the initial treatment of heartburn. This review explored whether published clinical trials provide evidence of a ceiling above which higher PPI doses do not provide additional clinical benefit over the lowest approved dose. All articles of randomized, controlled clinical trials in nonerosive gastroesophageal reflux disease (GERD) in which the effects of two or more doses of the same PPI on symptomatic relief of heartburn were quantified as a study endpoint were identified and analyzed through PubMed searches up to the end of September 2010. The majority of trials evaluated provided no evidence that higher PPI doses were superior to the lowest approved dose for the initial treatment of heartburn. There were no clinically relevant findings with respect to dose dependence and safety outcomes in these studies. Efficacy outcomes from the trials suggest there may be a dose ceiling effect and highlight the need for further research on the use of the lowest effective PPI doses as an appropriate strategy in the initial treatment of uncomplicated heartburn. Observational studies and some meta-analyses have suggested that long-term PPI pharmacotherapy might be associated with safety concerns, which necessitate the periodic evaluation of therapeutic benefit in terms of symptom resolution and regimen tolerability. However, evidence to date suggests that use of the lowest effective dose for the indication is not associated with significant adverse events, particularly in the short term. Clinical practice suggests that patients requiring long-term treatment should be maintained on the lowest dose necessary to control symptoms, and monitored for potentially confounding factors that may lead to safety concerns.

[Evaluation of the prescription of proton pump inhibitors in persons aged 75years and older in a geriatric acute-care unit].

PubMed

Dipanda, Mélanie; Pioro, Laureline; Buttard, Maxime; d'Athis, Philippe; Asgassou, Sanaa; Putot, Sophie; Deïdda, Martha; Laborde, Caroline; Putot, Alain; Manckoundia, Patrick

2017-12-01

Proton pump inhibitors (PPI) are widely prescribed in France and could be responsible for adverse drug reactions especially in elderly persons (EP). In order to reduce the misuse of PPI and the excess cost to the Social Security Agency, the French health authorities (Haute Autorité de santé [HAS]) have published strict guidelines for their prescription. We conducted a study in EP to determine the proportion of PPI prescriptions outside HAS guidelines. This was a prospective, single-centre observational study in persons aged≥75 years admitted to a geriatric acute-care unit over a period of 6months. The prevalence of prescriptions for PPI and the proportion of prescriptions outside the guidelines were calculated. The sociodemographic and medical characteristics of EP treated with PPI were studied as were the reasons for the prescription of PPI. Among the 818 patients hospitalized during the study period, 270 were taking PPI on admission (33%). Among these prescriptions, 60% were outside the HAS guidelines. Gastro-oesophageal reflux was the leading indication for PPI (30%), followed by dyspepsia (19%). This study confirms the high prevalence of prescriptions for PPI and their misuse. As these drugs are apparently well tolerated, prescriptions are often renewed with no medical re-evaluation. Copyright © 2017 Société française de pharmacologie et de thérapeutique. Published by Elsevier Masson SAS. All rights reserved.

Detection of interaction articles and experimental methods in biomedical literature.

PubMed

Schneider, Gerold; Clematide, Simon; Rinaldi, Fabio

2011-10-03

This article describes the approaches taken by the OntoGene group at the University of Zurich in dealing with two tasks of the BioCreative III competition: classification of articles which contain curatable protein-protein interactions (PPI-ACT) and extraction of experimental methods (PPI-IMT). Two main achievements are described in this paper: (a) a system for document classification which crucially relies on the results of an advanced pipeline of natural language processing tools; (b) a system which is capable of detecting all experimental methods mentioned in scientific literature, and listing them with a competitive ranking (AUC iP/R > 0.5). The results of the BioCreative III shared evaluation clearly demonstrate that significant progress has been achieved in the domain of biomedical text mining in the past few years. Our own contribution, together with the results of other participants, provides evidence that natural language processing techniques have become by now an integral part of advanced text mining approaches.

Integrating semantic information into multiple kernels for protein-protein interaction extraction from biomedical literatures.

PubMed

Li, Lishuang; Zhang, Panpan; Zheng, Tianfu; Zhang, Hongying; Jiang, Zhenchao; Huang, Degen

2014-01-01

Protein-Protein Interaction (PPI) extraction is an important task in the biomedical information extraction. Presently, many machine learning methods for PPI extraction have achieved promising results. However, the performance is still not satisfactory. One reason is that the semantic resources were basically ignored. In this paper, we propose a multiple-kernel learning-based approach to extract PPIs, combining the feature-based kernel, tree kernel and semantic kernel. Particularly, we extend the shortest path-enclosed tree kernel (SPT) by a dynamic extended strategy to retrieve the richer syntactic information. Our semantic kernel calculates the protein-protein pair similarity and the context similarity based on two semantic resources: WordNet and Medical Subject Heading (MeSH). We evaluate our method with Support Vector Machine (SVM) and achieve an F-score of 69.40% and an AUC of 92.00%, which show that our method outperforms most of the state-of-the-art systems by integrating semantic information.

IP-FCM measures physiologic protein-protein interactions modulated by signal transduction and small-molecule drug inhibition.

PubMed

Smith, Stephen E P; Bida, Anya T; Davis, Tessa R; Sicotte, Hugues; Patterson, Steven E; Gil, Diana; Schrum, Adam G

2012-01-01

Protein-protein interactions (PPI) mediate the formation of intermolecular networks that control biological signaling. For this reason, PPIs are of outstanding interest in pharmacology, as they display high specificity and may represent a vast pool of potentially druggable targets. However, the study of physiologic PPIs can be limited by conventional assays that often have large sample requirements and relatively low sensitivity. Here, we build on a novel method, immunoprecipitation detected by flow cytometry (IP-FCM), to assess PPI modulation during either signal transduction or pharmacologic inhibition by two different classes of small-molecule compounds. First, we showed that IP-FCM can detect statistically significant differences in samples possessing a defined PPI change as low as 10%. This sensitivity allowed IP-FCM to detect a PPI that increases transiently during T cell signaling, the antigen-inducible interaction between ZAP70 and the T cell antigen receptor (TCR)/CD3 complex. In contrast, IP-FCM detected no ZAP70 recruitment when T cells were stimulated with antigen in the presence of the src-family kinase inhibitor, PP2. Further, we tested whether IP-FCM possessed sufficient sensitivity to detect the effect of a second, rare class of compounds called SMIPPI (small-molecule inhibitor of PPI). We found that the first-generation non-optimized SMIPPI, Ro-26-4550, inhibited the IL-2:CD25 interaction detected by IP-FCM. This inhibition was detectable using either a recombinant CD25-Fc chimera or physiologic full-length CD25 captured from T cell lysates. Thus, we demonstrate that IP-FCM is a sensitive tool for measuring physiologic PPIs that are modulated by signal transduction and pharmacologic inhibition.

Large-scale protein-protein interaction analysis in Arabidopsis mesophyll protoplasts by split firefly luciferase complementation.

PubMed

Li, Jian-Feng; Bush, Jenifer; Xiong, Yan; Li, Lei; McCormack, Matthew

2011-01-01

Protein-protein interactions (PPIs) constitute the regulatory network that coordinates diverse cellular functions. There are growing needs in plant research for creating protein interaction maps behind complex cellular processes and at a systems biology level. However, only a few approaches have been successfully used for large-scale surveys of PPIs in plants, each having advantages and disadvantages. Here we present split firefly luciferase complementation (SFLC) as a highly sensitive and noninvasive technique for in planta PPI investigation. In this assay, the separate halves of a firefly luciferase can come into close proximity and transiently restore its catalytic activity only when their fusion partners, namely the two proteins of interest, interact with each other. This assay was conferred with quantitativeness and high throughput potential when the Arabidopsis mesophyll protoplast system and a microplate luminometer were employed for protein expression and luciferase measurement, respectively. Using the SFLC assay, we could monitor the dynamics of rapamycin-induced and ascomycin-disrupted interaction between Arabidopsis FRB and human FKBP proteins in a near real-time manner. As a proof of concept for large-scale PPI survey, we further applied the SFLC assay to testing 132 binary PPIs among 8 auxin response factors (ARFs) and 12 Aux/IAA proteins from Arabidopsis. Our results demonstrated that the SFLC assay is ideal for in vivo quantitative PPI analysis in plant cells and is particularly powerful for large-scale binary PPI screens.

Proton pump inhibitor co-prescription with dual antiplatelet therapy among patients with acute coronary syndrome in Qatar.

PubMed

Awaisu, Ahmed; Hamou, Fatima; Mekideche, Lylia; El Muabby, Nisrine; Mahfouz, Ahmed; Mohammed, Shaban; Saad, Ahmad

2016-04-01

There are increasing concerns about clinically significant interactions between proton pump inhibitors (PPIs) and clopidogrel, resulting in adverse cardiovascular outcomes in patients with acute coronary syndromes (ACS). However, published evidence on the prevalence and predictors of PPI use with dual antiplatelet therapy (DAPT) is scarce. This study investigated the prevalence of PPI use among patients with ACS receiving DAPT and possible predictors of co-prescribing the PPIs with the DAPT. Heart Hospital, a specialized tertiary care center in Qatar. A retrospective observational study of a prescription database was conducted. Subjects included 626 patients admitted between January and December 2012 with the diagnosis of ACS who received DAPT and discharged with or without a PPI. Univariate analysis and multivariate binary logistic regression analysis were performed to determine the predictors of PPI-DAPT co-prescription. Prevalence of PPI co-prescribing with DAPT in proportions and percentages and odd ratios for the predictors of PPI-DAPT co-prescribing. A total of 626 patients were analyzed for PPI prevalence, with 200 patients (32 %) being prescribed PPI with DAPT upon discharge. After controlling for confounders, PPI use on admission (aOR 14.5; 95 % CI 7.6-27.6, p < 0.001), nationality (aOR 3.2; 95 % CI 1.1-9.9, p = 0.041), and having a history of diabetes (aOR 0.5; 95 % CI 0.24-0.99, p = 0.046) significantly influenced PPI-DAPT co-prescribing. Users of PPI on admission compared to nonusers were about 15 times more likely to be prescribed PPI with DAPT upon discharge; likewise, having Qatari nationality increased the likelihood of co-prescribing PPI with DAPT upon discharge by three folds. Lastly, patients with a history of diabetes were 50 % less likely to be prescribed PPIs upon discharge compared to those with no history of diabetes. The rate of PPI co-prescribing with DAPT in the population studied was relatively high. The strongest predictor of PPI co-prescription with DAPT upon discharge was PPI use on admission. Furthermore, PPI prescribing was significantly predicted by nationality and not having diabetes. Further studies are warranted to better predict the factors associated with PPI-DAPT co-prescription and to investigate rational prescribing of PPIs among ACS patients.

Behavioral and Pharmacokinetic Interactions Between Monoamine Oxidase Inhibitors and the Hallucinogen 5-Methoxy-N,N-dimethyltryptamine

PubMed Central

Halberstadt, Adam L.

2016-01-01

Monoamine oxidase inhibitors (MAOIs) are often ingested together with tryptamine hallucinogens, but relatively little is known about the consequences of their combined use. We have shown previously that monoamine oxidase-A (MAO-A) inhibitors alter the locomotor profile of the hallucinogen 5-methoxy-N,N-dimethyltryptamine (5-MeO-DMT) in rats, and enhance its interaction with 5-HT2A receptors. The goal of the present studies was to investigate the mechanism for the interaction between 5-MeO-DMT and MAOIs, and to determine whether other behavioral responses to 5-MeO-DMT are similarly affected. Hallucinogens disrupt prepulse inhibition (PPI) in rats, an effect typically mediated by 5-HT2A activation. 5-MeO-DMT also disrupts PPI but the effect is primarily attributable to 5-HT1A activation. The present studies examined whether an MAOI can alter the respective contributions of 5-HT1A and 5-HT2A receptors to the effects of 5-MeO-DMT on PPI. A series of interaction studies using the 5-HT1A antagonist WAY-100635 and the 5-HT2A antagonist MDL 11,939 were performed to assess the respective contributions of these receptors to the behavioral effects of 5-MeO-DMT in rats pretreated with an MAOI. The effects of MAO-A inhibition on the pharmacokinetics of 5-MeO-DMT and its metabolism to bufotenine were assessed using liquid chromatography–electrospray ionization–selective reaction monitoring–tandem mass spectrometry (LC-ESI-SRM-MS/MS). 5-MeO-DMT (1 mg/kg) had no effect on PPI when tested 45-min post-injection but disrupted PPI in animals pretreated with the MAO-A inhibitor clorgyline or the MAO-A/B inhibitor pargyline. The combined effect of 5-MeO-DMT and pargyline on PPI was antagonized by pretreatment with either WAY-100635 or MDL 11,939. Inhibition of MAO-A increased the level of 5-MeO-DMT in plasma and whole brain, but had no effect on the conversion of 5-MeO-DMT to bufotenine, which was found to be negligible. The present results confirm that 5-MeO-DMT can disrupt PPI by activating 5-HT2A, and indicate that MAOIs alter 5-MeO-DMT pharmacodynamics by increasing its accumulation in the central nervous system. PMID:26780349

Pantoprazole-Induced Delirium: Review of a Case and Associated Literature.

PubMed

Razdan, Anupriya; Viswanathan, Ramaswamy; Tusher, Alan

2018-01-01

Proton pump inhibitors (PPIs) are frequently prescribed antiulcer agents in hospitals and are shown to be safer than H-2 blockers. We present a case report of PPI-induced delirium, regarding which not much has been written in the literature. We present a case of a 93-year-old woman with no known past psychiatric history, who was hospitalized for syncope workup and who developed delirium after a double dose of pantoprazole. Very few reports of PPI-induced delirium exist in the literature. In this case report, we attempt to highlight the mechanism of PPI induced delirium which in our case was most likely due to the primary effects of PPI and drug-drug interactions. Given the paucity of literature on this topic, we encourage further research into relationship between PPI and delirium and urge caution while using PPIs in geriatric population.

Controlled delivery of Gemcitabine Hydrochloride using mannosylated poly(propyleneimine) dendrimers

NASA Astrophysics Data System (ADS)

Soni, Namrata; Jain, Keerti; Gupta, Umesh; Jain, N. K.

2015-11-01

The aim of the present investigation was to deliver Gemcitabine Hydrochloride (GmcH), an anticancer bioactive, specifically to lung tumor cells using mannosylated 4.0G poly(propyleneimine) dendrimers (M-PPI). 4.0G poly(propyleneimine) (PPI) dendrimers was synthesized using ethylenediamine as core and conjugated with mannose by ring opening reactions, followed by Schiff's reaction in the presence of sodium acetate buffer (pH 4.0). Synthesized PPI dendrimers and mannose-conjugated dendrimers were characterized using IR, NMR spectroscopy, and scanning electron microscopy. GmcH was loaded into PPI and M-PPI dendrimers using equilibrium dialysis method to develop the formulations, GmcH-PPI and GmcH-M-PPI, respectively. The developed formulations were evaluated for drug loading, in vitro release kinetics, in vitro stability, hemolytic toxicity, cytotoxicity, pharmacokinetic, and biodistribution studies. The dendrimeric formulation of GmcH showed pH-sensitive release with faster release at acidic pH, i.e., pH 4.0 in comparison with physiological pH 7.4. M-PPI conjugate showed significant reduction in hemolytic toxicity as compared to plain 4.0G PPI dendrimers towards human erythrocytes. In the cytotoxicity studies with A-549 lung adenocarcinoma cell line, the GmcH-M-PPI formulation showed the lowest IC50 value. Further, the pharmacokinetic and tissue distribution studies of free drug GmcH, GmcH-PPI, and GmcH-M-PPI in albino rats of Sprague-Dawley strain suggested the mean residence time of GmcH-M-PPI conjugate to be significantly higher (24.85 h) than free GmcH and GmcH-PPI. Deposition of drug (396.1 ± 4.7 after 2 h) in lung was found to be significantly higher with GmcH-M-PPI formulation in comparison with Gmch and GmcH-PPI.

Development and application of a DNA microarray-based yeast two-hybrid system

PubMed Central

Suter, Bernhard; Fontaine, Jean-Fred; Yildirimman, Reha; Raskó, Tamás; Schaefer, Martin H.; Rasche, Axel; Porras, Pablo; Vázquez-Álvarez, Blanca M.; Russ, Jenny; Rau, Kirstin; Foulle, Raphaele; Zenkner, Martina; Saar, Kathrin; Herwig, Ralf; Andrade-Navarro, Miguel A.; Wanker, Erich E.

2013-01-01

The yeast two-hybrid (Y2H) system is the most widely applied methodology for systematic protein–protein interaction (PPI) screening and the generation of comprehensive interaction networks. We developed a novel Y2H interaction screening procedure using DNA microarrays for high-throughput quantitative PPI detection. Applying a global pooling and selection scheme to a large collection of human open reading frames, proof-of-principle Y2H interaction screens were performed for the human neurodegenerative disease proteins huntingtin and ataxin-1. Using systematic controls for unspecific Y2H results and quantitative benchmarking, we identified and scored a large number of known and novel partner proteins for both huntingtin and ataxin-1. Moreover, we show that this parallelized screening procedure and the global inspection of Y2H interaction data are uniquely suited to define specific PPI patterns and their alteration by disease-causing mutations in huntingtin and ataxin-1. This approach takes advantage of the specificity and flexibility of DNA microarrays and of the existence of solid-related statistical methods for the analysis of DNA microarray data, and allows a quantitative approach toward interaction screens in human and in model organisms. PMID:23275563

Cannabidiol Affects MK-801-Induced Changes in the PPI Learned Response of Capuchin Monkeys (Sapajus spp.).

PubMed

Saletti, Patricia G; Maior, Rafael S; Barros, Marilia; Nishijo, Hisao; Tomaz, Carlos

2017-01-01

There are several lines of evidence indicating a possible therapeutic action of cannabidiol (CBD) in schizophrenia treatment. Studies with rodents have demonstrated that CBD reverses MK-801 effects in prepulse inhibition (PPI) disruption, which may indicate that CBD acts by improving sensorimotor gating deficits. In the present study, we investigated the effects of CBD on a PPI learned response of capuchin monkeys ( Sapajus spp.). A total of seven monkeys were employed in this study. In Experiment 1, we evaluated the CBD (doses of 15, 30, 60 mg/kg, i.p.) effects on PPI. In Experiment 2, the effects of sub-chronic MK-801 (0.02 mg/kg, i.m.) on PPI were challenged by a CBD pre-treatment. No changes in PPI response were observed after CBD-alone administration. However, MK-801 increased the PPI response of our animals. CBD pre-treatment blocked the PPI increase induced by MK-801. Our findings suggest that CBD's reversal of the MK-801 effects on PPI is unlikely to stem from a direct involvement on sensorimotor mechanisms, but may possibly reflect its anxiolytic properties.

A novel dual-functional biosensor for fluorometric detection of inorganic pyrophosphate and pyrophosphatase activity based on globulin stabilized gold nanoclusters.

PubMed

Xu, Shenghao; Feng, Xiuying; Gao, Teng; Wang, Ruizhi; Mao, Yaning; Lin, Jiehua; Yu, Xijuan; Luo, Xiliang

2017-03-15

A novel ultrasensitive dual-functional biosensor for highly sensitive detection of inorganic pyrophosphate (PPi) and pyrophosphatase (PPase) activity was developed based on the fluorescent variation of globulin protected gold nanoclusters (Glo@Au NCs) with the assistance of Cu 2+ . Glo@Au NCs and PPi were used as the fluorescent indicator and substrate for PPase activity evaluation, respectively. In the presence of Cu 2+ , the fluorescence of the Glo@Au NCs will be quenched owing to the formation of Cu 2+ -Glo@Au NCs complex, while PPi can restore the fluorescence of the Cu 2+ -Glo@Au NCs complex because of its higher binding affinity with Cu 2+ . As PPase can catalyze the hydrolysis of PPi, it will lead to the release of Cu 2+ and re-quench the fluorescence of the Glo@Au NCs. Based on this mechanism, quantitative evaluation of the PPi and PPase activity can be achieved ranging from 0.05 μM to 218.125 μM for PPi and from 0.1 to 8 mU for PPase, with detection limits of 0.02 μM and 0.04 mU, respectively, which is much lower than that of other PPi and PPase assay methods. More importantly, this ultrasensitive dual-functional biosensor can also be successfully applied to evaluate the PPase activity in human serum, showing great promise for practical diagnostic applications. Copyright © 2016 Elsevier B.V. All rights reserved.

Effect of stress and attention on startle response and prepulse inhibition.

PubMed

De la Casa, Luis Gonzalo; Mena, Auxiliadora; Ruiz-Salas, Juan Carlos

2016-10-15

The startle reflex magnitude can be modulated when a weak stimulus is presented before the onset of the startle stimulus, a phenomenon termed prepulse inhibition (PPI). Previous research has demonstrated that emotional processes can modulate PPI and startle intensity, but the available evidence is inconclusive. In order to obtain additional evidence in this domain, we conducted two experiments intended to analyze the effect of induced stress and attentional load on PPI and startle magnitude. Specifically, in Experiment 1 we used a between subject strategy to evaluate the effect on startle response and PPI magnitude of performing a difficult task intended to induce stress in the participants, as compared to a group exposed to a control task. In Experiment 2 we evaluated the effect of diverting attention from the acoustic stimulus on startle and PPI intensity. The results seem to indicate that induced stress can reduce PPI, and that startle reflex intensity is reduced when attention is directed away from the auditory stimulus that induces the reflex. Copyright © 2016 Elsevier Inc. All rights reserved.

Discovery and Development of Kelch-like ECH-Associated Protein 1. Nuclear Factor Erythroid 2-Related Factor 2 (KEAP1:NRF2) Protein-Protein Interaction Inhibitors: Achievements, Challenges, and Future Directions.

PubMed

Jiang, Zheng-Yu; Lu, Meng-Chen; You, Qi-Dong

2016-12-22

The transcription factor Nrf2 is the primary regulator of the cellular defense system, and enhancing Nrf2 activity has potential usages in various diseases, especially chronic age-related and inflammatory diseases. Recently, directly targeting Keap1-Nrf2 protein-protein interaction (PPI) has been an emerging strategy to selectively and effectively activate Nrf2. This Perspective summarizes the progress in the discovery and development of Keap1-Nrf2 PPI inhibitors, including the Keap1-Nrf2 regulatory mechanisms, biochemical techniques for inhibitor identification, and approaches for identifying peptide and small-molecule inhibitors, as well as discusses privileged structures and future directions for further development of Keap1-Nrf2 PPI inhibitors.

Proton pump inhibitor chemosensitization in human osteosarcoma: from the bench to the patients’ bed

PubMed Central

2013-01-01

Background Major goals in translational oncology are to reduce systemic toxicity of current anticancer strategies and improve effectiveness. An extremely efficient cancer cell mechanism to avoid and/or reduce the effects of highly cytotoxic drugs is the establishment of an acidic microenvironment, an hallmark of all malignant tumors. The H + −rich milieu that anticancer drugs meet once they get inside the tumor leads to their protonation and neutralization, therefore hindering their access into tumor cells. We have previously shown that proton pump inhibitors (PPI) may efficiently counterattack this tumor advantage leading to a consistent chemosensitization of tumors. In this study, we investigated the effects of PPI in chemosensitizing osteosarcoma. Method MG-63 and Saos-2 cell lines were used as human osteosarcoma models. Cell proliferation after pretreatment with PPI and subsequent treatment with cisplatin was evaluated by using erythrosin B dye vital staining. Tumour growth was evaluated in xenograft treated with cisplatin after PPI pretreatment. Subsequently, a multi-centre historically controlled trial, was performed to evaluate the activity of a pre-treatment administration of PPIs as chemosensitizers during neoadjuvant chemotherapy based on methotrexate, cisplatin, and adriamycin. Results Preclinical experiments showed that PPI sensitize both human osteosarcoma cell lines and xenografts to cisplatin. A clinical study subsequently showed that pretreatment with PPI drug esomeprazole leads to an increase in the local effect of chemotherapy, as expressed by percentage of tumor necrosis. This was particularly evident in chondroblastic osteosarcoma, an histological subtype that normally shows a poor histological response. Notably, no significant increase in toxicity was recorded in PPI treated patients. Conclusion This study provides the first evidence that PPI may be beneficially added to standard regimens in combination to conventional chemotherapy. PMID:24156349

Proton pump inhibitor chemosensitization in human osteosarcoma: from the bench to the patients' bed.

PubMed

Ferrari, Stefano; Perut, Francesca; Fagioli, Franca; Brach Del Prever, Adalberto; Meazza, Cristina; Parafioriti, Antonina; Picci, Piero; Gambarotti, Marco; Avnet, Sofia; Baldini, Nicola; Fais, Stefano

2013-10-24

Major goals in translational oncology are to reduce systemic toxicity of current anticancer strategies and improve effectiveness. An extremely efficient cancer cell mechanism to avoid and/or reduce the effects of highly cytotoxic drugs is the establishment of an acidic microenvironment, an hallmark of all malignant tumors. The H +-rich milieu that anticancer drugs meet once they get inside the tumor leads to their protonation and neutralization, therefore hindering their access into tumor cells. We have previously shown that proton pump inhibitors (PPI) may efficiently counterattack this tumor advantage leading to a consistent chemosensitization of tumors. In this study, we investigated the effects of PPI in chemosensitizing osteosarcoma. MG-63 and Saos-2 cell lines were used as human osteosarcoma models. Cell proliferation after pretreatment with PPI and subsequent treatment with cisplatin was evaluated by using erythrosin B dye vital staining. Tumour growth was evaluated in xenograft treated with cisplatin after PPI pretreatment. Subsequently, a multi-centre historically controlled trial, was performed to evaluate the activity of a pre-treatment administration of PPIs as chemosensitizers during neoadjuvant chemotherapy based on methotrexate, cisplatin, and adriamycin. Preclinical experiments showed that PPI sensitize both human osteosarcoma cell lines and xenografts to cisplatin. A clinical study subsequently showed that pretreatment with PPI drug esomeprazole leads to an increase in the local effect of chemotherapy, as expressed by percentage of tumor necrosis. This was particularly evident in chondroblastic osteosarcoma, an histological subtype that normally shows a poor histological response. Notably, no significant increase in toxicity was recorded in PPI treated patients. This study provides the first evidence that PPI may be beneficially added to standard regimens in combination to conventional chemotherapy.

In silico prediction of protein-protein interactions in human macrophages

PubMed Central

2014-01-01

Background Protein-protein interaction (PPI) network analyses are highly valuable in deciphering and understanding the intricate organisation of cellular functions. Nevertheless, the majority of available protein-protein interaction networks are context-less, i.e. without any reference to the spatial, temporal or physiological conditions in which the interactions may occur. In this work, we are proposing a protocol to infer the most likely protein-protein interaction (PPI) network in human macrophages. Results We integrated the PPI dataset from the Agile Protein Interaction DataAnalyzer (APID) with different meta-data to infer a contextualized macrophage-specific interactome using a combination of statistical methods. The obtained interactome is enriched in experimentally verified interactions and in proteins involved in macrophage-related biological processes (i.e. immune response activation, regulation of apoptosis). As a case study, we used the contextualized interactome to highlight the cellular processes induced upon Mycobacterium tuberculosis infection. Conclusion Our work confirms that contextualizing interactomes improves the biological significance of bioinformatic analyses. More specifically, studying such inferred network rather than focusing at the gene expression level only, is informative on the processes involved in the host response. Indeed, important immune features such as apoptosis are solely highlighted when the spotlight is on the protein interaction level. PMID:24636261

IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model

PubMed Central

Xia, Kai; Dong, Dong; Han, Jing-Dong J

2006-01-01

Background Although protein-protein interaction (PPI) networks have been explored by various experimental methods, the maps so built are still limited in coverage and accuracy. To further expand the PPI network and to extract more accurate information from existing maps, studies have been carried out to integrate various types of functional relationship data. A frequently updated database of computationally analyzed potential PPIs to provide biological researchers with rapid and easy access to analyze original data as a biological network is still lacking. Results By applying a probabilistic model, we integrated 27 heterogeneous genomic, proteomic and functional annotation datasets to predict PPI networks in human. In addition to previously studied data types, we show that phenotypic distances and genetic interactions can also be integrated to predict PPIs. We further built an easy-to-use, updatable integrated PPI database, the Integrated Network Database (IntNetDB) online, to provide automatic prediction and visualization of PPI network among genes of interest. The networks can be visualized in SVG (Scalable Vector Graphics) format for zooming in or out. IntNetDB also provides a tool to extract topologically highly connected network neighborhoods from a specific network for further exploration and research. Using the MCODE (Molecular Complex Detections) algorithm, 190 such neighborhoods were detected among all the predicted interactions. The predicted PPIs can also be mapped to worm, fly and mouse interologs. Conclusion IntNetDB includes 180,010 predicted protein-protein interactions among 9,901 human proteins and represents a useful resource for the research community. Our study has increased prediction coverage by five-fold. IntNetDB also provides easy-to-use network visualization and analysis tools that allow biological researchers unfamiliar with computational biology to access and analyze data over the internet. The web interface of IntNetDB is freely accessible at . Visualization requires Mozilla version 1.8 (or higher) or Internet Explorer with installation of SVGviewer. PMID:17112386

Efficacy and safety of ultrasound-guided percutaneous polidocanol sclerotherapy in benign predominantly cystic thyroid nodules: a prospective study.

PubMed

Gong, Xiaohua; Zhou, Qi; Chen, Shuoping; Wang, Fang; Wu, Wenjun; Chen, Xiaojun

2017-08-01

To evaluate the efficacy and safety of percutaneous polidocanol injection (PPI) in treatment of predominantly cystic thyroid nodules. This prospective study included 111 patients with 122 benign predominantly cystic thyroid nodules inducing pressure symptoms or cosmetic problems. The nodules were randomized to a single aspiration with (n = 61) or without (n = 61) subsequent PPI and followed up after 1, 3, 6, and 12 months. Ten patients (12 nodules) declined to follow up after aspiration in group 2. Nodule volumes, symptoms scores, and cosmetic scores were evaluated before and after treatment. The therapeutic success rate and safety of PPI for treatment of predominantly cystic thyroid nodules were also evaluated. In the PPI group, the nodule volumes were reduced from 13.67 ± 9.90 to 2.60 ± 2.66 (p < .001). Therapeutic success rate (nodule volume reduction >50%) was obtained in 57 of 61 (93.44%) nodules in the PPI group, compared to seven of 49 (14.29%) in the aspiration group (p < .001). In the aspiration group, the nodule volume was not significantly reduced. The reduction in symptom scores was significantly higher in the PPI group (from 3.60 ± 1.65 to 1.60 ± 1.19) than in the aspiration group (from 3.62 ± 1.89 to 3.30 ± 1.06) (p < .001, between groups). The reduction in cosmetic scores showed a significant difference between groups (p < .001). In total, 4.92% of patients (3/61) in the PPI group and 85.71% (42/49) in the aspiration group showed recurrence during the follow-up period. There was a significant difference in the recurrence rate between groups (p < .001). No major side-effects occurred. US-guided PPI of benign recurrent predominantly cystic thyroid nodules is effective and safe. PPI is an important alternative to benign recurrent predominantly cystic thyroid nodules.

MCL-CAw: a refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure

PubMed Central

2010-01-01

Background The reconstruction of protein complexes from the physical interactome of organisms serves as a building block towards understanding the higher level organization of the cell. Over the past few years, several independent high-throughput experiments have helped to catalogue enormous amount of physical protein interaction data from organisms such as yeast. However, these individual datasets show lack of correlation with each other and also contain substantial number of false positives (noise). Over these years, several affinity scoring schemes have also been devised to improve the qualities of these datasets. Therefore, the challenge now is to detect meaningful as well as novel complexes from protein interaction (PPI) networks derived by combining datasets from multiple sources and by making use of these affinity scoring schemes. In the attempt towards tackling this challenge, the Markov Clustering algorithm (MCL) has proved to be a popular and reasonably successful method, mainly due to its scalability, robustness, and ability to work on scored (weighted) networks. However, MCL produces many noisy clusters, which either do not match known complexes or have additional proteins that reduce the accuracies of correctly predicted complexes. Results Inspired by recent experimental observations by Gavin and colleagues on the modularity structure in yeast complexes and the distinctive properties of "core" and "attachment" proteins, we develop a core-attachment based refinement method coupled to MCL for reconstruction of yeast complexes from scored (weighted) PPI networks. We combine physical interactions from two recent "pull-down" experiments to generate an unscored PPI network. We then score this network using available affinity scoring schemes to generate multiple scored PPI networks. The evaluation of our method (called MCL-CAw) on these networks shows that: (i) MCL-CAw derives larger number of yeast complexes and with better accuracies than MCL, particularly in the presence of natural noise; (ii) Affinity scoring can effectively reduce the impact of noise on MCL-CAw and thereby improve the quality (precision and recall) of its predicted complexes; (iii) MCL-CAw responds well to most available scoring schemes. We discuss several instances where MCL-CAw was successful in deriving meaningful complexes, and where it missed a few proteins or whole complexes due to affinity scoring of the networks. We compare MCL-CAw with several recent complex detection algorithms on unscored and scored networks, and assess the relative performance of the algorithms on these networks. Further, we study the impact of augmenting physical datasets with computationally inferred interactions for complex detection. Finally, we analyse the essentiality of proteins within predicted complexes to understand a possible correlation between protein essentiality and their ability to form complexes. Conclusions We demonstrate that core-attachment based refinement in MCL-CAw improves the predictions of MCL on yeast PPI networks. We show that affinity scoring improves the performance of MCL-CAw. PMID:20939868

Completing sparse and disconnected protein-protein network by deep learning.

PubMed

Huang, Lei; Liao, Li; Wu, Cathy H

2018-03-22

Protein-protein interaction (PPI) prediction remains a central task in systems biology to achieve a better and holistic understanding of cellular and intracellular processes. Recently, an increasing number of computational methods have shifted from pair-wise prediction to network level prediction. Many of the existing network level methods predict PPIs under the assumption that the training network should be connected. However, this assumption greatly affects the prediction power and limits the application area because the current golden standard PPI networks are usually very sparse and disconnected. Therefore, how to effectively predict PPIs based on a training network that is sparse and disconnected remains a challenge. In this work, we developed a novel PPI prediction method based on deep learning neural network and regularized Laplacian kernel. We use a neural network with an autoencoder-like architecture to implicitly simulate the evolutionary processes of a PPI network. Neurons of the output layer correspond to proteins and are labeled with values (1 for interaction and 0 for otherwise) from the adjacency matrix of a sparse disconnected training PPI network. Unlike autoencoder, neurons at the input layer are given all zero input, reflecting an assumption of no a priori knowledge about PPIs, and hidden layers of smaller sizes mimic ancient interactome at different times during evolution. After the training step, an evolved PPI network whose rows are outputs of the neural network can be obtained. We then predict PPIs by applying the regularized Laplacian kernel to the transition matrix that is built upon the evolved PPI network. The results from cross-validation experiments show that the PPI prediction accuracies for yeast data and human data measured as AUC are increased by up to 8.4 and 14.9% respectively, as compared to the baseline. Moreover, the evolved PPI network can also help us leverage complementary information from the disconnected training network and multiple heterogeneous data sources. Tested by the yeast data with six heterogeneous feature kernels, the results show our method can further improve the prediction performance by up to 2%, which is very close to an upper bound that is obtained by an Approximate Bayesian Computation based sampling method. The proposed evolution deep neural network, coupled with regularized Laplacian kernel, is an effective tool in completing sparse and disconnected PPI networks and in facilitating integration of heterogeneous data sources.

Detecting complexes from edge-weighted PPI networks via genes expression analysis.

PubMed

Zhang, Zehua; Song, Jian; Tang, Jijun; Xu, Xinying; Guo, Fei

2018-04-24

Identifying complexes from PPI networks has become a key problem to elucidate protein functions and identify signal and biological processes in a cell. Proteins binding as complexes are important roles of life activity. Accurate determination of complexes in PPI networks is crucial for understanding principles of cellular organization. We propose a novel method to identify complexes on PPI networks, based on different co-expression information. First, we use Markov Cluster Algorithm with an edge-weighting scheme to calculate complexes on PPI networks. Then, we propose some significant features, such as graph information and gene expression analysis, to filter and modify complexes predicted by Markov Cluster Algorithm. To evaluate our method, we test on two experimental yeast PPI networks. On DIP network, our method has Precision and F-Measure values of 0.6004 and 0.5528. On MIPS network, our method has F-Measure and S n values of 0.3774 and 0.3453. Comparing to existing methods, our method improves Precision value by at least 0.1752, F-Measure value by at least 0.0448, S n value by at least 0.0771. Experiments show that our method achieves better results than some state-of-the-art methods for identifying complexes on PPI networks, with the prediction quality improved in terms of evaluation criteria.

Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets

PubMed Central

Vinayagam, Arunachalam; Gibson, Travis E.; Lee, Ho-Joon; Yilmazel, Bahar; Roesel, Charles; Hu, Yanhui; Kwon, Young; Sharma, Amitabh; Liu, Yang-Yu; Perrimon, Norbert; Barabási, Albert-László

2016-01-01

The protein–protein interaction (PPI) network is crucial for cellular information processing and decision-making. With suitable inputs, PPI networks drive the cells to diverse functional outcomes such as cell proliferation or cell death. Here, we characterize the structural controllability of a large directed human PPI network comprising 6,339 proteins and 34,813 interactions. This network allows us to classify proteins as “indispensable,” “neutral,” or “dispensable,” which correlates to increasing, no effect, or decreasing the number of driver nodes in the network upon removal of that protein. We find that 21% of the proteins in the PPI network are indispensable. Interestingly, these indispensable proteins are the primary targets of disease-causing mutations, human viruses, and drugs, suggesting that altering a network’s control property is critical for the transition between healthy and disease states. Furthermore, analyzing copy number alterations data from 1,547 cancer patients reveals that 56 genes that are frequently amplified or deleted in nine different cancers are indispensable. Among the 56 genes, 46 of them have not been previously associated with cancer. This suggests that controllability analysis is very useful in identifying novel disease genes and potential drug targets. PMID:27091990

Proton pump inhibitors increase the incidence of bone fractures in hepatitis C patients.

PubMed

Mello, Michael; Weideman, Rick A; Little, Bertis B; Weideman, Mark W; Cryer, Byron; Brown, Geri R

2012-09-01

While proton pump inhibitors (PPI) may increase the risk of bone fractures, the incidence of new bone fractures in a chronic hepatitis C virus (HCV) infected cohort, with or without PPI exposure, has not been explored. A retrospective cohort study of the incidence of bone fractures over 10 years in 9,437 HCV antibody positive patients in the Dallas VA Hepatitis C Registry was performed. The study endpoint was the incidence of verified new bone fractures per patient-years (pt-yrs) in PPI users compared to non-PPI users. PPI use was defined as those taking a PPI for ≥360 days. Pt-yrs of exposure for PPI users began on the first PPI prescription date, and pt-yrs of exposure for non-PPI users began with first date of any non-PPI prescription. For both HCV groups, the final date of patients' study duration was defined by end of PPI exposure, bone fracture occurrence, death or end of study evaluation period. Exclusion criteria included use of bone health modifying medications ≥30 days. Statistical differences in fracture incidence between groups were determined by multivariate regression analysis. Among the total study population analyzed (n = 2,573), 109 bone fractures occurred. Unadjusted bone fracture incidences were 13.99/1,000 pt-yrs vs. 5.86/1,000 pt-yrs in PPI and non-PPI users, respectively. The adjusted hazard ratio for new bone fractures was 3.87 (95 % CI 2.46-6.08) (p < 0.001) in PPI users. In patients with chronic HCV, use of PPI for >1 year increased the risk of new bone fractures by more than threefold.

A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase

PubMed Central

Da, Lin-Tai; Pardo Avila, Fátima; Wang, Dong; Huang, Xuhui

2013-01-01

The dynamics of the PPi release during the transcription elongation of bacterial RNA polymerase and its effects on the Trigger Loop (TL) opening motion are still elusive. Here, we built a Markov State Model (MSM) from extensive all-atom molecular dynamics (MD) simulations to investigate the mechanism of the PPi release. Our MSM has identified a simple two-state mechanism for the PPi release instead of a more complex four-state mechanism observed in RNA polymerase II (Pol II). We observed that the PPi release in bacterial RNA polymerase occurs at sub-microsecond timescale, which is ∼3-fold faster than that in Pol II. After escaping from the active site, the (Mg-PPi)2− group passes through a single elongated metastable region where several positively charged residues on the secondary channel provide favorable interactions. Surprisingly, we found that the PPi release is not coupled with the TL unfolding but correlates tightly with the side-chain rotation of the TL residue R1239. Our work sheds light on the dynamics underlying the transcription elongation of the bacterial RNA polymerase. PMID:23592966

Evolution versus "intelligent design": comparing the topology of protein-protein interaction networks to the Internet.

PubMed

Yang, Q; Siganos, G; Faloutsos, M; Lonardi, S

2006-01-01

Recent research efforts have made available genome-wide, high-throughput protein-protein interaction (PPI) maps for several model organisms. This has enabled the systematic analysis of PPI networks, which has become one of the primary challenges for the system biology community. In this study, we attempt to understand better the topological structure of PPI networks by comparing them against man-made communication networks, and more specifically, the Internet. Our comparative study is based on a comprehensive set of graph metrics. Our results exhibit an interesting dichotomy. On the one hand, both networks share several macroscopic properties such as scale-free and small-world properties. On the other hand, the two networks exhibit significant topological differences, such as the cliqueishness of the highest degree nodes. We attribute these differences to the distinct design principles and constraints that both networks are assumed to satisfy. We speculate that the evolutionary constraints that favor the survivability and diversification are behind the building process of PPI networks, whereas the leading force in shaping the Internet topology is a decentralized optimization process geared towards efficient node communication.

Quality improvement of a rice-substituted fried noodle by utilizing the protein-polyphenol interaction between a pea protein isolate and green tea (Camellia sinensis) extract.

PubMed

Song, Youngwoon; Yoo, Sang-Ho

2017-11-15

The quality of rice-substituted fried noodles was improved by applying interaction between pea protein isolate (PPI) and green tea extract (GTE). Radical-scavenging activities of GTE were stably maintained when exposed to acidic pH, UV light, and fluorescent light, but decreased by approximately 65% when exposed to 80°C for 168h. The RVA profiles of noodle dough showed that peak viscosity and breakdown increased significantly but that setback and final viscosity remained unchanged with 20% rice flour replacement. PPI significantly decreased the viscosity parameters of rice-supplemented dough, and the addition of GTE recovered these values significantly. The cooking loss and viscoelasticity (R max ) of cooked rice-supplemented noodles were fully restored by combined treatment of PPI and GTE. GTE decreased the peroxide value of fried noodles by 14% after storage at 63°C for 16days. Therefore, PPI+GTE treatment has great potential for use in fried noodles owing to the reinforced network and antioxidant activity. Copyright © 2017 Elsevier Ltd. All rights reserved.

A patient and public involvement (PPI) toolkit for meaningful and flexible involvement in clinical trials - a work in progress.

PubMed

Bagley, Heather J; Short, Hannah; Harman, Nicola L; Hickey, Helen R; Gamble, Carrol L; Woolfall, Kerry; Young, Bridget; Williamson, Paula R

2016-01-01

Funders of research are increasingly requiring researchers to involve patients and the public in their research. Patient and public involvement (PPI) in research can potentially help researchers make sure that the design of their research is relevant, that it is participant friendly and ethically sound. Using and sharing PPI resources can benefit those involved in undertaking PPI, but existing PPI resources are not used consistently and this can lead to duplication of effort. This paper describes how we are developing a toolkit to support clinical trials teams in a clinical trials unit. The toolkit will provide a key 'off the shelf' resource to support trial teams with limited resources, in undertaking PPI. Key activities in further developing and maintaining the toolkit are to: ● listen to the views and experience of both research teams and patient and public contributors who use the tools; ● modify the tools based on our experience of using them; ● identify the need for future tools; ● update the toolkit based on any newly identified resources that come to light; ● raise awareness of the toolkit and ● work in collaboration with others to either develop or test out PPI resources in order to reduce duplication of work in PPI. Background Patient and public involvement (PPI) in research is increasingly a funder requirement due to the potential benefits in the design of relevant, participant friendly, ethically sound research. The use and sharing of resources can benefit PPI, but available resources are not consistently used leading to duplication of effort. This paper describes a developing toolkit to support clinical trials teams to undertake effective and meaningful PPI. Methods The first phase in developing the toolkit was to describe which PPI activities should be considered in the pathway of a clinical trial and at what stage these activities should take place. This pathway was informed through review of the type and timing of PPI activities within trials coordinated by the Clinical Trials Research Centre and previously described areas of potential PPI impact in trials. In the second phase, key websites around PPI and identification of resources opportunistically, e.g. in conversation with other trialists or social media, were used to identify resources. Tools were developed where gaps existed. Results A flowchart was developed describing PPI activities that should be considered in the clinical trial pathway and the point at which these activities should happen. Three toolkit domains were identified: planning PPI; supporting PPI; recording and evaluating PPI. Four main activities and corresponding tools were identified under the planning for PPI: developing a plan; identifying patient and public contributors; allocating appropriate costs; and managing expectations. In supporting PPI, tools were developed to review participant information sheets. These tools, which require a summary of potential trial participant characteristics and circumstances help to clarify requirements and expectations of PPI review. For recording and evaluating PPI, the planned PPI interventions should be monitored in terms of impact, and a tool to monitor public contributor experience is in development. Conclusions This toolkit provides a developing 'off the shelf' resource to support trial teams with limited resources in undertaking PPI. Key activities in further developing and maintaining the toolkit are to: listen to the views and experience of both research teams and public contributors using the tools, to identify the need for future tools, to modify tools based on experience of their use; to update the toolkit based on any newly identified resources that come to light; to raise awareness of the toolkit and to work in collaboration with others to both develop and test out PPI resources in order to reduce duplication of work in PPI.

Application of Machine Learning Approaches for Protein-protein Interactions Prediction.

PubMed

Zhang, Mengying; Su, Qiang; Lu, Yi; Zhao, Manman; Niu, Bing

2017-01-01

Proteomics endeavors to study the structures, functions and interactions of proteins. Information of the protein-protein interactions (PPIs) helps to improve our knowledge of the functions and the 3D structures of proteins. Thus determining the PPIs is essential for the study of the proteomics. In this review, in order to study the application of machine learning in predicting PPI, some machine learning approaches such as support vector machine (SVM), artificial neural networks (ANNs) and random forest (RF) were selected, and the examples of its applications in PPIs were listed. SVM and RF are two commonly used methods. Nowadays, more researchers predict PPIs by combining more than two methods. This review presents the application of machine learning approaches in predicting PPI. Many examples of success in identification and prediction in the area of PPI prediction have been discussed, and the PPIs research is still in progress. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Polypyrrole-MWCNT-Ag composites for electromagnetic shielding: Comparison between chemical deposition and UV-reduction approaches

NASA Astrophysics Data System (ADS)

Ebrahimi, Izadyar; Gashti, Mazeyar Parvinzadeh

2018-07-01

In this study, we focused on the synthesis of polypyrrole-MWCNT-Ag composites and we evaluated their electrical properties to determine the electromagnetic interference shielding performance. We reduced silver nanoparticles in composites using two different in situ methods: UV-reduction and chemical deposition. Composites were characterized using spectroscopic and microscopic tools for evaluation of the chemical, morphological, electrical conductivity and electromagnetic shielding effectiveness. Results from Fourier transform infrared spectroscopy and dispersive Raman microscope showed chemical interactions between silver and the polypyrrole-MWCNT composite due to the charge-transfer within the structure. X-ray diffraction confirmed appearance of two new peaks for silver nanoparticles embedded in polypyrrole-MWCNT independent to reduction method. According to microscopy images, silver nanoparticles were homogenously distributed at the PPy-MWCNTs interfaces by UV reduction, while, chemical reduction resulted to deposition of silver within the PPy matrix. Finally, our results revealed that the polypyrrole-MWCNT-Ag composite produced via UV-reduction has higher electrical conductivity and shielding effectiveness in comparison to chemically reduced one.

On the integration of protein-protein interaction networks with gene expression and 3D structural data: What can be gained?

NASA Astrophysics Data System (ADS)

Bertolazzi, Paola; Bock, Mary Ellen; Guerra, Concettina; Paci, Paola; Santoni, Daniele

2014-06-01

The biological role of proteins has been analyzed from different perspectives, initially by considering proteins as isolated biological entities, then as cooperating entities that perform their function by interacting with other molecules. There are other dimensions that are important for the complete understanding of the biological processes: time and location. However a protein is rarely annotated with temporal and spatial information. Experimental Protein-Proteins Interaction (PPI) data are static; furthermore they generally do not include transient interactions which are a considerable fraction of the interactome of many organisms. One way to incorporate temporal and condition information is to use other sources of information, such as gene expression data and 3D structural data. Here we review work done to understand the insight that can be gained by enriching PPI data with gene expression and 3D structural data. In particular, we address the following questions: Can the dynamics of a single protein or of an interaction be accurately derived from these data? Can the assembly-disassembly of protein complexes be traced over time? What type of topological changes occur in a PPI network architecture over time?

Polypropyleneimine and polyamidoamine dendrimer mediated enhanced solubilization of bortezomib: Comparison and evaluation of mechanistic aspects by thermodynamics and molecular simulations.

PubMed

Chaudhary, Sonam; Gothwal, Avinash; Khan, Iliyas; Srivastava, Shubham; Malik, Ruchi; Gupta, Umesh

2017-03-01

Bortezomib (BTZ) is the first proteasome inhibitor approved by the US-FDA is majorly used for the treatment of newly diagnosed and relapsed multiple myeloma including mantle cell lymphoma. BTZ is hydrophobic in nature and is a major cause for its minimal presence as marketed formulations. The present study reports the design, development and characterization of dendrimer based formulation for the improved solubility and effectivity of bortezomib. The study also equally focuses on the mechanistic elucidation of solubilization by two types of dendrimers i.e. fourth generation of poly (amidoamine) dendrimers (G4-PAMAM-NH 2 ) and fifth generation of poly (propylene) imine dendrimers (G5-PPI-NH 2 ). It was observed that aqueous solubility of BTZ was concentration and pH dependent. At 2mM G5-PPI-NH 2 concentration, the fold increase in bortezomib solubility was 1152.63 times in water, while approximately 3426.69 folds increase in solubility was observed at pH10.0, respectively (p<0.05). The solubility of the drug was increased to a greater extent with G5-PPI-NH 2 dendrimers because it has more hydrophobic interior than G4-PAMAM-NH 2 dendrimers. The release of BTZ from G5-PPI-NH 2 complex was comparatively slower than G4-PAMAM-NH 2 . The thermodynamic treatment of data proved that dendrimer drug complexes were stable at all pH with values of ΔG always negative. The experimental findings were also proven by molecular simulation studies and by calculating RMSD and intermolecular hydrogen bonding through Schrodinger software. It was concluded that PPI dendrimers were able to solubilize the drug more effectively than PAMAM dendrimers through electrostatic interactions. Copyright © 2016 Elsevier B.V. All rights reserved.

Polypyrrole-chitosan conductive biomaterial synchronizes cardiomyocyte contraction and improves myocardial electrical impulse propagation.

PubMed

Cui, Zhi; Ni, Nathan C; Wu, Jun; Du, Guo-Qing; He, Sheng; Yau, Terrence M; Weisel, Richard D; Sung, Hsing-Wen; Li, Ren-Ke

2018-01-01

Background: The post-myocardial infarction (MI) scar interrupts electrical impulse propagation and delays regional contraction, which contributes to ventricular dysfunction. We investigated the potential of an injectable conductive biomaterial to restore scar tissue conductivity and re-establish synchronous ventricular contraction. Methods: A conductive biomaterial was generated by conjugating conductive polypyrrole (PPY) onto chitosan (CHI) backbones. Trypan blue staining of neonatal rat cardiomyocytes (CMs) cultured on biomaterials was used to evaluate the biocompatibility of the conductive biomaterials. Ca 2+ imaging was used to visualize beating CMs. A cryoablation injury rat model was used to investigate the ability of PPY:CHI to improve cardiac electrical propagation in the injured heart in vivo . Electromyography was used to evaluate conductivity of scar tissue ex vivo . Results: Cell survival and morphology were similar between cells cultured on biomaterials-coated and uncoated-control dishes. PPY:CHI established synchronous contraction of two distinct clusters of spontaneously-beating CMs. Intramyocardial PPY:CHI injection into the cryoablation-induced injured region improved electrical impulse propagation across the scarred tissue and decreased the QRS interval, whereas saline- or CHI-injected hearts continued to have delayed propagation patterns and significantly reduced conduction velocity compared to healthy controls. Ex vivo evaluation found that scar tissue from PPY:CHI-treated rat hearts had higher signal amplitude compared to those from saline- or CHI-treated rat heart tissue. Conclusions: The PPY:CHI biomaterial is electrically conductive, biocompatible and injectable. It improved synchronous contraction between physically separated beating CM clusters in vitro . Intra-myocardial injection of PPY:CHI following cardiac injury improved electrical impulse propagation of scar tissue in vivo .

Use of proton pump inhibitors is associated with increased mortality due to nosocomial pneumonia in bedridden patients receiving tube feeding.

PubMed

Hamai, Kosuke; Iwamoto, Hiroshi; Ohshimo, Shinichiro; Wakabayashi, Yu; Ihara, Daisuke; Fujitaka, Kazunori; Hamada, Hironobu; Ono, Koichi; Hattori, Noboru

2018-05-22

To investigate the association between the use of proton pump inhibitors (PPI) and nosocomial pneumonia and gastrointestinal bleeding in bedridden patients receiving tube feeding. A total of 116 bedridden hospitalized patients receiving tube feeding, of which 80 were supported by percutaneous endoscopic gastrostomy and 36 by nasogastric tube, were included in the present study. The patients were divided into two groups: 62 patients treated with PPI (PPI group) and 54 patients without PPI (non-PPI group). Mortality due to nosocomial pneumonia was evaluated using the Kaplan-Meier approach and the log-rank test. A total of 36 patients (31%) died of nosocomial pneumonia during the observation period; the mortality rate due to nosocomial pneumonia was significantly higher in the PPI group than in the non-PPI group (P = 0.0395). Cox proportional hazard analysis showed that the use of PPI and lower levels of serum albumin were independent predictors of 2-year mortality due to nosocomial pneumonia. Gastrointestinal bleeding was observed in four patients in the non-PPI group (7.7%) and in one patient in the PPI group (1.6%); there was no significant difference between the two groups. The use of PPI in bedridden tube-fed patients was independently associated with mortality due to nosocomial pneumonia, and the PPI group had a non-significant lower incidence of gastrointestinal bleeding than the non-PPI group. Geriatr Gerontol Int 2018; ••: ••-••. © 2018 The Authors Geriatrics & Gerontology International published by John Wiley & Sons Australia, Ltd on behalf of Japan Geriatrics Society.

Feature generation and representations for protein-protein interaction classification.

PubMed

Lan, Man; Tan, Chew Lim; Su, Jian

2009-10-01

Automatic detecting protein-protein interaction (PPI) relevant articles is a crucial step for large-scale biological database curation. The previous work adopted POS tagging, shallow parsing and sentence splitting techniques, but they achieved worse performance than the simple bag-of-words representation. In this paper, we generated and investigated multiple types of feature representations in order to further improve the performance of PPI text classification task. Besides the traditional domain-independent bag-of-words approach and the term weighting methods, we also explored other domain-dependent features, i.e. protein-protein interaction trigger keywords, protein named entities and the advanced ways of incorporating Natural Language Processing (NLP) output. The integration of these multiple features has been evaluated on the BioCreAtIvE II corpus. The experimental results showed that both the advanced way of using NLP output and the integration of bag-of-words and NLP output improved the performance of text classification. Specifically, in comparison with the best performance achieved in the BioCreAtIvE II IAS, the feature-level and classifier-level integration of multiple features improved the performance of classification 2.71% and 3.95%, respectively.

ModuleRole: a tool for modulization, role determination and visualization in protein-protein interaction networks.

PubMed

Li, Guipeng; Li, Ming; Zhang, Yiwei; Wang, Dong; Li, Rong; Guimerà, Roger; Gao, Juntao Tony; Zhang, Michael Q

2014-01-01

Rapidly increasing amounts of (physical and genetic) protein-protein interaction (PPI) data are produced by various high-throughput techniques, and interpretation of these data remains a major challenge. In order to gain insight into the organization and structure of the resultant large complex networks formed by interacting molecules, using simulated annealing, a method based on the node connectivity, we developed ModuleRole, a user-friendly web server tool which finds modules in PPI network and defines the roles for every node, and produces files for visualization in Cytoscape and Pajek. For given proteins, it analyzes the PPI network from BioGRID database, finds and visualizes the modules these proteins form, and then defines the role every node plays in this network, based on two topological parameters Participation Coefficient and Z-score. This is the first program which provides interactive and very friendly interface for biologists to find and visualize modules and roles of proteins in PPI network. It can be tested online at the website http://www.bioinfo.org/modulerole/index.php, which is free and open to all users and there is no login requirement, with demo data provided by "User Guide" in the menu Help. Non-server application of this program is considered for high-throughput data with more than 200 nodes or user's own interaction datasets. Users are able to bookmark the web link to the result page and access at a later time. As an interactive and highly customizable application, ModuleRole requires no expert knowledge in graph theory on the user side and can be used in both Linux and Windows system, thus a very useful tool for biologist to analyze and visualize PPI networks from databases such as BioGRID. ModuleRole is implemented in Java and C, and is freely available at http://www.bioinfo.org/modulerole/index.php. Supplementary information (user guide, demo data) is also available at this website. API for ModuleRole used for this program can be obtained upon request.

Determining Effects of Non-synonymous SNPs on Protein-Protein Interactions using Supervised and Semi-supervised Learning

PubMed Central

Zhao, Nan; Han, Jing Ginger; Shyu, Chi-Ren; Korkin, Dmitry

2014-01-01

Single nucleotide polymorphisms (SNPs) are among the most common types of genetic variation in complex genetic disorders. A growing number of studies link the functional role of SNPs with the networks and pathways mediated by the disease-associated genes. For example, many non-synonymous missense SNPs (nsSNPs) have been found near or inside the protein-protein interaction (PPI) interfaces. Determining whether such nsSNP will disrupt or preserve a PPI is a challenging task to address, both experimentally and computationally. Here, we present this task as three related classification problems, and develop a new computational method, called the SNP-IN tool (non-synonymous SNP INteraction effect predictor). Our method predicts the effects of nsSNPs on PPIs, given the interaction's structure. It leverages supervised and semi-supervised feature-based classifiers, including our new Random Forest self-learning protocol. The classifiers are trained based on a dataset of comprehensive mutagenesis studies for 151 PPI complexes, with experimentally determined binding affinities of the mutant and wild-type interactions. Three classification problems were considered: (1) a 2-class problem (strengthening/weakening PPI mutations), (2) another 2-class problem (mutations that disrupt/preserve a PPI), and (3) a 3-class classification (detrimental/neutral/beneficial mutation effects). In total, 11 different supervised and semi-supervised classifiers were trained and assessed resulting in a promising performance, with the weighted f-measure ranging from 0.87 for Problem 1 to 0.70 for the most challenging Problem 3. By integrating prediction results of the 2-class classifiers into the 3-class classifier, we further improved its performance for Problem 3. To demonstrate the utility of SNP-IN tool, it was applied to study the nsSNP-induced rewiring of two disease-centered networks. The accurate and balanced performance of SNP-IN tool makes it readily available to study the rewiring of large-scale protein-protein interaction networks, and can be useful for functional annotation of disease-associated SNPs. SNIP-IN tool is freely accessible as a web-server at http://korkinlab.org/snpintool/. PMID:24784581

Structure-Based Design of Inhibitors of Protein–Protein Interactions: Mimicking Peptide Binding Epitopes

PubMed Central

Pelay-Gimeno, Marta; Glas, Adrian; Koch, Oliver; Grossmann, Tom N

2015-01-01

Protein–protein interactions (PPIs) are involved at all levels of cellular organization, thus making the development of PPI inhibitors extremely valuable. The identification of selective inhibitors is challenging because of the shallow and extended nature of PPI interfaces. Inhibitors can be obtained by mimicking peptide binding epitopes in their bioactive conformation. For this purpose, several strategies have been evolved to enable a projection of side chain functionalities in analogy to peptide secondary structures, thereby yielding molecules that are generally referred to as peptidomimetics. Herein, we introduce a new classification of peptidomimetics (classes A–D) that enables a clear assignment of available approaches. Based on this classification, the Review summarizes strategies that have been applied for the structure-based design of PPI inhibitors through stabilizing or mimicking turns, β-sheets, and helices. PMID:26119925

FACETS: multi-faceted functional decomposition of protein interaction networks

PubMed Central

Seah, Boon-Siew; Bhowmick, Sourav S.; Forbes Dewey, C.

2012-01-01

Motivation: The availability of large-scale curated protein interaction datasets has given rise to the opportunity to investigate higher level organization and modularity within the protein–protein interaction (PPI) network using graph theoretic analysis. Despite the recent progress, systems level analysis of high-throughput PPIs remains a daunting task because of the amount of data they present. In this article, we propose a novel PPI network decomposition algorithm called FACETS in order to make sense of the deluge of interaction data using Gene Ontology (GO) annotations. FACETS finds not just a single functional decomposition of the PPI network, but a multi-faceted atlas of functional decompositions that portray alternative perspectives of the functional landscape of the underlying PPI network. Each facet in the atlas represents a distinct interpretation of how the network can be functionally decomposed and organized. Our algorithm maximizes interpretative value of the atlas by optimizing inter-facet orthogonality and intra-facet cluster modularity. Results: We tested our algorithm on the global networks from IntAct, and compared it with gold standard datasets from MIPS and KEGG. We demonstrated the performance of FACETS. We also performed a case study that illustrates the utility of our approach. Contact: seah0097@ntu.edu.sg or assourav@ntu.edu.sg Supplementary information: Supplementary data are available at the Bioinformatics online. Availability: Our software is available freely for non-commercial purposes from: http://www.cais.ntu.edu.sg/∼assourav/Facets/ PMID:22908217

Deficient prepulse inhibition in schizophrenia in a multi-site cohort: Internal replication and extension.

PubMed

Swerdlow, Neal R; Light, Gregory A; Thomas, Michael L; Sprock, Joyce; Calkins, Monica E; Green, Michael F; Greenwood, Tiffany A; Gur, Raquel E; Gur, Ruben C; Lazzeroni, Laura C; Nuechterlein, Keith H; Radant, Allen D; Seidman, Larry J; Siever, Larry J; Silverman, Jeremy M; Stone, William S; Sugar, Catherine A; Tsuang, Debby W; Tsuang, Ming T; Turetsky, Bruce I; Braff, David L

2017-05-23

The Consortium on the Genetics of Schizophrenia (COGS) collected case-control endophenotype and genetic information from 2457 patients and healthy subjects (HS) across 5 test sites over 3.5 years. Analysis of the first "wave" (W1) of 1400 subjects identified prepulse inhibition (PPI) deficits in patients vs. HS. Data from the second COGS "wave" (W2), and the combined W(1+2), were used to assess: 1) the replicability of PPI deficits in this design; 2) the impact of response criteria on PPI deficits; and 3) PPI in a large cohort of antipsychotic-free patients. PPI in W2 HS (n=315) and schizophrenia patients (n=326) was compared to findings from W1; planned analyses assessed the impact of diagnosis, "wave" (1 vs. 2), and startle magnitude criteria. Combining waves allowed us to assess PPI in 120 antipsychotic-free patients, including many in the early course of illness. ANOVA of all W(1+2) subjects revealed robust PPI deficits in patients across "waves" (p<0.0004). Strict response criteria excluded almost 39% of all subjects, disproportionately impacting specific subgroups; ANOVA in this smaller cohort confirmed no significant effect of "wave" or "wave x diagnosis" interaction, and a significant effect of diagnosis (p<0.002). Antipsychotic-free, early-illness patients had particularly robust PPI deficits. Schizophrenia-linked PPI deficits were replicable across two multi-site "waves" of subjects collected over 3.5years. Strict response criteria disproportionately excluded older, male, non-Caucasian patients with low-normal hearing acuity. These findings set the stage for genetic analyses of PPI using the combined COGS wave 1 and 2 cohorts. Copyright © 2017 Elsevier B.V. All rights reserved.

Processable dodecylbenzene sulfonic acid (DBSA) doped poly(N-vinyl carbazole)-poly(pyrrole) for optoelectronic applications

PubMed Central

Hammed, W. A.; Rahman, M. S.; Mahmud, H. N. M. E.; Yahya, R.; Sulaiman, K.

2017-01-01

Abstract A soluble poly (n-vinyl carbazole)–polypyrrole (PNVC–Ppy) copolymer was prepared through oxidative chemical polymerization wherein dodecyl benzene sulfonic acid (DBSA) was used as a dopant to facilitate polymer-organic solvent interaction and ammonium persulfate (APS) was used as an oxidant. Compared with undoped PNVC–Ppy, the DBSA-doped PNVC–Ppy copolymer showed higher solubility in some selected organic solvents. The composition and structural characteristics of the DBSA-doped PNVC–Ppy were determined by Fourier transform infrared, ultraviolet–visible, and X-ray diffraction spectroscopic methods. Field emission scanning electron microscopic method was employed to observe the morphology of the DBSA-doped PNVC–Ppy copolymer. The electrical conductivity of the DBSA-doped PNVC–Ppy copolymer was measured at room temperature. The conductivity increased with increasing concentration of APS oxidant, and the highest conductivity was recorded at 0.004 mol/dm3 APS at a polymerization temperature of −5 °C. The increased conductivity can be explained by the extended half-life of pyrrole free radical at a lower temperature and a gradual increase in chain length over a prolonged time due to the slow addition of APS. Furthermore, the obtained soluble copolymer exhibits unique optical and thermal properties different from those of PNVC and Ppy. PMID:29491808

Novel in vitro protein fragment complementation assay applicable to high-throughput screening in a 1536-well format.

PubMed

Hashimoto, Junko; Watanabe, Taku; Seki, Tatsuya; Karasawa, Satoshi; Izumikawa, Miho; Seki, Tomoe; Iemura, Shun-Ichiro; Natsume, Tohru; Nomura, Nobuo; Goshima, Naoki; Miyawaki, Atsushi; Takagi, Motoki; Shin-Ya, Kazuo

2009-09-01

Protein-protein interactions (PPIs) play key roles in all cellular processes and hence are useful as potential targets for new drug development. To facilitate the screening of PPI inhibitors as anticancer drugs, the authors have developed a high-throughput screening (HTS) system using an in vitro protein fragment complementation assay (PCA) with monomeric Kusabira-Green fluorescent protein (mKG). The in vitro PCA system was established by the topological formation of a functional complex between 2 split inactive mKG fragments fused to target proteins, which fluoresces when 2 target proteins interact to allow complementation of the mKG fragments. Using this assay system, the authors screened inhibitors for TCF7/beta-catenin, PAC1/PAC2, and PAC3 homodimer PPIs from 123,599 samples in their natural product library. Compound TB1 was identified as a specific inhibitor for PPI of PAC3 homodimer. TB1 strongly inhibited the PPI of PAC3 homodimer with an IC(50) value of 0.020 microM and did not inhibit PPI between TCF7/beta-catenin and PAC1/PAC2 even at a concentration of 250 microM. The authors thus demonstrated that this in vitro PCA system applicable to HTS in a 1536-well format is capable of screening for PPI inhibitors from a huge natural product library.

HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks.

PubMed

Hashemifar, Somaye; Xu, Jinbo

2014-09-01

High-throughput experimental techniques have produced a large amount of protein-protein interaction (PPI) data. The study of PPI networks, such as comparative analysis, shall benefit the understanding of life process and diseases at the molecular level. One way of comparative analysis is to align PPI networks to identify conserved or species-specific subnetwork motifs. A few methods have been developed for global PPI network alignment, but it still remains challenging in terms of both accuracy and efficiency. This paper presents a novel global network alignment algorithm, denoted as HubAlign, that makes use of both network topology and sequence homology information, based upon the observation that topologically important proteins in a PPI network usually are much more conserved and thus, more likely to be aligned. HubAlign uses a minimum-degree heuristic algorithm to estimate the topological and functional importance of a protein from the global network topology information. Then HubAlign aligns topologically important proteins first and gradually extends the alignment to the whole network. Extensive tests indicate that HubAlign greatly outperforms several popular methods in terms of both accuracy and efficiency, especially in detecting functionally similar proteins. HubAlign is available freely for non-commercial purposes at http://ttic.uchicago.edu/∼hashemifar/software/HubAlign.zip. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Identification of Modules in Protein-Protein Interaction Networks

NASA Astrophysics Data System (ADS)

Erten, Sinan; Koyutürk, Mehmet

In biological systems, most processes are carried out through orchestration of multiple interacting molecules. These interactions are often abstracted using network models. A key feature of cellular networks is their modularity, which contributes significantly to the robustness, as well as adaptability of biological systems. Therefore, modularization of cellular networks is likely to be useful in obtaining insights into the working principles of cellular systems, as well as building tractable models of cellular organization and dynamics. A common, high-throughput source of data on molecular interactions is in the form of physical interactions between proteins, which are organized into protein-protein interaction (PPI) networks. This chapter provides an overview on identification and analysis of functional modules in PPI networks, which has been an active area of research in the last decade.

Prediction of Protein-Protein Interaction Sites by Random Forest Algorithm with mRMR and IFS

PubMed Central

Li, Bi-Qing; Feng, Kai-Yan; Chen, Lei; Huang, Tao; Cai, Yu-Dong

2012-01-01

Prediction of protein-protein interaction (PPI) sites is one of the most challenging problems in computational biology. Although great progress has been made by employing various machine learning approaches with numerous characteristic features, the problem is still far from being solved. In this study, we developed a novel predictor based on Random Forest (RF) algorithm with the Minimum Redundancy Maximal Relevance (mRMR) method followed by incremental feature selection (IFS). We incorporated features of physicochemical/biochemical properties, sequence conservation, residual disorder, secondary structure and solvent accessibility. We also included five 3D structural features to predict protein-protein interaction sites and achieved an overall accuracy of 0.672997 and MCC of 0.347977. Feature analysis showed that 3D structural features such as Depth Index (DPX) and surface curvature (SC) contributed most to the prediction of protein-protein interaction sites. It was also shown via site-specific feature analysis that the features of individual residues from PPI sites contribute most to the determination of protein-protein interaction sites. It is anticipated that our prediction method will become a useful tool for identifying PPI sites, and that the feature analysis described in this paper will provide useful insights into the mechanisms of interaction. PMID:22937126

Detection of Protein Complexes Based on Penalized Matrix Decomposition in a Sparse Protein⁻Protein Interaction Network.

PubMed

Cao, Buwen; Deng, Shuguang; Qin, Hua; Ding, Pingjian; Chen, Shaopeng; Li, Guanghui

2018-06-15

High-throughput technology has generated large-scale protein interaction data, which is crucial in our understanding of biological organisms. Many complex identification algorithms have been developed to determine protein complexes. However, these methods are only suitable for dense protein interaction networks, because their capabilities decrease rapidly when applied to sparse protein⁻protein interaction (PPI) networks. In this study, based on penalized matrix decomposition ( PMD ), a novel method of penalized matrix decomposition for the identification of protein complexes (i.e., PMD pc ) was developed to detect protein complexes in the human protein interaction network. This method mainly consists of three steps. First, the adjacent matrix of the protein interaction network is normalized. Second, the normalized matrix is decomposed into three factor matrices. The PMD pc method can detect protein complexes in sparse PPI networks by imposing appropriate constraints on factor matrices. Finally, the results of our method are compared with those of other methods in human PPI network. Experimental results show that our method can not only outperform classical algorithms, such as CFinder, ClusterONE, RRW, HC-PIN, and PCE-FR, but can also achieve an ideal overall performance in terms of a composite score consisting of F-measure, accuracy (ACC), and the maximum matching ratio (MMR).

Enduring sensorimotor gating abnormalities following predator exposure or corticotropin-releasing factor in rats: a model for PTSD-like information-processing deficits?

PubMed

Bakshi, Vaishali P; Alsene, Karen M; Roseboom, Patrick H; Connors, Elenora E

2012-02-01

A deficit in prepulse inhibition (PPI) can be one of the clinically observed features of post-traumatic stress disorder (PTSD) that is seen long after the acute traumatic episode has terminated. Thus, reduced PPI may represent an enduring psychophysiological marker of this illness in some patients. PPI is an operational measure of sensorimotor gating and refers to the phenomenon in which a weak stimulus presented immediately before an intense startling stimulus inhibits the magnitude of the subsequent startle response. The effects of stress on PPI have been relatively understudied, and in particular, there is very little information on PPI effects of ethologically relevant psychological stressors. We aimed to develop a paradigm for evaluating stress-induced sensorimotor gating abnormalities by comparing the effects of a purely psychological stressor (predator exposure) to those of a nociceptive physical stressor (footshock) on PPI and baseline startle responses in rats over an extended period of time following stressor presentation. Male Sprague-Dawley rats were exposed (within a protective cage) to ferrets for 5 min or left in their homecage and then tested for PPI immediately, 24 h, 48 h, and 9 days after the exposure. The effects of footshock were evaluated in a separate set of rats. The effects seen with stressor presentation were compared to those elicited by corticotropin-releasing factor (CRF; 0.5 and 3 μg/6 μl, intracerebroventricularly). Finally, the effects of these stressors and CRF administration on plasma corticosterone were measured. PPI was disrupted 24 h after ferret exposure; in contrast, footshock failed to affect PPI at any time. CRF mimicked the predator stress profile, with the lowdose producing a PPI deficit 24 h after infusion. Interestingly, the high dose also produced a PPI deficit 24 h after infusion, but with this dose, the PPI deficit was evident even 9d later. Plasma corticosterone levels were elevated acutely (before PPI deficits emerged) by both stressors and CRF, but returned to normal control levels 24 h later, when PPI deficits were present. Thus, predator exposure produces a delayed disruption of PPI, and stimulation of CRF receptors recapitulates these effects. Contemporaneous HPA axis activation is neither necessary nor sufficient for these PPI deficits. These results indicate that predator exposure, perhaps acting through CRF, may model the delayed-onset and persistent sensorimotor gating abnormalities that have been observed clinically in PTSD, and that further studies using this model may shed insight on the mechanisms of information-processing deficits in this disorder. This article is part of a Special Issue entitled 'Post-Traumatic Stress Disorder'. Copyright © 2011 Elsevier Ltd. All rights reserved.

Computational analysis of protein-protein interfaces involving an alpha helix: insights for terphenyl-like molecules binding.

PubMed

Isvoran, Adriana; Craciun, Dana; Martiny, Virginie; Sperandio, Olivier; Miteva, Maria A

2013-06-14

Protein-Protein Interactions (PPIs) are key for many cellular processes. The characterization of PPI interfaces and the prediction of putative ligand binding sites and hot spot residues are essential to design efficient small-molecule modulators of PPI. Terphenyl and its derivatives are small organic molecules known to mimic one face of protein-binding alpha-helical peptides. In this work we focus on several PPIs mediated by alpha-helical peptides. We performed computational sequence- and structure-based analyses in order to evaluate several key physicochemical and surface properties of proteins known to interact with alpha-helical peptides and/or terphenyl and its derivatives. Sequence-based analysis revealed low sequence identity between some of the analyzed proteins binding alpha-helical peptides. Structure-based analysis was performed to calculate the volume, the fractal dimension roughness and the hydrophobicity of the binding regions. Besides the overall hydrophobic character of the binding pockets, some specificities were detected. We showed that the hydrophobicity is not uniformly distributed in different alpha-helix binding pockets that can help to identify key hydrophobic hot spots. The presence of hydrophobic cavities at the protein surface with a more complex shape than the entire protein surface seems to be an important property related to the ability of proteins to bind alpha-helical peptides and low molecular weight mimetics. Characterization of similarities and specificities of PPI binding sites can be helpful for further development of small molecules targeting alpha-helix binding proteins.

Impact of New-Onset Left Bundle Branch Block and Periprocedural Permanent Pacemaker Implantation on Clinical Outcomes in Patients Undergoing Transcatheter Aortic Valve Replacement: A Systematic Review and Meta-Analysis.

PubMed

Regueiro, Ander; Abdul-Jawad Altisent, Omar; Del Trigo, María; Campelo-Parada, Francisco; Puri, Rishi; Urena, Marina; Philippon, François; Rodés-Cabau, Josep

2016-05-01

Available data on the clinical impact of new-onset left bundle branch block (LBBB) and permanent pacemaker implantation (PPI) after transcatheter aortic valve replacement (TAVR) remains controversial. We aimed to evaluate the impact of (1) periprocedural new-onset LBBB or PPI post-TAVR on cardiac mortality and all-cause 1-year mortality and (2) new-onset LBBB on the need for PPI at 1-year follow-up. We performed a systematic search from PubMed and EMBASE databases for studies reporting raw data on new-onset LBBB post-TAVR and the need for PPI or mortality at 1-year follow-up, or on 1-year mortality according to the need for periprocedural PPI post-TAVR. Data from 17 studies, including 4756 patients (8 studies) and 7032 patients (11 studies) for the evaluation of the impact of new-onset LBBB and periprocedural PPI post-TAVR were sourced, respectively (with 2 studies used for both outcomes). New-onset LBBB post-TAVR was associated with a higher risk of PPI (risk ratio [RR], 2.18; 95% confidence interval [CI], 1.28-3.70) and cardiac death (RR, 1.39; 95% CI, 1.04-1.86) during follow-up, as well with a tendency toward an increase in all-cause mortality (RR, 1.21; 95% CI, 0.98-1.50). Periprocedural PPI post-TAVR was not associated with any increased risk of all-cause mortality at 1 year (RR, 1.03; 95% CI, 0.9-1.18), yet a tendency toward a protective effect on cardiac death was observed (RR, 0.78; 95% CI, 0.60-1.03). New-onset LBBB post-TAVR is a marker of an increased risk of cardiac death and need for PPI at 1-year follow-up. The need for PPI early post-TAVR did not increase the risk of death. © 2016 American Heart Association, Inc.

Behavioral and pharmacokinetic interactions between monoamine oxidase inhibitors and the hallucinogen 5-methoxy-N,N-dimethyltryptamine.

PubMed

Halberstadt, Adam L

2016-04-01

Monoamine oxidase inhibitors (MAOIs) are often ingested together with tryptamine hallucinogens, but relatively little is known about the consequences of their combined use. We have shown previously that monoamine oxidase-A (MAO-A) inhibitors alter the locomotor profile of the hallucinogen 5-methoxy-N,N-dimethyltryptamine (5-MeO-DMT) in rats, and enhance its interaction with 5-HT2A receptors. The goal of the present studies was to investigate the mechanism for the interaction between 5-MeO-DMT and MAOIs, and to determine whether other behavioral responses to 5-MeO-DMT are similarly affected. Hallucinogens disrupt prepulse inhibition (PPI) in rats, an effect typically mediated by 5-HT2A activation. 5-MeO-DMT also disrupts PPI but the effect is primarily attributable to 5-HT1A activation. The present studies examined whether an MAOI can alter the respective contributions of 5-HT1A and 5-HT2A receptors to the effects of 5-MeO-DMT on PPI. A series of interaction studies using the 5-HT1A antagonist WAY-100,635 and the 5-HT2A antagonist MDL 11,939 were performed to assess the respective contributions of these receptors to the behavioral effects of 5-MeO-DMT in rats pretreated with an MAOI. The effects of MAO-A inhibition on the pharmacokinetics of 5-MeO-DMT and its metabolism to bufotenine were assessed using liquid chromatography-electrospray ionization-selective reaction monitoring-tandem mass spectrometry (LC-ESI-SRM-MS/MS). 5-MeO-DMT (1mg/kg) had no effect on PPI when tested 45-min post-injection but disrupted PPI in animals pretreated with the MAO-A inhibitor clorgyline or the MAO-A/B inhibitor pargyline. The combined effect of 5-MeO-DMT and pargyline on PPI was antagonized by pretreatment with either WAY-100,635 or MDL 11,939. Inhibition of MAO-A increased the level of 5-MeO-DMT in plasma and whole brain, but had no effect on the conversion of 5-MeO-DMT to bufotenine, which was found to be negligible. The present results confirm that 5-MeO-DMT can disrupt PPI by activating 5-HT2A, and indicate that MAOIs alter 5-MeO-DMT pharmacodynamics by increasing its accumulation in the central nervous system. Copyright © 2016 Elsevier Inc. All rights reserved.

Identification of potential crucial genes associated with steroid-induced necrosis of femoral head based on gene expression profile.

PubMed

Lin, Zhe; Lin, Yongsheng

2017-09-05

The aim of this study was to explore potential crucial genes associated with the steroid-induced necrosis of femoral head (SINFH) and to provide valid biological information for further investigation of SINFH. Gene expression profile of GSE26316, generated from 3 SINFH rat samples and 3 normal rat samples were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified using LIMMA package. After functional enrichment analyses of DEGs, protein-protein interaction (PPI) network and sub-PPI network analyses were conducted based on the STRING database and cytoscape. In total, 59 up-regulated DEGs and 156 downregulated DEGs were identified. The up-regulated DEGs were mainly involved in functions about immunity (e.g. Fcer1A and Il7R), and the downregulated DEGs were mainly enriched in muscle system process (e.g. Tnni2, Mylpf and Myl1). The PPI network of DEGs consisted of 123 nodes and 300 interactions. Tnni2, Mylpf, and Myl1 were the top 3 outstanding genes based on both subgraph centrality and degree centrality evaluation. These three genes interacted with each other in the network. Furthermore, the significant network module was composed of 22 downregulated genes (e.g. Tnni2, Mylpf and Myl1). These genes were mainly enriched in functions like muscle system process. The DEGs related to the regulation of immune system process (e.g. Fcer1A and Il7R), and DEGs correlated with muscle system process (e.g. Tnni2, Mylpf and Myl1) may be closely associated with the progress of SINFH, which is still needed to be confirmed by experiments. Copyright © 2017 Elsevier B.V. All rights reserved.

Demonstration of protein-fragment complementation assay using purified firefly luciferase fragments

PubMed Central

2013-01-01

Background Human interactome is predicted to contain 150,000 to 300,000 protein-protein interactions, (PPIs). Protein-fragment complementation assay (PCA) is one of the most widely used methods to detect PPI, as well as Förster resonance energy transfer (FRET). To date, successful applications of firefly luciferase (Fluc)-based PCA have been reported in vivo, in cultured cells and in cell-free lysate, owing to its high sensitivity, high signal-to-background (S/B) ratio, and reversible response. Here we show the assay also works with purified proteins with unexpectedly rapid kinetics. Results Split Fluc fragments both fused with a rapamycin-dependently interacting protein pair were made and expressed in E. coli system, and purified to homogeneity. When the proteins were used for PCA to detect rapamycin-dependent PPI, they enabled a rapid detection (~1 s) of PPI with high S/B ratio. When Fn7-8 domains (7 nm in length) that was shown to abrogate GFP mutant-based FRET was inserted between split Fluc and FKBP12 as a rigid linker, it still showed some response, suggesting less limitation in interacting partner’s size. Finally, the stability of the probe was investigated. Preincubation of the probes at 37 degreeC up to 1 h showed marked decrease of the luminescent signal to 1.5%, showing the limited stability of this system. Conclusion Fluc PCA using purified components will enable a rapid and handy detection of PPIs with high S/B ratio, avoiding the effects of concomitant components. Although the system might not be suitable for large-scale screening due to its limited stability, it can detect an interaction over larger distance than by FRET. This would be the first demonstration of Fluc PCA in vitro, which has a distinct advantage over other PPI assays. Our system enables detection of direct PPIs without risk of perturbation by PPI mediators in the complex cellular milieu. PMID:23536995

Increased proximal reflux in a hypersensitive esophagus might explain symptoms resistant to proton pump inhibitors in patients with gastroesophageal reflux disease.

PubMed

Rohof, Wout O; Bennink, Roelof J; de Jonge, Hugo; Boeckxstaens, Guy E

2014-10-01

Approximately 30% of patients with gastroesophageal reflux disease have symptoms resistant to treatment with proton pump inhibitors (PPIs). Several mechanisms such as esophageal hypersensitivity, increased mucosal permeability, and possibly the position of the gastric acid pocket might underlie a partial response to PPIs. To what extent these mechanisms interact and contribute to PPI-resistant symptoms, however, has not been investigated previously. In 18 gastroesophageal reflux disease patients (9 PPI responders and 9 PPI partial responders), esophageal sensitivity, mucosal permeability, and postprandial reflux parameters were determined during PPI use. Esophageal sensitivity for distension was measured by gradual balloon inflation at 5 and 15 cm above the lower esophageal sphincter. The mucosal permeability of 4 esophageal biopsy specimens per patient was determined in Ussing chambers by measuring the transepithelial electrical resistance and transmucosal flux of fluorescein. Postprandial reflux parameters were determined using concurrent high-resolution manometry/pH impedance after a standardized meal. In addition, the acid pocket was visualized using scintigraphy. No difference in the rate of postprandial acid reflux, in the pH of the acid pocket (PPI responders 3.7 ± 0.7 vs PPI partial responders 4.2 ± 0.4; P = .54), or in the position of the acid pocket was observed in PPI partial responders compared with PPI responders. In addition, the permeability of the esophageal mucosa was similar in both groups, as shown by a similar transepithelial electrical resistance and flux of fluorescein. PPI partial responders had more reflux episodes with a higher mean proximal extent, compared with PPI responders, and were more sensitive to balloon distension, both in the upper and lower esophagus. PPI-resistant symptoms most likely are explained by increased proximal reflux in a hypersensitive esophagus and less likely by increased mucosal permeability or the position of the acid pocket. Copyright © 2014 AGA Institute. Published by Elsevier Inc. All rights reserved.

T36. THE ANTIPSYCHOTIC-LIKE PROPERTIES OF EVENAMIDE (NW-3509) REFLECT THE MODULATION OF GLUTAMATERGIC DYSREGULATION

PubMed Central

Bortolato, Marco; Faravelli, Laura; Anand, Ravi

2018-01-01

Abstract Background The lack of adequate benefit with current 5HT2 / D2 antipsychotics in large proportions of schizophrenic patients suggests it is essential to modulate other mechanisms for improving symptoms of schizophrenia (SCZ). Increasing evidence implicates NMDAr hypofunction, and hippocampal hyperactivity, in the dysregulation not only of mesolimbic DA neurons but also of Glu neurons, leading to increasing synaptic activity of Glu in the PFC. Injection of NMDAr antagonists (PCP, ketamine) at doses that produce psychotomimetic effects lead to a downstream increase of Glu neurotransmission at non-NMDAr. The excessive firing and the hyper-glutamatergic tone represent alternative targets of treatment for SCZ ultimately affecting positive, negative, cognitive symptoms. The addition of Glu release inhibitors may augment the benefits of the antipsychotics in patients showing inadequate response. Evenamide uniquely does not interact with monoaminergic (DA, 5-HT, NA, H) pathways affected by current antipsychotics, or with more than 130 different targets that are involved in CNS activity, except sodium channels. Preclinical data suggests that by the modulation of the firing abnormalities, evenamide normalizes the aberrant spread of Glu excitatory transmission that occurs in the brains of patients with SCZ. Evenamide showed efficacy in animal models relevant to SCZ (sensory motor gating, mania, psychosis, depression, impulse control, cognition, social interaction), in monotherapy and as an add on to first or second generation antipsychotics irrespective of whether impairment was either spontaneous, induced by amphetamine or NMDAr antagonists or stress. Evenamide, has also shown significant benefit in a p.c phase 2 trial as an add-on to risperidone and aripiprazole in patients worsening on dopaminergic/serotoninergic antagonist medication, suggesting it acts through other mechanisms. New animal data further confirm evenamide’s activity in reducing SCZ symptoms provoked by Glu alteration. Methods Effects of evenamide (EVE 1.25, 5, 15 mg/kg PO) to restore the impaired information processing (a deficit observed in SCZ), were evaluated in the rat model of the Pre-Pulse Inhibition (PPI) deficit induced by injection of the NMDAr antagonist ketamine (KET 6 mg/kg, SC). Clozapine (CLO 7.5 mg/kg, IP) was used as a positive control. Results PPI analysis showed significant main effects for KET to lower PPI levels [F(1,264)=139.67, P<0.0001], for EVE [F(3,264)=3.14, P<0.05] and CLO to enhance PPI levels [F(1,98)=30.89, P<0.001]. Notably, significant EVE x KET [F(3,264)=2.79, P<0.05] and CLO x KET interactions [F(1,98)=5.45, P<0.05] were found. Post-hoc analyses (Tukey’s) revealed that KET significantly lowered PPI (P<0.0001) for each group; both EVE (5 mg/kg) and CLO significantly increased PPI in KET-treated rats (P=0.02; p<0.001). Discussion Evenamide as monotherapy has similar effect to clozapine in reversing ketamine- induced worsening of PPI. Together with previously demonstrated effects to reverse PCP-induced PPI and social interaction deficits, this further supports its potential to affect both positive and negative symptoms of SCZ by targeting altered Glu transmission. Efficacy of evenamide as an add-on to antipsychotics would revolutionize development of novel antipsychotics that would target aberrant firing and Glu transmission in SCZ. Two clinical trials have been planned to support the hypothesis that the addition of evenamide should add a non-dopaminergic mechanism for augmenting antipsychotic efficacy in patients who are not responding adequately to current antipsychotic, and in patients with treatment resistant SCZ who are not responding/worsening on clozapine.

From protein-protein interactions to protein co-expression networks: a new perspective to evaluate large-scale proteomic data.

PubMed

Vella, Danila; Zoppis, Italo; Mauri, Giancarlo; Mauri, Pierluigi; Di Silvestre, Dario

2017-12-01

The reductionist approach of dissecting biological systems into their constituents has been successful in the first stage of the molecular biology to elucidate the chemical basis of several biological processes. This knowledge helped biologists to understand the complexity of the biological systems evidencing that most biological functions do not arise from individual molecules; thus, realizing that the emergent properties of the biological systems cannot be explained or be predicted by investigating individual molecules without taking into consideration their relations. Thanks to the improvement of the current -omics technologies and the increasing understanding of the molecular relationships, even more studies are evaluating the biological systems through approaches based on graph theory. Genomic and proteomic data are often combined with protein-protein interaction (PPI) networks whose structure is routinely analyzed by algorithms and tools to characterize hubs/bottlenecks and topological, functional, and disease modules. On the other hand, co-expression networks represent a complementary procedure that give the opportunity to evaluate at system level including organisms that lack information on PPIs. Based on these premises, we introduce the reader to the PPI and to the co-expression networks, including aspects of reconstruction and analysis. In particular, the new idea to evaluate large-scale proteomic data by means of co-expression networks will be discussed presenting some examples of application. Their use to infer biological knowledge will be shown, and a special attention will be devoted to the topological and module analysis.

Proton Pump Inhibitor Use and Magnesium Concentrations in Hemodialysis Patients: A Cross-Sectional Study

PubMed Central

Nakashima, Akio; Ohkido, Ichiro; Yokoyama, Keitaro; Mafune, Aki; Urashima, Mitsuyoshi; Yokoo, Takashi

2015-01-01

Magnesium concentration is a proven predictor of mortality in hemodialysis patients. Recent reports have indicated that proton pump inhibitor (PPI) use affects serum magnesium levels, however few studies have investigated the relationship between PPI use and magnesium levels in hemodialysis patients. This study aimed to clarify the association between PPI use and serum magnesium levels in hemodialysis patients. We designed this cross sectional study and included 1189 hemodialysis patients in stable condition. Associations between PPI and magnesium-related factors, as well as other possible confounders, were evaluated using a multiple regression model. We defined hypomagnesemia as a value < 2.0 mg/dL, and created comparable logistic regression models to assess the association between PPI use and hypomagnesemia. PPI use is associated with a significantly lower mean serum magnesium level than histamine 2 (H2) receptor antagonists or no acid-suppressive medications (mean [SD] PPI: 2.52 [0.45] mg/dL; H2 receptor antagonist: 2.68 [0.41] mg/dL; no acid suppressive medications: 2.68 [0.46] mg/dL; P = 0.001). Hypomagnesemia remained significantly associated with PPI (adjusted OR, OR: 2.05; 95% CI: 1.14–3.69; P = 0.017). PPI use is associated with an increased risk of hypomagnesemia in hemodialysis patients. Future prospective studies are needed to explore magnesium replacement in PPI users on hemodialysis. PMID:26618538

Clopidogrel and proton pump inhibitors - where do we stand in 2012?

PubMed Central

Drepper, Michael D; Spahr, Laurent; Frossard, Jean Louis

2012-01-01

Clopidogrel in association with aspirine is considered state of the art of medical treatment for acute coronary syndrome by reducing the risk of new ischemic events. Concomitant treatment with proton pump inhibitors in order to prevent gastrointestinal side effects is recommended by clinical guidelines. Clopidogrel needs metabolic activation predominantly by the hepatic cytochrome P450 isoenzyme Cytochrome 2C19 (CYP2C19) and proton pump inhibitors (PPIs) are extensively metabolized by the CYP2C19 isoenzyme as well. Several pharmacodynamic studies investigating a potential clopidogrel-PPI interaction found a significant decrease of the clopidogrel platelet antiaggregation effect for omeprazole, but not for pantoprazole. Initial clinical cohort studies in 2009 reported an increased risk for adverse cardiovascular events, when under clopidogrel and PPI treatment at the same time. These observations led the United States Food and Drug Administration and the European Medecines Agency to discourage the combination of clopidogrel and PPI (especially omeprazole) in the same year. In contrast, more recent retrospective cohort studies including propensity score matching and the only existing randomized trial have not shown any difference concerning adverse cardiovascular events when concomitantly on clopidogrel and PPI or only on clopidogrel. Three meta-analyses report an inverse correlation between clopidogrel-PPI interaction and study quality, with high and moderate quality studies not reporting any association, rising concern about unmeasured confounders biasing the low quality studies. Thus, no definite evidence exists for an effect on mortality. Because PPI induced risk reduction clearly overweighs the possible adverse cardiovascular risk in patients with high risk of gastrointestinal bleeding, combination of clopidogrel with the less CYP2C19 inhibiting pantoprazole should be recommended. PMID:22611308

Control of intramolecular π-π stacking interaction in cationic iridium complexes via fluorination of pendant phenyl rings.

PubMed

He, Lei; Ma, Dongxin; Duan, Lian; Wei, Yongge; Qiao, Juan; Zhang, Deqiang; Dong, Guifang; Wang, Liduo; Qiu, Yong

2012-04-16

Intramolecular π-π stacking interaction in one kind of phosphorescent cationic iridium complexes has been controlled through fluorination of the pendant phenyl rings on the ancillary ligands. Two blue-green-emitting cationic iridium complexes, [Ir(ppy)(2)(F2phpzpy)]PF(6) (2) and [Ir(ppy)(2)(F5phpzpy)]PF(6) (3), with the pendant phenyl rings on the ancillary ligands substituted with two and five fluorine atoms, respectively, have been synthesized and compared to the parent complex, [Ir(ppy)(2)(phpzpy)]PF(6) (1). Here Hppy is 2-phenylpyridine, F2phpzpy is 2-(1-(3,5-difluorophenyl)-1H-pyrazol-3-yl)pyridine, F5phpzpy is 2-(1-pentafluorophenyl-1H-pyrazol-3-yl)-pyridine, and phpzpy is 2-(1-phenyl-1H-pyrazol-3-yl)pyridine. Single crystal structures reveal that the pendant phenyl rings on the ancillary ligands stack to the phenyl rings of the ppy ligands, with dihedral angles of 21°, 18°, and 5.0° between least-squares planes for complexes 1, 2, and 3, respectively, and centroid-centroid distances of 3.75, 3.65, and 3.52 Å for complexes 1, 2, and 3, respectively, indicating progressively reinforced intramolecular π-π stacking interactions from complexes 1 to 2 and 3. Compared to complex 1, complex 3 with a significantly reinforced intramolecular face-to-face π-π stacking interaction exhibits a significantly enhanced (by 1 order of magnitude) photoluminescent efficiency in solution. Theoretical calculations reveal that in complex 3 it is unfavorable in energy for the pentafluorophenyl ring to swing by a large degree and the intramolecular π-π stacking interaction remains on the lowest triplet state. © 2012 American Chemical Society

Recent Coselection in Human Populations Revealed by Protein–Protein Interaction Network

PubMed Central

Qian, Wei; Zhou, Hang; Tang, Kun

2015-01-01

Genome-wide scans for signals of natural selection in human populations have identified a large number of candidate loci that underlie local adaptations. This is surprising given the relatively short evolutionary time since the divergence of the human population. One hypothesis that has not been formally examined is whether and how the recent human evolution may have been shaped by coselection in the context of complex molecular interactome. In this study, genome-wide signals of selection were scanned in East Asians, Europeans, and Africans using 1000 Genome data, and subsequently mapped onto the protein–protein interaction (PPI) network. We found that the candidate genes of recent positive selection localized significantly closer to each other on the PPI network than expected, revealing substantial clustering of selected genes. Furthermore, gene pairs of shorter PPI network distances showed higher similarities of their recent evolutionary paths than those further apart. Last, subnetworks enriched with recent coselection signals were identified, which are substantially overrepresented in biological pathways related to signal transduction, neurogenesis, and immune function. These results provide the first genome-wide evidence for association of recent selection signals with the PPI network, shedding light on the potential mechanisms of recent coselection in the human genome. PMID:25532814

Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions.

PubMed

Zhou, Hufeng; Gao, Shangzhi; Nguyen, Nam Ninh; Fan, Mengyuan; Jin, Jingjing; Liu, Bing; Zhao, Liang; Xiong, Geng; Tan, Min; Li, Shijun; Wong, Limsoon

2014-04-08

H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are essential for understanding the infection mechanism of the formidable pathogen M. tuberculosis H37Rv. Computational prediction is an important strategy to fill the gap in experimental H. sapiens-M. tuberculosis H37Rv PPI data. Homology-based prediction is frequently used in predicting both intra-species and inter-species PPIs. However, some limitations are not properly resolved in several published works that predict eukaryote-prokaryote inter-species PPIs using intra-species template PPIs. We develop a stringent homology-based prediction approach by taking into account (i) differences between eukaryotic and prokaryotic proteins and (ii) differences between inter-species and intra-species PPI interfaces. We compare our stringent homology-based approach to a conventional homology-based approach for predicting host-pathogen PPIs, based on cellular compartment distribution analysis, disease gene list enrichment analysis, pathway enrichment analysis and functional category enrichment analysis. These analyses support the validity of our prediction result, and clearly show that our approach has better performance in predicting H. sapiens-M. tuberculosis H37Rv PPIs. Using our stringent homology-based approach, we have predicted a set of highly plausible H. sapiens-M. tuberculosis H37Rv PPIs which might be useful for many of related studies. Based on our analysis of the H. sapiens-M. tuberculosis H37Rv PPI network predicted by our stringent homology-based approach, we have discovered several interesting properties which are reported here for the first time. We find that both host proteins and pathogen proteins involved in the host-pathogen PPIs tend to be hubs in their own intra-species PPI network. Also, both host and pathogen proteins involved in host-pathogen PPIs tend to have longer primary sequence, tend to have more domains, tend to be more hydrophilic, etc. And the protein domains from both host and pathogen proteins involved in host-pathogen PPIs tend to have lower charge, and tend to be more hydrophilic. Our stringent homology-based prediction approach provides a better strategy in predicting PPIs between eukaryotic hosts and prokaryotic pathogens than a conventional homology-based approach. The properties we have observed from the predicted H. sapiens-M. tuberculosis H37Rv PPI network are useful for understanding inter-species host-pathogen PPI networks and provide novel insights for host-pathogen interaction studies.

Electrochemical direct immobilization of DNA sequences for label-free herpes virus detection

NASA Astrophysics Data System (ADS)

Tam, Phuong Dinh; Trung, Tran; Tuan, Mai Anh; Chien, Nguyen Duc

2009-09-01

DNA sequences/bio-macromolecules of herpes virus (5'-AT CAC CGA CCC GGA GAG GGA C-3') were directly immobilized into polypyrrole matrix by using the cyclic voltammetry method, and grafted onto arrays of interdigitated platinum microelectrodes. The morphology surface of the obtained PPy/DNA of herpes virus composite films was investigated by a FESEM Hitachi-S 4800. Fourier transform infrared spectroscopy (FTIR) was used to characterize the PPy/DNA film and to study the specific interactions that may exist between DNA biomacromolecules and PPy chains. Attempts are made to use these PPy/DNA composite films for label-free herpes virus detection revealed a response time of 60 s in solutions containing as low as 2 nM DNA concentration, and self life of six months when immerged in double distilled water and kept refrigerated.

A comparison of the psychometric properties of the psychopathic personality inventory full-length and short-form versions.

PubMed

Kastner, Rebecca M; Sellbom, Martin; Lilienfeld, Scott O

2012-03-01

The Psychopathic Personality Inventory (PPI) has shown promising construct validity as a measure of psychopathy. Because of its relative efficiency, a short-form version of the PPI (PPI-SF) was developed and has proven useful in many psychopathy studies. The validity of the PPI-SF, however, has not been thoroughly examined, and no studies have directly compared the validity of the short form with that of the full-length version. The current study was designed to compare the psychometric properties of both PPI versions, with an emphasis on convergent and discriminant validity in predicting external criteria conceptually relevant to psychopathy. We used both prison (n = 558) and college samples (n = 322) for this investigation. PPI scale scores were more reliable and more strongly correlated with the conceptually relevant criterion measures compared with the PPI-SF, particularly in the prison sample. There were no differences in relative discriminant validity. Thus, overall, the PPI full-length version showed more evidence of construct validity than did the short form, and the consequences of this psychometric difference should be considered when evaluating the clinical utility of each measure.

Poly(4-vinylphenylboronic acid) functionalized polypyrrole/graphene oxide nanosheets for simultaneous electrochemical determination of catechol and hydroquinone

NASA Astrophysics Data System (ADS)

Mao, Hui; Liu, Meihong; Cao, Zhenqian; Ji, Chunguang; Sun, Ying; Liu, Daliang; Wu, Shuyao; Zhang, Yu; Song, Xi-Ming

2017-10-01

Novel poly(4-vinylphenylboronic acid) (P4VPBA) functionalized polypyrrole/graphene oxide (PPy/GO) nanosheets, which combined the advantages of GO, PPy and PBA groups, were successfully prepared by a simple polymerization of 4-vinylphenylboronic acid (4VPBA) on the surface of pre-treated PPy/GO containing vinyl groups. Because of the synergistic effects of GO with excellent 2D structures and large surface area, PPy with good electronic conductivity and PBA with high recognition capability, P4VPBA/PPy/GO modified glassy carbon electrode presented excellent electrochemical sensing capabilities toward catechol (CC) and hydroquinone (HQ) with good stability, high sensitivity and selectivity, especially giving a large anodic peak potential difference between CC and HQ enough to well distinguish and simultaneously determine the two dihydroxybenzene isomers in their mixture. It is found that PBA groups on the surface of P4VPBA/PPy/GO nanosheets played an essential role for the discrimination and simultaneous electrochemical determination of CC and HQ, which may be due to the selective formation of stable cyclic esters by the covalent interaction between PBA groups and related molecules with a cis-diol in an alkaline aqueous solution. Therefore, P4VPBA/PPy/GO nanosheets can act as a good electrode material for building a steady electrochemical sensor for detecting the two dihydroxybenzene isomers with high sensitivity and selectivity.

Multiple kernel learning in protein-protein interaction extraction from biomedical literature.

PubMed

Yang, Zhihao; Tang, Nan; Zhang, Xiao; Lin, Hongfei; Li, Yanpeng; Yang, Zhiwei

2011-03-01

Knowledge about protein-protein interactions (PPIs) unveils the molecular mechanisms of biological processes. The volume and content of published biomedical literature on protein interactions is expanding rapidly, making it increasingly difficult for interaction database administrators, responsible for content input and maintenance to detect and manually update protein interaction information. The objective of this work is to develop an effective approach to automatic extraction of PPI information from biomedical literature. We present a weighted multiple kernel learning-based approach for automatic PPI extraction from biomedical literature. The approach combines the following kernels: feature-based, tree, graph and part-of-speech (POS) path. In particular, we extend the shortest path-enclosed tree (SPT) and dependency path tree to capture richer contextual information. Our experimental results show that the combination of SPT and dependency path tree extensions contributes to the improvement of performance by almost 0.7 percentage units in F-score and 2 percentage units in area under the receiver operating characteristics curve (AUC). Combining two or more appropriately weighed individual will further improve the performance. Both on the individual corpus and cross-corpus evaluation our combined kernel can achieve state-of-the-art performance with respect to comparable evaluations, with 64.41% F-score and 88.46% AUC on the AImed corpus. As different kernels calculate the similarity between two sentences from different aspects. Our combined kernel can reduce the risk of missing important features. More specifically, we use a weighted linear combination of individual kernels instead of assigning the same weight to each individual kernel, thus allowing the introduction of each kernel to incrementally contribute to the performance improvement. In addition, SPT and dependency path tree extensions can improve the performance by including richer context information. Copyright © 2010 Elsevier B.V. All rights reserved.

Rhizoma Dioscoreae extract protects against alveolar bone loss by regulating the cell cycle: A predictive study based on the protein‑protein interaction network.

PubMed

Zhang, Zhi-Guo; Song, Chang-Heng; Zhang, Fang-Zhen; Chen, Yan-Jing; Xiang, Li-Hua; Xiao, Gary Guishan; Ju, Da-Hong

2016-06-01

Rhizoma Dioscoreae extract (RDE) exhibits a protective effect on alveolar bone loss in ovariectomized (OVX) rats. The aim of this study was to predict the pathways or targets that are regulated by RDE, by re‑assessing our previously reported data and conducting a protein‑protein interaction (PPI) network analysis. In total, 383 differentially expressed genes (≥3‑fold) between alveolar bone samples from the RDE and OVX group rats were identified, and a PPI network was constructed based on these genes. Furthermore, four molecular clusters (A‑D) in the PPI network with the smallest P‑values were detected by molecular complex detection (MCODE) algorithm. Using Database for Annotation, Visualization and Integrated Discovery (DAVID) and Ingenuity Pathway Analysis (IPA) tools, two molecular clusters (A and B) were enriched for biological process in Gene Ontology (GO). Only cluster A was associated with biological pathways in the IPA database. GO and pathway analysis results showed that cluster A, associated with cell cycle regulation, was the most important molecular cluster in the PPI network. In addition, cyclin‑dependent kinase 1 (CDK1) may be a key molecule achieving the cell‑cycle‑regulatory function of cluster A. From the PPI network analysis, it was predicted that delayed cell cycle progression in excessive alveolar bone remodeling via downregulation of CDK1 may be another mechanism underling the anti‑osteopenic effect of RDE on alveolar bone.

Context-based retrieval of functional modules in protein-protein interaction networks.

PubMed

Dobay, Maria Pamela; Stertz, Silke; Delorenzi, Mauro

2017-03-27

Various techniques have been developed for identifying the most probable interactants of a protein under a given biological context. In this article, we dissect the effects of the choice of the protein-protein interaction network (PPI) and the manipulation of PPI settings on the network neighborhood of the influenza A virus (IAV) network, as well as hits in genome-wide small interfering RNA screen results for IAV host factors. We investigate the potential of context filtering, which uses text mining evidence linked to PPI edges, as a complement to the edge confidence scores typically provided in PPIs for filtering, for obtaining more biologically relevant network neighborhoods. Here, we estimate the maximum performance of context filtering to isolate a Kyoto Encyclopedia of Genes and Genomes (KEGG) network Ki from a union of KEGG networks and its network neighborhood. The work gives insights on the use of human PPIs in network neighborhood approaches for functional inference. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Insight into the fundamental interactions between LEDGF binding site inhibitors and integrase combining docking and molecular dynamics simulations.

PubMed

De Luca, Laura; Morreale, Francesca; Chimirri, Alba

2012-12-21

In recent years, HIV-1 integrase (IN) has emerged as an attractive target for novel anti-AIDS agents. In particular, nonactive-site-binding IN inhibitors would display synergy with current strand-transfer-specific IN inhibitors and other antiretroviral drugs in clinical use. An effective allosteric inhibitory approach would be the disruption of protein-protein interaction (PPI) between IN and cellular cofactors, such as LEDGF/p75. To date, several small molecules have been reported to be inhibitors of the PPI between IN and LEDGF/p75. In this study, we investigated the most relevant interactions between five selected PPI inhibitors and IN comparing them to the naturally occurring IN-LEDGF/p75 complex. We calculated the binding free energies by using the method of molecular mechanics-generalized Born surface area (MM-GBSA). Total energy was decomposed on per residue contribution, and hydrogen bond occupancies were monitored throughout the simulations. Considering all these results we obtained a good correlation with experimental activity and useful insights for the development of new inhibitors.

Enhanced magnetic performance of metal-organic nanowire arrays by FeCo/polypyrrole co-electrodeposition

NASA Astrophysics Data System (ADS)

Luo, X. J.; Xia, W. B.; Gao, J. L.; Zhang, S. Y.; Li, Y. L.; Tang, S. L.; Du, Y. W.

2013-05-01

FeCo/polypyrrole (PPy) composite nanowire array, which shows enhanced magnetic remanence and coercivity along the nanowires, was fabricated by AC electrodeposition using anodic aluminum oxide templates. High resolution transmission electron microscopy shows that PPy grows on the surface of FeCo nanowires forming a coaxial nanowire structure, with a coating layer of about 4 nm. It suggests that the decreased dipolar interaction due to the reduced nanowire diameters is responsible for the enhancement of magnetic performance. The possible mechanism of this coating may be that PPy is inclined to nucleate along the pore wall of the templates.

Impact of constitutional isomers of (BMes(2))phenylpyridine on structure, stability, phosphorescence, and Lewis acidity of mononuclear and dinuclear Pt(II) complexes.

PubMed

Rao, Ying-Li; Wang, Suning

2009-08-17

The impact of two constitutional isomers, 2-(4-BMes(2)-Ph)-pyridine (p-B-ppy, 1) and 5-BMes(2)-2-ph-pyridine (p-ppy-B, 2), as N,C-chelate ligands on the structures, stabilities, electronic and photophysical properties, and Lewis acidities of Pt(II) complexes has been investigated. Six Pt(II) complexes, Pt(p-B-ppy)Ph(DMSO) (1a), Pt(p-B-ppy)Ph(py) (1b), [Pt(p-B-ppy)Ph](2)(4,4'-bipy) (1c), Pt(p-ppy-B)Ph(DMSO) (2a), Pt(p-ppy-B)Ph(py) (2b), and [Pt(p-ppy-B)Ph](2)(4,4'-bipy) (2c), have been synthesized and fully characterized. The structures of 1a, 1c, 2a, and 2c were established by single-crystal X-ray diffraction analysis. All complexes adopt a cis geometry with the phenyl ligand being cis to the phenyl ring of the ppy chelate. The dinuclear complexes 2a and 2c were found to exist in two isomeric forms in solution, syn and anti, with respect to the relative orientation of the two BMes(2) groups in the molecule. While all complexes are stable in solution under ambient air, compound 2a was found to react with H(2)O slowly in solution and form complex 2a-OH, where one of the mesityl groups on the boron center was replaced by an OH group. This instability of 2a is attributed to an internal dimethylsulfoxide-directed hydrolysis process via hydrogen bonds. The electron-accepting ability of the free ligands and the complexes were examined by cyclic voltammetry, establishing that, for p-ppy-B, Pt(II) chelation enhances the electron-accepting ability while, for p-B-ppy, Pt(II) chelation has little impact. All Pt(II) complexes display oxygen-sensitive phosphorescence in solution at ambient temperature, dominated by B-ppy or ppy-B centered pi --> pi* transitions. The Lewis acidity of the complexes was examined by fluoride titration experiments using UV-vis, phosphorescence, and NMR spectroscopic methods, establishing that the p-ppy-B complexes have similar and strong binding constants while the p-B-ppy complexes have a much lower affinity toward F(-), compared to the free ligands. In the dinuclear complexes, weak electronic communication between the two Pt(II) units is evident in 1c but absent in 2c, attributable to the different steric interactions in the two molecules.

The effect of proton pump inhibitors on the CYP2C19 enzyme activity evaluated by the pantoprazole-13C breath test in GERD patients: clinical relevance for personalized medicine.

PubMed

Modak, Anil S; Klyarytska, Iryna; Kriviy, Valerij; Tsapyak, Tatjana; Rabotyagova, Yliya

2016-12-17

Patients with gastroesophageal reflux disease (GERD) are routinely prescribed one of the six FDA approved proton pump inhibitors (PPI). All of these PPI are inhibitors of CYP2C19 enzyme to varying degrees. The phenotype pantoprazole- 13 C breath test (Ptz-BT) was used to identify patients who are poor metabolizers (PM) and the extent of phenoconversion of CYP2C19 enzyme activity caused by four PPI (omeprazole, esomprazole pantoprazole and rabeprazole) in 54 newly diagnosed GERD patients prior to initiating randomly selected PPI therapy and 30 d after PPI therapy. The phenoconversion after 30 d of PPI therapy in GERD patients was statistically significant (p  =0.001) with omeprazole/esomeprazole (n  =  27) strong CYP2C19 inhibitors, while there was no change in CYP2C19 enzyme activity (p  =  0.8) with pantoprazole/ rabeprazole (n  =  27), weak CYP2C19 inhibitors. The concommitant use of omeprazole/esomeprazole, therefore, could have critical clinical relevance in individualizing medications metabolized primarily by CYP2C19 such as PPI, clopidogrel, phenytoin, cyclophosphamide, thalidomide, citalopram, clonazepam, diazepam, proguanil, tivantinib etc. The rapid (30 min), in vivo, and non-invasive phenotype Ptz-BT can evaluate CYP2C19 enzyme activity. More importantly, it can identify GERD patients with low CYP2C19 enzyme activity (PM), caused by PPI or other concomitant medications, who would benefit from dose adjustments to maintain efficacy and avoid toxicity. The existing CYP2C19 genotype tests cannot predict the phenotype nor can it detect phenoconversion due to non genetic factors.

Further Characterization of the Predictive Validity of the Brattleboro Rat Model for Antipsychotic Efficacy

PubMed Central

Feifel, D.; Shilling, P. D.; Melendez, G.

2014-01-01

Our laboratory and others have reported that Brattleboro (BRAT) rats, a Long Evans (LE) strain with a single gene mutation, have inherent deficits in prepulse inhibition (PPI) homologous to those observed in schizophrenia patients and that these deficits are reversed by antipsychotic drugs (APDs). To further evaluate the potential predictive validity of BRAT rat PPI for APDs, we compared the effects of acute subcutaneous administration of the typical APD chlorpromazine to that of three psychotropic drugs without antipsychotic efficacy, the antidepressant imipramine, the anxiolytic diazepam and the anticonvulsant mood stabilizer valproic acid on male and female BRAT rat PPI. Male and female BRAT rats exhibited baseline (saline treatment) PPI that was not different from each other (21.1 % and 21.3 %, respectively) and low compared to those historically exhibited by LE rats (approximately 59 %). Chlorpromazine facilitated PPI in male and female BRAT rats, whereas imipramine, diazepam, and valproic acid had no significant effect on PPI. These results suggest that PPI in the BRAT rat responds specifically to drugs with APD efficacy but not psychotropic drugs of different therapeutic families. PMID:21106605

Phosphorescence quenching of fac-tris(2-phenylpyridyl)iridium(iii) complexes in thin films on dielectric surfaces.

PubMed

Ribierre, J C; Ruseckas, A; Staton, S V; Knights, K; Cumpstey, N; Burn, P L; Samuel, I D W

2016-02-07

We study the influence of the film thickness on the time-resolved phosphorescence and the luminescence quantum yield of fac-tris(2-phenylpyridyl)iridium(iii) [Ir(ppy)3]-cored dendrimers deposited on dielectric substrates. A correlation is observed between the surface quenching velocity and the quenching rate by intermolecular interactions in the bulk film, which suggests that both processes are controlled by dipole-dipole interactions between Ir(ppy)3 complexes at the core of the dendrimers. It is also found that the surface quenching velocity decreases as the refractive index of the substrate is increased. This can be explained by partial screening of dipole-dipole interactions by the dielectric environment.

Evaluating Documents: The Case of Patient Package Inserts. Technical Report No. 2.

ERIC Educational Resources Information Center

Krug, Robert E.

To illustrate the types of factors that must be considered in evaluating public documents, this paper analyzes a number of possible outcomes resulting from one type of document, the patient package insert (PPI) designed to provide consumers of prescription drugs with information about the drugs. It first outlines the intended sequence for a PPI:…

Sustaining patient and public involvement in research: A case study of a research centre

PubMed Central

Jinks, Clare; Carter, Pam; Rhodes, Carol; Beech, Roger; Dziedzic, Krysia; Hughes, Rhian; Blackburn, Steven; Ong, Bie Nio

2013-01-01

The literature on patient and public involvement (PPI) in research covers a wide range of topics. However, one area of investigation that appears under developed is the sustainability and impact of PPI beyond involvement in time-limited research projects. This paper presents a case study of PPI development in one primary care research centre in England, and its approach to making this sustainable using documentary sources and material from a formal evaluation. We provide narrative accounts of the set-up, operation and main processes of PPI, and its perceived impact. PPI requires a long-term perspective with participation and trust growing over time, and both users and researchers learning what approaches work best. PPI is a complex interplay of clarity of purpose, defined roles and relationships, organised support (paid PPI staff) and a well-funded infrastructure. ‘Soft systems’ are equally important such as flexible and informal approaches to meetings, adapting timetables and environments to meet the needs of lay members and to create spaces for relationships to develop between researchers and lay members that are based on mutual trust and respect. This case study highlights that the right combination of ethos, flexible working practices, leadership, and secure funding goes a long way to embedding PPI beyond ad hoc involvement. This allows PPI in research to be integrated in the infrastructure and sustainable. PMID:26705412

Hyperbranched-dendrimer architectural copolymer gene delivery using hyperbranched PEI conjugated to poly(propyleneimine) dendrimers: synthesis, characterization, and evaluation of transfection efficiency

NASA Astrophysics Data System (ADS)

Alavi, Seyyed Jamal; Gholami, Leila; Askarian, Saeedeh; Darroudi, Majid; Massoudi, Abdolhossein; Rezaee, Mehdi; Kazemi Oskuee, Reza

2017-02-01

The applications of dendrimer-based vectors seem to be promising in non-viral gene delivery because of their potential for addressing the problems with viral vectors. In this study, generation 3 poly(propyleneimine) (G3-PPI) dendrimers with 1, 4-diaminobutane as a core initiator was synthesized using a divergent growth approach. To increase the hydrophobicity and reduce toxicity, 10% of primary amines of G3-PPI dendrimers were replaced with bromoalkylcarboxylates with different chain lengths (6-bromohexanoic and 10-bromodecanoic). Then, to retain the overall buffering capacity and enhance transfection, the alkylcarboxylate-PPIs were conjugated to 10 kDa branched polyethylenimine (PEI). The results showed that the modified PPI was able to form complexes with the diameter of less than 60 nm with net-positive surface charge around 20 mV. No significant toxicity was observed in modified PPIs; however, the hexanoate conjugated PPI-PEI (PPI-HEX-10% PEI) and the decanoate conjugated PPI-PEI (PPI-DEC-10%-PEI) showed the best transfection efficiency in murine neuroblastoma (Neuro-2a) cell line, even PPI-HEX-10%-PEI showed transfection efficiency equal to standard PEI 25 kDa with reduced toxicity. This study suggested a new series of hyperbranched (PEI)-dendrimer (PPI) architectural copolymers as non-viral gene delivery vectors with high transfection efficiency and low toxicity.

Stringent DDI-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions.

PubMed

Zhou, Hufeng; Rezaei, Javad; Hugo, Willy; Gao, Shangzhi; Jin, Jingjing; Fan, Mengyuan; Yong, Chern-Han; Wozniak, Michal; Wong, Limsoon

2013-01-01

H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are very important information to illuminate the infection mechanism of M. tuberculosis H37Rv. But current H. sapiens-M. tuberculosis H37Rv PPI data are very scarce. This seriously limits the study of the interaction between this important pathogen and its host H. sapiens. Computational prediction of H. sapiens-M. tuberculosis H37Rv PPIs is an important strategy to fill in the gap. Domain-domain interaction (DDI) based prediction is one of the frequently used computational approaches in predicting both intra-species and inter-species PPIs. However, the performance of DDI-based host-pathogen PPI prediction has been rather limited. We develop a stringent DDI-based prediction approach with emphasis on (i) differences between the specific domain sequences on annotated regions of proteins under the same domain ID and (ii) calculation of the interaction strength of predicted PPIs based on the interacting residues in their interaction interfaces. We compare our stringent DDI-based approach to a conventional DDI-based approach for predicting PPIs based on gold standard intra-species PPIs and coherent informative Gene Ontology terms assessment. The assessment results show that our stringent DDI-based approach achieves much better performance in predicting PPIs than the conventional approach. Using our stringent DDI-based approach, we have predicted a small set of reliable H. sapiens-M. tuberculosis H37Rv PPIs which could be very useful for a variety of related studies. We also analyze the H. sapiens-M. tuberculosis H37Rv PPIs predicted by our stringent DDI-based approach using cellular compartment distribution analysis, functional category enrichment analysis and pathway enrichment analysis. The analyses support the validity of our prediction result. Also, based on an analysis of the H. sapiens-M. tuberculosis H37Rv PPI network predicted by our stringent DDI-based approach, we have discovered some important properties of domains involved in host-pathogen PPIs. We find that both host and pathogen proteins involved in host-pathogen PPIs tend to have more domains than proteins involved in intra-species PPIs, and these domains have more interaction partners than domains on proteins involved in intra-species PPI. The stringent DDI-based prediction approach reported in this work provides a stringent strategy for predicting host-pathogen PPIs. It also performs better than a conventional DDI-based approach in predicting PPIs. We have predicted a small set of accurate H. sapiens-M. tuberculosis H37Rv PPIs which could be very useful for a variety of related studies.

Redox-induced surface stress of polypyrrole-based actuators.

PubMed

Tabard-Cossa, Vincent; Godin, Michel; Grütter, Peter; Burgess, Ian; Lennox, R B

2005-09-22

We measure the surface stress induced by electrochemical transformations of a thin conducting polymer film. One side of a micromechanical cantilever-based sensor is covered with an electropolymerized dodecyl benzenesulfonate-doped polypyrrole (PPyDBS) film. The microcantilever serves as both the working electrode (in a conventional three-electrode cell configuration) and as the mechanical transducer for simultaneous, in situ, and real-time measurements of the current and interfacial stress changes. A compressive change in surface stress of about -2 N/m is observed when the conducting polymer is electrochemically switched between its oxidized (PPy+) and neutral (PPy0) state by cyclic voltammetry. The surface stress sensor's response during the anomalous first reductive scan is examined. The effect of long-term cycling on the mechanical transformation ability of PPy(DBS) films in both surfactant and halide-based electrolytes is also discussed. We have identified two main competing origins of surface stress acting on the PPy(DBS)/ gold-coated microcantilever: one purely mechanical due to the volume change of the conducting polymer, and a second charge-induced, owing to the interaction of anions of the supporting electrolyte with the gold surface.

Value of the Gastroesophageal Reflux Disease Questionnaire (GerdQ) in predicting the proton pump inhibitor response in coronary artery disease patients with gastroesophageal reflux-related chest pain.

PubMed

He, S; Liu, Y; Chen, Y; Tang, Y; Xu, J; Tang, C

2016-05-01

Chest pain experienced by patients with coronary artery disease can be partly due to gastroesophageal reflux-induced chest pain (GERP). Empirical proton pump inhibitor (PPI) therapy has been recommended as an initial clinical approach for treating GERP. However, PPI use may lead to some health problems. The Gastroesophageal Reflux Disease Questionnaire (GerdQ) may represent a noninvasive and cost-effective approach for avoiding PPI misuse and for identifying the appropriate patients for the PPI trial test. The aim of this pilot study was to prospectively evaluate the association between GerdQ scores and PPI response in patients with coronary artery disease (CAD) and GERP to determine whether the GerdQ predicts the PPI response in patients with CAD and GERP and to further validate the clinical application value of the GerdQ. A total of 154 consecutive patients with potential GERP were recruited to complete a GerdQ with subsequent PPI therapy. Based on the PPI trial result, patients were divided into a PPI-positive response group and a PPI-negative response group. The difference in the GerdQ scores between the two groups was assessed. The receiver operating characteristic (ROC) curve of GerdQ score was drawn according to the PPI response as the gold standard. The ability of GerdQ to predict the PPI response was assessed. A total of 96 patients completed the entire study; 62 patients (64.6%) were assigned to the PPI-positive response group, and 34 patients (35.4%) to the PPI-negative response group. The GerdQ score of the PPI-positive response group (8.11 ± 3.315) was significantly higher than that of the PPI-negative response group (4.41 ± 2.743), and the difference was statistically significant (t = 5.863, P = 0.000). The ROC curve was drawn according to a PPI response assessment result with a score above 2 as the gold standard. The area under curve was 0.806. When the critical value of GerdQ score was 7.5, Youden index was up to 0.514, the diagnostic sensitivity was 0.661, and the diagnostic specificity was 0.853. A GerdQ score greater than 7.5 better predicts the response to the PPI trial therapy. There is a strong association between the GerdQ score and the response to PPI therapy. Higher GerdQ scores were predictive of a positive PPI response in CAD patients with GERP. The GerdQ may be a reasonable screening tool for GERP in patients with CAD who are prepared to accept PPI therapy. © 2015 International Society for Diseases of the Esophagus.

Risk of Community-Acquired Pneumonia with Outpatient Proton-Pump Inhibitor Therapy: A Systematic Review and Meta-Analysis

PubMed Central

Lambert, Allison A.; Lam, Jennifer O.; Paik, Julie J.; Ugarte-Gil, Cesar; Drummond, M. Bradley; Crowell, Trevor A.

2015-01-01

Background Proton-pump inhibitors (PPIs) are among the most frequently prescribed medications. Community-acquired pneumonia (CAP) is a common cause of morbidity, mortality and healthcare spending. Some studies suggest an increased risk of CAP among PPI users. We conducted a systematic review and meta-analysis to determine the association between outpatient PPI therapy and risk of CAP in adults. Methods We conducted systematic searches of MEDLINE, EMBASE, CINAHL, Cochrane Central Register of Controlled Trials, Scopus and Web of Science on February 3, 2014. Case-control studies, case-crossover, cohort studies and randomized controlled trials reporting outpatient PPI exposure and CAP diagnosis for patients ≥18 years old were eligible. Our primary outcome was the association between CAP and PPI therapy. A secondary outcome examined the risk of hospitalization for CAP and subgroup analyses evaluated the association between PPI use and CAP among patients of different age groups, by different PPI doses, and by different durations of PPI therapy. Results Systematic review of 33 studies was performed, of which 26 studies were included in the meta-analysis. These 26 studies included 226,769 cases of CAP among 6,351,656 participants. We observed a pooled risk of CAP with ambulatory PPI therapy of 1.49 (95% CI 1.16, 1.92; I2 99.2%). This risk was increased during the first month of therapy (OR 2.10; 95% CI 1.39, 3.16), regardless of PPI dose or patient age. PPI therapy also increased risk for hospitalization for CAP (OR 1.61; 95% CI: 1.12, 2.31). Discussion Outpatient PPI use is associated with a 1.5-fold increased risk of CAP, with the highest risk within the first 30 days after initiation of therapy. Providers should be aware of this risk when considering PPI use, especially in cases where alternative regimens may be available or the benefits of PPI use are uncertain. PMID:26042842

Evolutionary model selection and parameter estimation for protein-protein interaction network based on differential evolution algorithm

PubMed Central

Huang, Lei; Liao, Li; Wu, Cathy H.

2016-01-01

Revealing the underlying evolutionary mechanism plays an important role in understanding protein interaction networks in the cell. While many evolutionary models have been proposed, the problem about applying these models to real network data, especially for differentiating which model can better describe evolutionary process for the observed network urgently remains as a challenge. The traditional way is to use a model with presumed parameters to generate a network, and then evaluate the fitness by summary statistics, which however cannot capture the complete network structures information and estimate parameter distribution. In this work we developed a novel method based on Approximate Bayesian Computation and modified Differential Evolution (ABC-DEP) that is capable of conducting model selection and parameter estimation simultaneously and detecting the underlying evolutionary mechanisms more accurately. We tested our method for its power in differentiating models and estimating parameters on the simulated data and found significant improvement in performance benchmark, as compared with a previous method. We further applied our method to real data of protein interaction networks in human and yeast. Our results show Duplication Attachment model as the predominant evolutionary mechanism for human PPI networks and Scale-Free model as the predominant mechanism for yeast PPI networks. PMID:26357273

Prediction of protein-protein interaction network using a multi-objective optimization approach.

PubMed

Chowdhury, Archana; Rakshit, Pratyusha; Konar, Amit

2016-06-01

Protein-Protein Interactions (PPIs) are very important as they coordinate almost all cellular processes. This paper attempts to formulate PPI prediction problem in a multi-objective optimization framework. The scoring functions for the trial solution deal with simultaneous maximization of functional similarity, strength of the domain interaction profiles, and the number of common neighbors of the proteins predicted to be interacting. The above optimization problem is solved using the proposed Firefly Algorithm with Nondominated Sorting. Experiments undertaken reveal that the proposed PPI prediction technique outperforms existing methods, including gene ontology-based Relative Specific Similarity, multi-domain-based Domain Cohesion Coupling method, domain-based Random Decision Forest method, Bagging with REP Tree, and evolutionary/swarm algorithm-based approaches, with respect to sensitivity, specificity, and F1 score.

Core-Shell Composite Fibers for High-Performance Flexible Supercapacitor Electrodes.

PubMed

Lu, Xiaoyan; Shen, Chen; Zhang, Zeyang; Barrios, Elizabeth; Zhai, Lei

2018-01-31

Core-shell nanofibers containing poly(acrylic acid) (PAA) and manganese oxide nanoparticles as the core and polypyrrole (PPy) as the shell were fabricated through electrospinning the solution of PAA and manganese ions (PAA/Mn 2+ ). The obtained nanofibers were stabilized by Fe 3+ through the interaction between Fe 3+ ions and carboxylate groups. Subsequent oxidation of Mn 2+ by KMnO 4 produced uniform manganese dioxide (MnO 2 ) nanoparticles in the fibers. A PPy shell was created on the fibers by immersing the fibers in a pyrrole solution where the Fe 3+ ions in the fiber polymerized the pyrrole on the fiber surfaces. In the MnO 2 @PAA/PPy core-shell composite fibers, MnO 2 nanoparticles function as high-capacity materials, while the PPy shell prevents the loss of MnO 2 during the charge/discharge process. Such a unique structure makes the composite fibers efficient electrode materials for supercapacitors. The gravimetric specific capacity of the MnO 2 @PAA/PPy core-shell composite fibers was 564 F/g based on cyclic voltammetry curves at 10 mV/s and 580 F/g based on galvanostatic charge/discharge studies at 5 A/g. The MnO 2 @PAA/PPy core-shell composite fibers also present stable cycling performance with 100% capacitance retention after 5000 cycles.

Embedded Carbide-derived Carbon (CDC) particles in polypyrrole (PPy) for linear actuator

NASA Astrophysics Data System (ADS)

Zondaka, Zane; Valner, Robert; Aabloo, Alvo; Tamm, Tarmo; Kiefer, Rudolf

2016-04-01

Conducting polymer linear actuators, for example sodium dodecylbenzenesulfonate (NaDBS) doped polypyrrole (PPy/DBS), have shown moderate strain and stress. The goal of this work was to increase the obtainable strain and stress by adding additional active material to PPy/DBS. In recent year's carbide-derived carbon (CDC)-based materials have been applied in actuators; however, the obtained displacement and actuation speed has been low comparing to conducting polymer based actuators. In the present work, a CDC-PPy hybrid was synthesized electrochemically and polyoxometalate (POM) - phosphotungstic acid - was used to attach charge to CDC particles. The CDC-POM served in the presence of NaDBS as an additional electrolyte. Cyclic voltammetry and chronopotentiometric electrochemomechanical deformation (ECMD) measurements were performed in Lithium bis(trifluoromethanesulfonyl)- imide (LiTFSI) aqueous electrolyte. The ECMD measurements revealed that the hybrid CDC-PPy material exhibited higher force and strain in comparison to PPy/DBS films. The new material was investigated by scanning electron microscopy (SEM) to evaluate CDC particle embedding in the polymer network.

Prognostic factors and genes associated with endometrial cancer based on gene expression profiling by bioinformatics analysis.

PubMed

Zhang, Ying; Zhang, Wei; Li, Xinglan; Li, Dapeng; Zhang, Xiaoling; Yin, Yajie; Deng, Xiangyun; Sheng, Xiugui

2016-06-01

Endometrial cancer (EC) is the most prevalent malignancy worldwide. Although several efforts had been made to explore the molecular mechanism responsible for EC progression, it is still not fully understood. To evaluate the clinical characteristics and prognostic factors of patients with EC, and further to search for novel genes associated with EC progression. We recruited 328 patients with EC and analyzed prognostic factors using Cox proportional hazard regression model. Further, a gene expression profile of EC was used to identify the differentially expressed genes (DEGs) between normal samples and tumor samples. Subsequently, Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis ( http://www.genome.jp/kegg/ ) for DEGs were performed, and then protein-protein interaction (PPI) network of DEGs as well as the subnetwork of PPI were constructed with plug-in, MCODE by mapping DEGs into the Search Tool for the Retrieval of Interacting Genes database. Our results showed that body mass index (BMI), hypertension, myometrial invasion, pathological type, and Glut4 positive expression were prognostic factors in EC (P < 0.05). Bioinformatics analysis showed that upregulated DEGs were associated with cell cycle, and downregulated DEGs were related to MAPK pathway. Meanwhile, PPI network analysis revealed that upregulated CDK1 and CCNA2 as well as downregulated JUN and FOS were listed in top two nodes with high degrees. Patients with EC should be given more focused attentions in respect of pathological type, BMI, hypertension, and Glut4-positive expression. In addition, CDK1, CCNA2, JUN, and FOS might play important roles in EC development.

THE REELIN RECEPTORS VLDLR AND ApoER2 REGULATE SENSORIMOTOR GATING IN MICE

PubMed Central

Barr, Alasdair M.; Fish, Kenneth N.; Markou, Athina

2007-01-01

Summary Postmortem brain loss of reelin is noted in schizophrenia patients. Accordingly, heterozygous reeler mutant mice have been proposed as a putative model of this disorder. Little is known, however, about the involvement of the two receptors for reelin, Very-Low-Density Lipoprotein Receptor (VLDLR) and Apolipoprotein E Receptor 2 (ApoER2), on pre-cognitive processes of relevance to deficits seen in schizophrenia. Thus, we evaluated sensorimotor gating in mutant mice heterozygous or homozygous for the two reelin receptors. Mutant mice lacking one of these reelin receptors were tested for prepulse inhibition (PPI) of the acoustic startle reflex prior to and following puberty, and on a crossmodal PPI task, involving the presentation of acoustic and tactile stimuli. Furthermore, because schizophrenia patients show increased sensitivity to N-methyl-D-aspartate (NMDA) receptor blockade, we assessed the sensitivity of these mice to the PPI-disruptive effects of the NMDA receptor antagonist phencyclidine. The results demonstrated that acoustic PPI did not differ between mutant and wildtype mice. However, VLDLR homozygous mice displayed significant deficits in crossmodal PPI, while ApoER2 heterozygous and homozygous mice displayed significantly increased crossmodal PPI. Both ApoER2 and VLDLR heterozygous and homozygous mice exhibited greater sensitivity to the PPI-disruptive effects of phencyclidine than wildtype mice. These results indicate that partial or complete loss of either one of the reelin receptors results in a complex pattern of alterations in PPI function that include alterations in crossmodal, but not acoustic, PPI and increased sensitivity to NMDA receptor blockade. Thus, reelin receptor function appears to be critically involved in crossmodal PPI and the modulation of the PPI response by NMDA receptors. These findings have relevance to a range of neuropsychiatric disorders that involve sensorimotor gating deficits, including schizophrenia.. PMID:17261317

Novel degradable co-polymers of polypyrrole support cell proliferation and enhance neurite out-growth with electrical stimulation.

PubMed

Durgam, Hymavathi; Sapp, Shawn; Deister, Curt; Khaing, Zin; Chang, Emily; Luebben, Silvia; Schmidt, Christine E

2010-01-01

Synthetic polymers such as polypyrrole (PPy) are gaining significance in neural studies because of their conductive properties. We evaluated two novel biodegradable block co-polymers of PPy with poly(epsilon-caprolactone) (PCL) and poly(ethyl cyanoacrylate) (PECA) for nerve regeneration applications. PPy-PCL and PPy-PECA co-polymers can be processed from solvent-based colloidal dispersions and have essentially the same or greater conductivity (32 S/cm for PPy-PCL, 19 S/cm for PPy-PECA) compared to the PPy homo-polymer (22 S/cm). The PPy portions of the co-polymers permit electrical stimulation whereas the PCL or PECA blocks enable degradation by hydrolysis. For in vitro tests, films were prepared on polycarbonate sheets by air brushing layers of dispersions and pressing the films. We characterized the films for hydrolytic degradation, electrical conductivity, cell proliferation and neurite extension. The co-polymers were sufficient to carry out electrical stimulation of cells without the requirement of a metallic conductor underneath the co-polymer film. In vitro electrical stimulation of PPy-PCL significantly increased the number of PC12 cells bearing neurites compared to unstimulated PPy-PCL. For in vivo experiments, the PPy co-polymers were coated onto the inner walls of nerve guidance channels (NGCs) made of the commercially available non-conducting biodegradable polymer poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHB-HV). The NGCs were implanted in a 10 mm defect made in the sciatic nerve of rats, and harvested after 8 weeks. Histological staining showed axonal growth. The studies indicated that these new conducting degradable biomaterials have good biocompatibility and support proliferation and growth of PC12 cells in vitro (with and without electrical stimulation) and neurons in vivo (without electrical stimulation).

Identification of T1D susceptibility genes within the MHC region by combining protein interaction networks and SNP genotyping data

PubMed Central

Brorsson, C.; Hansen, N. T.; Lage, K.; Bergholdt, R.; Brunak, S.; Pociot, F.

2009-01-01

Aim To develop novel methods for identifying new genes that contribute to the risk of developing type 1 diabetes within the Major Histocompatibility Complex (MHC) region on chromosome 6, independently of the known linkage disequilibrium (LD) between human leucocyte antigen (HLA)-DRB1, -DQA1, -DQB1 genes. Methods We have developed a novel method that combines single nucleotide polymorphism (SNP) genotyping data with protein–protein interaction (ppi) networks to identify disease-associated network modules enriched for proteins encoded from the MHC region. Approximately 2500 SNPs located in the 4 Mb MHC region were analysed in 1000 affected offspring trios generated by the Type 1 Diabetes Genetics Consortium (T1DGC). The most associated SNP in each gene was chosen and genes were mapped to ppi networks for identification of interaction partners. The association testing and resulting interacting protein modules were statistically evaluated using permutation. Results A total of 151 genes could be mapped to nodes within the protein interaction network and their interaction partners were identified. Five protein interaction modules reached statistical significance using this approach. The identified proteins are well known in the pathogenesis of T1D, but the modules also contain additional candidates that have been implicated in β-cell development and diabetic complications. Conclusions The extensive LD within the MHC region makes it important to develop new methods for analysing genotyping data for identification of additional risk genes for T1D. Combining genetic data with knowledge about functional pathways provides new insight into mechanisms underlying T1D. PMID:19143816

Heteroprotein Complex Formation of Bovine Lactoferrin and Pea Protein Isolate: A Multiscale Structural Analysis.

PubMed

Adal, Eda; Sadeghpour, Amin; Connell, Simon; Rappolt, Michael; Ibanoglu, Esra; Sarkar, Anwesha

2017-02-13

Associative electrostatic interactions between two oppositely charged globular proteins, lactoferrin (LF) and pea protein isolate (PPI), the latter being a mixture of vicilin, legumin, and convicilin, was studied with a specific PPI/LF molar ratio at room temperature. Structural aspects of the electrostatic complexes probed at different length scales were investigated as a function of pH by means of different complementary techniques, namely, with dynamic light scattering, small-angle X-ray scattering (SAXS), turbidity measurements, and atomic force microscopy (AFM). Irrespective of the applied techniques, the results consistently displayed that complexation between LF and PPI did occur. In an optimum narrow range of pH 5.0-5.8, a viscous liquid phase of complex coacervate was obtained upon mild centrifugation of the turbid LF-PPI mixture with a maximum R h , turbidity and the ζ-potential being close to zero observed at pH 5.4. In particular, the SAXS data demonstrated that the coacervates were densely assembled with a roughly spherical size distribution exhibiting a maximum extension of ∼80 nm at pH 5.4. Equally, AFM image analysis showed size distributions containing most frequent cluster sizes around 40-80 nm with spherical to elliptical shapes (axis aspect ratio ≤ 2) as well as less frequent elongated to chainlike structures. The most frequently observed compact complexes, we identify as mainly leading to LF-PPI coacervation, whereas for the less frequent chain-like aggregates, we hypothesize that additionally PPI-PPI facilitated complexes exist.

Targeting protein-protein interactions in hematologic malignancies: still a challenge or a great opportunity for future therapies?

PubMed Central

Cierpicki, Tomasz; Grembecka, Jolanta

2015-01-01

Summary Over the past several years, there has been an increasing research effort focused on inhibition of protein-protein interactions (PPIs) to develop novel therapeutic approaches for cancer, including hematologic malignancies. These efforts have led to development of small molecule inhibitors of PPIs, some of which already advanced to the stage of clinical trials while others are at different stages of pre-clinical optimization, emphasizing PPIs as an emerging and attractive class of drug targets. Here, we review several examples of recently developed inhibitors of protein-protein interactions highly relevant to hematologic cancers. We address the existing skepticism about feasibility of targeting PPIs and emphasize potential therapeutic benefit from blocking PPIs in hematologic malignancies. We then use these examples to discuss the approaches for successful identification of PPI inhibitors and provide analysis of the protein-protein interfaces, with the goal to address ‘druggability’ of new PPIs relevant to hematology. We discuss lessons learned to improve the success of targeting new protein-protein interactions and evaluate prospects and limits of the research in this field. We conclude that not all PPIs are equally tractable for blocking by small molecules, and detailed analysis of PPI interfaces is critical for selection of those with the highest chance of success. Together, our analysis uncovers patterns that should help to advance drug discovery in hematologic malignancies by successful targeting of new protein-protein interactions. PMID:25510283

Small Bowel Bacterial Overgrowth Associated with Persistence of Abdominal Symptoms in Children Treated with a Proton Pump Inhibitor.

PubMed

Sieczkowska, Agnieszka; Landowski, Piotr; Zagozdzon, Pawel; Kaminska, Barbara; Lifschitz, Carlos

2015-05-01

Small bowel bacterial overgrowth (SBBO) was diagnosed in 22.5% of 40 children treated for 3 months with a proton pump inhibitor (PPI). Compared with those without SBBO, children with SBBO had higher frequency of abdominal pain, bloating, eructation, and flatulence. Patients with gastrointestinal symptoms after PPI treatment should be evaluated for SBBO rather than empirically prolonging PPI therapy. Copyright © 2015 Elsevier Inc. All rights reserved.

Is it worth it? Patient and public views on the impact of their involvement in health research and its assessment: a UK-based qualitative interview study.

PubMed

Crocker, Joanna C; Boylan, Anne-Marie; Bostock, Jennifer; Locock, Louise

2017-06-01

There are mounting calls for robust, critical evaluation of the impact of patient and public involvement (PPI) in health research. However, questions remain about how to assess its impact, and whether it should be assessed at all. The debate has thus far been dominated by professionals. To explore the views of PPI contributors involved in health research regarding the impact of PPI on research, whether and how it should be assessed. Qualitative interview study. Thirty-eight PPI contributors involved in health research across the UK. Participants felt that PPI has a beneficial impact on health research. They described various impactful roles, which we conceptualize as the 'expert in lived experience', the 'creative outsider', the 'free challenger', the 'bridger', the 'motivator' and the 'passive presence'. Participants generally supported assessing the impact of PPI, while acknowledging the challenges and concerns about the appropriateness and feasibility of measurement. They expressed a range of views about what impacts should be assessed, by whom and how. Individual feedback on impact was seen as an important driver of improved impact and motivation to stay involved. While there appears to be widespread support for PPI impact assessment among PPI contributors, their views on what to assess and how are diverse. PPI contributors should be involved as equal partners in debates and decisions about these issues. Individual feedback on impact may increase PPI contributors' potential impact and their motivation to stay involved. © 2016 The Authors. Health Expectations Published by John Wiley & Sons Ltd.

Gastroprotective strategies in chronic NSAID users: a cost-effectiveness analysis comparing single-tablet formulations with individual components.

PubMed

de Groot, N L; Spiegel, B M R; van Haalen, H G M; de Wit, N J; Siersema, P D; van Oijen, M G H

2013-01-01

To evaluate the cost-effectiveness of competing gastroprotective strategies, including single-tablet formulations, in the prevention of gastrointestinal (GI) complications in patients with chronic arthritis taking nonsteroidal anti-inflammatory drugs (NSAIDs). We performed a cost-utility analysis to compare eight gastroprotective strategies including NSAIDs, cyclooxygenase-2 inhibitors, proton pump inhibitors (PPIs), histamine-2 receptor antagonists, misoprostol, and single-tablet formulations. We derived estimates for outcomes and costs from medical literature. The primary outcome was incremental cost per quality-adjusted life-year gained. We performed sensitivity analyses to assess the effect of GI complications, compliance rates, and drug costs. For average-risk patients, NSAID + PPI cotherapy was most cost-effective. The NSAID/PPI single-tablet formulation became cost-effective only when its price decreased from €0.78 to €0.56 per tablet, or when PPI compliance fell below 51% in the NSAID + PPI strategy. All other strategies were more costly and less effective. The model was highly sensitive to the GI complication risk, costs of PPI and NSAID/PPI single-tablet formulation, and compliance to PPI. In patients with a threefold higher risk of GI complications, both NSAID + PPI cotherapy and single-tablet formulation were cost-effective. NSAID + PPI cotherapy is the most cost-effective strategy in all patients with chronic arthritis irrespective of their risk for GI complications. For patients with increased GI risk, the NSAID/PPI single-tablet formulation is also cost-effective. Copyright © 2013 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

atBioNet--an integrated network analysis tool for genomics and biomarker discovery.

PubMed

Ding, Yijun; Chen, Minjun; Liu, Zhichao; Ding, Don; Ye, Yanbin; Zhang, Min; Kelly, Reagan; Guo, Li; Su, Zhenqiang; Harris, Stephen C; Qian, Feng; Ge, Weigong; Fang, Hong; Xu, Xiaowei; Tong, Weida

2012-07-20

Large amounts of mammalian protein-protein interaction (PPI) data have been generated and are available for public use. From a systems biology perspective, Proteins/genes interactions encode the key mechanisms distinguishing disease and health, and such mechanisms can be uncovered through network analysis. An effective network analysis tool should integrate different content-specific PPI databases into a comprehensive network format with a user-friendly platform to identify key functional modules/pathways and the underlying mechanisms of disease and toxicity. atBioNet integrates seven publicly available PPI databases into a network-specific knowledge base. Knowledge expansion is achieved by expanding a user supplied proteins/genes list with interactions from its integrated PPI network. The statistically significant functional modules are determined by applying a fast network-clustering algorithm (SCAN: a Structural Clustering Algorithm for Networks). The functional modules can be visualized either separately or together in the context of the whole network. Integration of pathway information enables enrichment analysis and assessment of the biological function of modules. Three case studies are presented using publicly available disease gene signatures as a basis to discover new biomarkers for acute leukemia, systemic lupus erythematosus, and breast cancer. The results demonstrated that atBioNet can not only identify functional modules and pathways related to the studied diseases, but this information can also be used to hypothesize novel biomarkers for future analysis. atBioNet is a free web-based network analysis tool that provides a systematic insight into proteins/genes interactions through examining significant functional modules. The identified functional modules are useful for determining underlying mechanisms of disease and biomarker discovery. It can be accessed at: http://www.fda.gov/ScienceResearch/BioinformaticsTools/ucm285284.htm.

Discovery of direct inhibitors of Keap1-Nrf2 protein-protein interaction as potential therapeutic and preventive agents.

PubMed

Abed, Dhulfiqar Ali; Goldstein, Melanie; Albanyan, Haifa; Jin, Huijuan; Hu, Longqin

2015-07-01

The Keap1-Nrf2-ARE pathway is an important antioxidant defense mechanism that protects cells from oxidative stress and the Keap1-Nrf2 protein-protein interaction (PPI) has become an important drug target to upregulate the expression of ARE-controlled cytoprotective oxidative stress response enzymes in the development of therapeutic and preventive agents for a number of diseases and conditions. However, most known Nrf2 activators/ARE inducers are indirect inhibitors of Keap1-Nrf2 PPI and they are electrophilic species that act by modifying the sulfhydryl groups of Keap1׳s cysteine residues. The electrophilicity of these indirect inhibitors may cause "off-target" side effects by reacting with cysteine residues of other important cellular proteins. Efforts have recently been focused on the development of direct inhibitors of Keap1-Nrf2 PPI. This article reviews these recent research efforts including the development of high throughput screening assays, the discovery of peptide and small molecule direct inhibitors, and the biophysical characterization of the binding of these inhibitors to the target Keap1 Kelch domain protein. These non-covalent direct inhibitors of Keap1-Nrf2 PPI could potentially be developed into effective therapeutic or preventive agents for a variety of diseases and conditions.

Nature and consequences of protein-protein interactions in high protein concentration solutions.

PubMed

Saluja, Atul; Kalonia, Devendra S

2008-06-24

High protein concentration solutions are becoming increasingly important in the pharmaceutical industry. The solution behavior of proteins at high concentrations can markedly differ from that predicted based on dilute solution analysis due to thermodynamic non-ideality in these solutions. The non-ideality observed in these systems is related to the protein-protein interactions (PPI). Different types of forces play a key role in determining the overall nature and extent of these PPI and their relative contributions are affected by solute and solvent properties. However, individual contributions of these forces to the solution properties of concentrated protein solutions are not fully understood. The role of PPI, driven by these intermolecular forces, in governing solution rheology and physical stability of high protein concentration solutions is discussed from the point of view of pharmaceutical product development. Investigation of protein self-association and aggregation in concentrated protein solutions is crucial for ensuring the safety and efficacy of the final product for the duration of the desired product shelf life. Understanding rheology of high concentration protein solutions is critical for addressing issues during product manufacture and administration of final formulation to the patient. To this end, analysis of solution viscoelastic character can also provide an insight into the nature of PPI affecting solution rheology.

Electropolymerization of camphorsulfonic acid doped conductive polypyrrole anti-corrosive coating for 304SS bipolar plates

NASA Astrophysics Data System (ADS)

Jiang, Li; Syed, Junaid Ali; Gao, Yangzhi; Zhang, Qiuxiang; Zhao, Junfeng; Lu, Hongbin; Meng, Xiangkang

2017-12-01

Conductive polymer coating doped with large molecular organic acid is an alternative method used to protect stainless steel (SS) bipolar plates in proton exchange membrane fuel cells (PEMFCs). However, it is difficult to select the proper doping acid, which improves the corrosion resistance of the coating without affecting its conductivity. In this study, large spatial molecular group camphorsulfonic acid (CSA) doped polypyrrole (PPY) conductive coating was prepared by galvanostatic electropolymerization on 304SS. The electrochemical properties of the coating were evaluated in 0.1 M H2SO4 solution in order to simulate the PEMFC service environment. The results indicate that the coating increased the corrosion potential and shifted Ecorr towards more positive value, particularly the jcorr value of PPY-CSA coated 304SS was dropped from 97.3 to 0.00187 μA cm-2. The long-term immersion tests (660 h) show that the PPY-CSA coating exhibits better corrosion resistance in comparison with the small acid (SO42-) doped PPY-SO42- or PPY/PPY-SO42- coatings. Moreover, the PPY-CSA coating presents low contact resistance and maintains strong corrosion resistance during the prolonged exposure time due to barrier effect and anodic protection.

Detecting experimental techniques and selecting relevant documents for protein-protein interactions from biomedical literature.

PubMed

Wang, Xinglong; Rak, Rafal; Restificar, Angelo; Nobata, Chikashi; Rupp, C J; Batista-Navarro, Riza Theresa B; Nawaz, Raheel; Ananiadou, Sophia

2011-10-03

The selection of relevant articles for curation, and linking those articles to experimental techniques confirming the findings became one of the primary subjects of the recent BioCreative III contest. The contest's Protein-Protein Interaction (PPI) task consisted of two sub-tasks: Article Classification Task (ACT) and Interaction Method Task (IMT). ACT aimed to automatically select relevant documents for PPI curation, whereas the goal of IMT was to recognise the methods used in experiments for identifying the interactions in full-text articles. We proposed and compared several classification-based methods for both tasks, employing rich contextual features as well as features extracted from external knowledge sources. For IMT, a new method that classifies pair-wise relations between every text phrase and candidate interaction method obtained promising results with an F1 score of 64.49%, as tested on the task's development dataset. We also explored ways to combine this new approach and more conventional, multi-label document classification methods. For ACT, our classifiers exploited automatically detected named entities and other linguistic information. The evaluation results on the BioCreative III PPI test datasets showed that our systems were very competitive: one of our IMT methods yielded the best performance among all participants, as measured by F1 score, Matthew's Correlation Coefficient and AUC iP/R; whereas for ACT, our best classifier was ranked second as measured by AUC iP/R, and also competitive according to other metrics. Our novel approach that converts the multi-class, multi-label classification problem to a binary classification problem showed much promise in IMT. Nevertheless, on the test dataset the best performance was achieved by taking the union of the output of this method and that of a multi-class, multi-label document classifier, which indicates that the two types of systems complement each other in terms of recall. For ACT, our system exploited a rich set of features and also obtained encouraging results. We examined the features with respect to their contributions to the classification results, and concluded that contextual words surrounding named entities, as well as the MeSH headings associated with the documents were among the main contributors to the performance.

Imbalance in chemical space: How to facilitate the identification of protein-protein interaction inhibitors.

PubMed

Kuenemann, Mélaine A; Labbé, Céline M; Cerdan, Adrien H; Sperandio, Olivier

2016-04-01

Protein-protein interactions (PPIs) play vital roles in life and provide new opportunities for therapeutic interventions. In this large data analysis, 3,300 inhibitors of PPIs (iPPIs) were compared to 17 reference datasets of collectively ~566,000 compounds (including natural compounds, existing drugs, active compounds on conventional targets, etc.) using a chemoinformatics approach. Using this procedure, we showed that comparable classes of PPI targets can be formed using either the similarity of their ligands or the shared properties of their binding cavities, constituting a proof-of-concept that not only can binding pockets be used to group PPI targets, but that these pockets certainly condition the properties of their corresponding ligands. These results demonstrate that matching regions in both chemical space and target space can be found. Such identified classes of targets could lead to the design of PPI-class-specific chemical libraries and therefore facilitate the development of iPPIs to the stage of drug candidates.

MAPPI-DAT: data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform.

PubMed

Gupta, Surya; De Puysseleyr, Veronic; Van der Heyden, José; Maddelein, Davy; Lemmens, Irma; Lievens, Sam; Degroeve, Sven; Tavernier, Jan; Martens, Lennart

2017-05-01

Protein-protein interaction (PPI) studies have dramatically expanded our knowledge about cellular behaviour and development in different conditions. A multitude of high-throughput PPI techniques have been developed to achieve proteome-scale coverage for PPI studies, including the microarray based Mammalian Protein-Protein Interaction Trap (MAPPIT) system. Because such high-throughput techniques typically report thousands of interactions, managing and analysing the large amounts of acquired data is a challenge. We have therefore built the MAPPIT cell microArray Protein Protein Interaction-Data management & Analysis Tool (MAPPI-DAT) as an automated data management and analysis tool for MAPPIT cell microarray experiments. MAPPI-DAT stores the experimental data and metadata in a systematic and structured way, automates data analysis and interpretation, and enables the meta-analysis of MAPPIT cell microarray data across all stored experiments. MAPPI-DAT is developed in Python, using R for data analysis and MySQL as data management system. MAPPI-DAT is cross-platform and can be ran on Microsoft Windows, Linux and OS X/macOS. The source code and a Microsoft Windows executable are freely available under the permissive Apache2 open source license at https://github.com/compomics/MAPPI-DAT. jan.tavernier@vib-ugent.be or lennart.martens@vib-ugent.be. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions

PubMed Central

2014-01-01

Background H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are essential for understanding the infection mechanism of the formidable pathogen M. tuberculosis H37Rv. Computational prediction is an important strategy to fill the gap in experimental H. sapiens-M. tuberculosis H37Rv PPI data. Homology-based prediction is frequently used in predicting both intra-species and inter-species PPIs. However, some limitations are not properly resolved in several published works that predict eukaryote-prokaryote inter-species PPIs using intra-species template PPIs. Results We develop a stringent homology-based prediction approach by taking into account (i) differences between eukaryotic and prokaryotic proteins and (ii) differences between inter-species and intra-species PPI interfaces. We compare our stringent homology-based approach to a conventional homology-based approach for predicting host-pathogen PPIs, based on cellular compartment distribution analysis, disease gene list enrichment analysis, pathway enrichment analysis and functional category enrichment analysis. These analyses support the validity of our prediction result, and clearly show that our approach has better performance in predicting H. sapiens-M. tuberculosis H37Rv PPIs. Using our stringent homology-based approach, we have predicted a set of highly plausible H. sapiens-M. tuberculosis H37Rv PPIs which might be useful for many of related studies. Based on our analysis of the H. sapiens-M. tuberculosis H37Rv PPI network predicted by our stringent homology-based approach, we have discovered several interesting properties which are reported here for the first time. We find that both host proteins and pathogen proteins involved in the host-pathogen PPIs tend to be hubs in their own intra-species PPI network. Also, both host and pathogen proteins involved in host-pathogen PPIs tend to have longer primary sequence, tend to have more domains, tend to be more hydrophilic, etc. And the protein domains from both host and pathogen proteins involved in host-pathogen PPIs tend to have lower charge, and tend to be more hydrophilic. Conclusions Our stringent homology-based prediction approach provides a better strategy in predicting PPIs between eukaryotic hosts and prokaryotic pathogens than a conventional homology-based approach. The properties we have observed from the predicted H. sapiens-M. tuberculosis H37Rv PPI network are useful for understanding inter-species host-pathogen PPI networks and provide novel insights for host-pathogen interaction studies. Reviewers This article was reviewed by Michael Gromiha, Narayanaswamy Srinivasan and Thomas Dandekar. PMID:24708540

Analysis of nonformulary use of PPIs and excess drug cost in a Veterans Affairs population.

PubMed

Ajumobi, Adewale B; Vuong, Ronald; Ahaneku, Hycienth

2012-01-01

In the Veterans Affairs (VA) health care system, a formulary-based approach without beneficiary cost-share incentives is used to limit the pharmacy cost of proton pump inhibitors (PPIs). However, the effectiveness of this approach in reducing the cost of PPIs is unknown. To (a) compare cost differences between the formulary PPI (generic omeprazole) and nonformulary PPIs and (b) evaluate reasons for nonformulary PPI use in order to identify opportunities to increase formulary drug use and discourage unnecessary use of nonformulary PPIs. A list of patients with receipt of PPIs from July 1, 2008, through June 30, 2009, was obtained from the Loma Linda VA Healthcare System pharmacy. Subjects with receipt of at least 120 units (capsules or tablets) of any PPI in the study period were considered long-term users. Demographic information was collected. Pharmacy consult records were reviewed to identify reasons for nonformulary use and dosing regimen of the formulary PPI prior to the switch. Cost analysis was done based on the VA contract prices for the drugs at the time of the study. Of 58,605 unique patients seen in this VA health care system in the 12-month period from July 1, 2008, through June 30, 2009, 13,713 (23.4%) received a PPI, and of these, 10,483 (76.4%) received at least 120 PPI units and were defined as long-term users. Of the long-term users, 9,462 (90.3%) were on the formulary PPI generic omeprazole, and 1,021 were nonformulary PPI users. Use of nonformulary PPIs (esomeprazole, pantoprazole, lansoprazole, rabeprazole) accounted for 10.5% of the PPI units and 9.7% of the users but 57.3% of total PPI cost. This pattern resulted in $570,263 in excess spending (i.e., $570,263 would have been saved in the study period if the nonformulary PPI users had used the formulary drug). The most common reason for nonformulary long-term PPI use was persistent symptoms (n=901, 88.2%). Adverse reaction was cited by 111 (10.9%) of nonformulary PPI users, 33.3% (n=37) of whom reported diarrhea. Of those who switched to a nonformulary PPI due to persistent symptoms, 363 (40.3%) were on once-daily dosing prior to the switch; 379 (42.1%) were on twice-daily dosing; and 159 (17.6%) were transfers from other places in which prior dosing information was not available in the hospital pharmacy records. One-year PPI use prevalence was 23% in this VA population, and long-term use prevalence was 18%. Nonformulary PPI use accounted for 10.5% of the PPI units and 9.7% of the users but 57.3% of total PPI drug cost. Opportunities to reduce nonformulary PPI use in order to reduce overall expenditures on PPIs include verification of optimal formulary PPI use, titration to twice-daily dosing, and confirmation of adverse reaction as being attributable to PPI use.

Immobilization of antibacterial metallic cations (Ga3+, Zn2+ and Co2+) in a polypyrrole coating formed on Nitinol.

PubMed

Saugo, M; Brugnoni, L I; Flamini, D O; Saidman, S B

2018-05-01

Gallium, zinc and cobalt species were immobilized in hollow rectangular-sectioned microtubes of polypyrrole (PPy) electrosynthesized on Nitinol (NiTi) alloy by means of two different methods. One of them involved the immobilization after the PPy electropolymerization and the other one during the electrosynthesis process. The antibacterial activity of the coating against Escherichia coli (E. coli) was evaluated and the best results were obtained with gallium species. Characterization results demonstrated that gallium is incorporated into the PPy matrix as Ga 3+ ions. The PPy film with gallium species incorporated during the electropolymerization exhibited a good corrosion protection performance. Copyright © 2018 Elsevier B.V. All rights reserved.

Proton pump inhibitor for non-erosive reflux disease: A meta-analysis

PubMed Central

Zhang, Ji-Xiang; Ji, Meng-Yao; Song, Jia; Lei, Hong-Bo; Qiu, Shi; Wang, Jing; Ai, Ming-Hua; Wang, Jun; Lv, Xiao-Guang; Yang, Zi-Rong; Dong, Wei-Guo

2013-01-01

AIM: To evaluate the efficacy, safety and influential factors of proton pump inhibitor (PPI) treatment for non-erosive reflux disease (NERD). METHODS: PubMed, MEDLINE, EMBASE and the Cochrane Library were searched up to April 2013 to identify eligible randomized controlled trials (RCTs) that probed into the efficacy, safety and influential factors of PPI treatment for NERD. The rates of symptomatic relief and adverse events were measured as the outcomes. After RCT selection, assessment and data collection, the pooled RRs and 95%CI were calculated. This meta-analysis was performed using the Stata 12.0 software (Stata Corporation, College Station, Texas, United States). The level of evidence was estimated by the Grading of Recommendations Assessment, Development and Evaluation system. RESULTS: Seventeen RCTs including 6072 patients met the inclusion criteria. The results of the meta-analysis showed that PPI treatment was significantly superior to H2 receptor antagonists (H2RA) treatment (RR = 1.629, 95%CI: 1.422-1.867, P = 0.000) and placebo (RR = 1.903, 95%CI: 1.573-2.302, P = 0.000) for the symptomatic relief of NERD. However, there were no obvious differences between PPI and H2RA (RR = 0.928, 95%CI: 0.776-1.110, P = 0.414) or PPI and the placebo (RR = 1.000, 95%CI: 0.896-1.116, P = 0.997) regarding the rate of adverse events. The overall rate of symptomatic relief of PPI against NERD was 51.4% (95%CI: 0.433-0.595, P = 0.000), and relief was influenced by hiatal hernia (P = 0.030). The adverse rate of PPI against NERD was 21.0% (95%CI: 0.152-0.208, P = 0.000), and was affected by hiatal hernia (P = 0.081) and drinking (P = 0.053). CONCLUSION: PPI overmatched H2RA on symptomatic relief rate but not on adverse rate for NERD. Its relief rate and adverse rate were influenced by hiatal hernia and drinking. PMID:24363534

Surface amplification of pencil graphite electrode with polypyrrole and reduced graphene oxide for fabrication of a guanine/adenine DNA based electrochemical biosensors for determination of didanosine anticancer drug

NASA Astrophysics Data System (ADS)

Karimi-Maleh, Hassan; Bananezhad, Asma; Ganjali, Mohammad R.; Norouzi, Parviz; Sadrnia, Abdolhossein

2018-05-01

Didanosine is nucleoside analog reverse transcriptase inhibitors with many side effects such as nausea and vomiting, stomach pain, tingling, burning and numbness and determination of this drug is very important in biological samples. This paper presents a DNA biosensor for determination of didanosine (DDI) in pharmaceutical samples. A pencil graphite electrode modified with conductive materials such as polypyrrole (PPy) and reduced graphene oxide (rGO) (PGE/PPy/rGO) was used for this goal. The double-stranded DNA was successfully immobilized on PGE/PPy/rGO. The PGE/PPy/rGO was characterized by microscopic and electrochemical methods. Then, the interaction of DDI with DNA was identified by decreases in the oxidation currents of guanine and adenine by differential pulse voltammetric (DPV) method. The dynamic range of DDI identified in the range of 0.02-50.0 μM and this electrode provided a low limit of detection (LOD = 8.0 nM) for DDI. The PGE/PPy/rGO loaded with ds-DNA was utilized for the measurement of DDI in real samples and obtained data were compared with HPLC method. The statistical tests such as F-test and t-test were used for confirming ability of PGE/PPy/rGO loaded with ds-DNA for analysis of DDI in real samples.

Studies on gallium nitride doped ferrite-polypyrrole nanocomposites

NASA Astrophysics Data System (ADS)

Indrakanti, Rajani; Brahmaji Rao, V.; Udaya Kiran, C.

2018-06-01

This communication reports the synthesis and characterisation of two novel Intrinsic conducting polymer nano composites (ICPN s) with the formulae Ga (2x+2) N Fe 2(49-x) O3—PPY synthesized using Impregnation technique. The Gallium nitride ferrite nano particles were synthesized for x = 1 and x = 5 using the above stichiometric equation earlier by Sol—Gel route. The chemical composition in the assembly of the ICPNs were Ga4NFe96O3-3%,10%,30% Polypyrrole, Ga12NFe88O3-3%,10%,30% Polypyrrole by weight. The Sci-Finder software failed to trace any earlier articles or reviews related to these ICNPs synthesised by us in the literature. X-ray Diffractometric (Structural), Morphological, EDAX SAED, IR spectroscopic characterizations were done on the synthesized nanocomposites. Structural studies reveal the semi-crystalline nature of composites. The average crystallite size of nano composites is decreased when compared with nano ferrites. SEM findings reveal that the shape for higher percentage of PPY is nano rods; for lower percentage it is globular. TEM reveals good dispersion and average particle size from histograms are calculated. The FT- IR bands of PPY and GaNFe2O3 are observed which show strong interaction between PPY- GaNFe2O3. Also there is a shift of bands in GaNFe2O3-PPY nano composites when compared to the bands of PPY.

Polyurethane nanofiber strain sensors via in situ polymerization of polypyrrole and application to monitoring joint flexion

NASA Astrophysics Data System (ADS)

Kim, Inhwan; Cho, Gilsoo

2018-07-01

Strain sensors made of intrinsically conductive polymers (ICPs) and nanofibers were fabricated and tested for suitability for use in wearable technology. The sensors were fabricated and evaluated based on their surface appearances, and electrical, tensile, and chemical/thermal properties. Polypyrrole (PPy) was in situ polymerized onto polyurethane (PU) nanofiber substrates by exposing pyrrole monomers to ammonium persulfate as oxidant and 2,6-naphthalenedisulfonic acid disodium salt as doping agents in an aqueous bath. The PPy treated PU nanofibers were then coated with polydimethylsiloxane (PDMS). Both pyrrole concentrations and layer numbers were significantly related to change in electrical conductivity. Specimen treated with 0.1 M of PPy and having three layered structure showed the best electrical conductivity. Regarding tensile strength, the in situ polymerization process decreased tensile strength because the oxidant chemically degraded the PU fibers. Adding layers and PDMS treatment generally improved tensile properties while adding layers created fracture parts in the stress–strain curves. The treatment condition of 0.1 M of PPy, two layered, and PDMS treated specimen showed the best tensile properties as a strain sensor. The chemical property evaluation with Fourier transform infrared and x-ray photoelectron spectroscopy tests showed successful PPy polymerization and PDMS treatments. The functional groups and chemical bonds in polyol, urethane linkage, backbone ring structure in PPy, silicon-based functional groups in PDMS, and elemental content changes by treatment at each stage were characterized. The real-time data acquired from the dummy and five human subjects with repetition of motion at three different speeds of 0.16, 0.25 and 0.5 Hz generated similar trends and tendencies. The PU nanofiber sensors based on PPy and PDMS treatments in this study point to the possibility of developing textiles based wearable strain sensors developed using ICPs.

A retrospective analysis of the role of proton pump inhibitors in colorectal cancer disease survival

PubMed Central

Graham, C.; Orr, C.; Bricks, C.S.; Hopman, W.M.; Hammad, N.; Ramjeesingh, R.

2016-01-01

Background Proton pump inhibitors (ppis) are a commonly used medication. A limited number of studies have identified a weak-to-moderate association between ppi use and colorectal cancer (crc) risk, but none to date have identified an effect of ppi use on crc survival. We therefore postulated that an association between ppi use and crc survival might potentially exist. Methods We performed a retrospective chart review of 1304 crc patients diagnosed from January 2005 to December 2011 and treated at the Cancer Centre of Southeastern Ontario. Kaplan–Meier analysis and Cox proportional hazards regression models were used to evaluate overall survival (os). Results We identified 117 patients (9.0%) who were taking ppis at the time of oncology consult. Those taking a ppi were also more often taking asa or statins (or both) and had a statistically significantly increased rate of cardiac disease. No identifiable difference in tumour characteristics was evident in the two groups, including tumour location, differentiation, lymph node status, and stage. Univariate analysis identified a statistically nonsignificant difference in survival, with those taking a ppi experiencing lesser 1-year (82.1% vs. 86.7%, p = 0.161), 2-year (70.1% vs. 76.8%, p = 0.111), and 5-year os (55.2% vs. 62.9%, p = 0.165). When controlling for patient demographics and tumour characteristics, multivariate Cox regression analysis identified a statistically significant effect of ppi in our patient population (hazard ratio: 1.343; 95% confidence interval: 1.011 to 1.785; p = 0.042). Conclusions Our results suggest a potential adverse effect of ppi use on os in crc patients. These results need further evaluation in prospective analyses. PMID:28050148

Delocalization of π electrons and trapping action of ZnO nanoparticles in PPY matrix for hybrid solar cell application

NASA Astrophysics Data System (ADS)

Singh, Rajinder; Choudhary, Ram Bilash; Kandulna, Rohit

2018-03-01

Polypyrrole (PPY)-Zinc Oxide (ZnO) nanocomposites with varying concentration of ZnO (1:1-1:4) were prepared via in-situ polymerization technique by using pyrrole monomer in the presence of ammonium persulphate (APS) as oxidant. Globular morphology of PPY and sheet like structure of ZnO was examined using FESEM and EDAX. FTIR showed the presence of vibration modes in fingerprint region (1500 cm-1-500 cm-1) for metal oxides confirming the presence and interaction of ZnO with the polymer matrix in nanocomposites. Amorphous nature of PPY and hexagonal wurtzite structure of ZnO was confirmed using XRD with average crystallite size within 20 nm-30 nm. PANI-ZnO (1:1) exhibited blue shift in comparison to PPY (neat) and optimized optical band gap ∼ 1.81 eV. The effect of carrier concentration was investigated using electrochemical analyzer and maximum current was recorded for PANI-ZnO (1:1). The highest conductance was calculated for PANI-ZnO (1:1) ∼ 7.3242 × 10-3 S using current -voltage characteristics. Thermal stability was found to be increasing with the increase in ZnO concentration PANI-ZnO nanocomposite.

Stabilization of protein-protein interactions in drug discovery.

PubMed

Andrei, Sebastian A; Sijbesma, Eline; Hann, Michael; Davis, Jeremy; O'Mahony, Gavin; Perry, Matthew W D; Karawajczyk, Anna; Eickhoff, Jan; Brunsveld, Luc; Doveston, Richard G; Milroy, Lech-Gustav; Ottmann, Christian

2017-09-01

PPIs are involved in every disease and specific modulation of these PPIs with small molecules would significantly improve our prospects of developing therapeutic agents. Both industry and academia have engaged in the identification and use of PPI inhibitors. However in comparison, the opposite strategy of employing small-molecule stabilizers of PPIs is underrepresented in drug discovery. Areas covered: PPI stabilization has not been exploited in a systematic manner. Rather, this concept validated by a number of therapeutically used natural products like rapamycin and paclitaxel has been shown retrospectively to be the basis of the activity of synthetic molecules originating from drug discovery projects among them lenalidomide and tafamidis. Here, the authors cover the growing number of synthetic small-molecule PPI stabilizers to advocate for a stronger consideration of this as a drug discovery approach. Expert opinion: Both the natural products and the growing number of synthetic molecules show that PPI stabilization is a viable strategy for drug discovery. There is certainly a significant challenge to adapt compound libraries, screening techniques and downstream methodologies to identify, characterize and optimize PPI stabilizers, but the examples of molecules reviewed here in our opinion justify these efforts.

Titanium carbide nanocube core induced interfacial growth of crystalline polypyrrole/polyvinyl alcohol lamellar shell for wide-temperature range supercapacitors

NASA Astrophysics Data System (ADS)

Weng, Yu-Ting; Pan, Hsiao-An; Wu, Nae-Lih; Chen, Geroge Zheng

2015-01-01

This is the first investigation on electrically conducting polymers-based supercapacitor electrodes over a wide temperature range, from -18 °C to 60 °C. A high-performance supercapacitor electrode material consisting of TiC nanocube core and conformal crystalline polypyrrole (PPy)/poly-vinyl-alcohol (PVA) lamellar shell has been synthesized by heterogeneous nucleation-induced interfacial crystallization. PPy is induced to crystallize on the negatively charged TiC nanocube surfaces via strong interfacial interactions. In this organic-inorganic hybrid nanocomposite, the long chain PVA enables enhanced cycle life due to improved mechanical properties, and the TiC nanocube not only contributes to electron conduction, but also dictates the PPy morphology/crystallinity for maximizing the charging-discharging performance. The crystalline PPy/PAV layer on the TiC nanocube offers unprecedented high capacity (>350 F g-1-PPy at 300 mV s-1 with ΔV = 1.6 V) and cycling stability in a temperature range from -18 °C to 60 °C. The presented hybrid-filler and interfacial crystallization strategies can be applied to the exploration of new-generation high-power conducting polymer-based supercapacitor materials.

Mechanism of reactant and product dissociation from the anthrax edema factor: a locally enhanced sampling and steered molecular dynamics study.

PubMed

Martínez, Leandro; Malliavin, Thérèse E; Blondel, Arnaud

2011-05-01

The anthrax edema factor is a toxin overproducing damaging levels of cyclic adenosine monophosphate (cAMP) and pyrophosphate (PPi) from ATP. Here, mechanisms of dissociation of ATP and products (cAMP, PPi) from the active site are studied using locally enhanced sampling (LES) and steered molecular dynamics simulations. Various substrate conformations and ionic binding modes found in crystallographic structures are considered. LES simulations show that PPi and cAMP dissociate through different solvent accessible channels, while ATP dissociation requires significant active site exposure to solvent. The ionic content of the active site directly affects the dissociation of ATP and products. Only one ion dissociates along with ATP in the two-Mg(2+) binding site, suggesting that the other ion binds EF prior to ATP association. Dissociation of reaction products cAMP and PPi is impaired by direct electrostatic interactions between products and Mg(2+) ions. This provides an explanation for the inhibitory effect of high Mg(2+) concentrations on EF enzymatic activity. Breaking of electrostatic interactions is dependent on a competitive binding of water molecules to the ions, and thus on the solvent accessibility of the active site. Consequently, product dissociation seems to be a two-step process. First, ligands are progressively solvated while preserving the most important electrostatic interactions, in a process that is dependent on the flexibility of the active site. Second, breakage of the electrostatic bonds follows, and ligands diffuse into solvent. In agreement with this mechanism, product protonation facilitates dissociation.

Proton pump inhibitor resistance, the real challenge in gastro-esophageal reflux disease.

PubMed

Cicala, Michele; Emerenziani, Sara; Guarino, Michele Pier Luca; Ribolsi, Mentore

2013-10-21

Gastro-esophageal reflux disease (GERD) is one of the most prevalent chronic diseases. Although proton pump inhibitors (PPIs) represent the mainstay of treatment both for healing erosive esophagitis and for symptom relief, several studies have shown that up to 40% of GERD patients reported either partial or complete lack of response of their symptoms to a standard PPI dose once daily. Several mechanisms have been proposed as involved in PPIs resistance, including ineffective control of gastric acid secretion, esophageal hypersensitivity, ultrastructural and functional changes in the esophageal epithelium. The diagnostic evaluation of a refractory GERD patients should include an accurate clinical evaluation, upper endoscopy, esophageal manometry and ambulatory pH-impedance monitoring, which allows to discriminate non-erosive reflux disease patients from those presenting esophageal hypersensitivity or functional heartburn. Treatment has been primarily based on doubling the PPI dose or switching to another PPI. Patients with proven disease, not responding to PPI twice daily, are eligible for anti-reflux surgery.

Stringent DDI-based Prediction of H. sapiens-M. tuberculosis H37Rv Protein-Protein Interactions

PubMed Central

2013-01-01

Background H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are very important information to illuminate the infection mechanism of M. tuberculosis H37Rv. But current H. sapiens-M. tuberculosis H37Rv PPI data are very scarce. This seriously limits the study of the interaction between this important pathogen and its host H. sapiens. Computational prediction of H. sapiens-M. tuberculosis H37Rv PPIs is an important strategy to fill in the gap. Domain-domain interaction (DDI) based prediction is one of the frequently used computational approaches in predicting both intra-species and inter-species PPIs. However, the performance of DDI-based host-pathogen PPI prediction has been rather limited. Results We develop a stringent DDI-based prediction approach with emphasis on (i) differences between the specific domain sequences on annotated regions of proteins under the same domain ID and (ii) calculation of the interaction strength of predicted PPIs based on the interacting residues in their interaction interfaces. We compare our stringent DDI-based approach to a conventional DDI-based approach for predicting PPIs based on gold standard intra-species PPIs and coherent informative Gene Ontology terms assessment. The assessment results show that our stringent DDI-based approach achieves much better performance in predicting PPIs than the conventional approach. Using our stringent DDI-based approach, we have predicted a small set of reliable H. sapiens-M. tuberculosis H37Rv PPIs which could be very useful for a variety of related studies. We also analyze the H. sapiens-M. tuberculosis H37Rv PPIs predicted by our stringent DDI-based approach using cellular compartment distribution analysis, functional category enrichment analysis and pathway enrichment analysis. The analyses support the validity of our prediction result. Also, based on an analysis of the H. sapiens-M. tuberculosis H37Rv PPI network predicted by our stringent DDI-based approach, we have discovered some important properties of domains involved in host-pathogen PPIs. We find that both host and pathogen proteins involved in host-pathogen PPIs tend to have more domains than proteins involved in intra-species PPIs, and these domains have more interaction partners than domains on proteins involved in intra-species PPI. Conclusions The stringent DDI-based prediction approach reported in this work provides a stringent strategy for predicting host-pathogen PPIs. It also performs better than a conventional DDI-based approach in predicting PPIs. We have predicted a small set of accurate H. sapiens-M. tuberculosis H37Rv PPIs which could be very useful for a variety of related studies. PMID:24564941

Relevance of protein-protein interactions on the biological identity of nanoparticles.

PubMed

Vasti, Cecilia; Bonnet, Laura V; Galiano, Mauricio R; Rojas, Ricardo; Giacomelli, Carla E

2018-06-01

Considering that the use of nanoparticles (NPs) as carriers of therapeutic or theranostic agents has increased in the last years, it is mandatory to understand the interaction between NPs and living systems. In contact with biological fluids, the NPs (synthetic identity) are covered with biomolecules that form a protein corona, which defines the biological identity. It is well known that the protein corona formation is mediated by non-specific physical interactions, but protein-protein interactions (PPI), involving specific recognition sites of the polypeptides, are also involved. This work explores the relationship between the synthetic and biological identities of layered double hydroxides nanoparticles (LDH-NPs) and the effect of the protein corona on the cellular response. With such a purpose, the synthetic identity was modified by coating LDH-NPs with either a single protein or a complex mixture of them, followed by the characterization of the protein corona formed in a commonly used cell culture medium. A proteomic approach was used to identify the protein corona molecules and the PPI network was constructed with a novel bioinformatic tool. The coating on LDH-NPs defines the biological identity in such a way that the composition of the protein corona as well as PPI are changed. Electrostatic interactions appear not to be the only driving force regulating the interactions between NPs, proteins and cells since the specific recognition also play a fundamental role. However, the biological identity of LDH-NPs does not affect the interactions with cells that shows negligible cytotoxicity and high internalization levels. Copyright © 2018 Elsevier B.V. All rights reserved.

Taking patient and public involvement online: qualitative evaluation of an online forum for palliative care and rehabilitation research.

PubMed

Brighton, Lisa Jane; Pask, Sophie; Benalia, Hamid; Bailey, Sylvia; Sumerfield, Marion; Witt, Jana; de Wolf-Linder, Susanne; Etkind, Simon Noah; Murtagh, Fliss E M; Koffman, Jonathan; Evans, Catherine J

2018-01-01

Patient and public involvement (PPI) is increasingly recognised as important in research. Most PPI takes place face-to-face, but this can be difficult for people who are unwell or have caring responsibilities. As these challenges are particularly common in palliative care and rehabilitation research, we developed an online forum for PPI: www.csipublicinvolvement.co.uk. In this study, we explored how well the online forum worked, if it is a suitable method for PPI, and how PPI members and researchers reacted to using it. We used an existing theory about online interventions to help choose the 'right' questions to ask participants. We invited PPI members and researchers who had used the online forum to participate in focus groups, and identified the most important themes discussed. Within this study, PPI members have helped with the interview questions, analysis, and write up. Overall, four PPI members and five researchers participated in the focus groups. Participants felt the online forum worked well and had multiple benefits. From the discussions, we identified four key questions to consider when developing online methods for PPI: how does the forum work, how does it engage people, how does it empower people, and what is the impact? Participants suggested the forum could be improved by being more PPI and less researcher focused. We conclude that when developing online methods of PPI, a functioning forum is not enough: it also needs to be engaging and empowering to have an impact. Future work can use these four domains when developing their own online PPI methods. Patient and public involvement (PPI) in research is increasingly recognised as important. Most PPI activities take place face-to-face, yet this can be difficult for people with ill health or caring responsibilities, and may exclude people from hard-to-reach populations (e.g. living in vulnerable social circumstances and/or remote geographical locations). These challenges are particularly pertinent in palliative care and rehabilitation research where people often live with, or care for someone with, advanced illness. In response to this, we aimed to test the functionality, feasibility, and acceptability of an online forum for PPI for palliative care and rehabilitation research (www.csipublicinvolvement.co.uk). We conducted separate focus groups with PPI members and researchers who had used the online forum. Data collection was underpinned by DeLone and Mclean's model of information systems success. Focus groups were recorded, transcribed, and analysed using inductive thematic analysis. Dual coding by two authors ensured rigour, and attention was paid to divergent cases. Four PPI members and five researchers participated in the focus groups (two PPI focus groups, one researcher focus group). The online forum was perceived as functional, feasible, and acceptable. Our analysis identified four key questions to consider when developing online methods for PPI: (1) how does the forum work, (2) how does it engage people, (3) how does it empower people, and (4) what is the impact? PPI members felt that the online forum was too researcher led, and needed to be more PPI focussed. When developing online methods of PPI, a functioning forum is not enough: it also needs to be engaging and empowering to have an impact. To optimise online involvement, future work should refer to these four domains and balance the needs of researchers and PPI members.

Realistic expectations of prepulse inhibition in translational models for schizophrenia research

PubMed Central

Swerdlow, Neal R.; Weber, Martin; Qu, Ying; Light, Gregory A.; Braff, David L.

2009-01-01

Introduction Under specific conditions, a weak lead stimulus, or “prepulse”, can inhibit the startling effects of a subsequent intense abrupt stimulus. This startle-inhibiting effect of the prepulse, termed “prepulse inhibition” (PPI), is widely used in translational models to understand the biology of brain based inhibitory mechanisms and their deficiency in neuropsychiatric disorders. In 1981, four published reports with “prepulse inhibition” as an index term were listed on Medline; over the past 5 years, new published Medline reports with “prepulse inhibition” as an index term have appeared at a rate exceeding once every 2.7 days (n = 678). Most of these reports focus on the use of PPI in translational models of impaired sensorimotor gating in schizophrenia. This rapid expansion and broad application of PPI as a tool for understanding schizophrenia has, at times, outpaced critical thinking and falsifiable hypotheses about the relative strengths vs. limitations of this measure. Objectives This review enumerates the realistic expectations for PPI in translational models for schizophrenia research, and provides cautionary notes for the future applications of this important research tool. Conclusion In humans, PPI is not “diagnostic”; levels of PPI do not predict clinical course, specific symptoms, or individual medication responses. In preclinical studies, PPI is valuable for evaluating models or model organisms relevant to schizophrenia, “mapping” neural substrates of deficient PPI in schizophrenia, and advancing the discovery and development of novel therapeutics. Across species, PPI is a reliable, robust quantitative phenotype that is useful for probing the neurobiology and genetics of gating deficits in schizophrenia. PMID:18568339

Corrosion Protection Properties of PPy-ND Composite Coating: Sonoelectrochemical Synthesis and Design of Experiment

NASA Astrophysics Data System (ADS)

Ashassi-Sorkhabi, H.; Bagheri, R.; Rezaei-Moghadam, B.

2016-02-01

In this research, the nanocomposite coatings comprising the polypyrrole-nanodiamond, PPy-ND, on St-12 steel electrodes were electro-synthesized using in situ polymerization process under ultrasonic irradiation. The corrosion protection performance and morphology characterization of prepared coatings were investigated by electrochemical methods and scanning electron microscopy, SEM, respectively. Also, the experimental design was employed to determine the best values considering the effective parameters such as the concentration of nanoparticles, the applied current density and synthesis time to achieve the most protective films. A response surface methodology, RSM, involving a central composite design, CCD, was applied to the modeling and optimization of the PPy-ND nanocomposite deposition. Pareto graphic analysis of the parameters indicated that the applied current density and some of the interactions were effective on the response. The electrochemical results proved that the embedment of diamond nanoparticle, DNP, improves the corrosion resistance of PPy coatings significantly. Therefore, desirable correlation exists between predicted data and experimental results.

An unexpected way forward: towards a more accurate and rigorous protein-protein binding affinity scoring function by eliminating terms from an already simple scoring function.

PubMed

Swanson, Jon; Audie, Joseph

2018-01-01

A fundamental and unsolved problem in biophysical chemistry is the development of a computationally simple, physically intuitive, and generally applicable method for accurately predicting and physically explaining protein-protein binding affinities from protein-protein interaction (PPI) complex coordinates. Here, we propose that the simplification of a previously described six-term PPI scoring function to a four term function results in a simple expression of all physically and statistically meaningful terms that can be used to accurately predict and explain binding affinities for a well-defined subset of PPIs that are characterized by (1) crystallographic coordinates, (2) rigid-body association, (3) normal interface size, and hydrophobicity and hydrophilicity, and (4) high quality experimental binding affinity measurements. We further propose that the four-term scoring function could be regarded as a core expression for future development into a more general PPI scoring function. Our work has clear implications for PPI modeling and structure-based drug design.

Incorporation of hydrogel as a sensing medium for recycle of sensing material in chemical sensors

NASA Astrophysics Data System (ADS)

Hwang, Yunjung; Park, Jeong Yong; Kwon, Oh Seok; Joo, Seokwon; Lee, Chang-Soo; Bae, Joonwon

2018-01-01

A hydrogel, produced with agarose extracted from seaweed, was introduced as a reusable medium in ultrasensitive sensors employing conducting polymer nanomaterials and aptamers. A basic dopamine (DA) sensor was constructed by placing a hydrogel, containing a sensing material composed of aptamer-linked carboxylated polypyrrole nanotubes (PPy-COOH NTs), onto a micropatterned gold electrode. The hydrogel provided a benign electrochemical environment, facilitated specific interactions between DA and the PPy-COOH NT sensing material, and simplified the retrieval of PPy-COOH NTs after detection. It was demonstrated that the agarose hydrogel was successfully employed as a sensing medium for detection of DA, providing a benign environment for the electrode type sensor. PPy-COOH NTs were recovered by simply heating the hydrogel in water. The hydrogel also afforded stable signal intensity after repeated use with a limit of detection of 1 nmol and a clear, stable signal up to 100 nmol DA. This work provides relevant information for future research on reusable or recyclable sensors.

Ranking support vector machine for multiple kernels output combination in protein-protein interaction extraction from biomedical literature.

PubMed

Yang, Zhihao; Lin, Yuan; Wu, Jiajin; Tang, Nan; Lin, Hongfei; Li, Yanpeng

2011-10-01

Knowledge about protein-protein interactions (PPIs) unveils the molecular mechanisms of biological processes. However, the volume and content of published biomedical literature on protein interactions is expanding rapidly, making it increasingly difficult for interaction database curators to detect and curate protein interaction information manually. We present a multiple kernel learning-based approach for automatic PPI extraction from biomedical literature. The approach combines the following kernels: feature-based, tree, and graph and combines their output with Ranking support vector machine (SVM). Experimental evaluations show that the features in individual kernels are complementary and the kernel combined with Ranking SVM achieves better performance than those of the individual kernels, equal weight combination and optimal weight combination. Our approach can achieve state-of-the-art performance with respect to the comparable evaluations, with 64.88% F-score and 88.02% AUC on the AImed corpus. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Learning to work together - lessons from a reflective analysis of a research project on public involvement.

PubMed

Howe, A; Mathie, E; Munday, D; Cowe, M; Goodman, C; Keenan, J; Kendall, S; Poland, F; Staniszewska, S; Wilson, P

2017-01-01

Patient and public involvement (PPI) in research is very important, and funders and the NHS all expect this to happen. What this means in practice, and how to make it really successful, is therefore an important research question. This article analyses the experience of a research team using PPI, and makes recommendations on strengthening PPI in research. There were different PPI roles in our study - some people were part of the research team: some were on the advisory group; and there were patient groups who gave specific feedback on how to make research work better for their needs. We used minutes, other written documents, and structured individual and group reflections to learn from our own experiences over time. The main findings were:- for researchers and those in a PPI role to work in partnership, project structures must allow flexibility and responsiveness to different people's ideas and needs; a named link person can ensure support; PPI representatives need to feel fully included in the research; make clear what is expected for all roles; and ensure enough time and funding to allow meaningful involvement. Some roles brought more demands but also more rewards than others - highlighting that it is important that people giving up their time to help with research experience gains from doing so. Those contributing to PPI on a regular basis may want to learn new skills, rather than always doing the same things. Researchers and the public need to find ways to develop roles in PPI over time. We also found that, even for a team with expertise in PPI, there was a need both for understanding of different ways to contribute, and an evolving 'normalisation' of new ways of working together over time, which both enriched the process and the outputs. Background Patient and public involvement (PPI) is now an expectation of research funders, in the UK, but there is relatively little published literature on what this means in practice - nor is there much evaluative research about implementation and outputs. Policy literature endorses the need to include PPI representation at all stages of planning, performing and research dissemination, and recommends resource allocation to these roles; but details of how to make such inputs effective in practice are less common. While literature on power and participation informs the debate, there are relatively few published case studies of how this can play out through the lived experience of PPI in research; early findings highlight key issues around access to knowledge, resources, and interpersonal respect. This article describes the findings of a case study of PPI within a study about PPI in research. Methods The aim of the study was to look at how the PPI representatives' inputs had developed over time, key challenges and changes, and lessons learned. We used realist evaluation and normalisation process theory to frame and analyse the data, which was drawn from project documentation, minutes of meetings and workshops, field notes and observations made by PPI representatives and researchers; documented feedback after meetings and activities; and the structured feedback from two formal reflective meetings. Results Key findings included the need for named contacts who support, integrate and work with PPI contributors and researchers, to ensure partnership working is encouraged and supported to be as effective as possible. A structure for partnership working enabled this to be enacted systematically across all settings. Some individual tensions were nonetheless identified around different roles, with possible implications for clarifying expectations and deepening understandings of the different types of PPI contribution and of their importance. Even in a team with research expertise in PPI, the data showed that there were different phases and challenges to 'normalising' the PPI input to the project. Mutual commitment and flexibility, embedded through relationships across the team, led to inclusion and collaboration. Conclusion Work on developing relationships and teambuilding are as important for enabling partnership between PPI representatives and researchers as more practical components such as funding and information sharing. Early explicit exploration of the different roles and their contributions may assist effective participation and satisfaction.

Comparison of generation 3 polyamidoamine dendrimer and generation 4 polypropylenimine dendrimer on drug loading, complex structure, release behavior, and cytotoxicity

PubMed Central

Shao, Naimin; Su, Yunzhang; Hu, Jingjing; Zhang, Jiahai; Zhang, Hongfeng; Cheng, Yiyun

2011-01-01

Background Polyamidoamine (PAMAM) and polypropylenimine (PPI) dendrimers are the commercially available and most widely used dendrimers in pharmaceutical sciences and biomedical engineering. In the present study, the loading and release behaviors of generation 3 PAMAM and generation 4 PPI dendrimers with the same amount of surface amine groups (32 per dendrimer) were compared using phenylbutazone as a model drug. Methods The dendrimer-phenylbutazone complexes were characterized by 1H nuclear magnetic resonance and nuclear Overhauser effect techniques, and the cytotoxicity of each dendrimer was evaluated. Results Aqueous solubility results suggest that the generation 3 PAMAM dendrimer has a much higher loading ability towards phenylbutazone in comparison with the generation 4 PPI dendrimer at high phenylbutazone-dendrimer feeding ratios. Drug release was much slower from the generation 3 PAMAM matrix than from the generation 4 PPI dendrimer. In addition, the generation 3 PAMAM dendrimer is at least 50-fold less toxic than generation 4 PPI dendrimer on MCF-7 and A549 cell lines. Conclusion Although the nuclear Overhauser effect nuclear magnetic resonance results reveal that the generation 4 PPI dendrimer with a more hydrophobic interior encapsulates more phenylbutazone, the PPI dendrimer-phenylbutazone inclusion is not stable in aqueous solution, which poses a great challenge during drug development. PMID:22267921

Pacemaker implantation rate after transcatheter aortic valve implantation with early and new-generation devices: a systematic review.

PubMed

van Rosendael, Philippe J; Delgado, Victoria; Bax, Jeroen J

2018-06-01

The incidence of new-onset conduction abnormalities requiring permanent pacemaker implantation (PPI) after transcatheter aortic valve implantation (TAVI) with new-generation prostheses remains debated. This systematic review analyses the incidence of PPI after TAVI with new-generation devices and evaluates the electrical, anatomical, and procedural factors associated with PPI. In addition, the incidence of PPI after TAVI with early generation prostheses was reviewed for comparison. According to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses checklist, this systematic review screened original articles published between October 2010 and October 2017, reporting on the incidence of PPI after implantation of early and new-generation TAVI prostheses. Of the 1406 original articles identified in the first search for new-generation TAVI devices, 348 articles were examined for full text, and finally, 40 studies (n = 17 139) were included. The incidence of a PPI after the use of a new-generation TAVI prosthesis ranged between 2.3% and 36.1%. For balloon-expandable prostheses, the PPI rate remained low when using an early generation SAPIEN device (ranging between 2.3% and 28.2%), and with the new-generation SAPIEN 3 device, the PPI rate was between 4.0% and 24.0%. For self-expandable prostheses, the PPI rates were higher with the early generation CoreValve device (16.3-37.7%), and despite a reduction in PPI rates with the new Evolut R, the rates remained relatively higher (14.7-26.7%). When dividing the studies according to the highest (>26.0%) and the lowest (<12.1%) quintile of PPI rate, patients within the highest quintile were more frequently women when compared with the lowest quintile group (50.9% vs. 46.3%, P < 0.001). Pre-existent conduction abnormalities (electrical factor), calcification of the left ventricular outflow tract (anatomical factor), and balloon valvuloplasty and depth of implantation (procedural factors) were associated with increased risk of PPI. The rate of PPI after TAVI with new-generation devices is highly variable. Specific recommendations for implantation of each prosthesis, taking into consideration the presence of pre-existent conduction abnormalities and anatomical factors, may be needed to reduce the risk of PPI.

Integrative network alignment reveals large regions of global network similarity in yeast and human.

PubMed

Kuchaiev, Oleksii; Przulj, Natasa

2011-05-15

High-throughput methods for detecting molecular interactions have produced large sets of biological network data with much more yet to come. Analogous to sequence alignment, efficient and reliable network alignment methods are expected to improve our understanding of biological systems. Unlike sequence alignment, network alignment is computationally intractable. Hence, devising efficient network alignment heuristics is currently a foremost challenge in computational biology. We introduce a novel network alignment algorithm, called Matching-based Integrative GRAph ALigner (MI-GRAAL), which can integrate any number and type of similarity measures between network nodes (e.g. proteins), including, but not limited to, any topological network similarity measure, sequence similarity, functional similarity and structural similarity. Hence, we resolve the ties in similarity measures and find a combination of similarity measures yielding the largest contiguous (i.e. connected) and biologically sound alignments. MI-GRAAL exposes the largest functional, connected regions of protein-protein interaction (PPI) network similarity to date: surprisingly, it reveals that 77.7% of proteins in the baker's yeast high-confidence PPI network participate in such a subnetwork that is fully contained in the human high-confidence PPI network. This is the first demonstration that species as diverse as yeast and human contain so large, continuous regions of global network similarity. We apply MI-GRAAL's alignments to predict functions of un-annotated proteins in yeast, human and bacteria validating our predictions in the literature. Furthermore, using network alignment scores for PPI networks of different herpes viruses, we reconstruct their phylogenetic relationship. This is the first time that phylogeny is exactly reconstructed from purely topological alignments of PPI networks. Supplementary files and MI-GRAAL executables: http://bio-nets.doc.ic.ac.uk/MI-GRAAL/.

Prediction of Protein-Protein Interaction Sites with Machine-Learning-Based Data-Cleaning and Post-Filtering Procedures.

PubMed

Liu, Guang-Hui; Shen, Hong-Bin; Yu, Dong-Jun

2016-04-01

Accurately predicting protein-protein interaction sites (PPIs) is currently a hot topic because it has been demonstrated to be very useful for understanding disease mechanisms and designing drugs. Machine-learning-based computational approaches have been broadly utilized and demonstrated to be useful for PPI prediction. However, directly applying traditional machine learning algorithms, which often assume that samples in different classes are balanced, often leads to poor performance because of the severe class imbalance that exists in the PPI prediction problem. In this study, we propose a novel method for improving PPI prediction performance by relieving the severity of class imbalance using a data-cleaning procedure and reducing predicted false positives with a post-filtering procedure: First, a machine-learning-based data-cleaning procedure is applied to remove those marginal targets, which may potentially have a negative effect on training a model with a clear classification boundary, from the majority samples to relieve the severity of class imbalance in the original training dataset; then, a prediction model is trained on the cleaned dataset; finally, an effective post-filtering procedure is further used to reduce potential false positive predictions. Stringent cross-validation and independent validation tests on benchmark datasets demonstrated the efficacy of the proposed method, which exhibits highly competitive performance compared with existing state-of-the-art sequence-based PPIs predictors and should supplement existing PPI prediction methods.

Recent coselection in human populations revealed by protein-protein interaction network.

PubMed

Qian, Wei; Zhou, Hang; Tang, Kun

2014-12-21

Genome-wide scans for signals of natural selection in human populations have identified a large number of candidate loci that underlie local adaptations. This is surprising given the relatively short evolutionary time since the divergence of the human population. One hypothesis that has not been formally examined is whether and how the recent human evolution may have been shaped by coselection in the context of complex molecular interactome. In this study, genome-wide signals of selection were scanned in East Asians, Europeans, and Africans using 1000 Genome data, and subsequently mapped onto the protein-protein interaction (PPI) network. We found that the candidate genes of recent positive selection localized significantly closer to each other on the PPI network than expected, revealing substantial clustering of selected genes. Furthermore, gene pairs of shorter PPI network distances showed higher similarities of their recent evolutionary paths than those further apart. Last, subnetworks enriched with recent coselection signals were identified, which are substantially overrepresented in biological pathways related to signal transduction, neurogenesis, and immune function. These results provide the first genome-wide evidence for association of recent selection signals with the PPI network, shedding light on the potential mechanisms of recent coselection in the human genome. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Structure-based drug design, synthesis and biological assays of P. falciparum Atg3-Atg8 protein-protein interaction inhibitors

NASA Astrophysics Data System (ADS)

Villa, Stefania; Legnani, Laura; Colombo, Diego; Gelain, Arianna; Lammi, Carmen; Bongiorno, Daniele; Ilboudo, Denise P.; McGee, Kellen E.; Bosch, Jürgen; Grazioso, Giovanni

2018-03-01

The proteins involved in the autophagy (Atg) pathway have recently been considered promising targets for the development of new antimalarial drugs. In particular, inhibitors of the protein-protein interaction (PPI) between Atg3 and Atg8 of Plasmodium falciparum retarded the blood- and liver-stages of parasite growth. In this paper, we used computational techniques to design a new class of peptidomimetics mimicking the Atg3 interaction motif, which were then synthesized by click-chemistry. Surface plasmon resonance has been employed to measure the ability of these compounds to inhibit the Atg3-Atg8 reciprocal protein-protein interaction. Moreover, P. falciparum growth inhibition in red blood cell cultures was evaluated as well as the cyto-toxicity of the compounds.

Potential Interference of Protein-Protein Interactions by Graphyne.

PubMed

Luan, Binquan; Huynh, Tien; Zhou, Ruhong

2016-03-10

Graphyne has attracted tremendous attention recently due to its many potentially superior properties relative to those of graphene. Although extensive efforts have been devoted to explore the applicability of graphyne as an alternative nanomaterial for state-of-the-art nanotechnology (including biomedical applications), knowledge regarding its possible adverse effects to biological cells is still lacking. Here, using large-scale all-atom molecular dynamics simulations, we investigate the potential toxicity of graphyne by interfering a protein-protein interaction (ppI). We found that graphyne could indeed disrupt the ppIs by cutting through the protein-protein interface and separating the protein complex into noncontacting ones, due to graphyne's dispersive and hydrophobic interaction with the hydrophobic residues residing at the dimer interface. Our results help to elucidate the mechanism of interaction between graphyne and ppI networks within a biological cell and provide insights for its hazard reduction.

MEGADOCK: An All-to-All Protein-Protein Interaction Prediction System Using Tertiary Structure Data

PubMed Central

Ohue, Masahito; Matsuzaki, Yuri; Uchikoga, Nobuyuki; Ishida, Takashi; Akiyama, Yutaka

2014-01-01

The elucidation of protein-protein interaction (PPI) networks is important for understanding cellular structure and function and structure-based drug design. However, the development of an effective method to conduct exhaustive PPI screening represents a computational challenge. We have been investigating a protein docking approach based on shape complementarity and physicochemical properties. We describe here the development of the protein-protein docking software package “MEGADOCK” that samples an extremely large number of protein dockings at high speed. MEGADOCK reduces the calculation time required for docking by using several techniques such as a novel scoring function called the real Pairwise Shape Complementarity (rPSC) score. We showed that MEGADOCK is capable of exhaustive PPI screening by completing docking calculations 7.5 times faster than the conventional docking software, ZDOCK, while maintaining an acceptable level of accuracy. When MEGADOCK was applied to a subset of a general benchmark dataset to predict 120 relevant interacting pairs from 120 x 120 = 14,400 combinations of proteins, an F-measure value of 0.231 was obtained. Further, we showed that MEGADOCK can be applied to a large-scale protein-protein interaction-screening problem with accuracy better than random. When our approach is combined with parallel high-performance computing systems, it is now feasible to search and analyze protein-protein interactions while taking into account three-dimensional structures at the interactome scale. MEGADOCK is freely available at http://www.bi.cs.titech.ac.jp/megadock. PMID:23855673

Rice cyclophilin OsCYP18-2 is translocated to the nucleus by an interaction with SKIP and enhances drought tolerance in rice and Arabidopsis.

PubMed

Lee, Sang Sook; Park, Hyun Ji; Yoon, Dae Hwa; Kim, Beom-Gi; Ahn, Jun Cheul; Luan, Sheng; Cho, Hye Sun

2015-10-01

Cyclophilin 18-2 (CYP18-2) genes, homologues of human peptidyl-prolyl isomerase-like 1 (PPiL1), are conserved across multicellular organisms and Schizosaccharomyces pombe. Although PPiL1 is known to interact with ski-interacting protein (SKIP), a transcriptional co-regulator and spliceosomal component, there have been no functional analyses of PPiL1 homologues in plants. Rice cyclophilin 18-2 (OsCYP18-2) bound directly to amino acids 56-95 of OsSKIP and its binding was independent of cyclosporin A, a cyclophilin-binding drug. Moreover, OsCYP18-2 exhibited PPIase activity regardless of its interaction with OsSKIP. Therefore, the binding site for OsCYP18-2's interaction with SKIP was distinct from the PPIase active site. OsCYP18-2's interaction with SKIP full-length protein enabled OsCYP18-2's translocation from the cytoplasm into the nucleus and AtSKIP interacted in planta with both AtCYP18-2 and OsCYP18-2. Drought and salt stress induced similar expression of OsCYP18-2 and OsSKIP. Overexpression of OsCYP18-2 in transgenic rice and Arabidopsis thaliana plants enhanced drought tolerance and altered expression and pre-mRNA splicing patterns of stress-related genes in Arabidopsis under drought conditions. Furthermore, OsCYP18-2 caused transcriptional activation with/without OsSKIP in the GAL4 system of yeast; thus the OsSKIP-OsCYP18-2 interaction has an important role in the transcriptional and post-transcriptional regulation of stress-related genes and increases tolerance to drought stress. © 2015 John Wiley & Sons Ltd.

Prediction and redesign of protein–protein interactions

PubMed Central

Lua, Rhonald C.; Marciano, David C.; Katsonis, Panagiotis; Adikesavan, Anbu K.; Wilkins, Angela D.; Lichtarge, Olivier

2014-01-01

Understanding the molecular basis of protein function remains a central goal of biology, with the hope to elucidate the role of human genes in health and in disease, and to rationally design therapies through targeted molecular perturbations. We review here some of the computational techniques and resources available for characterizing a critical aspect of protein function – those mediated by protein–protein interactions (PPI). We describe several applications and recent successes of the Evolutionary Trace (ET) in identifying molecular events and shapes that underlie protein function and specificity in both eukaryotes and prokaryotes. ET is a part of analytical approaches based on the successes and failures of evolution that enable the rational control of PPI. PMID:24878423

Discovering disease-associated genes in weighted protein-protein interaction networks

NASA Astrophysics Data System (ADS)

Cui, Ying; Cai, Meng; Stanley, H. Eugene

2018-04-01

Although there have been many network-based attempts to discover disease-associated genes, most of them have not taken edge weight - which quantifies their relative strength - into consideration. We use connection weights in a protein-protein interaction (PPI) network to locate disease-related genes. We analyze the topological properties of both weighted and unweighted PPI networks and design an improved random forest classifier to distinguish disease genes from non-disease genes. We use a cross-validation test to confirm that weighted networks are better able to discover disease-associated genes than unweighted networks, which indicates that including link weight in the analysis of network properties provides a better model of complex genotype-phenotype associations.

High doses of salicylate causes prepulse facilitation of onset-gap induced acoustic startle response.

PubMed

Sun, Wei; Doolittle, Lauren; Flowers, Elizabeth; Zhang, Chao; Wang, Qiuju

2014-01-01

Prepulse inhibition of acoustic startle reflex (PPI), a well-established method for evaluating sensorimotor gating function, has been used to detect tinnitus in animal models. Reduced gap induced PPI (gap-PPI) was considered as a sign of tinnitus. The silent gap used in the test contains both onset and offset signals. Tinnitus may affect these cues differently. In this experiment, we studied the effects of a high dose of salicylate (250 mg/kg, i.p.), an inducer of reversible tinnitus and sensorineural hearing loss, on gap-PPI induced by three different gaps: an onset-gap with 0.1 ms onset and 25 ms offset time, an offset-gap with 25 ms onset and 0.1 ms offset time, and an onset-offset-gap with 0.1 ms onset and offset time. We found that the onset-gaps induced smaller inhibitions than the offset-gaps before salicylate treatment. The offset-gap induced PPI was significantly reduced 1-3h after salicylate treatment. However, the onset-gap caused a facilitation of startle response. These results suggest that salicylate induced reduction of gap-PPI was not only caused by the decrease of offset-gap induced PPI, but also by the facilitation induced by the onset-gap. Since the onset-gap induced PPI is caused by neural offset response, our results suggest that salicylate may cause a facilitation of neural response to an offset acoustical signal. Treatment of vigabatrin (60 mg/kg/day, 14 days), which elevates the GABA level in the brain, blocked the offset-gap induced PPI and onset-gap induced facilitation caused by salicylate. These results suggest that enhancing GABAergic activities can alleviate salicylate induced tinnitus. Published by Elsevier B.V.

Use of proton pump inhibitors among older Australians: national quality improvement programmes have led to sustained practice change.

PubMed

Pratt, Nicole L; Kalisch Ellett, Lisa M; Sluggett, Janet K; Gadzhanova, Svetla V; Ramsay, Emmae N; Kerr, Mhairi; LeBlanc, Vanessa T; Barratt, John D; Roughead, Elizabeth E

2017-02-01

To evaluate the impact of national multifaceted initiatives to improve use of proton pump inhibitors (PPIs) on the use of PPIs among older Australians. Interrupted time series analysis using administrative health claims data from the Australian Government Department of Veterans' Affairs (DVA). Australia. All veterans and dependents who received PPIs between January 2003 and December 2013. National, multifaceted interventions to improve PPI use were conducted by the Australian Government Department of Veterans' Affairs Veterans' MATES programme and Australia's NPS MedicineWise in April 2004, June 2006, May 2009 and August 2012. Trends in monthly rate of use of any PPI among the veteran population, and the monthly rate of use of low strength PPIs among all veterans dispensed a PPI. Interventions in 2004, 2006, 2009 and 2012 slowed the rate of increase in PPI use significantly, with the 2012 intervention resulting in a sustained 0.04% decrease in PPI use each month. The combined effect of all four interventions was a 20.9% (95% CI 7.8-33.9%) relative decrease in PPI use 12 months after the final intervention. The four interventions also resulted in a 42.2% (95% CI 19.9-64.5%) relative increase in low strength PPI use 12 months after the final intervention. National multifaceted programmes targeting clinicians and consumers were effective in reducing overall PPI use and increasing use of low strength PPIs. Interventions to improve PPI use should incorporate regular repetition of key messages to sustain practice change. © The Author 2016. Published by Oxford University Press in association with the International Society for Quality in Health Care. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Correction of hypophosphatasia (HPP) associated mineralization deficiencies in vitro by phosphate/pyrophosphate modulation in periodontal ligament cells

PubMed Central

Rodrigues, Thaisângela L.; Foster, Brian L.; Silverio, Karina G.; Martins, Luciane; Casati, Marcio Z.; Sallum, Enilson A.; Somerman, Martha J.; Nociti, Francisco H.

2013-01-01

Background Mutations in the Alpl gene in hypophosphatasia (HPP) reduce the function of tissue nonspecific alkaline phosphatase (TNAP), resulting in increased pyrophosphate (PPi) and a severe deficiency in acellular cementum. We hypothesized that exogenous phosphate (Pi) would rescue the in vitro mineralization capacity of periodontal ligament (PDL) cells harvested from HPP-diagnosed subjects, by correcting Pi/PPi ratio and modulating expression of genes involved with Pi/PPi metabolism. Methods Ex vivo and in vitro analyses were employed to identify mechanisms involved in HPP-associated PDL/tooth root deficiencies. Constitutive expression of PPi-associated genes was contrasted in PDL versus pulp tissues obtained from healthy subjects. Primary PDL cell cultures from HPP subjects (monozygotic twin males) were established to assay alkaline phosphatase activity (ALP), in vitro mineralization, and gene expression. Exogenous Pi was provided to correct Pi/PPi ratio. Results PDL tissues obtained from healthy individuals featured higher basal expression of key PPi regulators, genes Alpl, progressive ankylosis protein (Ankh) and ectonucleotide pyrophosphatase/phosphodiesterase 1 (Enpp1), versus paired pulp tissues. A novel Alpl mutation was identified in the twin HPP subjects enrolled in this study. Compared to controls, HPP-PDL cells exhibited significantly reduced ALP and mineralizing capacity, which were rescued by addition of 1mM Pi. Dysregulated expression of PPi regulatory genes Alpl, Ankh, and Enpp1 was also corrected by adding Pi, though other matrix markers evaluated in our study remained down-regulated. Conclusions These findings underscore the importance of controlling Pi/PPi ratio toward development of a functional periodontal apparatus, and support Pi/PPi imbalance as the etiology of HPP-associated cementum defects. PMID:22014174

Pharmacokinetics and pharmacodynamics of the proton pump inhibitors.

PubMed

Shin, Jai Moo; Kim, Nayoung

2013-01-01

Proton pump inhibitor (PPI) is a prodrug which is activated by acid. Activated PPI binds covalently to the gastric H(+), K(+)-ATPase via disulfide bond. Cys813 is the primary site responsible for the inhibition of acid pump enzyme, where PPIs bind. Omeprazole was the first PPI introduced in market, followed by pantoprazole, lansoprazole and rabeprazole. Though these PPIs share the core structures benzimidazole and pyridine, their pharmacokinetics and pharmacodynamics are a little different. Several factors must be considered in understanding the pharmacodynamics of PPIs, including: accumulation of PPI in the parietal cell, the proportion of the pump enzyme located at the canaliculus, de novo synthesis of new pump enzyme, metabolism of PPI, amounts of covalent binding of PPI in the parietal cell, and the stability of PPI binding. PPIs have about 1hour of elimination half-life. Area under the plasmic concentration curve and the intragastric pH profile are very good indicators for evaluating PPI efficacy. Though CYP2C19 and CYP3A4 polymorphism are major components of PPI metabolism, the pharmacokinetics and pharmacodynamics of racemic mixture of PPIs depend on the CYP2C19 genotype status. S-omeprazole is relatively insensitive to CYP2C19, so better control of the intragastric pH is achieved. Similarly, R-lansoprazole was developed in order to increase the drug activity. Delayed-release formulation resulted in a longer duration of effective concentration of R-lansoprazole in blood, in addition to metabolic advantage. Thus, dexlansoprazole showed best control of the intragastric pH among the present PPIs. Overall, PPIs made significant progress in the management of acid-related diseases and improved health-related quality of life.

Quantifying esophagogastric junction contractility with a novel HRM topographic metric, the EGJ-Contractile Integral: normative values and preliminary evaluation in PPI non-responders.

PubMed

Nicodème, F; Pipa-Muniz, M; Khanna, K; Kahrilas, P J; Pandolfino, J E

2014-03-01

Despite its obvious pathophysiological relevance, the clinical utility of measures of esophagogastric junction (EGJ) contractility is unsubstantiated. High-resolution manometry (HRM) may improve upon this with its inherent ability to integrate the magnitude of contractility over time and length of the EGJ. This study aimed to develop a novel HRM metric summarizing EGJ contractility and test its ability distinguish among subgroups of proton pump inhibitor non-responders (PPI-NRs). 75 normal controls and 88 PPI-NRs were studied. All underwent HRM. PPI-NRs underwent pH-impedance monitoring on PPI therapy scored in terms of acid exposure, number of reflux events, and reflux-symptom correlation and grouped as meeting all criteria, some criteria, or no criteria of abnormality. Control HRM studies were used to establish normal values for candidate EGJ contractility metrics, which were then compared in their ability to differentiate among PPI-NR subgroups. The EGJ contractile integral (EGJ-CI), a metric integrating contractility across the EGJ for three respiratory cycles, best distinguished the All Criteria PPI-NR subgroup from controls and other PPI-NR subgroups. Normal values (median, [IQR]) for this measure were 39 mmHg-cm [25-55 mmHg-cm]. The correlation between the EGJ-CI and a previously proposed metric, the lower esophageal sphincter-pressure integral, that used a fixed 10 s time frame and an atmospheric as opposed to gastric pressure reference was weak. Among HRM metrics tested, the EGJ-CI was best in distinguishing PPI-NRs meeting all criteria of abnormality on pH-impedance testing. Future prospective studies are required to explore its utility in management of broader groups of gastroesophageal reflux disease patients. © 2013 John Wiley & Sons Ltd.

Identifying protein complexes based on brainstorming strategy.

PubMed

Shen, Xianjun; Zhou, Jin; Yi, Li; Hu, Xiaohua; He, Tingting; Yang, Jincai

2016-11-01

Protein complexes comprising of interacting proteins in protein-protein interaction network (PPI network) play a central role in driving biological processes within cells. Recently, more and more swarm intelligence based algorithms to detect protein complexes have been emerging, which have become the research hotspot in proteomics field. In this paper, we propose a novel algorithm for identifying protein complexes based on brainstorming strategy (IPC-BSS), which is integrated into the main idea of swarm intelligence optimization and the improved K-means algorithm. Distance between the nodes in PPI network is defined by combining the network topology and gene ontology (GO) information. Inspired by human brainstorming process, IPC-BSS algorithm firstly selects the clustering center nodes, and then they are separately consolidated with the other nodes with short distance to form initial clusters. Finally, we put forward two ways of updating the initial clusters to search optimal results. Experimental results show that our IPC-BSS algorithm outperforms the other classic algorithms on yeast and human PPI networks, and it obtains many predicted protein complexes with biological significance. Copyright © 2016 Elsevier Inc. All rights reserved.

GraphCrunch 2: Software tool for network modeling, alignment and clustering.

PubMed

Kuchaiev, Oleksii; Stevanović, Aleksandar; Hayes, Wayne; Pržulj, Nataša

2011-01-19

Recent advancements in experimental biotechnology have produced large amounts of protein-protein interaction (PPI) data. The topology of PPI networks is believed to have a strong link to their function. Hence, the abundance of PPI data for many organisms stimulates the development of computational techniques for the modeling, comparison, alignment, and clustering of networks. In addition, finding representative models for PPI networks will improve our understanding of the cell just as a model of gravity has helped us understand planetary motion. To decide if a model is representative, we need quantitative comparisons of model networks to real ones. However, exact network comparison is computationally intractable and therefore several heuristics have been used instead. Some of these heuristics are easily computable "network properties," such as the degree distribution, or the clustering coefficient. An important special case of network comparison is the network alignment problem. Analogous to sequence alignment, this problem asks to find the "best" mapping between regions in two networks. It is expected that network alignment might have as strong an impact on our understanding of biology as sequence alignment has had. Topology-based clustering of nodes in PPI networks is another example of an important network analysis problem that can uncover relationships between interaction patterns and phenotype. We introduce the GraphCrunch 2 software tool, which addresses these problems. It is a significant extension of GraphCrunch which implements the most popular random network models and compares them with the data networks with respect to many network properties. Also, GraphCrunch 2 implements the GRAph ALigner algorithm ("GRAAL") for purely topological network alignment. GRAAL can align any pair of networks and exposes large, dense, contiguous regions of topological and functional similarities far larger than any other existing tool. Finally, GraphCruch 2 implements an algorithm for clustering nodes within a network based solely on their topological similarities. Using GraphCrunch 2, we demonstrate that eukaryotic and viral PPI networks may belong to different graph model families and show that topology-based clustering can reveal important functional similarities between proteins within yeast and human PPI networks. GraphCrunch 2 is a software tool that implements the latest research on biological network analysis. It parallelizes computationally intensive tasks to fully utilize the potential of modern multi-core CPUs. It is open-source and freely available for research use. It runs under the Windows and Linux platforms.

An enhanced functional interrogation/manipulation of intracellular signaling pathways with the peptide 'stapling' technology.

PubMed

He, Y; Chen, D; Zheng, W

2015-11-12

Specific protein-protein interactions (PPIs) constitute a key underlying mechanism for the presence of a multitude of intracellular signaling pathways, which are essential for the survival of normal and cancer cells. Specific molecular blockers for a crucial PPI would therefore be invaluable tools for an enhanced functional interrogation of the signaling pathway harboring this particular PPI. On the other hand, if a particular PPI is essential for the survival of cancer cells but is absent in or dispensable for the survival of normal cells, its specific molecular blockers could potentially be developed into effective anticancer therapeutics. Due to the flat and extended PPI interface, it would be conceivably difficult for small molecules to achieve an effective blockade, a problem which could be potentially circumvented with peptides or proteins. However, the well-documented proteolytic instability and cellular impermeability of peptides and proteins in general would make their developing into effective intracellular PPI blockers quite a challenge. With the advent of the peptide 'stapling' technology which was demonstrated to be able to stabilize the α-helical conformation of a peptide via bridging two neighboring amino-acid side chains with a 'molecular staple', a linear parent peptide could be transformed into a stronger PPI blocker with enhanced proteolytic stability and cellular permeability. This review will furnish an account on the peptide 'stapling' technology and its exploitation in efforts to achieve an enhanced functional interrogation or manipulation of intracellular signaling pathways especially those that are cancer relevant.

Proton pump inhibitor-refractory gastroesophageal reflux disease: challenges and solutions

PubMed Central

Mermelstein, Joseph; Chait Mermelstein, Alanna; Chait, Maxwell M

2018-01-01

A significant percentage of patients with gastroesophageal reflux disease (GERD) will not respond to proton pump inhibitor (PPI) therapy. The causes of PPI-refractory GERD are numerous and diverse, and include adherence, persistent acid, functional disorders, nonacid reflux, and PPI bioavailability. The evaluation should start with a symptom assessment and may progress to imaging, endoscopy, and monitoring of esophageal pH, impedance, and bilirubin. There are a variety of pharmacologic and procedural interventions that should be selected based on the underlying mechanism of PPI failure. Pharmacologic treatments can include antacids, prokinetics, alginates, bile acid binders, reflux inhibitors, and antidepressants. Procedural options include laparoscopic fundoplication and LINX as well as endoscopic procedures, such as transoral incisionless fundoplication and Stretta. Several alternative and complementary treatments of possible benefit also exist. PMID:29606884

Electrochemical characteristics of the reduced graphene oxide/carbon nanotube/polypyrrole composites for aqueous asymmetric supercapacitors

NASA Astrophysics Data System (ADS)

Peng, Yu-Jung; Wu, Tzu-Ho; Hsu, Chun-Tsung; Li, Shin-Ming; Chen, Ming-Guan; Hu, Chi-Chang

2014-12-01

Polypyrrole (PPy) has been polymerized onto reduced graphene oxide/carbon nanotube (rGO/CNT) to form an rGO/CNT/PPy composite using the chemical oxidation method. The electrochemical characteristics of the above composite in various aqueous electrolytes are systematically compared for the asymmetric supercapacitor application. The electrochemical characteristics of rGO/CNT/PPy in the electrolytes containing K+ show improved reversibility and higher stability. Introducing XC-72 in preparing the electrode has been found to enhance the specific capacitance and the cycle stability of rGO/CNT/PPy. The charge storage stability of rGO/CNT/PPy + XC-72 in various potential windows has been evaluated through the potential bias stress test. An asymmetric supercapacitor (ASC) with a positive electrode of Mn3O4 and a negative electrode of rGO/CNT/PPy + XC-72 is successfully demonstrated, which shows specific energy and power of 14. Wh kg-1 and 6.62 kW kg-1 with a cell voltage of 1.6 V. This ASC with a cell voltage of 1.6 V shows excellent charge-discharge cycle stability and ideal capacitive behavior in NaNO3 even after the application of 3250 charge-discharge cycles.

De Novo Synthesis and Functional Analysis of Polyphosphate-Loaded Poly(Ethylene) Glycol Hydrogel Nanoparticles Targeting Pyocyanin and Pyoverdin Production in Pseudomonas aeruginosa as a Model Intestinal Pathogen

PubMed Central

Yin, Yushu; Papavasiliou, Georgia; Zaborina, Olga Y.; Alverdy, John C.; Teymour, Fouad

2017-01-01

The human gastrointestinal tract is the primary site of colonization of multidrug resistant pathogens and the major source of life-threatening complications in critically ill and immunocompromised patients. Eradication measures using antibiotics carry further risk of antibiotic resistance. Furthermore, antibiotic treatment can adversely shift the intestinal microbiome toward domination by resistant pathogens. Therefore, approaches directed to prevent replacement of health promoting microbiota with resistant pathogens should be developed. The use of non-microbicidal drugs to create microenvironmental conditions that suppress virulence of pathogens is an attractive strategy to minimize the negative consequences of intestinal microbiome disruption. We have previously shown that phosphate is depleted in the intestinal tract following surgical injury, that this depletion is a major “cue” that triggers bacterial virulence, and that the maintenance of phosphate abundance prevents virulence expression. However, the use of inorganic phosphate may not be a suitable agent to deliver to the site of the host-pathogen interaction since it is readily adsorbed in small intestine. Here we propose a novel drug delivery approach that exploits the use of nanoparticles that allow for prolonged release of phosphates. We have synthesized phosphate (Pi) and polyphosphate (PPi) crosslinked poly (ethylene) glycol (PEG) hydrogel nanoparticles (NP-Pi and NP-PPi, respectively) that result in sustained delivery of Pi and PPi. NP-PPi demonstrated more prolonged release of PPi as compared to the release of Pi from NP-Pi. In vitro studies indicate that free PPi as well NP-PPi are effective compounds for suppressing pyoverdin and pyocyanin production, two global virulence systems of virulence of P. aeruginosa. These studies suggest that sustained release of polyphosphate from NP-PPi can be exploited as a target for virulence suppression of lethal pathogenic phenotypes in the gastrointestinal tract. PMID:27761766

Association between arginine vasopressin 1a receptor (AVPR1a) promoter region polymorphisms and prepulse inhibition.

PubMed

Levin, Raz; Heresco-Levy, Uriel; Bachner-Melman, Rachel; Israel, Salomon; Shalev, Idan; Ebstein, Richard P

2009-07-01

Arginine vasopressin and the arginine vasopressin 1a (AVPR1a) gene contribute to a range of social behaviors both in lower vertebrates and in humans. Human promoter-region microsatellite repeat regions (RS1 and RS3) in the AVPR1a gene region have been associated with autism spectrum disorders, prosocial behavior and social cognition. Prepulse inhibition (PPI) of the startle response to auditory stimuli is a largely autonomic response that resonates with social cognition in both animal models and humans. Reduced PPI has been observed in disorders including schizophrenia that are distinguished by deficits in social skills. In the current investigation association was examined between PPI and the AVPR1a RS1 and RS repeat regions and PPI in a group of 113 nonclinical subjects. Using a robust family-based strategy, association was observed between AVPR1a promoter-region repeat length, especially RS3) and PPI (30 ms: global p=0.04; 60 ms p=0.006; 120 ms p=0.008). Notably, longer RS3 alleles were associated with greater levels of prepulse inhibition. Using a short/long classification scheme for the repeat regions, significant association was also observed between all three PPI intervals (30, 60 and 120 ms) and both RS1 and RS3 polymorphisms (PBAT: FBAT-PC(2) statistic p=0.047). Tests of within-subject effects (SPSS GLM) showed significant sexxRS3 interactions at 30 ms (p=0.045) and 60 ms (p=0.01). Longer alleles, especially in male subjects, are associated with significantly higher PPI response, consistent with a role for the promoter repeat region in partially molding social behavior in both animals and humans. This is the first report in humans demonstrating a role of the AVPR1a gene in contributing to the PPI response to auditory stimuli.

Prediction of protein-protein interactions from amino acid sequences with ensemble extreme learning machines and principal component analysis.

PubMed

You, Zhu-Hong; Lei, Ying-Ke; Zhu, Lin; Xia, Junfeng; Wang, Bing

2013-01-01

Protein-protein interactions (PPIs) play crucial roles in the execution of various cellular processes and form the basis of biological mechanisms. Although large amount of PPIs data for different species has been generated by high-throughput experimental techniques, current PPI pairs obtained with experimental methods cover only a fraction of the complete PPI networks, and further, the experimental methods for identifying PPIs are both time-consuming and expensive. Hence, it is urgent and challenging to develop automated computational methods to efficiently and accurately predict PPIs. We present here a novel hierarchical PCA-EELM (principal component analysis-ensemble extreme learning machine) model to predict protein-protein interactions only using the information of protein sequences. In the proposed method, 11188 protein pairs retrieved from the DIP database were encoded into feature vectors by using four kinds of protein sequences information. Focusing on dimension reduction, an effective feature extraction method PCA was then employed to construct the most discriminative new feature set. Finally, multiple extreme learning machines were trained and then aggregated into a consensus classifier by majority voting. The ensembling of extreme learning machine removes the dependence of results on initial random weights and improves the prediction performance. When performed on the PPI data of Saccharomyces cerevisiae, the proposed method achieved 87.00% prediction accuracy with 86.15% sensitivity at the precision of 87.59%. Extensive experiments are performed to compare our method with state-of-the-art techniques Support Vector Machine (SVM). Experimental results demonstrate that proposed PCA-EELM outperforms the SVM method by 5-fold cross-validation. Besides, PCA-EELM performs faster than PCA-SVM based method. Consequently, the proposed approach can be considered as a new promising and powerful tools for predicting PPI with excellent performance and less time.

A novel method based on new adaptive LVQ neural network for predicting protein-protein interactions from protein sequences.

PubMed

Yousef, Abdulaziz; Moghadam Charkari, Nasrollah

2013-11-07

Protein-Protein interaction (PPI) is one of the most important data in understanding the cellular processes. Many interesting methods have been proposed in order to predict PPIs. However, the methods which are based on the sequence of proteins as a prior knowledge are more universal. In this paper, a sequence-based, fast, and adaptive PPI prediction method is introduced to assign two proteins to an interaction class (yes, no). First, in order to improve the presentation of the sequences, twelve physicochemical properties of amino acid have been used by different representation methods to transform the sequence of protein pairs into different feature vectors. Then, for speeding up the learning process and reducing the effect of noise PPI data, principal component analysis (PCA) is carried out as a proper feature extraction algorithm. Finally, a new and adaptive Learning Vector Quantization (LVQ) predictor is designed to deal with different models of datasets that are classified into balanced and imbalanced datasets. The accuracy of 93.88%, 90.03%, and 89.72% has been found on S. cerevisiae, H. pylori, and independent datasets, respectively. The results of various experiments indicate the efficiency and validity of the method. © 2013 Published by Elsevier Ltd.

Network-Based Comparative Analysis of Arabidopsis Immune Responses to Golovinomyces orontii and Botrytis cinerea Infections.

PubMed

Jiang, Zhenhong; Dong, Xiaobao; Zhang, Ziding

2016-01-11

A comprehensive exploration of common and specific plant responses to biotrophs and necrotrophs is necessary for a better understanding of plant immunity. Here, we compared the Arabidopsis defense responses evoked by the biotrophic fungus Golovinomyces orontii and the necrotrophic fungus Botrytis cinerea through integrative network analysis. Two time-course transcriptional datasets were integrated with an Arabidopsis protein-protein interaction (PPI) network to construct a G. orontii conditional PPI sub-network (gCPIN) and a B. cinerea conditional PPI sub-network (bCPIN). We found that hubs in gCPIN and bCPIN played important roles in disease resistance. Hubs in bCPIN evolved faster than hubs in gCPIN, indicating the different selection pressures imposed on plants by different pathogens. By analyzing the common network from gCPIN and bCPIN, we identified two network components in which the genes were heavily involved in defense and development, respectively. The co-expression relationships between interacting proteins connecting the two components were different under G. orontii and B. cinerea infection conditions. Closer inspection revealed that auxin-related genes were overrepresented in the interactions connecting these two components, suggesting a critical role of auxin signaling in regulating the different co-expression relationships. Our work may provide new insights into plant defense responses against pathogens with different lifestyles.

A novel one-class SVM based negative data sampling method for reconstructing proteome-wide HTLV-human protein interaction networks.

PubMed

Mei, Suyu; Zhu, Hao

2015-01-26

Protein-protein interaction (PPI) prediction is generally treated as a problem of binary classification wherein negative data sampling is still an open problem to be addressed. The commonly used random sampling is prone to yield less representative negative data with considerable false negatives. Meanwhile rational constraints are seldom exerted on model selection to reduce the risk of false positive predictions for most of the existing computational methods. In this work, we propose a novel negative data sampling method based on one-class SVM (support vector machine, SVM) to predict proteome-wide protein interactions between HTLV retrovirus and Homo sapiens, wherein one-class SVM is used to choose reliable and representative negative data, and two-class SVM is used to yield proteome-wide outcomes as predictive feedback for rational model selection. Computational results suggest that one-class SVM is more suited to be used as negative data sampling method than two-class PPI predictor, and the predictive feedback constrained model selection helps to yield a rational predictive model that reduces the risk of false positive predictions. Some predictions have been validated by the recent literature. Lastly, gene ontology based clustering of the predicted PPI networks is conducted to provide valuable cues for the pathogenesis of HTLV retrovirus.

Selective enhancement of NMDA receptor-mediated locomotor hyperactivity by male sex hormones in mice.

PubMed

van den Buuse, Maarten; Low, Jac Kee; Kwek, Perrin; Martin, Sally; Gogos, Andrea

2017-09-01

Altered glutamate NMDA receptor function is implicated in schizophrenia, and gender differences have been demonstrated in this illness. This study aimed to investigate the interaction of gonadal hormones with NMDA receptor-mediated locomotor hyperactivity and PPI disruption in mice. The effect of 0.25 mg/kg of MK-801 on locomotor activity was greater in male mice than in female mice. Gonadectomy (by surgical castration) significantly reduced MK-801-induced hyperlocomotion in male mice, but no effect of gonadectomy was seen in female mice or on amphetamine-induced locomotor hyperactivity. The effect of MK-801 on prepulse inhibition of startle (PPI) was similar in intact and castrated male mice and in ovariectomized (OVX) female mice. In contrast, there was no effect of MK-801 on PPI in intact female mice. Forebrain NMDA receptor density, as measured with [ 3 H]MK-801 autoradiography, was significantly higher in male than in female mice but was not significantly altered by either castration or OVX. These results suggest that male sex hormones enhance the effect of NMDA receptor blockade on psychosis-like behaviour. This interaction was not seen in female mice and was independent of NMDA receptor density in the forebrain. Male sex hormones may be involved in psychosis by an interaction with NMDA receptor hypofunction.

A systems biology approach to study systemic inflammation.

PubMed

Chen, Bor-Sen; Wu, Chia-Chou

2014-01-01

Systemic inflammation needs a precise control on the sequence and magnitude of occurring events. The high throughput data on the host-pathogen interactions gives us an opportunity to have a glimpse on the systemic inflammation. In this article, a dynamic Candida albicans-zebrafish interactive infectious network is built as an example to demonstrate how systems biology approach can be used to study systematic inflammation. In particular, based on microarray data of C. albicans and zebrafish during infection, the hyphal growth, zebrafish, and host-pathogen intercellular PPI networks were combined to form an integrated infectious PPI network that helps us understand the systematic mechanisms underlying the pathogenicity of C. albicans and the immune response of the host. The signaling pathways for morphogenesis and hyphal growth of C. albicans were 2 significant interactions found in the intercellular PPI network. Two cellular networks were also developed corresponding to the different infection stages (adhesion and invasion), and then compared with each other to identify proteins to gain more insight into the pathogenic role of hyphal development in the C. albicans infection process. Important defense-related proteins in zebrafish were predicted using the same approach. This integrated network consisting of intercellular invasion and cellular defense processes during infection can improve medical therapies and facilitate development of new antifungal drugs.

Facile preparation of polypyrrole/graphene oxide nanocomposites with large areal capacitance using electrochemical codeposition for supercapacitors

NASA Astrophysics Data System (ADS)

Zhou, Haihan; Han, Gaoyi; Xiao, Yaoming; Chang, Yunzhen; Zhai, Hua-Jin

2014-10-01

A simple and low-cost electrochemical codeposition method has been introduced to fabricate polypyrrole/graphene oxide (PPy/GO) nanocomposites and the areal capacitance of conducting polymer/GO composites is reported for the first time. Fourier transform infrared spectroscopy (FTIR), Transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), and X-ray diffraction (XRD) are implemented to determine the PPy/GO nanocomposites are successfully prepared and the interaction between PPy and GO. The as-prepared PPy/GO nanocomposites show the curly sheet-like morphology, superior capacitive behaviors and cyclic stability. Furthermore, the varying deposition time is implemented to investigate the impact of the loading amount on electrochemical behavior of the composites, and a high areal capacitance of 152 mF cm-2 is achieved at 10 mV s-1 CV scan. However, the thicker films caused by the long deposition time would result in larger diffusion resistance of electrolyte ions, consequently exhibit the relatively lower capacitance value at the high current density. The GCD tests indicate moderate deposition time is more suitable for the fast charge/discharge. Considering the very simple and effective synthetic process, the PPy/GO nanocomposites with relatively high areal capacitance are competitive candidate for supercapacitor application, and its capacitive performances can be easily tuned by varying the deposition time.

Identifying protein complex by integrating characteristic of core-attachment into dynamic PPI network.

PubMed

Shen, Xianjun; Yi, Li; Jiang, Xingpeng; He, Tingting; Yang, Jincai; Xie, Wei; Hu, Po; Hu, Xiaohua

2017-01-01

How to identify protein complex is an important and challenging task in proteomics. It would make great contribution to our knowledge of molecular mechanism in cell life activities. However, the inherent organization and dynamic characteristic of cell system have rarely been incorporated into the existing algorithms for detecting protein complexes because of the limitation of protein-protein interaction (PPI) data produced by high throughput techniques. The availability of time course gene expression profile enables us to uncover the dynamics of molecular networks and improve the detection of protein complexes. In order to achieve this goal, this paper proposes a novel algorithm DCA (Dynamic Core-Attachment). It detects protein-complex core comprising of continually expressed and highly connected proteins in dynamic PPI network, and then the protein complex is formed by including the attachments with high adhesion into the core. The integration of core-attachment feature into the dynamic PPI network is responsible for the superiority of our algorithm. DCA has been applied on two different yeast dynamic PPI networks and the experimental results show that it performs significantly better than the state-of-the-art techniques in terms of prediction accuracy, hF-measure and statistical significance in biology. In addition, the identified complexes with strong biological significance provide potential candidate complexes for biologists to validate.

Quantitative genetic-interaction mapping in mammalian cells

PubMed Central

Roguev, Assen; Talbot, Dale; Negri, Gian Luca; Shales, Michael; Cagney, Gerard; Bandyopadhyay, Sourav; Panning, Barbara; Krogan, Nevan J

2013-01-01

Mapping genetic interactions (GIs) by simultaneously perturbing pairs of genes is a powerful tool for understanding complex biological phenomena. Here we describe an experimental platform for generating quantitative GI maps in mammalian cells using a combinatorial RNA interference strategy. We performed ~11,000 pairwise knockdowns in mouse fibroblasts, focusing on 130 factors involved in chromatin regulation to create a GI map. Comparison of the GI and protein-protein interaction (PPI) data revealed that pairs of genes exhibiting positive GIs and/or similar genetic profiles were predictive of the corresponding proteins being physically associated. The mammalian GI map identified pathways and complexes but also resolved functionally distinct submodules within larger protein complexes. By integrating GI and PPI data, we created a functional map of chromatin complexes in mouse fibroblasts, revealing that the PAF complex is a central player in the mammalian chromatin landscape. PMID:23407553

Upper GI tract findings in patients with heartburn in whom proton pump inhibitor treatment failed versus those not receiving antireflux treatment.

PubMed

Poh, Choo Hean; Gasiorowska, Anita; Navarro-Rodriguez, Tomas; Willis, Marcia R; Hargadon, Deborah; Noelck, North; Mohler, Jane; Wendel, Christopher S; Fass, Ronnie

2010-01-01

Failure of proton pump inhibitor (PPI) treatment in patients with heartburn is very common. Because endoscopy is easily accessible, it is commonly used as the first evaluative tool in these patients. To compare GERD-related endoscopic and histologic findings in patients with heartburn in whom once-daily PPI therapy failed versus those not receiving antireflux treatment. Cross-sectional study. A Veterans Affairs hospital. Heartburn patients from the GI outpatient clinic. Recording of endoscopic results. Endoscopic findings and association between PPI treatment failure and esophageal mucosal injury by using logistic regression models. A total of 105 subjects (mean age 54.7 +/- 15.7 years; 71 men, 34 women) were enrolled in the PPI treatment failure group and 91 (mean age 53.4 +/- 15.8 years; 68 men, 23 women) were enrolled in the no-treatment group (P = not significant). Anatomic findings during upper endoscopy were significantly more common in the no-treatment group compared with the PPI treatment failure group (55.2% vs 40.7%, respectively; P = .04). GERD-related findings were significantly more common in the no-treatment group compared with the PPI treatment failure group (erosive esophagitis: 30.8% vs 6.7%, respectively; P < .05). Eosinophilic esophagitis was found in only 0.9% of PPI treatment failure patients. PPI treatment failure was associated with a significantly decreased odds ratio of erosive esophagitis compared with no treatment, adjusted for age, sex, and body mass index (adjusted odds ratio 0.11; 95% CI, 0.04-0.30). Heartburn patients in whom once-daily PPI treatment failed demonstrated a paucity of GERD-related findings compared with those receiving no treatment. Eosinophilic esophagitis was uncommon in PPI therapy failure patients. Upper endoscopy seems to have a very low diagnostic yield in this patient population. 2010 American Society for Gastrointestinal Endoscopy. Published by Mosby, Inc. All rights reserved.

Lifestyle factors among proton pump inhibitor users and nonusers: a cross-sectional study in a population-based setting.

PubMed

Hvid-Jensen, Frederik; Nielsen, Rikke B; Pedersen, Lars; Funch-Jensen, Peter; Drewes, Asbjørn Mohr; Larsen, Finn B; Thomsen, Reimar W

2013-01-01

Lifestyle factors may influence observed associations between proton pump inhibitor (PPI) usage and health outcomes. The aim of the study reported here was to examine characteristics and differences in lifestyle among PPI users and nonusers. This cross-sectional study utilized data from a 2006 population-based health survey of 21,637 persons in the Central Danish Region. All persons using prescribed PPIs were identified through linkage to a population-based prescription database. Biometric measures and prevalence of smoking, excessive alcohol consumption, diet, and physical exercise were analyzed, comparing PPI users with nonusers. Among 10,129 (46.8%) male and 11,508 (53.2%) female survey respondents, 1,356 (13.4%) males and 1,691 (14.7%) females reported ever use of PPIs. PPI users were more obese (16.7%) than nonusers (13.1%), with an age- and sex-standardized prevalence ratio (PR) of 1.3 (95% confidence interval [CI]: 1.2-1.4). The prevalence of smokers was also higher in the PPI group (26.2% vs 22.3% [PR =1.2, 95% CI: 1.1-1.3]), as was the prevalence of ex-smokers (41.0% vs 32.0% [PR =1.2, 95% CI: 1.1-1.2]). Unhealthy diet was slightly more common among PPI users than among nonusers (15.4% vs 13.0%), with a PR of 1.2 (95% CI: 1.1-1.3). Physical exercise level and alcohol consumption were similar in the two groups. Hospital-diagnosed comorbidity was observed in 35% of PPI users (a Charlson Comorbidity Index score of 1 or more) compared with only 15% among nonusers. PPI users are more obese, smoke more, and have significantly more comorbidities than PPI nonusers. These data are important when evaluating unmeasured confounding in observational studies of PPI effects.

Predictors of Need for Permanent Pacemaker Implantation and Conduction Abnormalities With a Novel Self-expanding Transcatheter Heart Valve.

PubMed

Pellegrini, Costanza; Husser, Oliver; Kim, Won-Keun; Holzamer, Andreas; Walther, Thomas; Rheude, Tobias; Mayr, Nicola Patrick; Trenkwalder, Teresa; Joner, Michael; Michel, Jonathan; Chaustre, Fabian; Kastrati, Adnan; Schunkert, Heribert; Burgdorf, Christof; Hilker, Michael; Möllmann, Helge; Hengstenberg, Christian

2018-03-15

The incidence of permanent pacemaker implantation (PPI) and new conduction abnormalities (CA) with the ACURATE neo (Symetis S.A., Eclubens, Switzerland) has not been studied in detail. We aimed to analyze their predictors, evaluating patient- and device-related factors, including implantation depth and device-to-annulus ratio (DAR). Two analyses of a multicenter population were performed: new PPI in pacemaker-naive patients (n = 283), and PPI/new-CA in patients without prior CA or pacemaker (n = 232). A new PPI was required in 9.9% of patients, who had a higher body mass index, higher rate of right bundle branch block and bradycardia. Neither implantation depth nor DAR differed in patients with PPI compared with those without. In the multivariable analysis neither DAR (OR, 1.010; 95%CI, 0.967-1.055; P = .7) nor implantation depth (OR, 0.972; 95%CI, 0.743-1.272; P = .8) predicted PPI. Only high body mass index, bradycardia and right bundle branch block persisted as independent predictors. PPI/new-onset CA occurred in 22.8% of patients and was associated with a higher logistic EuroSCORE. Neither implantation depth nor DAR differed in patients with PPI/new-CA vs those without (7.3 ± 1.9 vs 7.1 ± 1.5mm; P = .6 and 41.0 ± 7.9 vs 42.2 ± 10.1%; P = .4). The only predictor of PPI/new-CA was a higher logistic EuroSCORE (OR, 1.039; 95%CI, [1.008-1.071]; P = .013). New PPI and new-onset CA rates were low with the ACURATE neo. These were mainly influenced by patient characteristics and not by device-depending factors. Copyright © 2018 Sociedad Española de Cardiología. Published by Elsevier España, S.L.U. All rights reserved.

Proton pump inhibitors and potential interactions with clopidogrel: an update.

PubMed

Gerson, Lauren B

2013-06-01

Clopidogrel, an antiplatelet agent, is increasingly prescribed for patients with recent stroke, myocardial infarction, acute coronary syndrome, and/or patients post-coronary stent insertion to prevent recurrent cardiovascular events. Since clopidogrel can increase the risk of gastrointestinal hemorrhage, co-administration of proton pump inhibitors (PPIs) has been recommended, particularly in patients at high risk. In 2009, the FDA issued warnings about potential interactions between clopidogrel and PPIs, given the fact that both drugs are metabolized via the cytochrome P450 pathway. Prior studies have demonstrated significant reduction in platelet inhibition when PPI therapy is administered to subjects on clopidogrel therapy. Two meta-analyses were published in 2010 and 2011, the first suggesting association of PPIs with adverse cardiovascular events when observational studies were examined, but noting that the results were limited by the presence of significant heterogeneity. The second meta-analysis did not find a significant increase in the risk of adverse primary events (which included all cause mortality, cardiovascular death, myocardial infarction, or stroke), and concluded that analysis of the data from two randomized controlled trials yielded a risk difference of zero. An updated literature search was performed to assess clinical studies describing interactions between PPIs and clopidogrel published from 2011-2012. The majority of these studies did not show significant interactions when primary cardiac outcomes were considered. More importantly, the newer data demonstrated that PPI usage independently was a risk factor for adverse CV outcomes, since most PPI users were older patients who were more likely to have concomitant co-morbid conditions. Two updated reviews also concluded that the presence of confounding factors likely explained differences in results between studies, and that there were no significant differences in effects on clopidogrel between individual proton pump inhibitors. Overall, clinicians can assure their patients that combination therapy is safe when indicated in a patient at high risk of GI bleeding, but they should also stop PPI therapy if it is not clinically indicated.

The impact of newly produced protein and dietary fiber rich fractions of yellow pea (Pisum sativum L.) on the structure and mechanical properties of pasta-like sheets.

PubMed

Muneer, Faraz; Johansson, Eva; Hedenqvist, Mikael S; Plivelic, Tomás S; Markedal, Keld Ejdrup; Petersen, Iben Lykke; Sørensen, Jens Christian; Kuktaite, Ramune

2018-04-01

Two fractions from pea (Pisum sativum L.), protein isolate (PPI) and dietary fiber (PF), were newly produced by extraction-fractionation method and characterized in terms of particle size distribution and structural morphology using SEM. The newly produced PPI and PF fractions were processed into pasta-like sheets with varying protein to fiber ratios (100/0, 90/10, 80/20, 70/30 and 50/50, respectively) using high temperature compression molding. We studied protein polymerization, molecular structure and protein-fiber interactions, as well as mechanical performance and cooking characteristics of processed PPI-PF blends. Bi-modal particle size distribution and chemical composition of the PPI and PF fractions influenced significantly the physicochemical properties of the pasta-like sheets. Polymerization was most pronounced for the 100 PPI, 90/10 and 80/20 PPI-PF samples as studied by SE-HPLC, and polymerization decreased with addition of the PF fraction. The mechanical properties, as strength and extensibility, were likewise the highest for the 100 PPI and 90/10 PPI-PF blends, while the E-modulus was similar for all the studied blends (around 38 MPa). The extensibility decreased with the increasing amount of PF in the blend. The highest amounts of β-sheets were found in the pasta-like sheets with high amounts of PPI (100, 90 and 80%), by FT-IR. An increase in PF fraction in the blend, resulted into the high amounts of unordered structures as observed by FT-IR, as well as in an increase in the molecular scattering distances observed by SAXS. The water uptake increased and cooking loss decreased with increased proportions of the PF fraction, and the consistency of 10 min cooked pasta-like sheets were alike al dente texture. The new knowledge obtained in this study on the use of extraction-fractionation method to produce novel PPI and PF fractions for developing innovative high nutritious food can be of a great importance. The obtained knowledge on the pea protein and fiber processing behaviour could greatly contribute to a better control of functional properties of various temperature-processed products from yellow pea. Copyright © 2018 Elsevier Ltd. All rights reserved.

Measuring signal-to-noise ratio in partially parallel imaging MRI

PubMed Central

Goerner, Frank L.; Clarke, Geoffrey D.

2011-01-01

Purpose: To assess five different methods of signal-to-noise ratio (SNR) measurement for partially parallel imaging (PPI) acquisitions. Methods: Measurements were performed on a spherical phantom and three volunteers using a multichannel head coil a clinical 3T MRI system to produce echo planar, fast spin echo, gradient echo, and balanced steady state free precession image acquisitions. Two different PPI acquisitions, generalized autocalibrating partially parallel acquisition algorithm and modified sensitivity encoding with acceleration factors (R) of 2–4, were evaluated and compared to nonaccelerated acquisitions. Five standard SNR measurement techniques were investigated and Bland–Altman analysis was used to determine agreement between the various SNR methods. The estimated g-factor values, associated with each method of SNR calculation and PPI reconstruction method, were also subjected to assessments that considered the effects on SNR due to reconstruction method, phase encoding direction, and R-value. Results: Only two SNR measurement methods produced g-factors in agreement with theoretical expectations (g ≥ 1). Bland–Altman tests demonstrated that these two methods also gave the most similar results relative to the other three measurements. R-value was the only factor of the three we considered that showed significant influence on SNR changes. Conclusions: Non-signal methods used in SNR evaluation do not produce results consistent with expectations in the investigated PPI protocols. Two of the methods studied provided the most accurate and useful results. Of these two methods, it is recommended, when evaluating PPI protocols, the image subtraction method be used for SNR calculations due to its relative accuracy and ease of implementation. PMID:21978049

Preparation of PPy-Coated MnO2 Hybrid Micromaterials and Their Improved Cyclic Performance as Anode for Lithium-Ion Batteries

NASA Astrophysics Data System (ADS)

Feng, Lili; Zhang, Yinyin; Wang, Rui; Zhang, Yanli; Bai, Wei; Ji, Siping; Xuan, Zhewen; Yang, Jianhua; Zheng, Ziguang; Guan, Hongjin

2017-09-01

MnO2@PPy core-shell micromaterials are prepared by chemical polymerization of pyrrole on the MnO2 surface. The polypyrrole (PPy) is formed as a homogeneous organic shell on the MnO2 surface. The thickness of PPy shell can be adjusted by the usage of pyrrole. The analysis of SEM, FT-IR, X-ray photoelectron spectroscopy (XPS), thermo-gravimetric analysis (TGA), and XRD are used to confirm the formation of PPy shell. Galvanostatic cell cycling and electrochemical impedance spectroscopy (EIS) are used to evaluate the electrochemical performance as anode for lithium-ion batteries. The results show that after formation of MnO2@PPy core-shell micromaterials, the cyclic performance as anode for lithium-ion batteries is improved. Fifty microliters of PPy-coated caddice-clew-like MnO2 has the best cyclic performances as has 620 mAh g-1 discharge specific capacities after 300 cycles. As a comparison, the discharge specific capacity of bare MnO2 materials falls to below 200 mAh g-1 after 10 cycles. The improved lithium-storage cyclic stability of the MnO2@PPy samples attributes to the core-shell hybrid structure which can buffer the structural expansion and contraction of MnO2 caused by the repeated embedding and disengagement of Li ions and can prevent the pulverization of MnO2. This experiment provides an effective way to mitigate the problem of capacity fading of the transition metal oxide materials as anode materials for (lithium-ion batteries) LIBs.

Preparation of PPy-Coated MnO2 Hybrid Micromaterials and Their Improved Cyclic Performance as Anode for Lithium-Ion Batteries.

PubMed

Feng, Lili; Zhang, Yinyin; Wang, Rui; Zhang, Yanli; Bai, Wei; Ji, Siping; Xuan, Zhewen; Yang, Jianhua; Zheng, Ziguang; Guan, Hongjin

2017-09-02

MnO 2 @PPy core-shell micromaterials are prepared by chemical polymerization of pyrrole on the MnO 2 surface. The polypyrrole (PPy) is formed as a homogeneous organic shell on the MnO 2 surface. The thickness of PPy shell can be adjusted by the usage of pyrrole. The analysis of SEM, FT-IR, X-ray photoelectron spectroscopy (XPS), thermo-gravimetric analysis (TGA), and XRD are used to confirm the formation of PPy shell. Galvanostatic cell cycling and electrochemical impedance spectroscopy (EIS) are used to evaluate the electrochemical performance as anode for lithium-ion batteries. The results show that after formation of MnO 2 @PPy core-shell micromaterials, the cyclic performance as anode for lithium-ion batteries is improved. Fifty microliters of PPy-coated caddice-clew-like MnO 2 has the best cyclic performances as has 620 mAh g -1 discharge specific capacities after 300 cycles. As a comparison, the discharge specific capacity of bare MnO 2 materials falls to below 200 mAh g -1 after 10 cycles. The improved lithium-storage cyclic stability of the MnO 2 @PPy samples attributes to the core-shell hybrid structure which can buffer the structural expansion and contraction of MnO 2 caused by the repeated embedding and disengagement of Li ions and can prevent the pulverization of MnO 2 . This experiment provides an effective way to mitigate the problem of capacity fading of the transition metal oxide materials as anode materials for (lithium-ion batteries) LIBs.

Modification of Aspergillus niger by conducting polymer, Polypyrrole, and the evaluation of electrochemical properties of modified cells.

PubMed

Apetrei, Roxana-Mihaela; Carac, Geta; Bahrim, Gabriela; Ramanaviciene, Almira; Ramanavicius, Arunas

2018-06-01

The enhancement of bioelectrochemical properties of microorganism by in situ formation of conducting polymer within the cell structures (e.g. cell wall) was performed. The synthesis of polypyrrole (Ppy) within fungi (Aspergillus niger) cells was achieved. Two different Aspergillus niger strains were selected due to their ability to produce glucose oxidase, which initiated the Ppy formation through products of enzymatic reaction. The evolution of Ppy structural features was investigated by absorption spectroscopy, cyclic voltammetry and Fourier transform infrared spectroscopy. Copyright © 2018 Elsevier B.V. All rights reserved.

The use of proton pump inhibitors in an Italian hospital: focus on oncologic and critical non-ICU patients.

PubMed

Meli, Maria; Raffa, Maria Pia; Malta, Renato; Morreale, Ilaria; Aprea, Luigi; D'Alessandro, Natale

2015-12-01

Proton pump inhibitors (PPIs) are among the most misused drugs both at the community and hospital level. Recently, possible risks have been underscored, suggesting the importance of limiting PPI use to proven indications. To survey the appropriateness of PPI use in a University hospital in Italy. Setting Azienda Ospedaliera Universitaria Policlinico 'P. Giaccone', in Palermo, Italy. A one day-observational study, reviewing patients' medical records to identify treatments with PPIs and the indications for their use. After discharge, a subgroup of the cohort was followed up to assess the continuation of therapy at home. Appropriateness was evaluated according to the indications stated in the official product information sheet and supported by the AIFA notes. Prevalence and appropriateness of PPI use in the hospital and after discharge. In the index day 62.9 % of 343 evaluable patients received a PPI. In only 29.1 % of these, the treatment could be considered appropriate. The most frequent reasons for inappropriate treatment were stress ulcer prophylaxis in low risk patients and unwarranted gastro-protection in drug treated patients. 30.9 % of patients received PPIs for uncertain indications: of these, 25.7 % were "critical" patients admitted in non-ICU wards. Furthermore, as much as 88.2 % of anticancer drug treated patients received PPIs as gastroprotective agents. At discharge 48.6 % of patients received a prescription to continue PPI therapy at home and 75.9 % of the 83 followed up patients were found to be still taking these drugs after on average 3 months from discharge. This study confirms a high proportion of inappropriate PPI therapy into the hospital that translates in a prolonged unnecessary administration in the community setting. Further studies are needed to assess the cost-effectiveness of PPI therapy in subgroups of patients at moderate risk for gastric complications to optimize current guidelines.

[Value of the palliative prognostic index, controlling nutritional status, and prognostic nutritional index for objective evaluation during transition from chemotherapy to palliative care in cases of advanced or recurrent gastrointestinal cancer].

PubMed

Fukushima, Tsuyoshi; Annen, Kazuya; Kawamukai, Yuji; Onuma, Noritomo; Kawashima, Mayu

2014-07-01

We investigated whether objective evaluation by using the palliative prognostic index(PPI), controlling nutritional status(COUNT), and prognostic nutritional index(PNI)can provide prognostic information during the transition from chemotherapy to palliative care in patients with advanced or recurrent gastrointestinal cancer. The subjects were 28 patients with gastrointestinal cancer who died of their disease between January 2009 and June 2012. We compared the PPI, COUNT, and PNI scores between patients who died within 90 days of completing chemotherapy(Group A, n=14)and patients who survived for 90 or more days(Group B, n=14). The PPI score for Group A(4.0)was significantly higher than that for Group B(0.8)(p<0.001). The COUNT score was also significantly higher for Group A(6.3)than for Group B (3.9)(p=0.033). A significant difference in survival was evident when the cutoff value for PNI was set at 40 in the critical region(68/118, p=0.04). Our study suggests that the PPI, COUNT, and PNI may be useful for objective evaluation during the transition from chemotherapy to palliative care.

Synergistic Effect of Polypyrrole-Intercalated Graphene for Enhanced Corrosion Protection of Aqueous Coating in 3.5% NaCl Solution.

PubMed

Qiu, Shihui; Li, Wei; Zheng, Wenru; Zhao, Haichao; Wang, Liping

2017-10-04

Dispersion of graphene in water and its incorporation into waterborne resin have been rarely researched and hardly achieved owing to its hydrophobicity. Furthermore, it has largely been reported that graphene with impermeability contributed to the improved anticorrosion property. Here, we show that highly concentrated graphene aqueous solution up to 5 mg/mL can be obtained by synthesizing hydrophilic polypyrrole (PPy) nanocolloids as intercalators and ultrasonic vibration. On the basis of π-π interaction between PPy and graphene, stacked graphene sheets are exfoliated to the thickness of three to five layers without increasing defects. The corrosion performance of coatings without and with PPy and graphene is obtained by potential and impedance measurements, Tafel curves, and fitted pore resistance by immersing in a 3.5 wt % NaCl solution. It turns out that composite coating with 0.5 wt % graphene additive exhibits superior anticorrosive ability. The mechanism of intercalated graphene-based coating is interpreted as the synergistic protection of impermeable graphene sheets and self-healing PPy and proved by the identification of corrosion products and the scanning vibrating electrode technique.

Targeting Hsp90-Cdc37: A Promising Therapeutic Strategy by Inhibiting Hsp90 Chaperone Function.

PubMed

Wang, Lei; Li, Li; Gu, Kai; Xu, Xiao-Li; Sun, Yuan; You, Qi-Dong

2017-01-01

The Hsp90 chaperone protein regulates the folding, maturation and stability of a wide variety of oncoproteins. In recent years, many Hsp90 inhibitors have entered into the clinical trials while all of them target ATPase showing similar binding capacity and kinds of side-effects so that none have reached to the market. During the regulation progress, numerous protein- protein interactions (PPI) such as Hsp90 and client proteins or cochaperones are involved. With the Hsp90-cochaperones PPI networks being more and more clear, many cancerous proteins have been reported to be tightly correlated to Hsp90-cochaperones PPI. Among them, Hsp90-Cdc37 PPI has been widely reported to associate with numerous protein kinases, making it a novel target for the treatment of cancers. In this paper, we briefly review the strategies and modulators targeting Hsp90-Cdc37 complex including direct and indirect regulation mechanism. Through these discussions we expect to present inspirations for new insights into an alternative way to inhibit Hsp90 chaperone function. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Detecting experimental techniques and selecting relevant documents for protein-protein interactions from biomedical literature

PubMed Central

2011-01-01

Background The selection of relevant articles for curation, and linking those articles to experimental techniques confirming the findings became one of the primary subjects of the recent BioCreative III contest. The contest’s Protein-Protein Interaction (PPI) task consisted of two sub-tasks: Article Classification Task (ACT) and Interaction Method Task (IMT). ACT aimed to automatically select relevant documents for PPI curation, whereas the goal of IMT was to recognise the methods used in experiments for identifying the interactions in full-text articles. Results We proposed and compared several classification-based methods for both tasks, employing rich contextual features as well as features extracted from external knowledge sources. For IMT, a new method that classifies pair-wise relations between every text phrase and candidate interaction method obtained promising results with an F1 score of 64.49%, as tested on the task’s development dataset. We also explored ways to combine this new approach and more conventional, multi-label document classification methods. For ACT, our classifiers exploited automatically detected named entities and other linguistic information. The evaluation results on the BioCreative III PPI test datasets showed that our systems were very competitive: one of our IMT methods yielded the best performance among all participants, as measured by F1 score, Matthew’s Correlation Coefficient and AUC iP/R; whereas for ACT, our best classifier was ranked second as measured by AUC iP/R, and also competitive according to other metrics. Conclusions Our novel approach that converts the multi-class, multi-label classification problem to a binary classification problem showed much promise in IMT. Nevertheless, on the test dataset the best performance was achieved by taking the union of the output of this method and that of a multi-class, multi-label document classifier, which indicates that the two types of systems complement each other in terms of recall. For ACT, our system exploited a rich set of features and also obtained encouraging results. We examined the features with respect to their contributions to the classification results, and concluded that contextual words surrounding named entities, as well as the MeSH headings associated with the documents were among the main contributors to the performance. PMID:22151769

Concurrent Validity of the Psychopathic Personality Inventory with Offender and Community Samples

PubMed Central

Malterer, Melanie B.; Lilienfeld, Scott O.; Neumann, Craig S.; Newman, Joseph P.

2009-01-01

The Psychopathy Checklist - Revised (PCL-R; Hare, 2003) is a frequently used and well-validated measure of psychopathy, but is relatively time-intensive and expensive to administer. The Psychopathic Personality Inventory (PPI; Lilienfeld & Andrews, 1996) is a self-report measure that provides a less time-intensive and less expensive method for identifying psychopathic individuals. Using three independent samples and two different versions of the PCL (i.e., PCL-R, PCL:SV), we evaluated the extent to which the PPI and PCL overlap in their measurement of the psychopathy construct. Across three studies, PPI total and Factor 2 scores correlated moderately to strongly with PCL total and Factor 2 scores. Results for PPI and PCL Factor 1 scores were less positive. These findings raise important questions concerning the integration of results obtained using alternative psychopathy assessments. PMID:19955107

SPR Biosensors in Direct Molecular Fishing: Implications for Protein Interactomics.

PubMed

Florinskaya, Anna; Ershov, Pavel; Mezentsev, Yuri; Kaluzhskiy, Leonid; Yablokov, Evgeniy; Medvedev, Alexei; Ivanov, Alexis

2018-05-18

We have developed an original experimental approach based on the use of surface plasmon resonance (SPR) biosensors, applicable for investigation of potential partners involved in protein⁻protein interactions (PPI) as well as protein⁻peptide or protein⁻small molecule interactions. It is based on combining a SPR biosensor, size exclusion chromatography (SEC), mass spectrometric identification of proteins (LC-MS/MS) and direct molecular fishing employing principles of affinity chromatography for isolation of potential partner proteins from the total lysate of biological samples using immobilized target proteins (or small non-peptide compounds) as ligands. Applicability of this approach has been demonstrated within the frame of the Human Proteome Project (HPP) and PPI regulation by a small non-peptide biologically active compound, isatin.

Contractor Past Performance Information (PPI) in Source Selection: A Comparison Study of Public and Private Sector

DTIC Science & Technology

2005-05-01

efficiencies similar to those in the private sector . However, along the way, Government and private sector industry have begun to disagree about how PPI is...double that of the private sector due to an evaluation process that is cumbersome, time-consuming, and lacking the efficiencies enjoyed by private

Impact of a pharmacist-driven protocol to decrease proton pump inhibitor use in non-intensive care hospitalized adults.

PubMed

Michal, Jessica; Henry, Thomas; Street, Connie

2016-09-01

Results of a pharmacist-driven protocol to decrease proton pump inhibitor (PPI) use in non-intensive care unit (ICU) hospitalized adults are presented. This concurrent preintervention and postintervention study included subjects at least 18 years of age receiving PPIs while hospitalized in general medical or surgical beds. Patients were identified for inclusion in the postintervention group using a daily list of hospitalized patients with active PPI orders. A pharmacist evaluated these subjects for PPI appropriateness, and then recommended discontinuing or changing PPIs to histamine H2-receptor antagonists. Per protocol, the pharmacist could change PPIs to H2-antagonists if prescribers did not respond to recommendations. Preintervention group patients were gathered retrospectively and treated as the retrospective control group. Patients were excluded if they had cumulative ICU or ICU step-down stays of at least two days, had predefined appropriate indications for PPIs, or were not evaluated within one day of PPI orders. The primary outcome was the rate of PPI use. Secondary objectives included rates of prescriber acceptance of pharmacist recommendations and hospital-onset Clostridium difficile infections (HO-CDI). PPIs were discontinued in 66.0% (n = 62) of postintervention group patients compared to 41.1% (n = 39) of the preintervention group (absolute risk reduction, 24.9%; p = 0.001). In the postintervention group, 31.9% (n = 30) of recommendations were accepted, whereas 11.7% (n = 11) were rejected. No subjects in either group were diagnosed with HO-CDI during the study period. The pharmacist-driven protocol described in this study decreased PPI use in non-ICU hospitalized adults. Copyright © 2016 by the American Society of Health-System Pharmacists, Inc. All rights reserved.

Second-line rescue triple therapy with levofloxacin after failure of non-bismuth quadruple "sequential" or "concomitant" treatment to eradicate H. pylori infection.

PubMed

Gisbert, Javier P; Molina-Infante, Javier; Marin, Alicia C; Vinagre, Gemma; Barrio, Jesus; McNicholl, Adrian Gerald

2013-06-01

Non-bismuth quadruple "sequential" and "concomitant" regimens, including a proton pump inhibitor (PPI), amoxicillin, clarithromycin and a nitroimidazole, are increasingly used as first-line treatments for Helicobacter pylori infection. Eradication with rescue regimens may be challenging after failure of key antibiotics such as clarithromycin and nitroimidazoles. To evaluate the efficacy and tolerability of a second-line levofloxacin-containing triple regimen (PPI-amoxicillin-levofloxacin) in the eradication of H. pylori after non-bismuth quadruple-containing treatment failure. prospective multicenter study. in whom a non-bismuth quadruple regimen, administered either sequentially (PPI + amoxicillin for 5 days followed by PPI + clarithromycin + metronidazole for 5 more days) or concomitantly (PPI + amoxicillin + clarithromycin + metronidazole for 10 days) had previously failed. levofloxacin (500 mg b.i.d.), amoxicillin (1 g b.i.d.) and PPI (standard dose b.i.d.) for 10 days. eradication was confirmed with (13)C-urea breath test 4-8 weeks after therapy. Compliance and tolerance: compliance was determined through questioning and recovery of empty medication envelopes. Incidence of adverse effects was evaluated by means of a questionnaire. 100 consecutive patients were included (mean age 50 years, 62% females, 12% peptic ulcer and 88% dyspepsia): 37 after "sequential", and 63 after "concomitant" treatment failure. All patients took all medications correctly. Overall, per-protocol and intention-to-treat H. pylori eradication rates were 75.5% (95% CI 66-85%) and 74% (65-83%). Respective intention-to-treat cure rates for "sequential" and "concomitant" failure regimens were 74.4% and 71.4%, respectively. Adverse effects were reported in six (6%) patients; all of them were mild. Ten-day levofloxacin-containing triple therapy constitutes an encouraging second-line strategy in patients with previous non-bismuth quadruple "sequential" or "concomitant" treatment failure.

Proton pump inhibitors are associated with increased risk of development of chronic kidney disease.

PubMed

Arora, Pradeep; Gupta, Anu; Golzy, Mojgan; Patel, Nilang; Carter, Randolph L; Jalal, Kabir; Lohr, James W

2016-08-03

Acute interstitial nephritis secondary to proton pump inhibitors (PPIs) frequently goes undiagnosed due to its subacute clinical presentation, which may later present as chronic kidney disease (CKD). We investigated the association of PPI use with the development of CKD and death. Two separate retrospective case-control study designs were employed with a prospective logistic regression analysis of data to evaluate the association of development of CKD and death with PPI use. The population included 99,269 patients who were seen in primary care VISN2 clinics from 4/2001 until 4/2008. For evaluation of the CKD outcome, 22,807 with preexisting CKD at the first observation in Veterans Affairs Health Care Upstate New York (VISN2) network data system were excluded. Data obtained included use of PPI (Yes/No), demographics, laboratory data, pre-PPI comorbidity variables. A total of 19,311/76,462 patients developed CKD. Of those who developed CKD 24.4 % were on PPI. Patients receiving PPI were less likely to have vascular disease, COPD, cancer and diabetes. Of the total of 99,269 patients analyzed for mortality outcome, 11,758 died. A prospective logistic analysis of case-control data showed higher odds for development of CKD (OR 1.10 95 % CI 1.05-1.16) and mortality (OR 1.76, 95 % CI 1.67-1.84) among patients taking PPIs versus those not on PPIs. Use of proton pump inhibitors is associated with increased risk of development of CKD and death. With the large number of patients being treated with proton pump inhibitors, healthcare providers need to be better educated about the potential side effects of these medications.

Esophageal Motility and Rikkunshito Treatment for Proton Pump Inhibitor-Refractory Nonerosive Reflux Disease: A Prospective, Uncontrolled, Open-Label Pilot Study Trial.

PubMed

Odaka, Takeo; Yamato, Shigeru; Yokosuka, Osamu

2017-01-01

Only a few reports focused on esophageal motility in patients with proton pump inhibitor (PPI)-refractory nonerosive reflux disease (NERD) and there has been no established strategy for treatment. To clarify the characteristics of esophageal motility in patients with PPI-refractory NERD, we evaluated esophageal function using combined multichannel intraluminal impedance and esophageal manometry (MII-EM). In addition, we evaluated the efficacy of rikkunshito (RKT), which is a gastrointestinal prokinetic agent. Thirty patients with NERD were enrolled and underwent MII-EM. After 8 weeks of RKT (7.5 g/d) treatment, MII-EM was repeated on patients with PPI-refractory NERD. Symptoms were assessed by the Gastrointestinal Symptom Rating Scale. In patients with PPI-refractory NERD, measures of complete bolus transit, peristaltic contractions, and residual pressure of the lower esophageal sphincter during swallowing deviated from the standard values and esophageal clearance was found to be deteriorated. RKT significantly improved the peristaltic contractions ( P < 0.05), the complete bolus transit ( P < 0.01), and the residual pressure of lower esophageal sphincter ( P < 0.05) in these patients. The overall score ( P < 0.01) and the subscale scores of acid reflux syndrome ( P < 0.05), abdominal pain ( P < 0.05), and indigestion syndrome ( P < 0.01) in the Gastrointestinal Symptom Rating Scale were significantly improved by the 8-week RKT treatment. In the pilot study, patients with PPI-refractory NERD had disorders of esophageal and lower esophageal sphincter motility that were improved by RKT. Further studies examining esophageal motor activity of RKT in PPI-refractory NERD are required. University hospital Medical Information Network (UMIN) Clinical Trial Registry identifier: UMIN000003092.

Comparative study of therapeutic effects of PPI and H2RA on ulcers during continuous aspirin therapy

PubMed Central

Nema, Hiroaki; Kato, Mototsugu

2010-01-01

AIM: To compare the therapeutic effects of proton pump inhibitors (PPI) and histamine 2 receptor antagonists (H2RA) on gastroduodenal ulcers under continuous use of low-dose aspirin. METHODS: Sixty patients who had a gastroduodenal ulcer on screening endoscopy but required continuous use of low-dose aspirin were randomly assigned to receive PPI (lansoprazole 30 mg, n = 30) or H2RA (famotidine 40 mg or if famotidine had been administered before assignment, ranitidine 300 mg, n = 30). The therapeutic effects were evaluated by endoscopy after 8-wk treatment. The presence or absence of Helicobacter pylori (H. pylori) was determined by urea breath test before treatment. Abdominal symptoms were compared with the gastrointestinal symptom rating scale (GSRS) questionnaire before and after treatment. RESULTS: Twenty-six patients in the PPI group and 26 patients in the H2RA group, excluding dropouts, were analyzed. There were no significant differences in median age, sex, underlying disease, smoking status, H. pylori infection, prevalence of ulcers before treatment, and lesion site between the two groups. The therapeutic effects were endoscopically evaluated as healed in 23 patients (88.5%) and not healed in 3 patients in the PPI group and as healed in 22 patients (84.6%) and not healed in 4 patients in the H2RA group. Abdominal symptoms before treatment were uncommon in both groups; the GSRS scores were not significantly reduced after treatment as compared with before treatment. CONCLUSION: The healing rate of gastroduodenal ulcers during continuous use of low-dose aspirin was greater than 80% in both the PPI group and the H2RA group, with no significant difference between the two groups. PMID:21072898

The association between the use of proton pump inhibitors and the risk of hypomagnesemia: a systematic review and meta-analysis.

PubMed

Park, Chan Hyuk; Kim, Eun Hye; Roh, Yun Ho; Kim, Ha Yan; Lee, Sang Kil

2014-01-01

Although many case reports have described patients with proton pump inhibitor (PPI)-induced hypomagnesemia, the impact of PPI use on hypomagnesemia has not been fully clarified through comparative studies. We aimed to evaluate the association between the use of PPI and the risk of developing hypomagnesemia by conducting a systematic review with meta-analysis. We conducted a systematic search of MEDLINE, EMBASE, and the Cochrane Library using the primary keywords "proton pump," "dexlansoprazole," "esomeprazole," "ilaprazole," "lansoprazole," "omeprazole," "pantoprazole," "rabeprazole," "hypomagnesemia," "hypomagnesaemia," and "magnesium." Studies were included if they evaluated the association between PPI use and hypomagnesemia and reported relative risks or odds ratios or provided data for their estimation. Pooled odds ratios with 95% confidence intervals were calculated using the random effects model. Statistical heterogeneity was assessed with Cochran's Q test and I2 statistics. Nine studies including 115,455 patients were analyzed. The median Newcastle-Ottawa quality score for the included studies was seven (range, 6-9). Among patients taking PPIs, the median proportion of patients with hypomagnesemia was 27.1% (range, 11.3-55.2%) across all included studies. Among patients not taking PPIs, the median proportion of patients with hypomagnesemia was 18.4% (range, 4.3-52.7%). On meta-analysis, pooled odds ratio for PPI use was found to be 1.775 (95% confidence interval 1.077-2.924). Significant heterogeneity was identified using Cochran's Q test (df = 7, P<0.001, I2 = 98.0%). PPI use may increase the risk of hypomagnesemia. However, significant heterogeneity among the included studies prevented us from reaching a definitive conclusion.

Influence of Aripiprazole, Risperidone, and Amisulpride on Sensory and Sensorimotor Gating in Healthy ‘Low and High Gating' Humans and Relation to Psychometry

PubMed Central

Csomor, Philipp A; Preller, Katrin H; Geyer, Mark A; Studerus, Erich; Huber, Theodor; Vollenweider, Franz X

2014-01-01

Despite advances in the treatment of schizophrenia spectrum disorders with atypical antipsychotics (AAPs), there is still need for compounds with improved efficacy/side-effect ratios. Evidence from challenge studies suggests that the assessment of gating functions in humans and rodents with naturally low-gating levels might be a useful model to screen for novel compounds with antipsychotic properties. To further evaluate and extend this translational approach, three AAPs were examined. Compounds without antipsychotic properties served as negative control treatments. In a placebo-controlled, within-subject design, healthy males received either single doses of aripiprazole and risperidone (n=28), amisulpride and lorazepam (n=30), or modafinil and valproate (n=30), and placebo. Prepulse inhibiton (PPI) and P50 suppression were assessed. Clinically associated symptoms were evaluated using the SCL-90-R. Aripiprazole, risperidone, and amisulpride increased P50 suppression in low P50 gaters. Lorazepam, modafinil, and valproate did not influence P50 suppression in low gaters. Furthermore, low P50 gaters scored significantly higher on the SCL-90-R than high P50 gaters. Aripiprazole increased PPI in low PPI gaters, whereas modafinil and lorazepam attenuated PPI in both groups. Risperidone, amisulpride, and valproate did not influence PPI. P50 suppression in low gaters appears to be an antipsychotic-sensitive neurophysiologic marker. This conclusion is supported by the association of low P50 suppression and higher clinically associated scores. Furthermore, PPI might be sensitive for atypical mechanisms of antipsychotic medication. The translational model investigating differential effects of AAPs on gating in healthy subjects with naturally low gating can be beneficial for phase II/III development plans by providing additional information for critical decision making. PMID:24801767

BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference.

PubMed

Garcia-Garcia, Javier; Schleker, Sylvia; Klein-Seetharaman, Judith; Oliva, Baldo

2012-07-01

Protein-protein interactions (PPIs) play a crucial role in biology, and high-throughput experiments have greatly increased the coverage of known interactions. Still, identification of complete inter- and intraspecies interactomes is far from being complete. Experimental data can be complemented by the prediction of PPIs within an organism or between two organisms based on the known interactions of the orthologous genes of other organisms (interologs). Here, we present the BIANA (Biologic Interactions and Network Analysis) Interolog Prediction Server (BIPS), which offers a web-based interface to facilitate PPI predictions based on interolog information. BIPS benefits from the capabilities of the framework BIANA to integrate the several PPI-related databases. Additional metadata can be used to improve the reliability of the predicted interactions. Sensitivity and specificity of the server have been calculated using known PPIs from different interactomes using a leave-one-out approach. The specificity is between 72 and 98%, whereas sensitivity varies between 1 and 59%, depending on the sequence identity cut-off used to calculate similarities between sequences. BIPS is freely accessible at http://sbi.imim.es/BIPS.php.

High-Affinity Small-Molecule Inhibitors of the Menin-Mixed Lineage Leukemia (MLL) Interaction Closely Mimic a Natural Protein-Protein Interaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Shihan; Senter, Timothy J.; Pollock, Jonathan

2014-10-02

The protein–protein interaction (PPI) between menin and mixed lineage leukemia (MLL) plays a critical role in acute leukemias, and inhibition of this interaction represents a new potential therapeutic strategy for MLL leukemias. We report development of a novel class of small-molecule inhibitors of the menin–MLL interaction, the hydroxy- and aminomethylpiperidine compounds, which originated from HTS of ~288000 small molecules. We determined menin–inhibitor co-crystal structures and found that these compounds closely mimic all key interactions of MLL with menin. Extensive crystallography studies combined with structure-based design were applied for optimization of these compounds, resulting in MIV-6R, which inhibits the menin–MLL interactionmore » with IC 50 = 56 nM. Treatment with MIV-6 demonstrated strong and selective effects in MLL leukemia cells, validating specific mechanism of action. Our studies provide novel and attractive scaffold as a new potential therapeutic approach for MLL leukemias and demonstrate an example of PPI amenable to inhibition by small molecules.« less

Clopidogrel-Proton Pump Inhibitor Drug-Drug Interaction and Risk of Adverse Clinical Outcomes Among PCI-Treated ACS Patients: A Meta-analysis.

PubMed

Serbin, Michael A; Guzauskas, Gregory F; Veenstra, David L

2016-08-01

Uncertainty regarding clopidogrel effectiveness attenuation because of a drug-drug interaction with proton pump inhibitors (PPI) has led to conflicting guidelines on concomitant therapy. In particular, the effect of this interaction in patients who undergo a percutaneous coronary intervention (PCI), a population known to have increased risk of adverse cardiovascular events, has not been systematically evaluated. To synthesize the evidence of the effect of clopidogrel-PPI drug interaction on adverse cardiovascular outcomes in a PCI patient population. We conducted a systematic literature review for studies reporting clinical outcomes in patients who underwent a PCI and were initiated on clopidogrel with or without a PPI. Studies were included in the analysis if they reported at least 1 of the clinical outcomes of interest (major adverse cardiovascular event [MACE], cardiovascular death, all-cause death, myocardial infarction, stroke, stent thrombosis, and bleed events). We excluded studies that were not exclusive to PCI patients or had no PCI subgroup analysis and/or did not report at least a 6-month follow-up. Statistical and clinical heterogeneity were evaluated and HRs and 95% CIs for adverse clinical events were pooled using the DerSimonian and Laird random-effects meta-analysis method. We identified 12 studies comprising 50,277 PCI patients that met our inclusion and exclusion criteria. Our analysis included retrospective analyses of randomized controlled trials (2), health registries (3), claims databases (2), and institutional records (5); no prospective studies of PCI patients were identified. On average, patients were in their mid-60s, male, and had an array of comorbidities, including hyperlipidemia, diabetes, hypertension, and smoking history. Concomitant therapy following PCI resulted in statistically significant increases in composite MACE (HR = 1.28; 95% CI = 1.24-1.32), myocardial infarction (HR = 1.51; 95% CI = 1.40-1.62), and stroke (HR = 1.46; 95% CI = 1.15-1.86). However, concomitant therapy had no statistically significant effect on stent thrombosis, mortality measured by all-cause or cardiovascular death, or major bleeding before or after the grouping of studies that reported a major or minor bleed outcome. Only 1 study reported on gastrointestinal bleed, and pooled analysis could not be conducted. Statistical testing suggested heterogeneity among studies, but subgroup analysis did not reveal a clear source. Based on the results from this meta-analysis of retrospective analyses of randomized controlled trials and observational studies, concomitant clopidogrel-PPI therapy following PCI appears to be significantly associated with adverse cardiovascular events. Further research on the effect of individual PPIs is needed. Serbin, Guzauskas, and Veenstra were supported by the NIH Common Fund and NIA (1U01AG047109-01, Veenstra, PI) via the Personalized Medicine Economics Research (PriMER) project. The authors do not report any conflicting interests. All authors contributed to the study concept and design. Serbin took the lead in data collection; data interpretation was performed primarily by Serbin, with assistance from the other authors. The manuscript was written primarily by Serbin, along with Guzauskas, and revised by Guzauskas and Veenstra, with assistance from Serbin.

Partial response to proton pump inhibitor therapy for GERD: observational study of patient characteristics, burden of disease, and costs in the USA.

PubMed

Stålhammar, Nils-Olov; Spiegel, Brennan M; Granstedt Löfman, Helena; Karlsson, Maria; Wahlqvist, Peter; Næsdal, Jørgen; Nelson, M Todd; Despiégel, Nicolas

2012-01-01

Disease burden and associated costs are not well understood among patients with gastroesophageal reflux disease (GERD) who have persistent symptoms despite optimized proton pump inhibitor (PPI) therapy. The aim of this study was to investigate disease burden and costs of GERD in partial responders to PPI therapy. The Partial Response to PPI treatment: the Cost to Society and the Burden to the Patient in the US (REMAIN US) study was a 12-month, multicenter, noninterventional, observational study of 552 partial PPI responders in the USA. Participating sites were comprised of family practice (n = 30), internal medicine (n = 8), and specialist (gastroenterologist) centers (n = 15). GERD symptoms, health-related quality of life (HRQL), and impact on productivity were evaluated from patient-reported outcome instruments. Resource utilization data were also collected. Patients had a high symptom burden, impaired HRQL, and reduced productivity while at work and in daily activities, despite optimized PPI therapy. Mean annual GERD-related costs were US$9944 per patient, comprising total direct costs and mean productivity loss costs of US$4068 and US$5876 per patient, respectively. Patients with GERD and a partial response to PPI therapy have considerable direct and indirect costs, along with substantial impairments in HRQL and productivity.

High sensitivity Schottky junction diode based on monolithically grown aligned polypyrrole nanofibers: Broad range detection of m-dihydroxybenzene.

PubMed

Ameen, Sadia; Akhtar, M Shaheer; Seo, Hyung-Kee; Shin, Hyung Shik

2015-07-30

Aligned p-type polypyrrole (PPy) nanofibers (NFs) thin film was grown on n-type silicon (100) substrate by an electrochemical technique to fabricate Schottky junction diode for the efficient detection of m-dihydroxybenzene chemical. The highly dense and well aligned PPy NFs with the average diameter (∼150-200 nm) were grown on n-type Si substrate. The formation of aligned PPy NFs was confirmed by elucidating the structural, compositional and the optical properties. The electrochemical behavior of the fabricated Pt/p-aligned PPy NFs/n-silicon Schottky junction diode was evaluated by cyclovoltametry (CV) and current (I)-voltage (V) measurements with the variation of m-dihydroxybenzene concentration in the phosphate buffer solution (PBS). The fabricated Pt/p-aligned PPy NFs/n-silicon Schottky junction diode exhibited the rectifying behavior of I-V curve with the addition of m-dihydroxybenzene chemical, while a weak rectifying I-V behavior was observed without m-dihydroxybenzene chemical. This non-linear I-V behavior suggested the formation of Schottky barrier at the interface of Pt layer and p-aligned PPy NFs/n-silicon thin film layer. By analyzing the I-V characteristics, the fabricated Pt/p-aligned PPy NFs/n-silicon Schottky junction diode displayed reasonably high sensitivity ∼23.67 μAmM(-1)cm(-2), good detection limit of ∼1.51 mM with correlation coefficient (R) of ∼0.9966 and short response time (10 s). Copyright © 2015 Elsevier B.V. All rights reserved.

Intersystem-crossing and phosphorescence rates in fac-Ir(III)(ppy)3: a theoretical study involving multi-reference configuration interaction wavefunctions.

PubMed

Kleinschmidt, Martin; van Wüllen, Christoph; Marian, Christel M

2015-03-07

We have employed combined density functional theory and multi-reference configuration interaction methods including spin-orbit coupling (SOC) effects to investigate the photophysics of the green phosphorescent emitter fac-tris-(2-phenylpyridine)iridium (fac-Ir(ppy)3). A critical evaluation of our quantum chemical approaches shows that a perturbational treatment of SOC is the method of choice for computing the UV/Vis spectrum of this heavy transition metal complex while multi-reference spin-orbit configuration interaction is preferable for calculating the phosphorescence rates. The particular choice of the spin-orbit interaction operator is found to be of minor importance. Intersystem crossing (ISC) rates have been determined by Fourier transformation of the time correlation function of the transition including Dushinsky rotations. In the electronic ground state, fac-Ir(ppy)3 is C3 symmetric. The calculated UV/Vis spectrum is in excellent agreement with experiment. The effect of SOC is particularly pronounced for the metal-to-ligand charge transfer (MLCT) band in the visible region of the absorption spectrum which does not only extend its spectral onset towards longer wavelengths but also experiences a blue shift of its maximum. Pseudo-Jahn-Teller interaction leads to asymmetric coordinate displacements in the lowest MLCT states. Substantial electronic SOC and a small energy gap make ISC an ultrafast process in fac-Ir(ppy)3. For the S1↝T1 non-radiative transition, we compute a rate constant of kISC = 6.9 × 10(12) s(-1) which exceeds the rate constant of radiative decay to the electronic ground state by more than six orders of magnitude, in agreement with the experimental observation of a subpicosecond ISC process and a triplet quantum yield close to unity. As a consequence of the geometric distortion in the T1 state, the T1 → S0 transition densities are localized on one of the phenylpyridyl moieties. In our best quantum chemical model, we obtain phosphorescence decay times of 264 μs, 13 μs, and 0.9 μs, respectively, for the T1,I, T1,II, and T1,III fine-structure levels in dichloromethane (DCM) solution. In addition to reproducing the correct orders of magnitude for the individual phosphorescence emission probabilities, our theoretical study gives insight into the underlying mechanisms. In terms of intensity borrowing from spin-allowed transitions, the low emission probability of the T1,I substate is caused by the mutual cancellation of contributions from several singlet states to the total transition dipole moment. Their contributions do not cancel but add up in case of the much faster T1,III → S0 emission while the T1,II → S0 emission is dominated by intensity borrowing from a single spin-allowed process, i.e., the S2 → S0 transition.

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text.

PubMed

Krallinger, Martin; Vazquez, Miguel; Leitner, Florian; Salgado, David; Chatr-Aryamontri, Andrew; Winter, Andrew; Perfetto, Livia; Briganti, Leonardo; Licata, Luana; Iannuccelli, Marta; Castagnoli, Luisa; Cesareni, Gianni; Tyers, Mike; Schneider, Gerold; Rinaldi, Fabio; Leaman, Robert; Gonzalez, Graciela; Matos, Sergio; Kim, Sun; Wilbur, W John; Rocha, Luis; Shatkay, Hagit; Tendulkar, Ashish V; Agarwal, Shashank; Liu, Feifan; Wang, Xinglong; Rak, Rafal; Noto, Keith; Elkan, Charles; Lu, Zhiyong; Dogan, Rezarta Islamaj; Fontaine, Jean-Fred; Andrade-Navarro, Miguel A; Valencia, Alfonso

2011-10-03

Determining usefulness of biomedical text mining systems requires realistic task definition and data selection criteria without artificial constraints, measuring performance aspects that go beyond traditional metrics. The BioCreative III Protein-Protein Interaction (PPI) tasks were motivated by such considerations, trying to address aspects including how the end user would oversee the generated output, for instance by providing ranked results, textual evidence for human interpretation or measuring time savings by using automated systems. Detecting articles describing complex biological events like PPIs was addressed in the Article Classification Task (ACT), where participants were asked to implement tools for detecting PPI-describing abstracts. Therefore the BCIII-ACT corpus was provided, which includes a training, development and test set of over 12,000 PPI relevant and non-relevant PubMed abstracts labeled manually by domain experts and recording also the human classification times. The Interaction Method Task (IMT) went beyond abstracts and required mining for associations between more than 3,500 full text articles and interaction detection method ontology concepts that had been applied to detect the PPIs reported in them. A total of 11 teams participated in at least one of the two PPI tasks (10 in ACT and 8 in the IMT) and a total of 62 persons were involved either as participants or in preparing data sets/evaluating these tasks. Per task, each team was allowed to submit five runs offline and another five online via the BioCreative Meta-Server. From the 52 runs submitted for the ACT, the highest Matthew's Correlation Coefficient (MCC) score measured was 0.55 at an accuracy of 89% and the best AUC iP/R was 68%. Most ACT teams explored machine learning methods, some of them also used lexical resources like MeSH terms, PSI-MI concepts or particular lists of verbs and nouns, some integrated NER approaches. For the IMT, a total of 42 runs were evaluated by comparing systems against manually generated annotations done by curators from the BioGRID and MINT databases. The highest AUC iP/R achieved by any run was 53%, the best MCC score 0.55. In case of competitive systems with an acceptable recall (above 35%) the macro-averaged precision ranged between 50% and 80%, with a maximum F-Score of 55%. The results of the ACT task of BioCreative III indicate that classification of large unbalanced article collections reflecting the real class imbalance is still challenging. Nevertheless, text-mining tools that report ranked lists of relevant articles for manual selection can potentially reduce the time needed to identify half of the relevant articles to less than 1/4 of the time when compared to unranked results. Detecting associations between full text articles and interaction detection method PSI-MI terms (IMT) is more difficult than might be anticipated. This is due to the variability of method term mentions, errors resulting from pre-processing of articles provided as PDF files, and the heterogeneity and different granularity of method term concepts encountered in the ontology. However, combining the sophisticated techniques developed by the participants with supporting evidence strings derived from the articles for human interpretation could result in practical modules for biological annotation workflows.

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text

PubMed Central

2011-01-01

Background Determining usefulness of biomedical text mining systems requires realistic task definition and data selection criteria without artificial constraints, measuring performance aspects that go beyond traditional metrics. The BioCreative III Protein-Protein Interaction (PPI) tasks were motivated by such considerations, trying to address aspects including how the end user would oversee the generated output, for instance by providing ranked results, textual evidence for human interpretation or measuring time savings by using automated systems. Detecting articles describing complex biological events like PPIs was addressed in the Article Classification Task (ACT), where participants were asked to implement tools for detecting PPI-describing abstracts. Therefore the BCIII-ACT corpus was provided, which includes a training, development and test set of over 12,000 PPI relevant and non-relevant PubMed abstracts labeled manually by domain experts and recording also the human classification times. The Interaction Method Task (IMT) went beyond abstracts and required mining for associations between more than 3,500 full text articles and interaction detection method ontology concepts that had been applied to detect the PPIs reported in them. Results A total of 11 teams participated in at least one of the two PPI tasks (10 in ACT and 8 in the IMT) and a total of 62 persons were involved either as participants or in preparing data sets/evaluating these tasks. Per task, each team was allowed to submit five runs offline and another five online via the BioCreative Meta-Server. From the 52 runs submitted for the ACT, the highest Matthew's Correlation Coefficient (MCC) score measured was 0.55 at an accuracy of 89% and the best AUC iP/R was 68%. Most ACT teams explored machine learning methods, some of them also used lexical resources like MeSH terms, PSI-MI concepts or particular lists of verbs and nouns, some integrated NER approaches. For the IMT, a total of 42 runs were evaluated by comparing systems against manually generated annotations done by curators from the BioGRID and MINT databases. The highest AUC iP/R achieved by any run was 53%, the best MCC score 0.55. In case of competitive systems with an acceptable recall (above 35%) the macro-averaged precision ranged between 50% and 80%, with a maximum F-Score of 55%. Conclusions The results of the ACT task of BioCreative III indicate that classification of large unbalanced article collections reflecting the real class imbalance is still challenging. Nevertheless, text-mining tools that report ranked lists of relevant articles for manual selection can potentially reduce the time needed to identify half of the relevant articles to less than 1/4 of the time when compared to unranked results. Detecting associations between full text articles and interaction detection method PSI-MI terms (IMT) is more difficult than might be anticipated. This is due to the variability of method term mentions, errors resulting from pre-processing of articles provided as PDF files, and the heterogeneity and different granularity of method term concepts encountered in the ontology. However, combining the sophisticated techniques developed by the participants with supporting evidence strings derived from the articles for human interpretation could result in practical modules for biological annotation workflows. PMID:22151929

Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines

PubMed Central

2010-01-01

Background Protein-protein interaction (PPI) plays essential roles in cellular functions. The cost, time and other limitations associated with the current experimental methods have motivated the development of computational methods for predicting PPIs. As protein interactions generally occur via domains instead of the whole molecules, predicting domain-domain interaction (DDI) is an important step toward PPI prediction. Computational methods developed so far have utilized information from various sources at different levels, from primary sequences, to molecular structures, to evolutionary profiles. Results In this paper, we propose a computational method to predict DDI using support vector machines (SVMs), based on domains represented as interaction profile hidden Markov models (ipHMM) where interacting residues in domains are explicitly modeled according to the three dimensional structural information available at the Protein Data Bank (PDB). Features about the domains are extracted first as the Fisher scores derived from the ipHMM and then selected using singular value decomposition (SVD). Domain pairs are represented by concatenating their selected feature vectors, and classified by a support vector machine trained on these feature vectors. The method is tested by leave-one-out cross validation experiments with a set of interacting protein pairs adopted from the 3DID database. The prediction accuracy has shown significant improvement as compared to InterPreTS (Interaction Prediction through Tertiary Structure), an existing method for PPI prediction that also uses the sequences and complexes of known 3D structure. Conclusions We show that domain-domain interaction prediction can be significantly enhanced by exploiting information inherent in the domain profiles via feature selection based on Fisher scores, singular value decomposition and supervised learning based on support vector machines. Datasets and source code are freely available on the web at http://liao.cis.udel.edu/pub/svdsvm. Implemented in Matlab and supported on Linux and MS Windows. PMID:21034480

Protein-Protein Interactions (PPI) reagents: | Office of Cancer Genomics

Cancer.gov

The CTD2 Center at Emory University has a library of genes used to study protein-protein interactions in mammalian cells. These genes are cloned in different mammalian expression vectors. A list of available cancer-associated genes can be accessed below.

Modulators of 14-3-3 Protein–Protein Interactions

PubMed Central

2017-01-01

Direct interactions between proteins are essential for the regulation of their functions in biological pathways. Targeting the complex network of protein–protein interactions (PPIs) has now been widely recognized as an attractive means to therapeutically intervene in disease states. Even though this is a challenging endeavor and PPIs have long been regarded as “undruggable” targets, the last two decades have seen an increasing number of successful examples of PPI modulators, resulting in growing interest in this field. PPI modulation requires novel approaches and the integrated efforts of multiple disciplines to be a fruitful strategy. This perspective focuses on the hub-protein 14-3-3, which has several hundred identified protein interaction partners, and is therefore involved in a wide range of cellular processes and diseases. Here, we aim to provide an integrated overview of the approaches explored for the modulation of 14-3-3 PPIs and review the examples resulting from these efforts in both inhibiting and stabilizing specific 14-3-3 protein complexes by small molecules, peptide mimetics, and natural products. PMID:28968506

Transient protein-protein interactions perturb E. coli metabolome and cause gene dosage toxicity

PubMed Central

Bhattacharyya, Sanchari; Bershtein, Shimon; Yan, Jin; Argun, Tijda; Gilson, Amy I; Trauger, Sunia A; Shakhnovich, Eugene I

2016-01-01

Gene dosage toxicity (GDT) is an important factor that determines optimal levels of protein abundances, yet its molecular underpinnings remain unknown. Here, we demonstrate that overexpression of DHFR in E. coli causes a toxic metabolic imbalance triggered by interactions with several functionally related enzymes. Though deleterious in the overexpression regime, surprisingly, these interactions are beneficial at physiological concentrations, implying their functional significance in vivo. Moreover, we found that overexpression of orthologous DHFR proteins had minimal effect on all levels of cellular organization – molecular, systems, and phenotypic, in sharp contrast to E. coli DHFR. Dramatic difference of GDT between ‘E. coli’s self’ and ‘foreign’ proteins suggests the crucial role of evolutionary selection in shaping protein-protein interaction (PPI) networks at the whole proteome level. This study shows how protein overexpression perturbs a dynamic metabolon of weak yet potentially functional PPI, with consequences for the metabolic state of cells and their fitness. DOI: http://dx.doi.org/10.7554/eLife.20309.001 PMID:27938662

The TEMPO Trial at 5 Years: Transoral Fundoplication (TIF 2.0) Is Safe, Durable, and Cost-effective.

PubMed

Trad, Karim S; Barnes, William E; Prevou, Elizabeth R; Simoni, Gilbert; Steffen, Jennifer A; Shughoury, Ahmad B; Raza, Mamoon; Heise, Jeffrey A; Fox, Mark A; Mavrelis, Peter G

2018-04-01

Questions remain about the therapeutic durability of transoral incisionless fundoplication (TIF). In this study, clinical outcomes were evaluated at 5 years post-TIF 2.0. A total of 63 chronic gastroesophageal reflux disease (GERD) sufferers with troublesome symptoms refractory to proton pump inhibitor (PPI) therapy, absent or ≤2 cm hiatal hernia, and abnormal esophageal acid exposure were randomized to the TIF group or PPI group. Following the 6-month evaluation, all patients in the PPI group elected for crossover to TIF; therefore, all 63 patients underwent TIF 2.0 with EsophyX 2 device. Primary outcome was elimination of daily troublesome regurgitation and atypical symptoms at the 5-year follow-up. Secondary outcomes were improvement in symptom scores, PPI use, reoperations, and patient health satisfaction. The cost-effectiveness of TIF 2.0 was also estimated. Of 63 patients, 60 were available at 1 year, 52 at 3 years, and 44 at 5 years for evaluation. Troublesome regurgitation was eliminated in 88% of patients at 1 year, 90% at 3 years, and 86% at 5 years. Resolution of troublesome atypical symptoms was achieved in 82% of patients at 1 year, 88% at 3 years, and 80% at 5 years. No serious adverse events occurred. There were 3 reoperations by the end of the 5-year follow-up. At the 5-year follow-up, 34% of patients were on daily PPI therapy as compared with 100% of patients at screening. The total GERD Health-related quality-of-life score improved by decreasing from 22.2 to 6.8 at 5 years ( P < .001). In this patient population, the TIF 2.0 procedure provided safe and sustained long-term elimination of troublesome GERD symptoms.

Inhibitors of protein-protein interactions (PPIs): an analysis of scaffold choices and buried surface area.

PubMed

Ran, Xu; Gestwicki, Jason E

2018-06-13

Protein-protein interactions (PPI) were once considered 'undruggable', but clinical successes, driven by advanced methods in drug discovery, have challenged that notion. Here, we review the last three years of literature on PPI inhibitors to understand what is working and why. From the 66 recently reported PPI inhibitors, we found that the average molecular weight was significantly greater than 500Da, but that this trend was driven, in large part, by the contribution of peptide-based compounds. Despite differences in average molecular weight, we found that compounds based on small molecules or peptides were almost equally likely to be potent inhibitors (K D <1μM). Finally, we found PPIs with buried surface area (BSA) less than 2000Å 2 were more likely to be inhibited by small molecules, while PPIs with larger BSA values were typically inhibited by peptides. PPIs with BSA values over 4000Å 2 seemed to create a particular challenge, especially for orthosteric small molecules. Thus, it seems important to choose the inhibitor scaffold based on the properties of the target interaction. Moreover, this survey suggests a (more nuanced) conclusion to the question of whether PPIs are good drug targets; namely, that some PPIs are readily 'druggable' given the right choice of scaffold, while others still seem to deserve the 'undruggable' moniker. Copyright © 2018 Elsevier Ltd. All rights reserved.

Discovering protein complexes in protein interaction networks via exploring the weak ties effect

PubMed Central

2012-01-01

Background Studying protein complexes is very important in biological processes since it helps reveal the structure-functionality relationships in biological networks and much attention has been paid to accurately predict protein complexes from the increasing amount of protein-protein interaction (PPI) data. Most of the available algorithms are based on the assumption that dense subgraphs correspond to complexes, failing to take into account the inherence organization within protein complex and the roles of edges. Thus, there is a critical need to investigate the possibility of discovering protein complexes using the topological information hidden in edges. Results To provide an investigation of the roles of edges in PPI networks, we show that the edges connecting less similar vertices in topology are more significant in maintaining the global connectivity, indicating the weak ties phenomenon in PPI networks. We further demonstrate that there is a negative relation between the weak tie strength and the topological similarity. By using the bridges, a reliable virtual network is constructed, in which each maximal clique corresponds to the core of a complex. By this notion, the detection of the protein complexes is transformed into a classic all-clique problem. A novel core-attachment based method is developed, which detects the cores and attachments, respectively. A comprehensive comparison among the existing algorithms and our algorithm has been made by comparing the predicted complexes against benchmark complexes. Conclusions We proved that the weak tie effect exists in the PPI network and demonstrated that the density is insufficient to characterize the topological structure of protein complexes. Furthermore, the experimental results on the yeast PPI network show that the proposed method outperforms the state-of-the-art algorithms. The analysis of detected modules by the present algorithm suggests that most of these modules have well biological significance in context of complexes, suggesting that the roles of edges are critical in discovering protein complexes. PMID:23046740

Proton-pump inhibitors adverse effects: a review of the evidence and position statement by the Sociedad Española de Patología Digestiva.

PubMed

de la Coba Ortiz, Cristóbal; Argüelles Arias, Federico; Martín de Argila de Prados, Carlos; Júdez Gutiérrez, Javier; Linares Rodríguez, Antonio; Ortega Alonso, Aida; Rodríguez de Santiago, Enrique; Rodríguez-Téllez, Manuel; Vera Mendoza, María Isabel; Aguilera Castro, Lara; Álvarez Sánchez, Ángel; Andrade Bellido, Raúl Jesús; Bao Pérez, Fidencio; Castro Fernández, Manuel; Giganto Tomé, Froilán

2016-04-01

In the last few years a significant number of papers have related the use of proton-pump inhibitors (PPIs) to potential serious adverse effects that have resulted in social unrest. The goal of this paper was to provide a literature review for the development of an institutional position statement by Sociedad Española de Patología Digestiva (SEPD) regarding the safety of long-term PPI use. A comprehensive review of the literature was performed to draw conclusions based on a critical assessment of the following: a) current PPI indications; b) vitamin B12 deficiency and neurological disorders; c) magnesium deficiency; d) bone fractures; e) enteric infection and pneumonia; f) interactions with thienopyridine derivatives; e) complications in cirrhotic patients. Current PPI indications have remained unchanged for years now, and are well established. A general screening of vitamin B12 levels is not recommended for all patients on a PPI; however, it does seem necessary that magnesium levels be measured at therapy onset, and then monitored in subjects on other drugs that may induce hypomagnesemia. A higher risk for bone fractures is present, even though causality cannot be concluded for this association. The association between PPIs and infection with Clostridium difficile is mild to moderate, and the risk for pneumonia is low. In patients with cardiovascular risk receiving thienopyridines derivatives it is prudent to adequately consider gastrointestinal and cardiovascular risks, given the absence of definitive evidence regardin potential drug-drug interactions; if gastrointestinal risk is found to be moderate or high, effective prevention should be in place with a PPI. PPIs should be cautiously indicated in patients with decompensated cirrhosis. PPIs are safe drugs whose benefits outweigh their potential side effects both short-term and long-term, provided their indication, dosage, and duration are appropriate.

Indication of acid suppression therapy and predictors for the prophylactic use of protonpump inhibitors vs. histamine-2 receptor antagonists in a Malaysian tertiary hospital

PubMed Central

Oh, Ai L.; Tan, Andrew G.; Phan, Hui S.; Lee, Basil C.; Jumaat, Nafisah; Chew, Soo P.; Wong, Siok H.; Ting, Shee H.; Subramaniam, Theebaa

2015-01-01

Background: Proton-pump inhibitors (PPI) and histamine-2 receptor antagonists (H2RA) are common acid suppressants used in gastrointestinal disorders. The trend of usage in Malaysia has changed from predominantly H2RA to PPI from 2007 to 2008, 3.46 versus 2.87 and 2.99 versus 3.24 DDD (Defined Daily Dose)/1000 population/day respectively. This raises concerns as PPI overutilization amounts to higher cost expenditure and are associated with various untoward consequences such as Clostridium difficile-associated diarrhea, pneumonia, and osteoporosis. Objectives: To evaluate the indication of acid suppression therapy (AST) and to look for predictors associated with the prophylactic use of PPI as compared to H2RA. Methods: Data collection was conducted via a standardized surveillance form over a 2-month period in the general medical wards of Sarawak General Hospital. All patients who received at least one dose of PPI or H2RA in any dosage form were included in the study. Appropriateness of prophylaxis was determined using current available guidelines. Selected risk factors were analysed using simple logistic regression to look for predictors associated with the choice of PPI in prophylactic AST. Results: Out of 212 cases in the present cohort, about three quarters (75.5%, n=160) of acid suppressants were given as prophylaxis. Over half of these did not have appropriate indications for prophylactic AST (58.1%, n=93). Among all cases given prophylactic AST, 75.0% (n=120) of them were given PPI. Renal insufficiency was identified as the only predictor associated with the use of prophylactic PPI in preference to H2RA (OR=2.86, 95%CI 1.21:6.72, p=0.011). Conclusion: Inappropriate prophylactic AST is a major concern and may even be underestimated due to the lack of appropriate guidelines. More data is required to guide the selection between PPI and H2RA, specifically the more cost-effective use of H2RA in patients with lower gastrointestinal risk or in whom PPI has no clear advantage. PMID:26445624

Highly efficient near ultraviolet organic light-emitting diode based on a meta-linked donor–acceptor molecule† †Electronic supplementary information (ESI) available: The details of the synthesis; the ground state and excited state geometries in PPI, TPA–PPI and mTPA–PPI; absorption and emission properties of PPI, TPA–PPI and mTPA–PPI in the gas phase; detailed absorption peak positions, emission peak positions and ηPL values of PPI and mTPA–PPI in different solvents; HOMO and LUMO of mTPA–PPI at ground state; NTO for the S0 → S1 absorption transition in PPI, TPA–PPI and mTPA–PPI; NTO for S0 → Sn electronic transition character in mTPA–PPI; lifetime measurement, radiative transition rates and non-radiative transition rates of PPI and mTPA–PPI in hexane and THF solutions; low-temperature fluorescence and phosphorescence spectra of PPI and mTPA–PPI; CV curves of PPI and mTPA–PPI, and schematic diagram of design principle of mTPA–PPI; TGA and DSC graphs of PPI and mTPA–PPI; current efficiency–current density–power efficiency curves and EL spectra at different driving voltages of PPI and mTPA–PPI devices. See DOI: 10.1039/c5sc01131k

PubMed Central

Liu, Haichao; Bai, Qing; Yao, Liang; Zhang, Haiyan; Xu, Hai; Zhang, Shitong; Li, Weijun; Gao, Yu; Li, Jinyu; Lu, Ping; Wang, Hongyan; Ma, Yuguang

2015-01-01

A novel near ultraviolet (NUV) emitter with a meta-linked donor–acceptor (D–A) structure between triphenylamine (TPA) and phenanthroimidazole (PPI), mTPA–PPI, was designed and synthesized. This molecular design is expected to resolve the conflict between the non-red-shifted emission and the introduction of a charge-transfer (CT) state in the D–A system, aiming at NUV organic light-emitting diodes (OLEDs) with high-efficiency and colour-purity. Theoretical calculations and photophysical experiments were implemented to verify the unique excited state properties of mTPA–PPI. The mTPA–PPI device exhibited excellent NUV electroluminescence (EL) performance with an emission peak at 404 nm, a full width at half maximum (FWHM) of only 47 nm corresponding to a CIE coordinate of (0.161, 0.049), and a maximum external quantum efficiency (EQE) of 3.33%, which is among the best results for NUV OLEDs. This work not only demonstrates the promising potential of mTPA–PPI in NUV OLEDs, but also provides a valuable strategy for the rational design of NUV materials by using the meta-linked D–A architecture. PMID:29218149

Macrocyclic peptide inhibitors for the protein-protein interaction of Zaire Ebola virus protein 24 and karyopherin alpha 5.

PubMed

Song, Xiao; Lu, Lu-Yi; Passioura, Toby; Suga, Hiroaki

2017-06-21

Ebola virus infection leads to severe hemorrhagic fever in human and non-human primates with an average case fatality rate of 50%. To date, numerous potential therapies are in development, but FDA-approved drugs or vaccines are yet unavailable. Ebola viral protein 24 (VP24) is a multifunctional protein that plays critical roles in the pathogenesis of Ebola virus infection, e.g. innate immune suppression by blocking the interaction between KPNA and PY-STAT1. Here we report macrocyclic peptide inhibitors of the VP24-KPNA5 protein-protein interaction (PPI) by means of the RaPID (Random non-standard Peptides Integrated Discovery) system. These macrocyclic peptides showed remarkably high affinity to recombinant Zaire Ebola virus VP24 (eVP24), with a dissociation constant in the single digit nanomolar range, and could also successfully disrupt the eVP24-KPNA interaction. This work provides for the first time a chemical probe capable of modulating this PPI interaction and is the starting point for the development of unique anti-viral drugs against the Ebola virus.

Plank fence penetration into automobiles-implications for prevention initiatives.

PubMed

Procter, Levi; Bernard, Andrew; Ginn, Gary; Kearney, Paul; Pienkowski, David

2011-01-01

The wooden plank fence presents a deadly but unrecognized hazard to motorists. We hypothesize that fence plank injury is prevalent and results in significant morbidity and mortality. Databases of the University of Kentucky's Level I Trauma Center and the Fayette County Coroner were retrospectively analyzed over a 12-year period (1995-2006). One hundred and twenty-eight subjects were involved in vehicle contact with wooden plank fences. One hundred and twenty-three subjects were evaluated at the Emergency Department of our trauma center; 35 (27%) had a patient-plank interaction (PPI). Men (30/35) were more frequently involved (86%), and average age was 32.8 years. Thirty-two (91%) were drivers; 14/35 (40%) died from PPI-related injuries. The most common cause of death was blunt head trauma in 13 of these 14 fatally injured subjects (93%). This study provides new data underscoring the frequency, lethality, and economic consequences of this injury mechanism. Further research is needed to quantify the national prevalence of this problem and develop injury-mitigating strategies pertaining to roadway or fence design. © 2010 American Academy of Forensic Sciences.

Proton Pump Inhibitor Use and Risk of Chronic Kidney Disease

PubMed Central

Lazarus, Benjamin; Chen, Yuan; Wilson, Francis P.; Sang, Yingying; Chang, Alex R.; Coresh, Josef; Grams, Morgan E.

2016-01-01

Context Proton pump inhibitors (PPIs) are among the most commonly used drugs worldwide, and have been linked to acute interstitial nephritis. Less is known about the relationship between PPI use and chronic kidney disease (CKD). Objective To quantify the association between PPI use and incident CKD in a population-based cohort. Design, Setting and Participants 10,482 participants in the Atherosclerosis Risk in Communities (ARIC) study with an estimated glomerular filtration rate (eGFR) of ≥60mL/min/1.73m2 were followed from a baseline visit (1996–1999) to December 31, 2011. Findings were replicated in an administrative cohort of 248,751 patients with eGFR ≥60mL/min/1.73m2 from Geisinger Health System. Exposure Self-reported PPI use in ARIC, or an outpatient PPI prescription in the replication cohort. Histamine-2 receptor (H2) antagonist use was considered a negative control and active comparator. Main Outcome Measure Incident CKD, using diagnostic codes indicating CKD at hospital discharge or death. In the replication cohort, incident CKD was defined by outpatient eGFR <60 mL/min/1.73 m2. Results Compared to non-users, PPI-users were more often white, obese, and taking antihypertensive medication. In ARIC, PPI use was associated with incident CKD in unadjusted analysis (hazard ratio [HR], 1.45; 95% confidence interval [CI], 1.11–1.90), analysis adjusted for demographic, socioeconomic, and clinical parameters (HR, 1.50; 95% CI, 1.14–1.96), and in analysis with PPI ever-use modeled as a time-varying variable (adjusted HR, 1.35; 95% CI, 1.17–1.55). The association persisted when baseline PPI users were compared directly to H2-antagonist users (adjusted HR, 1.39; 95% CI, 1.01–1.91), and to propensity-score matched non-users (HR, 1.76; 95% CI, 1.13–2.74). In the replication cohort, PPI use was associated with CKD in all analyses, including a time-varying new user design (adjusted HR 1.24; 95% CI, 1.20–1.28). Twice-daily PPI dosing was associated with a higher risk (adjusted HR, 1.46; 95% CI, 1.28–1.67) than once-daily dosing (adjusted HR, 1.15; 95% CI, 1.09–1.21). Conclusions PPI use is associated with a 20%–50% higher risk of incident CKD. Future research should evaluate whether limiting PPI use reduces the incidence of CKD. PMID:26752337

Up-regulated expression of cartilage intermediate-layer protein and ANK in articular hyaline cartilage from patients with calcium pyrophosphate dihydrate crystal deposition disease.

PubMed

Hirose, Jun; Ryan, Lawrence M; Masuda, Ikuko

2002-12-01

Excess accumulation of extracellular inorganic pyrophosphate (ePPi) in aged human cartilage is crucial in calcium pyrophosphate dihydrate (CPPD) crystal formation in cartilage matrix. Two sources of ePPi are ePPi-generating ectoenzymes (NTPPPH) and extracellular transport of intracellular PPi by ANK. This study was undertaken to evaluate the role of NTPPPH and ANK in ePPi elaboration, by investigating expression of NTPPPH enzymes (cartilage intermediate-layer protein [CILP] and plasma cell membrane glycoprotein 1 [PC-1]) and ANK in human chondrocytes from osteoarthritic (OA) articular cartilage containing CPPD crystals and without crystals. Chondrocytes were harvested from knee cartilage at the time of arthroplasty (OA with CPPD crystals [CPPD], n = 8; OA without crystals [OA], n = 10). Normal adult human chondrocytes (n = 1) were used as a control. Chondrocytes were cultured with transforming growth factor beta1 (TGFbeta1), which stimulates ePPi elaboration, and/or insulin-like growth factor 1 (IGF-1), which inhibits ePPi elaboration. NTPPPH and ePPi were measured in the media at 48 hours. Media CILP, PC-1, and ANK were determined by dot-immunoblot analysis. Chondrocyte messenger RNA (mRNA) was extracted for reverse transcriptase-polymerase chain reaction to study expression of mRNA for CILP, PC-1, and ANK. NTPPPH and ANK mRNA and protein were also studied in fresh frozen cartilage. Basal ePPi elaboration and NTPPPH activity in conditioned media from CPPD chondrocytes were elevated compared with normal chondrocytes, and tended to be higher compared with OA chondrocytes. Basal expression of mRNA for CILP (chondrocytes) and ANK (cartilage) was higher in both CPPD chondrocytes and CPPD cartilage extract than in OA or normal samples. PC-1 mRNA was less abundant in CPPD chondrocytes and cartilage extract than in OA chondrocytes and extract, although the difference was not significant. CILP, PC-1, and ANK protein levels were similar in CPPD, OA, and normal chondrocytes or cartilage extracts. Both CILP and ANK mRNA expression and ePPi elaboration were stimulated by TGFbeta1 and inhibited by IGF-1 in chondrocytes from all sources. CILP and ANK mRNA expression correlates with chondrocyte ePPi accumulation around CPPD and OA chondrocytes, and all respond similarly to growth factor stimulation. These findings suggest that up-regulated CILP and ANK expression contributes to higher ePPi accumulation from CPPD crystal-forming cartilage.

L-GRAAL: Lagrangian graphlet-based network aligner.

PubMed

Malod-Dognin, Noël; Pržulj, Nataša

2015-07-01

Discovering and understanding patterns in networks of protein-protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary conserved pathways, protein complexes and functional orthologs. A few methods have been proposed for global PPI network alignments, but because of NP-completeness of underlying sub-graph isomorphism problem, producing topologically and biologically accurate alignments remains a challenge. We introduce a novel global network alignment tool, Lagrangian GRAphlet-based ALigner (L-GRAAL), which directly optimizes both the protein and the interaction functional conservations, using a novel alignment search heuristic based on integer programming and Lagrangian relaxation. We compare L-GRAAL with the state-of-the-art network aligners on the largest available PPI networks from BioGRID and observe that L-GRAAL uncovers the largest common sub-graphs between the networks, as measured by edge-correctness and symmetric sub-structures scores, which allow transferring more functional information across networks. We assess the biological quality of the protein mappings using the semantic similarity of their Gene Ontology annotations and observe that L-GRAAL best uncovers functionally conserved proteins. Furthermore, we introduce for the first time a measure of the semantic similarity of the mapped interactions and show that L-GRAAL also uncovers best functionally conserved interactions. In addition, we illustrate on the PPI networks of baker's yeast and human the ability of L-GRAAL to predict new PPIs. Finally, L-GRAAL's results are the first to show that topological information is more important than sequence information for uncovering functionally conserved interactions. L-GRAAL is coded in C++. Software is available at: http://bio-nets.doc.ic.ac.uk/L-GRAAL/. n.malod-dognin@imperial.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Synthesis and electromagnetic interference shielding of cellulose-derived carbon aerogels functionalized with α-Fe2O3 and polypyrrole.

PubMed

Wan, Caichao; Li, Jian

2017-04-01

Eco-friendly cellulose-derived carbon aerogels (CDCA) were employed as porous substrate to integrate with α-Fe 2 O 3 and polypyrrole (PPy) via pyrolysis and vapor-phase polymerization. The SEM and TEM observations present that the wrinkled PPy sheets and the α-Fe 2 O 3 nanoparticles were well dispersed in CDCA. The strong interactions (such as hydrogen bonding) between the substrate and the nanomaterials were demonstrated by the FTIR and XPS analysis. When utilized as electromagnetic interference (EMI) shielding materials, the α-Fe 2 O 3 /PPy/CDCA (FPCA) composite has the highest total shielding effectiveness (SE total ) of 39.4dB, about 2.0, 2.9, and 1.3 times that of the acid-treated CDCA (19.3dB), PPy (13.6dB), and α-Fe 2 O 3 /CDCA (29.3dB), respectively. Moreover, the shielding effectiveness due to absorption accounts for 78.2%-84.2% of SE total for FPCA, indicative of the absorption-dominant shielding mechanism contributing to alleviating secondary radiation. These features make the composite a useful alternative candidate for EMI shielding. Copyright © 2017 Elsevier Ltd. All rights reserved.

Prioritizing chronic obstructive pulmonary disease (COPD) candidate genes in COPD-related networks

PubMed Central

Zhang, Yihua; Li, Wan; Feng, Yuyan; Guo, Shanshan; Zhao, Xilei; Wang, Yahui; He, Yuehan; He, Weiming; Chen, Lina

2017-01-01

Chronic obstructive pulmonary disease (COPD) is a multi-factor disease, which could be caused by many factors, including disturbances of metabolism and protein-protein interactions (PPIs). In this paper, a weighted COPD-related metabolic network and a weighted COPD-related PPI network were constructed base on COPD disease genes and functional information. Candidate genes in these weighted COPD-related networks were prioritized by making use of a gene prioritization method, respectively. Literature review and functional enrichment analysis of the top 100 genes in these two networks suggested the correlation of COPD and these genes. The performance of our gene prioritization method was superior to that of ToppGene and ToppNet for genes from the COPD-related metabolic network or the COPD-related PPI network after assessing using leave-one-out cross-validation, literature validation and functional enrichment analysis. The top-ranked genes prioritized from COPD-related metabolic and PPI networks could promote the better understanding about the molecular mechanism of this disease from different perspectives. The top 100 genes in COPD-related metabolic network or COPD-related PPI network might be potential markers for the diagnosis and treatment of COPD. PMID:29262568

Prioritizing chronic obstructive pulmonary disease (COPD) candidate genes in COPD-related networks.

PubMed

Zhang, Yihua; Li, Wan; Feng, Yuyan; Guo, Shanshan; Zhao, Xilei; Wang, Yahui; He, Yuehan; He, Weiming; Chen, Lina

2017-11-28

Chronic obstructive pulmonary disease (COPD) is a multi-factor disease, which could be caused by many factors, including disturbances of metabolism and protein-protein interactions (PPIs). In this paper, a weighted COPD-related metabolic network and a weighted COPD-related PPI network were constructed base on COPD disease genes and functional information. Candidate genes in these weighted COPD-related networks were prioritized by making use of a gene prioritization method, respectively. Literature review and functional enrichment analysis of the top 100 genes in these two networks suggested the correlation of COPD and these genes. The performance of our gene prioritization method was superior to that of ToppGene and ToppNet for genes from the COPD-related metabolic network or the COPD-related PPI network after assessing using leave-one-out cross-validation, literature validation and functional enrichment analysis. The top-ranked genes prioritized from COPD-related metabolic and PPI networks could promote the better understanding about the molecular mechanism of this disease from different perspectives. The top 100 genes in COPD-related metabolic network or COPD-related PPI network might be potential markers for the diagnosis and treatment of COPD.

PdCo porous nanostructures decorated on polypyrrole @ MWCNTs conductive nanocomposite-Modified glassy carbon electrode as a powerful catalyst for ethanol electrooxidation

NASA Astrophysics Data System (ADS)

Fard, Leyla Abolghasemi; Ojani, Reza; Raoof, Jahan Bakhsh; Zare, Ehsan Nazarzadeh; Lakouraj, Moslem Mansour

2017-04-01

In the current study, well-defined PdCo porous nanostructure (PdCo PNS) is prepared by a simple one-pot wet-chemical method and polypyrrole@multi-walled carbon nanotubes (PPy@MWCNTs) nanocomposite is used as a catalyst support. The morphology and the structural properties of the prepared catalyst were studied by scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). The electrocatalytic performance of PdCo PNS/PPy@MWCNTs on glassy carbon electrode has been evaluated by cyclic voltammetry (CV), chronoamperometry (CA) and electrochemical impedance spectroscopy (EIS) techniques. The specific activity of PdCo PNS/PPy@MWCNTs for ethanol electrooxidation (1.65 mA cm-2) is higher than those of other compared electrocatalysts. Also, PdCo PNS/PPy@MWCNTs catalyst represented higher electrocatalytic activity, better long-term stability and high level of poisoning tolerance to the carbonaceous oxidative intermediates for ethanol electrooxidation reaction in alkaline media. Furthermore, the presence of PPY@MWCNTs on the surface of GCE produce a high activity to electrocatalyst, which might be due to the easier charge transfer at polymer/carbon nanotubes interfaces, higher electrochemically accessible surface areas and electronic conductivity. The superior catalytic activity of PdCo PNS/PPy@MWCNTs suggests it to be as a promising electrocatalyst for future direct ethanol fuel cells.

Step-by-step management of refractory gastresophageal reflux disease.

PubMed

Hershcovici, T; Fass, R

2013-01-01

Up to a third of the patients who receive proton pump inhibitor (PPI) once daily will demonstrate lack or partial response to treatment. There are various mechanisms that contribute to PPI failure and they include residual acid reflux, weakly acidic and weakly alkaline reflux, esophageal hypersensitivity, and psychological comorbidity, among others. Some of these underlying mechanisms may coincide in the same patient. Evaluation for proper compliance and adequate dosing time of PPIs should be the first management step before ordering invasive diagnostic tests. Doubling the PPI dose or switching to another PPI is the second step of management. Upper endoscopy and pH testing appear to have limited diagnostic value in patients who failed PPI treatment. In contrast, esophageal impedance with pH testing (multichannel intraluminal impedance MII-pH) on therapy appears to provide the most insightful information about the subsequent management of these patients (step 3). In step 4, treatment should be tailored to the specific underlying mechanism of patient's PPI failure. For those who demonstrate weakly acidic or weakly alkaline reflux as the underlying cause of their residual symptoms, transient lower esophageal sphincter relaxation reducers, endoscopic treatment, antireflux surgery and pain modulators should be considered. In those with functional heartburn, pain modulators are the cornerstone of therapy. © 2012 Copyright the Authors. Journal compilation © 2012, Wiley Periodicals, Inc. and the International Society for Diseases of the Esophagus.

Protein-Protein Interaction Reagents | Office of Cancer Genomics

Cancer.gov

The CTD2 Center at Emory University has a library of genes used to study protein-protein interactions in mammalian cells. These genes are cloned in different mammalian expression vectors. A list of available cancer-associated genes can be accessed below. Emory_CTD^2_PPI_Reagents.xlsx Contact: Haian Fu

Emory University: High-Throughput Protein-Protein Interaction Analysis for Hippo Pathway Profiling | Office of Cancer Genomics

Cancer.gov

The CTD2 Center at Emory University used high-throughput protein-protein interaction (PPI) mapping for Hippo signaling pathway profiling to rapidly unveil promising PPIs as potential therapeutic targets and advance functional understanding of signaling circuitry in cells. Read the abstract.

Differences in the Language and Design of Four PPIs for Valium. Technical Assistance Report No. 1.

ERIC Educational Resources Information Center

Redish, Janice C.

As part of the evaluation of four different versions of a patient package insert (PPI) for diazepam (Valium) created by the Food and Drug Administration (FDA), the content, organization, language, and design of the PPIs were compared. One PPI was a short prose piece with clear organization that did not particularly highlight warnings or, indeed,…

The Interactomic Analysis Reveals Pathogenic Protein Networks in Phomopsis longicolla Underlying Seed Decay of Soybean.

PubMed

Li, Shuxian; Musungu, Bryan; Lightfoot, David; Ji, Pingsheng

2018-01-01

Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla ) is the primary cause of Phomopsis seed decay (PSD) in soybean, Glycine max (L.) Merrill. This disease results in poor seed quality and is one of the most economically important seed diseases in soybean. The objectives of this study were to infer protein-protein interactions (PPI) and to identify conserved global networks and pathogenicity subnetworks in P. longicolla including orthologous pathways for cell signaling and pathogenesis. The interlog method used in the study identified 215,255 unique PPIs among 3,868 proteins. There were 1,414 pathogenicity related genes in P. longicolla identified using the pathogen host interaction (PHI) database. Additionally, 149 plant cell wall degrading enzymes (PCWDE) were detected. The network captured five different classes of carbohydrate degrading enzymes, including the auxiliary activities, carbohydrate esterases, glycoside hydrolases, glycosyl transferases, and carbohydrate binding molecules. From the PPI analysis, novel interacting partners were determined for each of the PCWDE classes. The most predominant class of PCWDE was a group of 60 glycoside hydrolases proteins. The glycoside hydrolase subnetwork was found to be interacting with 1,442 proteins within the network and was among the largest clusters. The orthologous proteins FUS3, HOG, CYP1, SGE1, and the g5566t.1 gene identified in this study could play an important role in pathogenicity. Therefore, the P. longicolla protein interactome (PiPhom) generated in this study can lead to a better understanding of PPIs in soybean pathogens. Furthermore, the PPI may aid in targeting of genes and proteins for further studies of the pathogenicity mechanisms.

The Interactomic Analysis Reveals Pathogenic Protein Networks in Phomopsis longicolla Underlying Seed Decay of Soybean

PubMed Central

Li, Shuxian; Musungu, Bryan; Lightfoot, David; Ji, Pingsheng

2018-01-01

Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla) is the primary cause of Phomopsis seed decay (PSD) in soybean, Glycine max (L.) Merrill. This disease results in poor seed quality and is one of the most economically important seed diseases in soybean. The objectives of this study were to infer protein–protein interactions (PPI) and to identify conserved global networks and pathogenicity subnetworks in P. longicolla including orthologous pathways for cell signaling and pathogenesis. The interlog method used in the study identified 215,255 unique PPIs among 3,868 proteins. There were 1,414 pathogenicity related genes in P. longicolla identified using the pathogen host interaction (PHI) database. Additionally, 149 plant cell wall degrading enzymes (PCWDE) were detected. The network captured five different classes of carbohydrate degrading enzymes, including the auxiliary activities, carbohydrate esterases, glycoside hydrolases, glycosyl transferases, and carbohydrate binding molecules. From the PPI analysis, novel interacting partners were determined for each of the PCWDE classes. The most predominant class of PCWDE was a group of 60 glycoside hydrolases proteins. The glycoside hydrolase subnetwork was found to be interacting with 1,442 proteins within the network and was among the largest clusters. The orthologous proteins FUS3, HOG, CYP1, SGE1, and the g5566t.1 gene identified in this study could play an important role in pathogenicity. Therefore, the P. longicolla protein interactome (PiPhom) generated in this study can lead to a better understanding of PPIs in soybean pathogens. Furthermore, the PPI may aid in targeting of genes and proteins for further studies of the pathogenicity mechanisms. PMID:29666630

Prediction of protein-protein interactions from amino acid sequences with ensemble extreme learning machines and principal component analysis

PubMed Central

2013-01-01

Background Protein-protein interactions (PPIs) play crucial roles in the execution of various cellular processes and form the basis of biological mechanisms. Although large amount of PPIs data for different species has been generated by high-throughput experimental techniques, current PPI pairs obtained with experimental methods cover only a fraction of the complete PPI networks, and further, the experimental methods for identifying PPIs are both time-consuming and expensive. Hence, it is urgent and challenging to develop automated computational methods to efficiently and accurately predict PPIs. Results We present here a novel hierarchical PCA-EELM (principal component analysis-ensemble extreme learning machine) model to predict protein-protein interactions only using the information of protein sequences. In the proposed method, 11188 protein pairs retrieved from the DIP database were encoded into feature vectors by using four kinds of protein sequences information. Focusing on dimension reduction, an effective feature extraction method PCA was then employed to construct the most discriminative new feature set. Finally, multiple extreme learning machines were trained and then aggregated into a consensus classifier by majority voting. The ensembling of extreme learning machine removes the dependence of results on initial random weights and improves the prediction performance. Conclusions When performed on the PPI data of Saccharomyces cerevisiae, the proposed method achieved 87.00% prediction accuracy with 86.15% sensitivity at the precision of 87.59%. Extensive experiments are performed to compare our method with state-of-the-art techniques Support Vector Machine (SVM). Experimental results demonstrate that proposed PCA-EELM outperforms the SVM method by 5-fold cross-validation. Besides, PCA-EELM performs faster than PCA-SVM based method. Consequently, the proposed approach can be considered as a new promising and powerful tools for predicting PPI with excellent performance and less time. PMID:23815620

Global De Novo Protein-Protein Interactome Elucidates Interactions of Drought-Responsive Proteins in Horse Gram (Macrotyloma uniflorum).

PubMed

Bhardwaj, Jyoti; Gangwar, Indu; Panzade, Ganesh; Shankar, Ravi; Yadav, Sudesh Kumar

2016-06-03

Inspired by the availability of de novo transcriptome of horse gram (Macrotyloma uniflorum) and recent developments in systems biology studies, the first ever global protein-protein interactome (PPI) map was constructed for this highly drought-tolerant legume. Large-scale studies of PPIs and the constructed database would provide rationale behind the interplay at cascading translational levels for drought stress-adaptive mechanisms in horse gram. Using a bidirectional approach (interolog and domain-based), a high-confidence interactome map and database for horse gram was constructed. Available transcriptomic information for shoot and root tissues of a sensitive (M-191; genotype 1) and a drought-tolerant (M-249; genotype 2) genotype of horse gram was utilized to draw comparative PPI subnetworks under drought stress. High-confidence 6804 interactions were predicted among 1812 proteins covering about one-fourth of the horse gram proteome. The highest number of interactions (33.86%) in horse gram interactome matched with Arabidopsis PPI data. The top five hub nodes mostly included ubiquitin and heat-shock-related proteins. Higher numbers of PPIs were found to be responsive in shoot tissue (416) and root tissue (2228) of genotype 2 compared with shoot tissue (136) and root tissue (579) of genotype 1. Characterization of PPIs using gene ontology analysis revealed that kinase and transferase activities involved in signal transduction, cellular processes, nucleocytoplasmic transport, protein ubiquitination, and localization of molecules were most responsive to drought stress. Hence, these could be framed in stress adaptive mechanisms of horse gram. Being the first legume global PPI map, it would provide new insights into gene and protein regulatory networks for drought stress tolerance mechanisms in horse gram. Information compiled in the form of database (MauPIR) will provide the much needed high-confidence systems biology information for horse gram genes, proteins, and involved processes. This information would ease the effort and increase the efficacy for similar studies on other legumes. Public access is available at http://14.139.59.221/MauPIR/ .

The extent, quality and impact of patient and public involvement in primary care research: a mixed methods study.

PubMed

Blackburn, Steven; McLachlan, Sarah; Jowett, Sue; Kinghorn, Philip; Gill, Paramjit; Higginbottom, Adele; Rhodes, Carol; Stevenson, Fiona; Jinks, Clare

2018-01-01

In the UK, more patients go to primary care than other parts of the health service. Therefore it is important for research into primary care to include the insights and views of people who receive these services. To explore the extent, quality and impact of patient and public involvement (PPI) in primary care research, we examined documents of 200 projects and surveyed 191 researchers.We found that about half of studies included PPI to develop research ideas and during the study itself. Common activities included designing study materials, advising on methods, and managing the research. Some studies did not undertake the PPI activities initially planned and funded for. PPI varied by study design, health condition and study population. We found pockets of good practice: having a PPI budget, supporting PPI contributors, and PPI informing recruitment issues. However, good practice was lacking in other areas. Few projects offered PPI contributors training, used PPI to develop information for participants about study progress and included PPI to advise on publishing findings.Researchers reported beneficial impacts of PPI. Most impact was reported when the approach to PPI included more indicators of good practice. The main cost of PPI for researchers was their time. Many reported difficulties providing information about PPI.In partnership with PPI contributors, we have used these findings to develop:a new Cost and Consequences Framework for PPI highlighting financial and non-financial costs, benefits and harms of PPIFifteen co-produced recommendations to improve the practice and delivery of PPI. Background: To improve the lives of patients in primary care requires the involvement of service users in primary care research. We aimed to explore the extent, quality and impact of patient and public involvement (PPI) in primary care research. Methods: We extracted information about PPI from grant applications, reports and an electronic survey of researchers of studies funded by the NIHR School for Primary Care Research (SPCR). We applied recognised quality indicators to assess the quality of PPI and assessed its impact on research. Results: We examined 200 grant applications and reports of 181 projects. PPI was evident in the development of 47 (24%) grant applications. 113 (57%) grant applications included plans for PPI during the study, mostly in study design, oversight, and dissemination. PPI during projects was reported for 83 (46%) projects, including designing study materials and managing the research. We identified inconsistencies between planned and reported PPI. PPI varied by study design, health condition and study population.Of 46 (24%) of 191 questionnaires completed, 15 reported PPI activity. Several projects showed best practice according to guidelines, in terms of having a PPI budget, supporting PPI contributors, and PPI informing recruitment issues. However few projects offered PPI contributors training, used PPI to develop information for participants about study progress, and had PPI in advising on dissemination.Beneficial impacts of PPI in designing studies and writing participant information was frequently reported. Less impact was reported on developing funding applications, managing or carrying out the research. The main cost of PPI for researchers was their time. Many researchers found it difficult to provide information about PPI activities.Our findings informed:a new Cost and Consequences Framework for PPI in primary care research highlighting financial and non-financial costs, plus the benefits and harms of PPIFifteen co-produced recommendations to improve PPI in research and within the SPCR. Conclusions: The extent, quality and impact of PPI in primary care research is inconsistent across research design and topics. Pockets of good practice were identified making a positive impact on research. The new Cost and Consequences Framework may help others assess the impact of PPI.

Identification of key genes related to high-risk gastrointestinal stromal tumors using bioinformatics analysis.

PubMed

Jin, Shuan; Zhu, Wenhua; Li, Jun

2018-01-01

The purpose of this study was to identify predictive biomarkers used for clinical therapy and prognostic evaluation of high-risk gastrointestinal stromal tumors (GISTs). In this study, microarray data GSE31802 were used to identify differentially expressed genes (DEGs) between high-risk GISTs and low-risk GISTs. Then, enrichment analysis of DEGs was conducted based on the gene ontology and kyoto encyclopedia of genes and genomes pathway database. In addition, the transcription factors and cancer-related genes in DEGs were screened according to the TRANSFAC, TSGene, and TAG database. Finally, protein-protein interaction (PPI) network was constructed and analyzed to look for critical genes involved in high-risk GISTs. A total of forty DEGs were obtained and these genes were mainly involved in four pathways, including melanogenesis, neuroactive ligand-receptor interaction, malaria, and hematopoietic cell lineage. The enriched biological processes were related to the regulation of insulin secretion, integrin activation, and neuropeptide signaling pathway. Transcription factor analysis of DEGs indicated that POU domain, class 2, associating factor 1 (POU2AF1) was significantly downregulated in high-risk GISTs. By constructing the PPI network of DEGs, ten genes with high degrees formed local networks, such as PNOC, P2RY14, and SELP. Four genes as POU2AF1, PNOC, P2RY14, and SELP might be used as biomarkers for prognosis of high-risk GISTs.

PPP insights in South Africa.

PubMed

du Toit, Japie

2003-01-01

After functioning for some time in an increasingly regulated and structured environment in dealing with the private sector in South Africa, it was important to Government, to carefully review the terminology used in this evolving playing field. As the definitions and mechanisms impacting on this form of interaction became clear, it was essential to find a broader definition to encompass all forms of commercial intervention between the two sectors. In preparation for the first South African National Health Summit during 2001, the term public private interaction became a general term used in this context. In the South African healthcare sectors this term is used specifically to indicate that all forms of interaction between the two sectors should be considered, rather than merely focussing on specific Public Private Partnerships (PPPs), that have a much more narrow definition. Recent health policy documents in South Africa all stress four key goals--equity, coherence, quality of care and efficiency--which provide a useful basis for decision-making about PPIs. The range of public-private interactions that may support or constrain the South African health system's development are set within the overall public/private mix of the country. In developing an equitable, efficient, coherent and high quality health system in South Africa, there is considerable potential for constructive engagement (collaboration and co-operation) between the public and the private health care sectors. Both sectors should embrace this opportunity and therefore it is useful to propose some basic guidelines for engagement based on the vision and goals of the national health system. In deciding whether or not to pursue any new PPI within the health sector, or in evaluating whether an existing PPI should continue or be revised, it is necessary to assess its merits in relation to the achievement of health system goals.

VANLO - Interactive visual exploration of aligned biological networks

PubMed Central

Brasch, Steffen; Linsen, Lars; Fuellen, Georg

2009-01-01

Background Protein-protein interaction (PPI) is fundamental to many biological processes. In the course of evolution, biological networks such as protein-protein interaction networks have developed. Biological networks of different species can be aligned by finding instances (e.g. proteins) with the same common ancestor in the evolutionary process, so-called orthologs. For a better understanding of the evolution of biological networks, such aligned networks have to be explored. Visualization can play a key role in making the various relationships transparent. Results We present a novel visualization system for aligned biological networks in 3D space that naturally embeds existing 2D layouts. In addition to displaying the intra-network connectivities, we also provide insight into how the individual networks relate to each other by placing aligned entities on top of each other in separate layers. We optimize the layout of the entire alignment graph in a global fashion that takes into account inter- as well as intra-network relationships. The layout algorithm includes a step of merging aligned networks into one graph, laying out the graph with respect to application-specific requirements, splitting the merged graph again into individual networks, and displaying the network alignment in layers. In addition to representing the data in a static way, we also provide different interaction techniques to explore the data with respect to application-specific tasks. Conclusion Our system provides an intuitive global understanding of aligned PPI networks and it allows the investigation of key biological questions. We evaluate our system by applying it to real-world examples documenting how our system can be used to investigate the data with respect to these key questions. Our tool VANLO (Visualization of Aligned Networks with Layout Optimization) can be accessed at . PMID:19821976

Influence of Protein Abundance on High-Throughput Protein-Protein Interaction Detection

DTIC Science & Technology

2009-06-05

the interaction data sets we determined, via comparisons with strict randomized simulations , the propensity for essential proteins to selectively...and analysis of high- quality PPI data sets. Materials and Methods We analyzed protein interaction networks for yeast and E. coli determined from Y2H...we reinvestigated the centrality-lethality rule, which implies that proteins having more interactions are more likely to be essential. From analysis

Examining the reliability and validity of an abbreviated Psychopathic Personality Inventory-Revised (PPI-R) in four samples.

PubMed

Ruchensky, Jared R; Edens, John F; Donnellan, M Brent; Witt, Edward A

2017-02-01

A recently developed 40-item short-form of the Psychopathic Personality Inventory-Revised (PPI-R; Lilienfeld & Widows, 2005) has shown considerable promise as an alternative to the long-form of the instrument (Eisenbarth, Lilienfeld, & Yarkoni, 2015). Beyond the initial construction of the short-form, however, Eisenbarth et al. only evaluated a small number of external correlates in a German college student sample. In this study, we evaluate the internal consistency of the short-form scales in 4 samples previously administered the full PPI-R (3 U.S. college student samples and 1 U.S. forensic psychiatric inpatient sample) and examine a wide range of external correlates to compare the nomological nets of the short- and long-forms. Across all 4 samples, correlations between each short-form scale and its corresponding long-form scale were uniformly high (all rs > .75). In terms of external correlates, the pattern of associations was exceedingly similar, for the short-form and long-form composites with a largely trivial reduction in effect size. Collectively, our findings offer considerable support for the utility of this new short-form as a substitute for the full PPI-R. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Proton pump inhibitors and vascular function: A prospective cross-over pilot study.

PubMed

Ghebremariam, Yohannes T; Cooke, John P; Khan, Fouzia; Thakker, Rahul N; Chang, Peter; Shah, Nigam H; Nead, Kevin T; Leeper, Nicholas J

2015-08-01

Proton pump inhibitors (PPIs) are commonly used drugs for the treatment of gastric reflux. Recent retrospective cohorts and large database studies have raised concern that the use of PPIs is associated with increased cardiovascular (CV) risk. However, there is no prospective clinical study evaluating whether the use of PPIs directly causes CV harm. We conducted a controlled, open-label, cross-over pilot study among 21 adults aged 18 and older who are healthy (n=11) or have established clinical cardiovascular disease (n=10). Study subjects were assigned to receive a PPI (Prevacid; 30 mg) or a placebo pill once daily for 4 weeks. After a 2-week washout period, participants were crossed over to receive the alternate treatment for the ensuing 4 weeks. Subjects underwent evaluation of vascular function (by the EndoPAT technique) and had plasma levels of asymmetric dimethylarginine (ADMA, an endogenous inhibitor of endothelial function previously implicated in PPI-mediated risk) measured prior to and after each treatment interval. We observed a marginal inverse correlation between the EndoPAT score and plasma levels of ADMA (r = -0.364). Subjects experienced a greater worsening in plasma ADMA levels while on PPI than on placebo, and this trend was more pronounced amongst those subjects with a history of vascular disease. However, these trends did not reach statistical significance, and PPI use was also not associated with an impairment in flow-mediated vasodilation during the course of this study. In conclusion, in this open-label, cross-over pilot study conducted among healthy subjects and coronary disease patients, PPI use did not significantly influence vascular endothelial function. Larger, long-term and blinded trials are needed to mechanistically explain the correlation between PPI use and adverse clinical outcomes, which has recently been reported in retrospective cohort studies. © The Author(s) 2015.

The Association between the Use of Proton Pump Inhibitors and the Risk of Hypomagnesemia: A Systematic Review and Meta-Analysis

PubMed Central

Park, Chan Hyuk; Kim, Eun Hye; Roh, Yun Ho; Kim, Ha Yan; Lee, Sang Kil

2014-01-01

Background Although many case reports have described patients with proton pump inhibitor (PPI)-induced hypomagnesemia, the impact of PPI use on hypomagnesemia has not been fully clarified through comparative studies. We aimed to evaluate the association between the use of PPI and the risk of developing hypomagnesemia by conducting a systematic review with meta-analysis. Methods We conducted a systematic search of MEDLINE, EMBASE, and the Cochrane Library using the primary keywords “proton pump,” “dexlansoprazole,” “esomeprazole,” “ilaprazole,” “lansoprazole,” “omeprazole,” “pantoprazole,” “rabeprazole,” “hypomagnesemia,” “hypomagnesaemia,” and “magnesium.” Studies were included if they evaluated the association between PPI use and hypomagnesemia and reported relative risks or odds ratios or provided data for their estimation. Pooled odds ratios with 95% confidence intervals were calculated using the random effects model. Statistical heterogeneity was assessed with Cochran’s Q test and I 2 statistics. Results Nine studies including 115,455 patients were analyzed. The median Newcastle-Ottawa quality score for the included studies was seven (range, 6–9). Among patients taking PPIs, the median proportion of patients with hypomagnesemia was 27.1% (range, 11.3–55.2%) across all included studies. Among patients not taking PPIs, the median proportion of patients with hypomagnesemia was 18.4% (range, 4.3–52.7%). On meta-analysis, pooled odds ratio for PPI use was found to be 1.775 (95% confidence interval 1.077–2.924). Significant heterogeneity was identified using Cochran’s Q test (df = 7, P<0.001, I 2 = 98.0%). Conclusions PPI use may increase the risk of hypomagnesemia. However, significant heterogeneity among the included studies prevented us from reaching a definitive conclusion. PMID:25394217

Correlative Förster Resonance Electron Transfer-Proximity Ligation Assay (FRET-PLA) Technique for Studying Interactions Involving Membrane Proteins.

PubMed

Ivanusic, Daniel; Denner, Joachim; Bannert, Norbert

2016-08-01

This unit provides a guide and detailed protocol for studying membrane protein-protein interactions (PPI) using the acceptor-sensitized Förster resonance electron transfer (FRET) method in combination with the proximity ligation assay (PLA). The protocol in this unit is focused on the preparation of FRET-PLA samples and the detection of correlative FRET/PLA signals as well as on the analysis of FRET-PLA data and interpretation of correlative results when using cyan fluorescent protein (CFP) as a FRET donor and yellow fluorescent protein (YFP) as a FRET acceptor. The correlative application of FRET and PLA combines two powerful tools for monitoring PPI, yielding results that are more reliable than with either technique alone. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

Psychophysiological interaction between superior temporal gyrus (STG) and cerebellum: An fMRI study

NASA Astrophysics Data System (ADS)

Yusoff, A. N.; Teng, X. L.; Ng, S. B.; Hamid, A. I. A.; Mukari, S. Z. M.

2016-03-01

This study aimed to model the psychophysiological interaction (PPI) between the bilateral STG and cerebellum (lobule VI and lobule VII) during an arithmetic addition task. Eighteen young adults participated in this study. They were instructed to solve single-digit addition tasks in quiet and noisy backgrounds during an fMRI scan. Results showed that in both hemispheres, the response in the cerebellum was found to be linearly influenced by the activity in STG (vice-versa) for both in-quiet and in-noise conditions. However, the influence of the cerebellum on STG seemed to be modulated by noise. A two-way PPI model between STG and cerebellum is suggested. The connectivity between the two regions during a simple addition task in a noisy condition is modulated by the participants’ higher attention to perceive.

Therapeutic Efficacy of a New Procedure for Male Urinary Incontinence Combining a Suburethral Polypropylene Mesh and Cardiovascular Patch

PubMed Central

Jiang, Yuan-Hong

2017-01-01

Purpose Stress urinary incontinence (SUI) in men is a complication secondary to prostatectomy or resulting from neurological lesions. This study presents our experiences with male suburethral slings over the past decade. Methods In this study, we considered patients who presented with SUI and were diagnosed with an intrinsic sphincteric deficiency due to postprostatectomy incontinence (PPI) or other causes (non-PPI). Patients who underwent the suburethral sling procedure using a polypropylene mesh and a cardiovascular patch were retrospectively included. An urodynamic study was performed before and after the operation. Global response assessment (GRA) and SUI grading were used for surgical outcome. The revision rate and the infection rate were also evaluated. Results A total 31 patients were enrolled in this study; the mean patient age was 59.5±18.9 years, and the mean follow-up period was 36.9±29.4 months. Fourteen patients comprised the non-PPI group and 17 were in the PPI group. The preoperative SUI of all patients were categorized as a moderate to severe problem according to the SUI grade, with a mean score of 2.32±0.48 before the operation and 0.48±0.57 after the operation. With a mean score of 2.35±0.71, GRA showed that the patients were satisfied with the treatment. After the sling procedure, 4 patients (13%) reported a mild improvement, 12 (38.7%) a moderate improvement, while 15 (48.4%) reported an excellent improvement. Six patients (19.4%), including 5 from the non-PPI group (35.7%) and 1 (5.9%) from the PPI group (P=0.037), underwent sling removal because of infection. Conclusions The male suburethral sling procedure using a polypropylene mesh and a cardiovascular patch is a safe, efficacious, and inexpensive surgical procedure for PPI. In cases of neurological incontinence, however, the higher infection rate in non-PPI patients means that they should be carefully managed. PMID:28361511

3D-DIVIMP(HC) code modeling of DIII-D DiMES porous plug injector experiments

NASA Astrophysics Data System (ADS)

Mu, Y.; Elder, J. D.; Stangeby, P. C.; McLean, A. G.

2011-08-01

A Porous Plug Injector (PPI) system for the Divertor Material Evaluation System (DiMES) on DIII-D has been employed for in situ study of chemical erosion in the tokamak divertor environment. The 3D-DIVIMP(HC) code has been applied to the interpretation of the CI, CII and other spectroscopic measurements made at the PPI location, for (a) the synthetic source due to injection of CH4 through the PPI, and (b) the natural emission from the PPI head itself, which was inserted above surrounding graphite tiles by ˜0.3 mm.The code successfully replicated the MDS (spectrometer)-measured absolute emissions of CH, CI, CII 427 nm, 514 nm, and 658 nm [1] and the DiMES TV-measured spatial shapes of the CH, CI, and CII 514 nm [1] emission "clouds" to within the combined uncertainties. It is thus concluded that the most important physics and chemistry of chemical sputtering have most likely been included in the model.

A new method based on the Butler-Volmer formalism to evaluate voltammetric cation and anion sensors.

PubMed

Cano, Manuel; Rodríguez-Amaro, Rafael; Fernández Romero, Antonio J

2008-12-11

A new method based on the Butler-Volmer formalism is applied to assess the capability of two voltammetric ion sensors based on polypyrrole films: PPy/DBS and PPy/ClO4 modified electrodes were studied as voltammetric cation and anion sensors, respectively. The reversible potential versus electrolyte concentrations semilogarithm plots provided positive calibration slopes for PPy/DBS and negative ones for PPy/ClO4, as was expected from the proposed method and that based on the Nernst equation. The slope expressions deduced from Butler-Volmer include the electron-transfer coefficient, which allows slope values different from the ideal Nernstian value to be explained. Both polymeric films exhibited a degree of ion-selectivity when they were immersed in mixed-analyte solutions. Selectivity coefficients for the two proposed voltammetric cation and anion sensors were obtained by several experimental methods, including the separated solution method (SSM) and matched potential method (MPM). The K values acquired by the different methods were very close for both polymeric sensors.

Pantoprazole for the treatment of peptic ulcer bleeding and prevention of rebleeding.

PubMed

van Rensburg, Christo J; Cheer, Susan

2012-01-01

Adding proton pump inhibitors (PPIs) to endoscopic therapy has become the mainstay of treatment for peptic ulcer bleeding, with current consensus guidelines recommending high-dose intravenous (IV) PPI therapy (IV bolus followed by continuous therapy). However, whether or not high-dose PPI therapy is more effective than low-dose PPI therapy is still debated. Furthermore, maintaining pH ≥ 4 appears to prevent mucosal bleeding in patients with acute stress ulcers; thus, stress ulcer prophylaxis with acid-suppressing therapy has been increasingly recommended in intensive care units (ICUs). This review evaluates the evidence for the efficacy of IV pantoprazole, a PPI, in preventing ulcer rebleeding after endoscopic hemostasis, and in controlling gastric pH and protecting against upper gastrointestinal (GI) bleeding in high-risk ICU patients. The review concludes that IV pantoprazole provides an effective option in the treatment of upper GI bleeding, the prevention of rebleeding, and for the prophylaxis of acute bleeding stress ulcers.

Pantoprazole for the Treatment of Peptic Ulcer Bleeding and Prevention of Rebleeding

PubMed Central

van Rensburg, Christo J.; Cheer, Susan

2012-01-01

Adding proton pump inhibitors (PPIs) to endoscopic therapy has become the mainstay of treatment for peptic ulcer bleeding, with current consensus guidelines recommending high-dose intravenous (IV) PPI therapy (IV bolus followed by continuous therapy). However, whether or not high-dose PPI therapy is more effective than low-dose PPI therapy is still debated. Furthermore, maintaining pH ≥ 4 appears to prevent mucosal bleeding in patients with acute stress ulcers; thus, stress ulcer prophylaxis with acid-suppressing therapy has been increasingly recommended in intensive care units (ICUs). This review evaluates the evidence for the efficacy of IV pantoprazole, a PPI, in preventing ulcer rebleeding after endoscopic hemostasis, and in controlling gastric pH and protecting against upper gastrointestinal (GI) bleeding in high-risk ICU patients. The review concludes that IV pantoprazole provides an effective option in the treatment of upper GI bleeding, the prevention of rebleeding, and for the prophylaxis of acute bleeding stress ulcers. PMID:24833934

Interfacial Constructing Flexible V2O5@Polypyrrole Core-Shell Nanowire Membrane with Superior Supercapacitive Performance.

PubMed

Wang, Jian-Gan; Liu, Huanyan; Liu, Hongzhen; Hua, Wei; Shao, Minhua

2018-06-06

Flexible membrane consisting of ultralong V 2 O 5 @conducting polypyrrole (V 2 O 5 @PPy) core-shell nanowires is prepared by a facile in situ interfacial synthesis approach. The V 2 O 5 is for the first time demonstrated to show versatile function of reactive template to initiate the uniform and conformal polymerization of PPy nanocoating without the need for extra oxidants. The freestanding PPy-encapsulated V 2 O 5 nanowire membrane is of great benefit in achieving strong electrochemical harvest by increasing electrical conductivity, shortening ion/electron transport distance, and enlarging electrode/electrolyte contact area. When evaluated as binder- and additive-free supercapacitor electrodes, the V 2 O 5 @PPy core-shell hybrid delivers a significantly enhanced specific capacitance of 334 F g -1 along with superior rate capability and improved cycling stability. The present work would provide a simple yet powerful interfacial strategy for elaborate constructing V 2 O 5 /conducting polymers toward various energy-storage technologies.

Fabricate BC/Fe3O4@PPy 3D nanofiber film as flexible electrode for supercapacitor application

NASA Astrophysics Data System (ADS)

Lv, Xvdan; Li, Guohui; Pang, Zengyuan; Li, Dawei; Lei, Luo; Lv, Pengfei; Mushtaq, Muhammad; Wei, Qufu

2018-05-01

For flexible film supercapacitor, high areal capacitance is a main evaluating indicator. In this paper, bacterial cellulose (BC) with special three-dimensional structure was used as the natural flexible base material. Fe3O4 nanoparticles with average diameter of 20 nm were synthesized on the surface of BC fibers. The conductive path polypyrrole (PPy) was introduced as shell of BC/Fe3O4 fibers to further improve the pseudo capacitance in 1 mol/L H2SO4 solution. Besides, the BC/Fe3O4@PPy was used for supercapacitor application in acid electrolyte, and delivered higher areal capacitance compared to other Fe3O4 composites in previous reports. The obtained BC/Fe3O4@PPy film showed excellent mechanical strength (tensile strength reached 11 MPa), high areal specific capacitance (5.4 F cm-2 at active mass of 8.4 mg cm-2), and long cycle life (1.95 F cm-2 over 3500 cycles).

Development and Validation of Triarchic Construct Scales from the Psychopathic Personality Inventory

PubMed Central

Hall, Jason R.; Drislane, Laura E.; Patrick, Christopher J.; Morano, Mario; Lilienfeld, Scott O.; Poythress, Norman G.

2014-01-01

The Triarchic model of psychopathy describes this complex condition in terms of distinct phenotypic components of boldness, meanness, and disinhibition. Brief self-report scales designed specifically to index these psychopathy facets have thus far demonstrated promising construct validity. The present study sought to develop and validate scales for assessing facets of the Triarchic model using items from a well-validated existing measure of psychopathy—the Psychopathic Personality Inventory (PPI). A consensus rating approach was used to identify PPI items relevant to each Triarchic facet, and the convergent and discriminant validity of the resulting PPI-based Triarchic scales were evaluated in relation to multiple criterion variables (i.e., other psychopathy inventories, antisocial personality disorder features, personality traits, psychosocial functioning) in offender and non-offender samples. The PPI-based Triarchic scales showed good internal consistency and related to criterion variables in ways consistent with predictions based on the Triarchic model. Findings are discussed in terms of implications for conceptualization and assessment of psychopathy. PMID:24447280

Development and validation of Triarchic construct scales from the psychopathic personality inventory.

PubMed

Hall, Jason R; Drislane, Laura E; Patrick, Christopher J; Morano, Mario; Lilienfeld, Scott O; Poythress, Norman G

2014-06-01

The Triarchic model of psychopathy describes this complex condition in terms of distinct phenotypic components of boldness, meanness, and disinhibition. Brief self-report scales designed specifically to index these psychopathy facets have thus far demonstrated promising construct validity. The present study sought to develop and validate scales for assessing facets of the Triarchic model using items from a well-validated existing measure of psychopathy-the Psychopathic Personality Inventory (PPI). A consensus-rating approach was used to identify PPI items relevant to each Triarchic facet, and the convergent and discriminant validity of the resulting PPI-based Triarchic scales were evaluated in relation to multiple criterion variables (i.e., other psychopathy inventories, antisocial personality disorder features, personality traits, psychosocial functioning) in offender and nonoffender samples. The PPI-based Triarchic scales showed good internal consistency and related to criterion variables in ways consistent with predictions based on the Triarchic model. Findings are discussed in terms of implications for conceptualization and assessment of psychopathy.

Evaluation of poultry protein isolate as a food ingredient: physicochemical properties and sensory characteristics of marinated chicken breasts.

PubMed

Khiari, Zied; Omana, Dileep A; Pietrasik, Zeb; Betti, Mirko

2013-07-01

The possibilities of replacing soy protein isolate (SPI) and reducing the amount of phosphate in marinated chicken breasts using poultry protein isolate (PPI) were investigated. PPI, prepared from mechanically separated turkey meat through the pH-shift technology, was used as a marinade ingredient for chicken breasts at 2 different concentrations (1.0% and 1.5%, w/w on a dry weight basis). Product characteristics were compared to samples marinated with salt, phosphate, or SPI. All the 5 treatments were subjected to instrumental and sensory analyses. Tumbling yield, drip, and cooking losses as well as expressible moisture showed that PPI can be used as a substitute for SPI in brine. The sensory analysis revealed that there were no differences among treatments in terms of appearance, color, flavor, saltiness, juiciness, tenderness, and overall acceptability of the marinated chicken breasts. However, chicken breasts marinated with phosphate had significantly higher aroma acceptability scores than those treated with 1% PPI. © 2013 Institute of Food Technologists®

Yeast-assisted synthesis of polypyrrole: Quantification and influence on the mechanical properties of the cell wall.

PubMed

Andriukonis, Eivydas; Stirke, Arunas; Garbaras, Andrius; Mikoliunaite, Lina; Ramanaviciene, Almira; Remeikis, Vidmantas; Thornton, Barry; Ramanavicius, Arunas

2018-04-01

In this study, the metabolism of yeast cells (Saccharomyces cerevisiae) was utilized for the synthesis of the conducting polymer - polypyrrole (Ppy).Yeast cells were modified in situ by synthesized Ppy. The Ppy was formed in the cell wall by redox-cycling of [Fe(CN) 6 ] 3-/4- , performed by the yeast cells. Fluorescence microscopy, enzymatic digestions, atomic force microscopy and isotope ratio mass spectroscopy were applied to determine both the polymerization reaction itself and the polymer location in yeast cells. Ppy formation resulted in enhanced resistance to lytic enzymes, significant increase of elasticity and alteration of other mechanical cell wall properties evaluated by atomic force microscopy (AFM). The suggested method of polymer synthesis allows the introduction of polypyrrole structures within the cell wall, which is build up from polymers consisting of carbohydrates. This cell wall modification strategy could increase the usefulness of yeast as an alternative energy source in biofuel cells, and in cell based biosensors. Copyright © 2018 Elsevier B.V. All rights reserved.

A validity assessment of the Progress out of Poverty Index (PPI)™.

PubMed

Desiere, Sam; Vellema, Wytse; D'Haese, Marijke

2015-04-01

Development organisations need easy-to-use and quick-to-implement indicators to quantify poverty when requested to measure program impact. In this paper we assess the validity of the Progress out of Poverty Index (PPI)™, a country-specific indicator based on ten closed questions on directly observable household characteristics, by its compliance to the SMART criteria. Each response receives a pre-determined score, such that the sum of these scores can be converted into the likelihood the household is living below the poverty line. We focus on the PPI scorecard for Rwanda, which was validated using two national household surveys conducted in 2005/06 and 2010/11. The PPI is Specific, Measurable, Available cost effectively, and Timely available. Yet, its Relevance depends on the way it is used. Although it accurately distinguishes poor from non-poor households, making it a useful reporting tool, its limited sensitivity to changes in poverty status restricts its usefulness for evaluating the impact of development projects. Copyright © 2014 Elsevier Ltd. All rights reserved.

Association between prepulse inhibition of the startle response and latent inhibition of two-way avoidance acquisition: A study with heterogeneous NIH-HS rats.

PubMed

Sánchez-González, Ana; Esnal, Aitor; Río-Álamos, Cristóbal; Oliveras, Ignasi; Cañete, Toni; Blázquez, Gloria; Tobeña, Adolf; Fernández-Teruel, Alberto

2016-03-01

This study presents the first evaluation of the associations between responses in two paradigms related to schizophrenia in the genetically heterogeneous NIH-HS rat stock. NIH-HS rats are a stock of genetically heterogeneous animals that have been derived from eight different inbred strains. A rotational breeding schedule has been followed for more than eighty generations, leading to a high level of genetic recombination that makes the NIH-HS rats a unique tool for studying the genetic basis of (biological, behavioral, disease-related) complex traits. Previous work has dealt with the characterization of coping styles, cognitive and anxiety/fear-related profiles of NIH-HS rats. In the present study we have completed their characterization in two behavioral models, prepulse inhibition (PPI) and latent inhibition (LI) of the two-way active avoidance response, that appear to be related to schizophrenia or to schizophrenia-relevant symptoms. We have found that these rats display PPI for each of the four prepulse intensities tested, allowing their stratification in high, medium and low PPI subgroups. When testing these three subgroups for LI of two-way active avoidance acquisition it has been observed that the LowPPI and MediumPPI subgroups present impaired LI, which, along with the fact that the HighPPI group presents significant LI, allows us to hypothesize that responses in these two paradigms are somehow related and that selection of NIH-HS rats for Low vs HighPPI could make a promising animal model for the study of clusters of schizophrenia-relevant symptoms and their underlying neurobiological mechanisms. Copyright © 2015 Elsevier Inc. All rights reserved.

Implementation of Global Strategies to Prevent Hospital-Onset Clostridium difficile Infection: Targeting Proton Pump Inhibitors and Probiotics.

PubMed

Lewis, Paul O; Lundberg, Timothy S; Tharp, Jennifer L; Runnels, Clay W

2017-10-01

Proton pump inhibitors (PPIs) have been identified as a significant risk factor for the development of Clostridium difficile infection (CDI). Probiotics given concurrently with antibiotics have been shown to have a moderate impact on preventing CDI. To evaluate the effectiveness of hospital-wide interventions designed to reduce PPI use and increase probiotics and whether these interventions were associated with a change in the incidence of hospital onset (HO)-CDI. This retrospective cohort study compared 2 fiscal years: July 2013 to June 2014 (FY14) and July 2014 to June 2015 (FY15). In July of FY15, global educational initiatives were launched targeting PPIs. Additionally, a HO-CDI prevention bundle was added to antibiotic-containing order sets targeting probiotics. Overall PPI use, probiotic use, and incidence of HO-CDI were recorded and compared for each cohort. Charts were also reviewed for patients who developed HO-CDI for the presence and appropriateness of a PPI and presence of probiotics. The interventions resulted in a decrease in PPI use by 14% or 96 doses/1000 patient days (TPD; P = 0.0002) and a reduction in IV PPI use by 31% or 71 doses/TPD ( P = 0.0008). Probiotic use increased by 130% or 126 doses/TPD ( P = 0.0006). The incidence of HO-CDI decreased by 20% or 0.1 cases/TPD ( P = 0.04). A collaborative, multifaceted educational initiative directed at highlighting the risks associated with PPI use was effective in reducing PPI prescribing. The implementation of a probiotic bundle added to antibiotic order sets was effective in increasing probiotic use. These interventions were associated with a decrease in incidence of HO-CDI.

Helicobacter pylori first-line and rescue treatments in the presence of penicillin allergy.

PubMed

Gisbert, Javier P; Barrio, Jesús; Modolell, Inés; Molina-Infante, Javier; Aisa, Angeles Perez; Castro-Fernández, Manuel; Rodrigo, Luis; Cosme, Angel; Gisbert, Jose Luis; Fernández-Bermejo, Miguel; Marcos, Santiago; Marín, Alicia C; McNicholl, Adrián G

2015-02-01

Helicobacter pylori eradication is a challenge in penicillin allergy. To assess the efficacy and safety of first-line and rescue treatments in patients allergic to penicillin. Prospective multicenter study. Patients allergic to penicillin were given a first-line treatment comprising (a) 7-day omeprazole-clarithromycin-metronidazole and (b) 10-day omeprazole-bismuth-tetracycline-metronidazole. Rescue treatments were as follows: (a) bismuth quadruple therapy; (b) 10-day PPI-clarithromycin-levofloxacin; and (c) 10-day PPI-clarithromycin-rifabutin. Eradication was confirmed by (13)C-urea breath test. Compliance was determined through questioning and recovery of empty medication envelopes. Adverse effects were evaluated by questionnaires. In total, 267 consecutive treatments were included. (1) First-line treatment: Per-protocol and intention-to-treat eradication rates with omeprazole-clarithromycin-metronidazole were 59 % (62/105; 95 % CI 49-62 %) and 57 % (64/112; 95 % CI 47-67 %). Respective figures for PPI-bismuth-tetracycline-metronidazole were 75 % (37/49; 95 % CI 62-89 %) and 74 % (37/50; 95 % CI (61-87 %) (p < 0.05). Compliance with treatment was 94 and 98 %, respectively. Adverse events were reported in 14 % with both regimens (all mild). (2) Second-line treatment: Intention-to-treat eradication rate with omeprazole-clarithromycin-levofloxacin was 64 % both after triple and quadruple failure; compliance was 88-100 %, with 23-29 % adverse effects (all mild). (3) Third-/fourth-line treatment: Intention-to-treat eradication rate with PPI-clarithromycin-rifabutin was 22 %. In allergic to penicillin patients, a first-line treatment with a bismuth-containing quadruple therapy (PPI-bismuth-tetracycline-metronidazole) seems to be a better option than the triple PPI-clarithromycin-metronidazole regimen. A levofloxacin-based regimen (together with a PPI and clarithromycin) represents a second-line rescue option in the presence of penicillin allergy.

Evidence-based clinical practice guidelines for gastroesophageal reflux disease 2015.

PubMed

Iwakiri, Katsuhiko; Kinoshita, Yoshikazu; Habu, Yasuki; Oshima, Tadayuki; Manabe, Noriaki; Fujiwara, Yasuhiro; Nagahara, Akihito; Kawamura, Osamu; Iwakiri, Ryuichi; Ozawa, Soji; Ashida, Kiyoshi; Ohara, Shuichi; Kashiwagi, Hideyuki; Adachi, Kyoichi; Higuchi, Kazuhide; Miwa, Hiroto; Fujimoto, Kazuma; Kusano, Motoyasu; Hoshihara, Yoshio; Kawano, Tatsuyuki; Haruma, Ken; Hongo, Michio; Sugano, Kentaro; Watanabe, Mamoru; Shimosegawa, Tooru

2016-08-01

As an increase in gastroesophageal reflux disease (GERD) has been reported in Japan, and public interest in GERD has been increasing, the Japanese Society of Gastroenterology published the Evidence-based Clinical Practice Guidelines for GERD (1st edition) in 2009. Six years have passed since its publication, and there have been a large number of reports in Japan concerning the epidemiology, pathophysiology, treatment, and Barrett's esophagus during this period. By incorporating the contents of these reports, the guidelines were completely revised, and a new edition was published in October 2015. The revised edition consists of eight items: epidemiology, pathophysiology, diagnosis, internal treatment, surgical treatment, esophagitis after surgery of the upper gastrointestinal tract, extraesophageal symptoms, and Barrett's esophagus. This paper summarizes these guidelines, particularly the parts related to the treatment for GERD. In the present revision, aggressive proton pump inhibitor (PPI) maintenance therapy is recommended for severe erosive GERD, and on-demand therapy or continuous maintenance therapy is recommended for mild erosive GERD or PPI-responsive non-erosive GERD. Moreover, PPI-resistant GERD (insufficient symptomatic improvement and/or esophageal mucosal break persisting despite the administration of PPI at a standard dose for 8 weeks) is defined, and a standard-dose PPI twice a day, change in PPI, change in the PPI timing of dosing, addition of a prokinetic drug, addition of rikkunshito (traditional Japanese herbal medicine), and addition of histamine H2-receptor antagonist are recommended for its treatment. If no improvement is observed even after these treatments, pathophysiological evaluation with esophageal impedance-pH monitoring or esophageal manometry at an expert facility for diseases of the esophagus is recommended.

Urodynamic assessment of bladder and urethral function among men with lower urinary tract symptoms after radical prostatectomy: A comparison between men with and without urinary incontinence.

PubMed

Lee, Hansol; Kim, Ki Bom; Lee, Sangchul; Lee, Sang Wook; Kim, Myong; Cho, Sung Yong; Oh, Seung-June; Jeong, Seong Jin

2015-12-01

We compared bladder and urethral functions following radical prostatectomy (RP) between men with and without urinary incontinence (UI), using a large-scale database from SNU-experts-of-urodynamics-leading (SEOUL) Study Group. Since July 2004, we have prospectively collected data on urodynamics from 303 patients with lower urinary tract symptoms (LUTS) following RP at three affiliated hospitals of SEOUL Study Group. After excluding 35 patients with neurogenic abnormality, pelvic irradiation after surgery, or a history of surgery on the lower urinary tract, 268 men were evaluated. We compared the urodynamic findings between men who had LUTS with UI (postprostatectomy incontinence [PPI] group) and those who had LUTS without UI (non-PPI group). The mean age at an urodynamic study was 68.2 years. Overall, a reduced bladder compliance (≤20 mL/cmH2O) was shown in 27.2% of patients; and 31.3% patients had idiopathic detrusor overactivity. The patients in the PPI group were older (p=0.001) at an urodynamic study and had a lower maximum urethral closure pressure (MUCP) (p<0.001), as compared with those in the non-PPI group. Bladder capacity and detrusor pressure during voiding were also significantly lower in the PPI group. In the logistic regression, only MUCP and maximum cystometric capacity were identified as the related factor with the presence of PPI. In our study, significant number of patients with LUTS following RP showed a reduced bladder compliance and detrusor overactivity. PPI is associated with both impairment of the urethral closuring mechanism and bladder storage dysfunction.

Identifying Dynamic Protein Complexes Based on Gene Expression Profiles and PPI Networks

PubMed Central

Li, Min; Chen, Weijie; Wang, Jianxin; Pan, Yi

2014-01-01

Identification of protein complexes from protein-protein interaction networks has become a key problem for understanding cellular life in postgenomic era. Many computational methods have been proposed for identifying protein complexes. Up to now, the existing computational methods are mostly applied on static PPI networks. However, proteins and their interactions are dynamic in reality. Identifying dynamic protein complexes is more meaningful and challenging. In this paper, a novel algorithm, named DPC, is proposed to identify dynamic protein complexes by integrating PPI data and gene expression profiles. According to Core-Attachment assumption, these proteins which are always active in the molecular cycle are regarded as core proteins. The protein-complex cores are identified from these always active proteins by detecting dense subgraphs. Final protein complexes are extended from the protein-complex cores by adding attachments based on a topological character of “closeness” and dynamic meaning. The protein complexes produced by our algorithm DPC contain two parts: static core expressed in all the molecular cycle and dynamic attachments short-lived. The proposed algorithm DPC was applied on the data of Saccharomyces cerevisiae and the experimental results show that DPC outperforms CMC, MCL, SPICi, HC-PIN, COACH, and Core-Attachment based on the validation of matching with known complexes and hF-measures. PMID:24963481

Different effects of isolation-rearing and neonatal MK-801 treatment on attentional modulations of prepulse inhibition of startle in rats.

PubMed

Wu, Zhe-Meng; Ding, Yu; Jia, Hong-Xiao; Li, Liang

2016-09-01

Prepulse inhibition (PPI) is suppression of the startle reflex by a weaker sensory stimulus (prepulse) preceding the startling stimulus. In people with schizophrenia, impairment of attentional modulation of PPI, but not impairment of baseline PPI, is correlated with symptom severity. In rats, both fear conditioning of prepulse and perceptually spatial separation between the conditioned prepulse and a noise masker enhance PPI (the paradigms of attentional modulation of PPI). As a neurodevelopmental model of schizophrenia, isolation rearing impairs both baseline PPI and attentional modulations of PPI in rats. This study examined in Sprague-Dawley male rats whether neonatally blocking N-methyl-D-aspartate (NMDA) receptors specifically affects attentional modulations of PPI during adulthood. Both socially reared rats with neonatal exposure to the NMDA receptor antagonist MK-801 and isolation-reared rats exhibited augmented startle responses, but only isolation rearing impaired baseline PPI. Fear conditioning of the prepulse enhanced PPI in socially reared rats, but MK-801-treated rats lost the prepulse feature specificity. Perceptually spatial separation between the conditioned prepulse and a noise masker further enhanced PPI only in normally reared rats. Clozapine administration during adulthood generally weakened startle, enhanced baseline PPI in neonatally interrupted rats, and restored the fear conditioning-induced PPI enhancement in isolation-reared rats with a loss of the prepulse feature specificity. Clozapine administration also abolished both the perceptual separation-induced PPI enhancement in normally reared rats and the fear conditioning-induced PPI enhancement in MK-801-treated rats. Isolation rearing impairs both baseline PPI and attentional modulations of PPI, but neonatally disrupting NMDA receptor-mediated transmissions specifically impair attentional modulations of PPI. Clozapine has limited alleviating effects.

Intersystem-crossing and phosphorescence rates in fac-Ir{sup III}(ppy){sub 3}: A theoretical study involving multi-reference configuration interaction wavefunctions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kleinschmidt, Martin; Marian, Christel M., E-mail: Christel.Marian@hhu.de; Wüllen, Christoph van

2015-03-07

We have employed combined density functional theory and multi-reference configuration interaction methods including spin–orbit coupling (SOC) effects to investigate the photophysics of the green phosphorescent emitter fac-tris-(2-phenylpyridine)iridium (fac-Ir(ppy){sub 3}). A critical evaluation of our quantum chemical approaches shows that a perturbational treatment of SOC is the method of choice for computing the UV/Vis spectrum of this heavy transition metal complex while multi-reference spin–orbit configuration interaction is preferable for calculating the phosphorescence rates. The particular choice of the spin–orbit interaction operator is found to be of minor importance. Intersystem crossing (ISC) rates have been determined by Fourier transformation of the timemore » correlation function of the transition including Dushinsky rotations. In the electronic ground state, fac-Ir(ppy){sub 3} is C{sub 3} symmetric. The calculated UV/Vis spectrum is in excellent agreement with experiment. The effect of SOC is particularly pronounced for the metal-to-ligand charge transfer (MLCT) band in the visible region of the absorption spectrum which does not only extend its spectral onset towards longer wavelengths but also experiences a blue shift of its maximum. Pseudo-Jahn-Teller interaction leads to asymmetric coordinate displacements in the lowest MLCT states. Substantial electronic SOC and a small energy gap make ISC an ultrafast process in fac-Ir(ppy){sub 3}. For the S{sub 1}↝T{sub 1} non-radiative transition, we compute a rate constant of k{sub ISC} = 6.9 × 10{sup 12} s{sup −1} which exceeds the rate constant of radiative decay to the electronic ground state by more than six orders of magnitude, in agreement with the experimental observation of a subpicosecond ISC process and a triplet quantum yield close to unity. As a consequence of the geometric distortion in the T{sub 1} state, the T{sub 1} → S{sub 0} transition densities are localized on one of the phenylpyridyl moieties. In our best quantum chemical model, we obtain phosphorescence decay times of 264 μs, 13 μs, and 0.9 μs, respectively, for the T{sub 1,I}, T{sub 1,II}, and T{sub 1,III} fine-structure levels in dichloromethane (DCM) solution. In addition to reproducing the correct orders of magnitude for the individual phosphorescence emission probabilities, our theoretical study gives insight into the underlying mechanisms. In terms of intensity borrowing from spin-allowed transitions, the low emission probability of the T{sub 1,I} substate is caused by the mutual cancellation of contributions from several singlet states to the total transition dipole moment. Their contributions do not cancel but add up in case of the much faster T{sub 1,III} → S{sub 0} emission while the T{sub 1,II} → S{sub 0} emission is dominated by intensity borrowing from a single spin-allowed process, i.e., the S{sub 2} → S{sub 0} transition.« less

Impact of self-reported gastroesophageal reflux disease in subjects from COPDGene cohort.

PubMed

Martinez, Carlos H; Okajima, Yuka; Murray, Susan; Washko, George R; Martinez, Fernando J; Silverman, Edwin K; Lee, Jin Hwa; Regan, Elizabeth A; Crapo, James D; Curtis, Jeffrey L; Hatabu, Hiroto; Han, MeiLan K

2014-06-03

The coexistence of gastroesophageal reflux disease (GERD) and COPD has been recognized, but there has been no comprehensive evaluation of the impact of GERD on COPD-related health status and patient-centered outcomes. Cross-sectional and longitudinal study of 4,483 participants in the COPDGene cohort who met GOLD criteria for COPD. Physician-diagnosed GERD was ascertained by questionnaire. Clinical features, spirometry and imaging were compared between COPD subjects without versus with GERD. We evaluated the relationship between GERD and symptoms, exacerbations and markers of microaspiration in univariate and multivariate models. Associations were additionally tested for the confounding effect of covariates associated with a diagnosis of GERD and the use of proton-pump inhibitor medications (PPIs). To determine whether GERD is simply a marker for the presence of other conditions independently associated with worse COPD outcomes, we also tested models incorporating a GERD propensity score. GERD was reported by 29% of subjects with female predominance. Subjects with GERD were more likely to have chronic bronchitis symptoms, higher prevalence of prior cardiovascular events (combined myocardial infarction, coronary artery disease and stroke 21.3% vs. 13.4.0%, p < 0.0001). Subjects with GERD also had more severe dyspnea (MMRC score 2.2 vs. 1.8, p < 0.0001), and poorer quality of life (QOL) scores (St. George's Respiratory Questionnaire (SGRQ) total score 41.8 vs. 34.9, p < 0.0001; SF36 Physical Component Score 38.2 vs. 41.4, p < 0.0001). In multivariate models, a significant relationship was detected between GERD and SGRQ (3.4 points difference, p < 0.001) and frequent exacerbations at baseline (≥2 exacerbation per annum at inclusion OR 1.40, p = 0.006). During a mean follow-up time of two years, GERD was also associated with frequent (≥2/year exacerbations OR 1.40, p = 0.006), even in models in which PPIs, GERD-PPI interactions and a GERD propensity score were included. PPI use was associated with frequent exacerbator phenotype, but did not meaningfully influence the GERD-exacerbation association. In COPD the presence of physician-diagnosed GERD is associated with increased symptoms, poorer QOL and increased frequency of exacerbations at baseline and during follow-up. These associations are maintained after controlling for PPI use. The PPI-exacerbations association could result from confounding-by-indication.

Construction of a Turn Off-On-Off Fluorescent System Based on Competitive Coordination of Cu2+ between 6,7-Dihydroxycoumarin and Pyrophosphate Ion for Sensitive Assay of Pyrophosphatase Activity

PubMed Central

Zhao, Liu; Miao, Yanqing; Liu, Chunye; Zhang, Chenxiao

2016-01-01

The detection of pyrophosphatase (PPase) activity is of great significance in diagnosing diseases and understanding the function of PPase-related biological events. This study constructed a turn off-on-off fluorescent system for PPase activity assay based on PPase-regulated competitive coordination of Cu2+ between a water-soluble fluorescent probe 6,7-dihydroxycoumarin (DHC) and pyrophosphate (PPi). The probe DHC can coordinate with Cu2+ and consequently display on-off type fluorescence response. Furthermore, the in situ formed nonfluorescent Cu2+-DHC complex can act as an effective off-on type fluorescent probe for sensing PPi due to the higher coordination reactivity between Cu2+ and PPi than that between Cu2+ and DHC. The subsequent addition of PPase to the mixture containing Cu2+, DHC, and PPi leads to the fluorescence requenching of the system again (an off state) because PPase catalyzes the hydrolysis of PPi into orthophosphate in the reaction system. Under the optimum conditions, the decrease of the fluorescence intensity of DHC-Cu2+-PPi system was linear with the increase of the PPase activity in the range from 0.1 to 0.3 U. The detection limit was down to 0.028 U PPase (S/N = 3). Moreover, the as-established system was also applied to evaluate PPase inhibitor. This study offers a simple yet effective method for the detection of PPase activity. PMID:27766179

Differential reward network functional connectivity in cannabis dependent and non-dependent users☆

PubMed Central

Filbey, Francesca M.; Dunlop, Joseph

2015-01-01

Background Emergent studies show that similar to other substances of abuse, cue-reactivity to cannabis is also associated with neural response in the brain’s reward pathway (Filbey et al., 2009). However, the inter-relatedness of brain regions during cue-reactivity in cannabis users remains unknown. Methods In this study, we conducted a series of investigations to determine functional connectivity during cue-reactivity in 71 cannabis users. First, we used psychophysiological interaction (PPI) analysis to examine coherent neural response to cannabis cues. Second, we evaluated whether these patterns of network functional connectivity differentiated dependent and non-dependent users. Finally, as an exploratory analysis, we determined the directionality of these connections via Granger connectivity analyses. Results PPI analyses showed reward network functional connectivity with the nucleus accumbens (NAc) seed region during cue exposure. Between-group contrasts found differential effects of dependence status. Dependent users (N = 31) had greater functional connectivity with amygdala and anterior cingulate gyrus (ACG) seeds while the non-dependent users (N = 24) had greater functional connectivity with the NAc, orbitofrontal cortex (OFC) and hippocampus seeds. Granger analyses showed that hippocampal and ACG activation preceded neural response in reward areas. Conclusions Both PPI and Granger analyses demonstrated strong functional coherence in reward regions during exposure to cannabis cues in current cannabis users. Functional connectivity (but not regional activation) in the reward network differentiated dependent from non-dependent cannabis users. Our findings suggest that repeated cannabis exposure causes observable changes in functional connectivity in the reward network and should be considered in intervention strategies. PMID:24838032

The autophagy interaction network of the aging model Podospora anserina.

PubMed

Philipp, Oliver; Hamann, Andrea; Osiewacz, Heinz D; Koch, Ina

2017-03-27

Autophagy is a conserved molecular pathway involved in the degradation and recycling of cellular components. It is active either as response to starvation or molecular damage. Evidence is emerging that autophagy plays a key role in the degradation of damaged cellular components and thereby affects aging and lifespan control. In earlier studies, it was found that autophagy in the aging model Podospora anserina acts as a longevity assurance mechanism. However, only little is known about the individual components controlling autophagy in this aging model. Here, we report a biochemical and bioinformatics study to detect the protein-protein interaction (PPI) network of P. anserina combining experimental and theoretical methods. We constructed the PPI network of autophagy in P. anserina based on the corresponding networks of yeast and human. We integrated PaATG8 interaction partners identified in an own yeast two-hybrid analysis using ATG8 of P. anserina as bait. Additionally, we included age-dependent transcriptome data. The resulting network consists of 89 proteins involved in 186 interactions. We applied bioinformatics approaches to analyze the network topology and to prove that the network is not random, but exhibits biologically meaningful properties. We identified hub proteins which play an essential role in the network as well as seven putative sub-pathways, and interactions which are likely to be evolutionary conserved amongst species. We confirmed that autophagy-associated genes are significantly often up-regulated and co-expressed during aging of P. anserina. With the present study, we provide a comprehensive biological network of the autophagy pathway in P. anserina comprising PPI and gene expression data. It is based on computational prediction as well as experimental data. We identified sub-pathways, important hub proteins, and evolutionary conserved interactions. The network clearly illustrates the relation of autophagy to aging processes and enables further specific studies to understand autophagy and aging in P. anserina as well as in other systems.

Ligand-bridged dinuclear cyclometalated Ir(III) complexes: from metallamacrocycles to discrete dimers.

PubMed

Chandrasekhar, Vadapalli; Hajra, Tanima; Bera, Jitendra K; Rahaman, S M Wahidur; Satumtira, Nisa; Elbjeirami, Oussama; Omary, Mohammad A

2012-02-06

Metallamacrocycles 1, 2, and 3 of the general formula [{Ir(ppy)(2)}(2)(μ-BL)(2)](OTf)(2) (ppyH = 2-phenyl pyridine; BL = 1,2-bis(4-pyridyl)ethane (bpa) (1), 1,3-bis(4-pyridyl)propane (bpp) (2), and trans-1,2-bis(4-pyridyl)ethylene (bpe) (3)) have been synthesized by the reaction of [{(ppy)(2)Ir}(2)(μ-Cl)(2)], first with AgOTf to effect dechlorination and later with various bridging ligands. Open-frame dimers [{Ir(ppy)(2)}(2)(μ-BL)](OTf)(2) were obtained in a similar manner by utilizing N,N'-bis(2-pyridyl)methylene-hydrazine (abp) and N,N'-(bis(2-pyridyl)formylidene)ethane-1,2-diamine (bpfd) (for compounds 4 and 5, respectively) as bridging ligands. Molecular structures of 1, 3, 4, and 5 were established by X-ray crystallography. Cyclic voltammetry experiments reveal weakly interacting "Ir(ppy)(2)" units bridged by ethylene-linked bpe ligand in 3; on the contrary the metal centers are electronically isolated in 1 and 2 where the bridging ligands are based on ethane and propane linkers. The dimer 4 exhibits two accessible reversible reduction couples separated by 570 mV indicating the stability of the one-electron reduced species located on the diimine-based bridge abp. The "Ir(ppy)(2)" units in compound 5 are noninteracting as the electronic conduit is truncated by the ethane spacer in the bpfd bridge. The dinuclear compounds 1-5 show ligand centered (LC) transitions involving ppy ligands and mixed metal to ligand/ligand to ligand charge transfer (MLCT/LLCT) transitions involving both the cyclometalating ppy and bridging ligands (BL) in the UV-vis spectra. For the conjugated bridge bpe in compound 3 and abp in compound 4, the lowest-energy charge-transfer absorptions are red-shifted with enhanced intensity. In accordance with their similar electronic structures, compounds 1 and 2 exhibit identical emissions. The presence of vibronic structures in these compounds indicates a predominantly (3)LC excited states. On the contrary, broad and unstructured phosphorescence bands in compounds 3-5 strongly suggest emissive states of mixed (3)MLCT/(3)LLCT character. Density functional theory (DFT) calculations have been carried out to gain insight on the frontier orbitals, and to rationalize the electrochemical and photophysical properties of the compounds based on their electronic structures.

APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks

PubMed Central

Alonso-López, Diego; Gutiérrez, Miguel A.; Lopes, Katia P.; Prieto, Carlos; Santamaría, Rodrigo; De Las Rivas, Javier

2016-01-01

APID (Agile Protein Interactomes DataServer) is an interactive web server that provides unified generation and delivery of protein interactomes mapped to their respective proteomes. This resource is a new, fully redesigned server that includes a comprehensive collection of protein interactomes for more than 400 organisms (25 of which include more than 500 interactions) produced by the integration of only experimentally validated protein–protein physical interactions. For each protein–protein interaction (PPI) the server includes currently reported information about its experimental validation to allow selection and filtering at different quality levels. As a whole, it provides easy access to the interactomes from specific species and includes a global uniform compendium of 90,379 distinct proteins and 678,441 singular interactions. APID integrates and unifies PPIs from major primary databases of molecular interactions, from other specific repositories and also from experimentally resolved 3D structures of protein complexes where more than two proteins were identified. For this purpose, a collection of 8,388 structures were analyzed to identify specific PPIs. APID also includes a new graph tool (based on Cytoscape.js) for visualization and interactive analyses of PPI networks. The server does not require registration and it is freely available for use at http://apid.dep.usal.es. PMID:27131791

Quantitative determination and evaluation of Paris polyphylla var. yunnanensis with different harvesting times using UPLC-UV-MS and FT-IR spectroscopy in combination with partial least squares discriminant analysis.

PubMed

Yang, Yuan-Gui; Zhang, Ji; Zhao, Yan-Li; Zhang, Jin-Yu; Wang, Yuan-Zhong

2017-07-01

A rapid method was developed and validated by ultra-performance liquid chromatography-triple quadrupole mass spectroscopy with ultraviolet detection (UPLC-UV-MS) for simultaneous determination of paris saponin I, paris saponin II, paris saponin VI and paris saponin VII. Partial least squares discriminant analysis (PLS-DA) based on UPLC and Fourier transform infrared (FT-IR) spectroscopy was employed to evaluate Paris polyphylla var. yunnanensis (PPY) at different harvesting times. Quantitative determination implied that the various contents of bioactive compounds with different harvesting times may lead to different pharmacological effects; the average content of total saponins for PPY harvested at 8 years was higher than that from other samples. The PLS-DA of FT-IR spectra had a better performance than that of UPLC for discrimination of PPY from different harvesting times. Copyright © 2016 John Wiley & Sons, Ltd.

How perfect can protein interactomes be?

PubMed

Levy, Emmanuel D; Landry, Christian R; Michnick, Stephen W

2009-03-03

Any engineered device should certainly not contain nonfunctional components, for this would be a waste of energy and money. In contrast, evolutionary theory tells us that biological systems need not be optimized and may very well accumulate nonfunctional elements. Mutational and demographic processes contribute to the cluttering of eukaryotic genomes and transcriptional networks with "junk" DNA and spurious DNA binding sites. Here, we question whether such a notion should be applied to protein interactomes-that is, whether these protein interactomes are expected to contain a fraction of nonselected, nonfunctional protein-protein interactions (PPIs), which we term "noisy." We propose a simple relationship between the fraction of noisy interactions expected in a given organism and three parameters: (i) the number of mutations needed to create and destroy interactions, (ii) the size of the proteome, and (iii) the fitness cost of noisy interactions. All three parameters suggest that noisy PPIs are expected to exist. Their existence could help to explain why PPIs determined from large-scale studies often lack functional relationships between interacting proteins, why PPIs are poorly conserved across organisms, and why the PPI space appears to be immensely large. Finally, we propose experimental strategies to estimate the fraction of evolutionary noise in PPI networks.

Identification of Small Molecule Translesion Synthesis Inhibitors That Target the Rev1-CT/RIR Protein-Protein Interaction.

PubMed

Sail, Vibhavari; Rizzo, Alessandro A; Chatterjee, Nimrat; Dash, Radha C; Ozen, Zuleyha; Walker, Graham C; Korzhnev, Dmitry M; Hadden, M Kyle

2017-07-21

Translesion synthesis (TLS) is an important mechanism through which proliferating cells tolerate DNA damage during replication. The mutagenic Rev1/Polζ-dependent branch of TLS helps cancer cells survive first-line genotoxic chemotherapy and introduces mutations that can contribute to the acquired resistance so often observed with standard anticancer regimens. As such, inhibition of Rev1/Polζ-dependent TLS has recently emerged as a strategy to enhance the efficacy of first-line chemotherapy and reduce the acquisition of chemoresistance by decreasing tumor mutation rate. The TLS DNA polymerase Rev1 serves as an integral scaffolding protein that mediates the assembly of the active multiprotein TLS complexes. Protein-protein interactions (PPIs) between the C-terminal domain of Rev1 (Rev1-CT) and the Rev1-interacting region (RIR) of other TLS DNA polymerases play an essential role in regulating TLS activity. To probe whether disrupting the Rev1-CT/RIR PPI is a valid approach for developing a new class of targeted anticancer agents, we designed a fluorescence polarization-based assay that was utilized in a pilot screen for small molecule inhibitors of this PPI. Two small molecule scaffolds that disrupt this interaction were identified, and secondary validation assays confirmed that compound 5 binds to Rev1-CT at the RIR interface. Finally, survival and mutagenesis assays in mouse embryonic fibroblasts and human fibrosarcoma HT1080 cells treated with cisplatin and ultraviolet light indicate that these compounds inhibit mutagenic Rev1/Polζ-dependent TLS in cells, validating the Rev1-CT/RIR PPI for future anticancer drug discovery and identifying the first small molecule inhibitors of TLS that target Rev1-CT.

Identifying Hierarchical and Overlapping Protein Complexes Based on Essential Protein-Protein Interactions and “Seed-Expanding” Method

PubMed Central

Ren, Jun; Zhou, Wei; Wang, Jianxin

2014-01-01

Many evidences have demonstrated that protein complexes are overlapping and hierarchically organized in PPI networks. Meanwhile, the large size of PPI network wants complex detection methods have low time complexity. Up to now, few methods can identify overlapping and hierarchical protein complexes in a PPI network quickly. In this paper, a novel method, called MCSE, is proposed based on λ-module and “seed-expanding.” First, it chooses seeds as essential PPIs or edges with high edge clustering values. Then, it identifies protein complexes by expanding each seed to a λ-module. MCSE is suitable for large PPI networks because of its low time complexity. MCSE can identify overlapping protein complexes naturally because a protein can be visited by different seeds. MCSE uses the parameter λ_th to control the range of seed expanding and can detect a hierarchical organization of protein complexes by tuning the value of λ_th. Experimental results of S. cerevisiae show that this hierarchical organization is similar to that of known complexes in MIPS database. The experimental results also show that MCSE outperforms other previous competing algorithms, such as CPM, CMC, Core-Attachment, Dpclus, HC-PIN, MCL, and NFC, in terms of the functional enrichment and matching with known protein complexes. PMID:25143945

Poly(zwitterionic liquids) functionalized polypyrrole/graphene oxide nanosheets for electrochemically detecting dopamine at low concentration.

PubMed

Mao, Hui; Liang, Jiachen; Ji, Chunguang; Zhang, Haifeng; Pei, Qi; Zhang, Yuyang; Zhang, Yu; Hisaeda, Yoshio; Song, Xi-Ming

2016-08-01

Poly(3-(1-vinylimidazolium-3-yl)propane-1-sulfonate) (PVIPS), a novel kind of poly(zwitterionic liquids) (PZILs) containing both imidazolium cation and sulfonate anion, was successfully modified on the surface of polypyrrole/graphene oxide nanosheets (PPy/GO) by covalent bonding. The obtained novel PZILs functionalized PPy/GO nanosheets (PVIPS/PPy/GO) modified glassy carbon electrode (GCE) presented the excellent electrochemical catalytic activity towards dopamine (DA) with high stability, sensitivity, selectivity and wide linear range (40-1220nM), especially having a lower detection limit (17.3nM). The excellent analytical performance is attributed to the strongly negative charges on the surface of modified GCE in aqueous solution, which is different from conventional poly(ionic liquids) modified GCE. DA cations could be quickly enriched on the electrode surface by electrostatic interaction in solution due to the existence of SO3(-) groups with negative charge at the end of pendant groups in zwitterionic PVIPS, resulting in a change of the electrons transmission mode in the oxidation of DA, that is, from a typical diffusion-controlled process at conventional poly(1-vinyl-3-ethylimidazole bromide) (PVEIB)/PPy/GO modified GCE to a typical surface-controlled process. Copyright © 2016 Elsevier B.V. All rights reserved.

Medial prefrontal cortex lesions in the female rat affect sexual and maternal behavior and their sequential organization.

PubMed

Afonso, Veronica M; Sison, Margarette; Lovic, Vedran; Fleming, Alison S

2007-06-01

Temporal sequences of sexual and maternal behaviors in female rats and their correlation with each other and with performance on a sensory-motor gating response inhibition task assessed by prepulse inhibition (PPI) were investigated following medial prefrontal cortex (mPFC) lesions. Following excitotoxic mPFC (n = 10) or sham (n = 9) lesions, sexual behaviors across the ovarian cycle were scored. After mating and parturition, maternal interactions were scored until pups reached postnatal Day 10. After resumption of the ovarian cycle, the female rats were tested for PPI. Compared with sham lesions, mPFC lesions impaired proceptive behaviors and some maternal behaviors (e.g., pup retrieval, pup licking) but did not affect others (e.g., nest building, pup mouthing). Lesions disrupted temporal sequences of solicitations (number of male orientations followed, within 4 s, by a level change) and pup retrievals (number of pup retrievals followed, within 5 s, by another retrieval). These sequential behavior patterns were significantly correlated with each other and with PPI. However, when PPI effects were partialled out, group differences were less strong, but persisted. This study demonstrated that mPFC manipulations affect actions rich in sequential structure in response to biologically relevant stimuli. Copyright (c) 2007 APA, all rights reserved.

The effects of Eph-ephrin mutations on pre-pulse inhibition in mice.

PubMed

Liuzzo, Andrea; Gray, Lincoln; Wallace, Matthew; Gabriele, Mark

2014-08-01

Eph-ephrin signaling is known to be important in directing topographic projections in the afferent auditory pathway, including connections to various subdivisions of the inferior colliculus (IC). The acoustic startle-response (ASR) is a reliable reflexive behavioral response in mammals elicited by an unexpected intense acoustic startle-eliciting stimulus (ES). It is mediated by a sub-cortical pathway that includes the IC. The ASR amplitude can be measured with an accelerometer under the subject and can be decreased in amplitude by presenting a less intense, non-startling stimulus 5-300ms before the ES. This reflexive decrement in ASR is called pre-pulse inhibition (PPI) and indicates that the relatively soft pre-pulse was heard. PPI is a general trait among mammals. Mice have been used recently to study this response and to reveal how genetic mutations affect neural circuits and hence the ASR and PPI. In this experiment, we measured the effect of Eph-ephrin mutations using control mice (C57BL/6J), mice with compromised EphA4 signaling (EphA4(lacZ/+), EphA4(lacZ/lacZ)), and knockout ephrin-B3 mice (ephrin-B3 (+/-, -/-)). Control and EphA4(lacZ/+s)trains showed robust PPI (up to 75% decrement in ASR) to an offset of a 70dB SPL background noise at 50ms before the ES. Ephrin-B3 knockout mice and EphA4 homozygous mutants were only marginally significant in PPI (<25% decrement and <33% decrement, respectively) to the same conditions. This decrement in PPI highlights the importance of ephrin-B3 and EphA4 interactions in ordering auditory behavioral circuits. Thus, different mutations in certain members of the signaling family produce a full range of changes in PPI, from minimal to nearly maximal. This technique can be easily adapted to study other aspects of hearing in a wider range of mutations. Along with ongoing neuroanatomical studies, this allows careful quantification of how the auditory anatomical, physiological and now behavioral phenotype is affected by changes in Eph-ephrin expression and functionality. Copyright © 2014 Elsevier Inc. All rights reserved.

Description and Evaluation of the First National Patient and Public Involvement Day for Thyroid Eye Disease in the United Kingdom

PubMed Central

Porteous, Carol; Bunce, Catey; Bonstein, Karen; Hickey, Janis; Dayan, Colin M.; Adams, Gill; Rose, Geoff E.; Ezra, Daniel G.

2014-01-01

Background: To ensure appropriate patient-focused outcomes, the National Institute for Health Research (NIHR) in the United Kingdom has made consultation with patients, caregivers, and the public a prerequisite to providing research funding. One method of encouraging engagement with research is through patient and public involvement (PPI) events. We describe the planning and implementation of a PPI day for thyroid eye disease (TED) and evaluate our own event using feedback from delegates. Methods: The Moorfields NIHR Biomedical Research Centre, in partnership with TED charities, arranged the first national PPI day for TED in the United Kingdom. The event included didactic lectures; pre-event and postevent questionnaires; an exhibition with stalls, posters, and an interactive voting wall to determine research priorities; focus group sessions to explore patient experiences and perceptions of research; and one-on-one interviews recording individual patient stories. Results: Of 100 attendees, 70 completed questionnaires. When asked whether the day had provided what they wanted, 48 of 52 (92%) said yes; 3 of 52 (6%) said no. Overall 6 of 52 (12%) rated the event as good; 28 of 52 (54%), very good; and 18 of 52 (34%), excellent. Thirty-six patients registered to participate in further research, identifying “finding the cause for TED,” “improving psychological support,” and “achieving a better cosmetic outcome” as key priorities. A poor understanding of TED among medical professionals was a common complaint. Conclusions: The event received positive feedback and achieved its key objective of engaging patients, researchers, and clinicians in a two-way discussion about research priorities and improved study design. An invaluable insight was gained into patients' needs for a better quality of life, and we have demonstrated that important data can be captured from such events, providing an evidential basis consistent with the NIHR principles of patient-centered research. PMID:24936890

The roles of 5-HT1A and 5-HT2 receptors in the effects of 5-MeO-DMT on locomotor activity and prepulse inhibition in rats.

PubMed

Krebs-Thomson, Kirsten; Ruiz, Erbert M; Masten, Virginia; Buell, Mahalah; Geyer, Mark A

2006-12-01

The hallucinogen 5-methoxy-N,N-dimethyltryptamine (5-MeO-DMT) is structurally similar to other indoleamine hallucinogens such as LSD. The present study examined the effects of 5-MeO-DMT in rats using the Behavioral Pattern Monitor (BPM), which enables analyses of patterns of locomotor activity and exploration, and the prepulse inhibition of startle (PPI) paradigm. A series of interaction studies using the serotonin (5-HT)(1A) antagonist WAY-100635 (1.0 mg/kg), the 5-HT(2A) antagonist M100907 (1.0 mg/kg), and the 5-HT(2C) antagonist SER-082 (0.5 mg/kg) were performed to assess the respective contributions of these receptors to the behavioral effects of 5-MeO-DMT (0.01, 0.1, and 1.0 mg/kg) in the BPM and PPI paradigms. 5-MeO-DMT decreased locomotor activity, investigatory behavior, the time spent in the center of the BPM chamber, and disrupted PPI. All of these effects were antagonized by WAY-100635 pretreatment. M100907 pretreatment failed to attenuate any of these effects, while SER-082 pretreatment only antagonized the PPI disruption produced by 5-MeO-DMT. While the prevailing view was that the activation of 5-HT(2) receptors is solely responsible for hallucinogenic drug effects, these results support a role for 5-HT(1A) receptors in the effects of the indoleamine hallucinogen 5-MeO-DMT on locomotor activity and PPI in rats.

Effects of long-term PPI treatment on producing bowel symptoms and SIBO.

PubMed

Compare, Debora; Pica, Loredana; Rocco, Alba; De Giorgi, Francesco; Cuomo, Rosario; Sarnelli, Giovanni; Romano, Marco; Nardone, Gerardo

2011-04-01

Gastroesophageal reflux disease (GERD), including erosive reflux disease and non-erosive reflux disease (NERD), is a chronic disease with a significant negative effect on quality of life. State-of-the-art treatment involves proton pump inhibitors (PPIs). However, relapse of symptoms occurs in the majority of the patients who require recurrent or continuous therapy. Although PPIs are well tolerated, little information is available about gastrointestinal side effects. To evaluate the effects of long-term PPI treatment on development of bowel symptoms and/or small intestinal bacterial overgrowth (SIBO). Patients with NERD not complaining of bowel symptoms were selected by upper endoscopy, 24-h pH-metry and a structured questionnaire concerning severity and frequency of bloating, flatulence, abdominal pain, diarrhoea and constipation. Patients were treated with esomeprazole 20 mg bid for 6 months. Prior to and after 8 weeks and 6 months of therapy, patients received the structured questionnaire and underwent evaluation of SIBO by glucose hydrogen breath test (GHBT). Forty-two patients with NERD were selected out of 554 eligible patients. After 8 weeks of PPI treatment, patients complained of bloating, flatulence, abdominal pain and diarrhoea in 43%, 17%, 7% and 2%, respectively. After 6 months, the incidence of bowel symptoms further increased and GHBT was found positive in 11/42 (26%) patients. By a post hoc analysis, a significant (P < 0·05) percentage of patients (8/42) met Rome III criteria for irritable bowel syndrome. Prolonged PPI treatment may produce bowel symptoms and SIBO; therefore, the strategy of step-down or on-demand PPI therapy should be encouraged in GERD. © 2010 The Authors. European Journal of Clinical Investigation © 2010 Stichting European Society for Clinical Investigation Journal Foundation.

Nonsteroid anti-inflammatory drug-induced gastroduodenal injury.

PubMed

Lai, Larry H; Chan, Francis K L

2009-11-01

This article reviews selected publications related to nonsteroid anti-inflammatory drug (NSAID)-induced gastroduodenal toxicity in recent years. This article provides a comprehensive review of the latest evidence on the epidemiology of NSAID-induced gastroduodenal injury, recommendations on optimal gastroprotective regimens among patients in need of NSAID, risk stratification approach by considering gastrointestinal and cardiovascular risks, and negative interaction between proton pump inhibitors (PPIs) and clopidogrel. Current evidence indicates that a PPI and a cyclooxygenase (COX)-2-selective NSAID provides the best gastric protection. In light of potential cardiovascular hazard of NSAIDs, physicians should select an NSAID according to individual patients' cardiovascular risk (i.e., naproxen vs. a nonnaproxen NSAID). The choice of gastroprotective therapy depends on the number and nature of gastrointestinal risk factors. PPI co-therapy is recommended in patients with high gastrointestinal risk on aspirin. Whether there is any clinically important interaction between PPIs and clopidogrel remains uncertain.

Optical band gap determination of calcium doped lanthanum manganite nano particle tailored with polypyrrole

NASA Astrophysics Data System (ADS)

Gopalakrishna, Smitha Mysore; Murugendrappa, Malalkere Veerappa

2018-05-01

In this paper we bring forth the effect of La0.7Ca0.3MnO3 (LCM) perovskite nano particle on the optical band gap in composition with conducting Polypyrrole (PPy) prepared by chemical oxidation method. The morphology and crystalline phase were determined by SEM, TEM and X-Ray diffraction studies. The Optical band gap studies were analyzed using the UV-VIS spectrometer scanned in the range 200 nm to 600 nm for pure PPy and PPy/LCM composites. There is a characteristic peak observed for the composites situated around 315 nm for pure PPy, PPy/LCM10 and PPy/LCM50. But for higher compositions of LCM weight percentage like 30%, 40% and 50% the peak shift slightly to higher wavelength side. The peak shifts to 320 nm, 325 nm and 335 nm respectively. The optical band gap increased for Pure PPy, PPy/LCM10 and PPy/LCM20 and found to decrease gradually for PPy/LCM30, PPy/LCM40 and PPy/LCM50. The studies suggest that LCM composition in the PPy chain has a role in modifying the wavelength and in turn its band gap. The study may find application in organic devices working at high frequency and voltage.

A computational interactome for prioritizing genes associated with complex agronomic traits in rice (Oryza sativa).

PubMed

Liu, Shiwei; Liu, Yihui; Zhao, Jiawei; Cai, Shitao; Qian, Hongmei; Zuo, Kaijing; Zhao, Lingxia; Zhang, Lida

2017-04-01

Rice (Oryza sativa) is one of the most important staple foods for more than half of the global population. Many rice traits are quantitative, complex and controlled by multiple interacting genes. Thus, a full understanding of genetic relationships will be critical to systematically identify genes controlling agronomic traits. We developed a genome-wide rice protein-protein interaction network (RicePPINet, http://netbio.sjtu.edu.cn/riceppinet) using machine learning with structural relationship and functional information. RicePPINet contained 708 819 predicted interactions for 16 895 non-transposable element related proteins. The power of the network for discovering novel protein interactions was demonstrated through comparison with other publicly available protein-protein interaction (PPI) prediction methods, and by experimentally determined PPI data sets. Furthermore, global analysis of domain-mediated interactions revealed RicePPINet accurately reflects PPIs at the domain level. Our studies showed the efficiency of the RicePPINet-based method in prioritizing candidate genes involved in complex agronomic traits, such as disease resistance and drought tolerance, was approximately 2-11 times better than random prediction. RicePPINet provides an expanded landscape of computational interactome for the genetic dissection of agronomically important traits in rice. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Influence of pea protein aggregates on the structure and stability of pea protein/soybean polysaccharide complex emulsions.

PubMed

Yin, Baoru; Zhang, Rujing; Yao, Ping

2015-03-20

The applications of plant proteins in the food and beverage industry have been hampered by their precipitation in acidic solution. In this study, pea protein isolate (PPI) with poor dispersibility in acidic solution was used to form complexes with soybean soluble polysaccharide (SSPS), and the effects of PPI aggregates on the structure and stability of PPI/SSPS complex emulsions were investigated. Under acidic conditions, high pressure homogenization disrupts the PPI aggregates and the electrostatic attraction between PPI and SSPS facilitates the formation of dispersible PPI/SSPS complexes. The PPI/SSPS complex emulsions prepared from the PPI containing aggregates prove to possess similar droplet structure and similar stability compared with the PPI/SSPS emulsions produced from the PPI in which the aggregates have been previously removed by centrifugation. The oil droplets are protected by PPI/SSPS complex interfacial films and SSPS surfaces. The emulsions show long-term stability against pH and NaCl concentration changes. This study demonstrates that PPI aggregates can also be used to produce stable complex emulsions, which may promote the applications of plant proteins in the food and beverage industry.

High-Content Positional Biosensor Screening Assay for Compounds to Prevent or Disrupt Androgen Receptor and Transcriptional Intermediary Factor 2 Protein–Protein Interactions

PubMed Central

Hua, Yun; Shun, Tong Ying; Strock, Christopher J.

2014-01-01

Abstract The androgen receptor–transcriptional intermediary factor 2 (AR-TIF2) positional protein–protein interaction (PPI) biosensor assay described herein combines physiologically relevant cell-based assays with the specificity of binding assays by incorporating structural information of AR and TIF2 functional domains along with intracellular targeting sequences and fluorescent reporters. Expression of the AR-red fluorescent protein (RFP) “prey” and TIF2-green fluorescent protein (GFP) “bait” components of the biosensor was directed by recombinant adenovirus constructs that expressed the ligand binding and activation function 2 surface domains of AR fused to RFP with nuclear localization and nuclear export sequences, and three α-helical LXXLL motifs from TIF2 fused to GFP and an HIV Rev nucleolar targeting sequence. In unstimulated cells, AR-RFP was localized predominantly to the cytoplasm and TIF2-GFP was localized to nucleoli. Dihydrotestosterone (DHT) treatment induced AR-RFP translocation into the nucleus where the PPIs between AR and TIF2 resulted in the colocalization of both biosensors within the nucleolus. We adapted the translocation enhanced image analysis module to quantify the colocalization of the AR-RFP and TIF2-GFP biosensors in images acquired on the ImageXpress platform. DHT induced a concentration-dependent AR-TIF2 colocalization and produced a characteristic condensed punctate AR-RFP PPI nucleolar distribution pattern. The heat-shock protein 90 inhibitor 17-N-allylamino-17-demethoxygeldanamycin (17-AAG) and antiandrogens flutamide and bicalutamide inhibited DHT-induced AR-TIF2 PPI formation with 50% inhibition concentrations (IC50s) of 88.5±12.5 nM, 7.6±2.4 μM, and 1.6±0.4 μM, respectively. Images of the AR-RFP distribution phenotype allowed us to distinguish between 17-AAG and flutamide, which prevented AR translocation, and bicalutamide, which blocked AR-TIF2 PPIs. We screened the Library of Pharmacologically Active Compounds (LOPAC) set for compounds that inhibited AR-TIF2 PPI formation or disrupted preexisting complexes. Eleven modulators of steroid family nuclear receptors (NRs) and 6 non-NR ligands inhibited AR-TIF2 PPI formation, and 10 disrupted preexisting complexes. The hits appear to be either AR antagonists or nonspecific inhibitors of NR activation and trafficking. Given that the LOPAC set represents such a small and restricted biological and chemical diversity, it is anticipated that screening a much larger and more diverse compound library will be required to find AR-TIF2 PPI inhibitors/disruptors. The AR-TIF2 protein–protein interaction biosensor (PPIB) approach offers significant promise for identifying molecules with potential to modulate AR transcriptional activity in a cell-specific manner that is distinct from the existing antiandrogen drugs that target AR binding or production. Small molecules that disrupt AR signaling at the level of AR-TIF2 PPIs may also overcome the development of resistance and progression to castration-resistant prostate cancer. PMID:25181412

PPI, paradoxes and Plato: who's sailing the ship?

PubMed

Ives, Jonathan; Damery, Sarah; Redwod, Sabi

2013-03-01

Over the last decade, patient and public involvement (PPI) has become a requisite in applied health research. Some funding bodies demand explicit evidence of PPI, while others have made a commitment to developing PPI in the projects they fund. Despite being commonplace, there remains a dearth of engagement with the ethical and theoretical underpinnings of PPI processes and practices. More specifically, while there is a small (but growing) body of literature examining the effectiveness and impact of PPI, there has been relatively little reflection on whether the concept/practice of PPI is internally coherent. Here, the authors unpick a 'paradox' within PPI, which highlights a tension between its moral and pragmatic motivations and its implementation. The authors argue that this 'professionalisation paradox' means we need to rethink the practice, and purpose, of PPI in research.

A novel highly selective and sensitive detection of serotonin based on Ag/polypyrrole/Cu2O nanocomposite modified glassy carbon electrode.

PubMed

Selvarajan, S; Suganthi, A; Rajarajan, M

2018-06-01

A silver/polypyrrole/copper oxide (Ag/PPy/Cu 2 O) ternary nanocomposite was prepared by sonochemical and oxidative polymerization simple way, in which Cu 2 O was decorated with Ag nanoparticles, and covered by polyprrole (PPy) layer. The as prepared materials was characterized by UV-vis-spectroscopy (UV-vis), FT-IR, X-ray diffraction (XRD), thermo-gravimetric analysis (TGA), scanning electron microscopy (SEM) with EDX, high resolution transmission electron microscopy (HR-TEM) and X-ray photoelectron spectroscopy (XPS). Sensing of serotonin (5HT) was evaluated electrocatalyst using polypyrrole/glassy carbon electrode (PPy/GCE), polypyrrole/copper oxide/glassy carbon electrode (PPy/Cu 2 O/GCE) and silver/polypyrrole/copper oxide/glassy carbon electrode (Ag/PPy/Cu 2 O/GCE). The Ag/PPy/Cu 2 O/GCE was electrochemically treated in 0.1MPBS solution through cyclic voltammetry (CV) and differential pulse voltammetry (DPV). The peak current response increases linearly with 5-HT concentration from 0.01 to 250 µmol L -1 and the detection limit was found to be 0.0124 μmol L -1 . It exhibits high electrocatalytic activity, satisfactory repeatability, stability, fast response and good selectivity against potentially interfering species, which suggests its potential in the development of sensitive, selective, easy-operation and low-cost serotonin sensor for practical routine analyses. The proposed method is potential to expand the possible applied range of the nanocomposite material for detection of various concerned electro active substances. Copyright © 2018 Elsevier B.V. All rights reserved.

Routine post-weaning handling of rats prevents isolation rearing-induced deficit in prepulse inhibition.

PubMed

Rosa, M L N M; Silva, R C B; Moura-de-Carvalho, F T; Brandão, M L; Guimarães, F S; Del Bel, E A

2005-11-01

Rats reared under isolation conditions from weaning present a number of behavioral changes compared to animals reared under social conditions (group housing). These changes include deficits in prepulse inhibition (PPI) of the startle reflex to a loud sound. PPI refers to the reduction of the magnitude of the startle reflex when a relatively weak stimulus (the prepulse) precedes by an appropriate time interval the intense startle-elicing stimulus (the pulse). PPI is useful for studying sensorimotor integration. The present study evaluated the effect of handling on the impairment of PPI induced by isolation-rearing. Male Wistar rats (N = 11-15/group) were housed in groups (5 per cage and handled three times a week) or isolated (housed individually) since weaning (21 days) for 10 weeks when they reach approximately 150 g. The isolated rats were divided into "minimally handled" animals (handled once a week for cleaning purposes only) or "handled" animals (handled three times a week). This handling consisted of grasping the rat by the tail and moving it to a clean cage (approximately 5 s). A statistically significant reduction (52%) in the PPI test was found only in the isolated group with minimal handling while no difference was seen between grouped animals and isolated handled animals. These results indicate that isolation rearing causes disruption in the PPI at adult age, which serves as an index of attention deficit. This change in the sensory processing of information induced by post-weaning isolation can be prevented by handling during the development of the animal.

Associations between gastro-oesophageal reflux, its management and exacerbations of chronic obstructive pulmonary disease.

PubMed

Benson, Victoria S; Müllerová, Hana; Vestbo, Jørgen; Wedzicha, Jadwiga A; Patel, Anant; Hurst, John R

2015-09-01

To determine factors, overall and by sex, associated with self-reported gastro-oesophageal reflux disease (GORD) in chronic obstructive pulmonary disease (COPD) patients, and to evaluate relationships between GORD, its modification by acid suppression medications (Proton Pump Inhibitors [PPI]/histamine-2 receptor antagonists [H2RA]) and exacerbations of COPD and mortality. Logistic regression was used to determine factors associated with GORD; Cox proportional hazards models were used to calculate adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) for GORD and risk of exacerbation and death. Among 2135 COPD patients from the ECLIPSE cohort, 547 patients self-reported GORD, with female preponderance; 237 were taking PPI/H2RA. Risk factors for GORD did not differ by sex. When compared to patients who did not report GORD or use of PPI/H2RA, patients with GORD and taking PPI/H2RA had a significantly increased risk of exacerbation (HR = 1.58, 95%CI = 1.35-1.86); risk was also increased for patients reporting GORD only or PPI/H2RA use only (HR = 1.21 [1.04-1.40] and 1.33 [1.08-1.65], respectively). Similar findings were observed for risk of hospitalised exacerbation. GORD was not associated with mortality. GORD in COPD patients is highly prevalent, and risk factors did not differ by sex. Use of PPI/H2RA and self-reported GORD were associated with increased risk of moderate-to-severe and hospitalised exacerbations. Copyright © 2015 Elsevier Ltd. All rights reserved.

Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding

PubMed Central

Cannistraci, Carlo Vittorio; Alanis-Lobato, Gregorio; Ravasi, Timothy

2013-01-01

Motivation: Most functions within the cell emerge thanks to protein–protein interactions (PPIs), yet experimental determination of PPIs is both expensive and time-consuming. PPI networks present significant levels of noise and incompleteness. Predicting interactions using only PPI-network topology (topological prediction) is difficult but essential when prior biological knowledge is absent or unreliable. Methods: Network embedding emphasizes the relations between network proteins embedded in a low-dimensional space, in which protein pairs that are closer to each other represent good candidate interactions. To achieve network denoising, which boosts prediction performance, we first applied minimum curvilinear embedding (MCE), and then adopted shortest path (SP) in the reduced space to assign likelihood scores to candidate interactions. Furthermore, we introduce (i) a new valid variation of MCE, named non-centred MCE (ncMCE); (ii) two automatic strategies for selecting the appropriate embedding dimension; and (iii) two new randomized procedures for evaluating predictions. Results: We compared our method against several unsupervised and supervisedly tuned embedding approaches and node neighbourhood techniques. Despite its computational simplicity, ncMCE-SP was the overall leader, outperforming the current methods in topological link prediction. Conclusion: Minimum curvilinearity is a valuable non-linear framework that we successfully applied to the embedding of protein networks for the unsupervised prediction of novel PPIs. The rationale for our approach is that biological and evolutionary information is imprinted in the non-linear patterns hidden behind the protein network topology, and can be exploited for predicting new protein links. The predicted PPIs represent good candidates for testing in high-throughput experiments or for exploitation in systems biology tools such as those used for network-based inference and prediction of disease-related functional modules. Availability: https://sites.google.com/site/carlovittoriocannistraci/home Contact: kalokagathos.agon@gmail.com or timothy.ravasi@kaust.edu.sa Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23812985

Polypyrrole-based nanotheranostics for activatable fluorescence imaging and chemo/photothermal dual therapy of triple-negative breast cancer

NASA Astrophysics Data System (ADS)

Park, Dongjin; Ahn, Kyung-Ohk; Jeong, Kyung-Chae; Choi, Yongdoo

2016-05-01

Here, we fabricated polypyrrole nanoparticles (PPys) (termed HA10-PPy, HA20-PPy, and HA40-PPy) doped with different average molecular weight hyaluronic acids (HAs) (10, 20, and 40 kDa, respectively), and evaluated the effect of molecular weight of doped HA on photothermal induction, fluorescence quenching, and drug loading efficiencies. Doxorubicin-loaded HA-doped PPys (DOX@HA-PPys) could be used for imaging and therapy of triple-negative breast cancer (TNBC). Fluorescence turn-on, stimuli-responsive drug release, and photo-induced heating of DOX@HA-PPys enabled not only activatable fluorescence imaging but also subsequent chemo/photothermal dual therapy for TNBC. In particular, we illustrated the potential usefulness of the photothermal effect of the nanoparticles for overcoming chemoresistance in TNBC.

Detection of membrane protein-protein interaction in planta based on dual-intein-coupled tripartite split-GFP association.

PubMed

Liu, Tzu-Yin; Chou, Wen-Chun; Chen, Wei-Yuan; Chu, Ching-Yi; Dai, Chen-Yi; Wu, Pei-Yu

2018-05-01

Despite the great interest in identifying protein-protein interactions (PPIs) in biological systems, only a few attempts have been made at large-scale PPI screening in planta. Unlike biochemical assays, bimolecular fluorescence complementation allows visualization of transient and weak PPIs in vivo at subcellular resolution. However, when the non-fluorescent fragments are highly expressed, spontaneous and irreversible self-assembly of the split halves can easily generate false positives. The recently developed tripartite split-GFP system was shown to be a reliable PPI reporter in mammalian and yeast cells. In this study, we adapted this methodology, in combination with the β-estradiol-inducible expression cassette, for the detection of membrane PPIs in planta. Using a transient expression assay by agroinfiltration of Nicotiana benthamiana leaves, we demonstrate the utility of the tripartite split-GFP association in plant cells and affirm that the tripartite split-GFP system yields no spurious background signal even with abundant fusion proteins readily accessible to the compartments of interaction. By validating a few of the Arabidopsis PPIs, including the membrane PPIs implicated in phosphate homeostasis, we proved the fidelity of this assay for detection of PPIs in various cellular compartments in planta. Moreover, the technique combining the tripartite split-GFP association and dual-intein-mediated cleavage of polyprotein precursor is feasible in stably transformed Arabidopsis plants. Our results provide a proof-of-concept implementation of the tripartite split-GFP system as a potential tool for membrane PPI screens in planta. © 2018 The Authors The Plant Journal © 2018 John Wiley & Sons Ltd.

Target gene screening and evaluation of prognostic values in non-small cell lung cancers by bioinformatics analysis.

PubMed

Piao, Junjie; Sun, Jie; Yang, Yang; Jin, Tiefeng; Chen, Liyan; Lin, Zhenhua

2018-03-20

Non-small cell lung cancer (NSCLC) is the major leading cause of cancer-related deaths worldwide. This study aims to explore molecular mechanism of NSCLC. Microarray dataset was obtained from the Gene Expression Omnibus (GEO) database, and analyzed by using GEO2R. Functional and pathway enrichment analysis were performed based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Then, STRING, Cytoscape and MCODE were applied to construct the Protein-protein interaction (PPI) network and screen hub genes. Following, overall survival (OS) analysis of hub genes was performed by using the Kaplan-Meier plotter online tool. Moreover, miRecords was also applied to predict the targets of the differentially expressed microRNAs (DEMs). A total of 228 DEGs were identified, and they were mainly enriched in the terms of cell adhesion molecules, leukocyte transendothelial migration and ECM-receptor interaction. A PPI network was constructed, and 16 hub genes were identified, including TEK, ANGPT1, MMP9, VWF, CDH5, EDN1, ESAM, CCNE1, CDC45, PRC1, CCNB2, AURKA, MELK, CDC20, TOP2A and PTTG1. Among the genes, expressions of 14 hub genes were associated with prognosis of NSCLC patients. Additionally, a total of 11 DEMs were also identified. Our results provide some potential underlying biomarkers for NSCLC. Further studies are required to elucidate the pathogenesis of NSCLC. Copyright © 2018 Elsevier B.V. All rights reserved.

A little more conversation please? Qualitative study of researchers' and patients' interview accounts of training for patient and public involvement in clinical trials.

PubMed

Dudley, Louise; Gamble, Carrol; Allam, Alison; Bell, Philip; Buck, Deborah; Goodare, Heather; Hanley, Bec; Preston, Jennifer; Walker, Alison; Williamson, Paula; Young, Bridget

2015-04-27

Training in patient and public involvement (PPI) is recommended, yet little is known about what training is needed. We explored researchers' and PPI contributors' accounts of PPI activity and training to inform the design of PPI training for both parties. We used semi-structured qualitative interviews with researchers (chief investigators and trial managers) and PPI contributors, accessed through a cohort of clinical trials, which had been funded between 2006 and 2010. An analysis of transcripts of audio-recorded interviews drew on the constant comparative method. We interviewed 31 researchers and 17 PPI contributors from 28 trials. Most researchers could see some value in PPI training for researchers, although just under half had received such training themselves, and some had concerns about the purpose and evidence base for PPI training. PPI contributors were evenly split in their perceptions of whether researchers needed training in PPI. Few PPI contributors had themselves received training for their roles. Many informants across all groups felt that training PPI contributors was unnecessary because they already possessed the skills needed. Informants were also concerned that training would professionalise PPI contributors, limiting their ability to provide an authentic patient perspective. However, informants welcomed informal induction 'conversations' to help contributors understand their roles and support them in voicing their opinions. Informants believed that PPI contributors should be confident, motivated, intelligent, focussed on helping others and have relevant experience. Researchers looked for these qualities when selecting contributors, and spoke of how finding 'the right' contributor was more important than accessing 'the right' training. While informants were broadly receptive to PPI training for researchers, they expressed considerable reluctance to training PPI contributors. Providers of training will need to address these reservations. Our findings point to the importance of reconsidering how training is conceptualised, designed and promoted and of providing flexible, learning opportunities in ways that flow from researchers' and contributors' needs and preferences. We also identify some areas of training content and the need for further consideration to be given to the selection of PPI contributors and models for implementing PPI to ensure clinical trials benefit from a diversity of patient perspectives.

Potentiometric glucose biosensor based on core-shell Fe3O4-enzyme-polypyrrole nanoparticles.

PubMed

Yang, Zhengpeng; Zhang, Chunjing; Zhang, Jianxin; Bai, Wanbei

2014-01-15

Core-shell Fe3O4-enzyme-polypyrrole (Ppy) nanoparticles with excellent magnetism and conductivity were successfully prepared via the surface modification and enzyme self-encapsulation within Ppy. A novel potentiometric glucose biosensor has been constructed by effectively attaching the proposed Fe3O4-enzyme-Ppy nanoparticles to the surface of the magnetic glassy carbon electrode (MGCE). The optimum biosensing conditions could be provided with polymerization time of pyrrole for 6h and 0.42 mg immobilization amount of Fe3O4-enzyme-Ppy nanoparticles on MGCE. The performance of the developed glucose biosensor was evaluated and the results indicated that a sensitive glucose biosensor could be fabricated. The obtained glucose biosensor presents shorter response time (6 s), wider linear range (0.5 μM to 34 mM), lower limit of detection (LOD, 0.3 μM), high-selectivity monitoring of glucose and good stability (with about 98.1% of the initial response signal retained after 20 days). The analytical application of the glucose biosensor confirms the feasibility of glucose detection in serum sample. © 2013 Elsevier B.V. All rights reserved.

Electromagnetic interference attenuation and shielding effect of quaternary Epoxy-PPy/Fe3O4-ZnO nanocomposite as a broad band microwave-absorber

NASA Astrophysics Data System (ADS)

Olad, Ali; Shakoori, Sahar

2018-07-01

An increase in the electromagnetic wave pollution generated from wireless telecommunication devices has devoted to a great request for exploiting microwave absorbing materials for themselves. The combination of inherently conducting polymers such as polypyrrole (PPy) with metal oxides has led to design ideal microwave absorbing materials which benefit both advantage effects of ICPs and metal oxide nanoparticles. Herein, the quaternary nanocomposite of Epoxy-PPy/Fe3O4-ZnO was prepared and tested for the absorption of X-band microwaves. Simultaneous application of metal oxides and conducting polypyrrole in the epoxy matrix was evaluated in order to increase the absorption intensity and broadness of microwaves in X-band region. The morphology, microstructure, and phase structure of Fe3O4, ZnO, and PPy, as well as quaternary nanocomposite were characterized and studied using FTIR, XRD, FESEM and TEM techniques. The presence of nanoparticles in the quaternary nanocomposite was confirmed by EDS. The magnetization of iron oxide was studied by VSM. The synergetic effect of iron oxide and zinc oxide nanoparticles in different weight ratios (Fe3O4/ZnO) on the electromagnetic wave absorption was evaluated. The electromagnetic parameters have been evaluated by the vector network analyzer in the frequency range of 8.2-12.4 GHz which is named as X-band region and is adequate for radar applications. The electromagnetic wave absorbing outcomes indicated that Epoxy-PPy/Fe3O4-ZnO quaternary nanocomposite has wide absorption area and high attenuation, which is believed to be due to dielectric loss properties related to the polypyrrole, magnetic loss factor of Fe3O4, and synergetic effects of components. The maximum reflection loss reached to -32.53 dB at 9.96 GHz with a nanocomposite thickness of 2 mm which is dedicated to the Epoxy-PPy/Fe3O4-ZnO with iron oxide to zinc oxide ratio of 2:1. The absorption bandwidth with the reflection loss lower than -10 dB (90% attenuation) was up to 4.2 GHz that covering a frequency range of 8.2-12.4 GHz. Results showed that absorber having %15 (w/w) polypyrrole/epoxy resin in Epoxy-PPy/Fe3O4-ZnO nanocomposite with iron oxide to zinc oxide ratio of 2:1 displays the best reflection loss properties. The loss curves illustrated the values of dielectric loss tangent and magnetic loss tangent of prepared nanocomposites which are in the range of 0.25-0.7 and -0.08 to 0.09 respectively. Therefore, microwave absorption mechanism is probably attributed to dielectric loss.

Computational Framework for Prediction of Peptide Sequences That May Mediate Multiple Protein Interactions in Cancer-Associated Hub Proteins.

PubMed

Sarkar, Debasree; Patra, Piya; Ghosh, Abhirupa; Saha, Sudipto

2016-01-01

A considerable proportion of protein-protein interactions (PPIs) in the cell are estimated to be mediated by very short peptide segments that approximately conform to specific sequence patterns known as linear motifs (LMs), often present in the disordered regions in the eukaryotic proteins. These peptides have been found to interact with low affinity and are able bind to multiple interactors, thus playing an important role in the PPI networks involving date hubs. In this work, PPI data and de novo motif identification based method (MEME) were used to identify such peptides in three cancer-associated hub proteins-MYC, APC and MDM2. The peptides corresponding to the significant LMs identified for each hub protein were aligned, the overlapping regions across these peptides being termed as overlapping linear peptides (OLPs). These OLPs were thus predicted to be responsible for multiple PPIs of the corresponding hub proteins and a scoring system was developed to rank them. We predicted six OLPs in MYC and five OLPs in MDM2 that scored higher than OLP predictions from randomly generated protein sets. Two OLP sequences from the C-terminal of MYC were predicted to bind with FBXW7, component of an E3 ubiquitin-protein ligase complex involved in proteasomal degradation of MYC. Similarly, we identified peptides in the C-terminal of MDM2 interacting with FKBP3, which has a specific role in auto-ubiquitinylation of MDM2. The peptide sequences predicted in MYC and MDM2 look promising for designing orthosteric inhibitors against possible disease-associated PPIs. Since these OLPs can interact with other proteins as well, these inhibitors should be specific to the targeted interactor to prevent undesired side-effects. This computational framework has been designed to predict and rank the peptide regions that may mediate multiple PPIs and can be applied to other disease-associated date hub proteins for prediction of novel therapeutic targets of small molecule PPI modulators.

Proton Pump Inhibitor-Responsive Oesophageal Eosinophilia: An Entity Challenging Current Diagnostic Criteria for Eosinophilic Oesophagitis

PubMed Central

Molina-Infante, Javier; Bredenoord, Albert J.; Cheng, Edaire; Dellon, Evan S.; Furuta, Glenn T.; Gupta, Sandeep K.; Hirano, Ikuo; Katzka, David A.; Moawad, Fouad J.; Rothenberg, Marc E.; Schoepfer, Alain; Spechler, Stuart; Wen, Ting; Straumann, Alex; Lucendo, Alfredo J.

2016-01-01

Consensus diagnostic recommendations to distinguish gastro-oesophageal reflux disease (GORD) from eosinophilic oesophagitis (EoE) by response to a trial of proton pump inhibitors (PPI) unexpectedly uncovered an entity called “PPI-responsive oesophageal eosinophilia” (PPI-REE). PPI-REE refers to patients with clinical and histologic features of EoE that remit with PPI treatment. Recent and evolving evidence, mostly from adults, shows that PPI-REE and EoE patients at baseline are clinically, endoscopically and histologically indistinguishable, and have significant overlap in terms of features of Th2 immune-mediated inflammation and gene expression. Furthermore, PPI therapy restores oesophageal mucosal integrity, reduces Th2 inflammation and reverses the abnormal gene expression signature in PPI-REE patients, similar to the effects of topical steroids in EoE patients. Additionally, recent series have reported that EoE patients responsive to diet/topical steroids may also achieve remission on PPI therapy. This mounting evidence supports the concept that PPI-REE represents a continuum of the same immunologic mechanisms that underlie EoE. Accordingly, it seems counterintuitive to differentiate PPI-REE from EoE based on a differential response to PPI therapy when their phenotypic, molecular, mechanistic, and therapeutic features cannot be reliably distinguished. For patients with symptoms and histologic features of EoE, it is reasonable to consider PPI therapy not as a diagnostic test, but as a therapeutic agent. Due to its safety profile, ease of administration and high response rates (up to 50%), PPI can be considered a first-line treatment, before diet and topical steroids. The reasons why some EoE patients respond to PPI, while others do not, remain to be elucidated. PMID:26685124

Preparation of Different Substitued Polypyridine Ligands, Ruthenium(II)-Bridged Complexes and Spectoscopıc Studies.

PubMed

Obali, Aslihan Yilmaz; Ucan, Halil Ismet

2016-09-01

Novel different substitued polypyridine ligands 4-((4-(1H-imidazo[4,5-f][1,10]phenanthroline-2-yl)phenoxy)methyl)benzaldehyde (BA-PPY), (E)-N-(4-((4-(1H-imidazo[4,5-f][1,10]phenanthroline-2-yl)phenoxy)methyl)benzylidene)-pyrene-4-amine (PR-PPY), (E)-N-(4-((4-(1H-imidazo[4,5-f][1,10] phenanthroline-2-yl)phenoxy)methyl)benzylidene)-1,10-phenanthroline-5amine (FN-PPY), 2-(4-(bromomethyl)phenyl)-1H-imidazo[4,5-f][1,10] phenanthroline (BR-PPY), 2-(4-(azidomethyl)phenyl)-1H-imidazo[4,5-f][1,10]phenanthroline (N3-PPY) and triazole containing polypyridine ligand 3,4-bis[(4-(metoxy)-1,2,3-triazole)1-methylphenyl)-1H-imidazo[4,5-f][1,10]phenanthroline)] benzaldehyde (BA-DIPPY) and Ruthenium(II) complexes were synthesized and characterized. Their photopysical properties were investigated. The complexes RuP(PR-PPY), RuB(PR-PPY, RuP(FN-PPY) and RuB(FN-PPY) exhibited a broad absorption bands at 485, 475, 476, and 453 nm, respectively, assignable to the spin-allowed MLCT (dπ-π*) transition. The emission maxima of the pyrene-appended polypyridine ligand PR-PPY was observed at λems = 616 nm and the phenanthroline-appended polypyridine ligand FN-PPY was observed at λems = 668 nm. And the emission maxima of the complexes RuP(PR-PPY), RuB(PR-PPY), RuP(FN-PPY) and RuB(FN-PPY) were observed at λems = 646, 646, 685 and 685 nm, respectively. As seen in fluorescence spectra, the fluorescence intensities of the ligands are higher than their metal complexes. This is because of quenching effect of Ruthenium(II) metal on chromophore groups.

Same-session dorsal vein ligation and testing by intracavernous injection prior to penile prosthesis implantation (DVL-ICI-PPI).

PubMed

Shaeer, Osama; Shaeer, Kamal

2014-09-01

Complications of penile prosthesis implantation (PPI) are rare, nevertheless can be grave. In cases with veno-occlusive dysfunction (VOD), alternative surgical techniques such as dorsal vein ligation (DVL) are controversial. Some patients may opt for trial at DVL to avoid the possible complications of PPI. However, this may be associated with disappointment if DVL fails and another procedure is required. The aim if this study is to evaluate the results of a combined approach involving DVL, same-session testing by intracavernous injection (ICI) of prostaglandin E1 (PGE1), and immediate implantation of a penile prosthesis (PPI) in case of poor response to DVL. Long-term erectile function in cases with favorable intraoperative response to DVL. Twenty-six patients with refractory VOD were operated upon. Through a peno-pubic incision, DVL was performed, followed by ICI of 20 µg PGE1 in two divided doses, 10 µg each, 15 minutes apart. Group 1 exhibited full rigidity in response to the first dose. Group 2 exhibited full rigidity in response to the second dose. PPI was not performed for either. Group 3 exhibited suboptimal response to both doses, and PPI was performed through the same incision. Patients were followed up from 24 to 48 months using International Index of Erectile Function-5 scoring. For Group 1 (n = 8), six patients experienced normal erectile function following DVL throughout the whole follow-up period of 48 months (23.1% of all patients), and two patients relapsed. Group 2 (n = 6) (23.1%) reported normal erectile function for an average of 6 months, then relapsed. Group 3 (n = 12) had a penile prosthesis implanted in the same setting. Combined DVL-ICI-PPI can spare around 23.1% of young patients with VOD from PPI, at no additional risk. Full response to 10 µg PGE1 at intraoperative testing carries good prognosis to DVL on the long run. Investigation of a larger number of patients is necessary before reaching a final conclusion. © 2014 International Society for Sexual Medicine.

A novel feature extraction scheme with ensemble coding for protein-protein interaction prediction.

PubMed

Du, Xiuquan; Cheng, Jiaxing; Zheng, Tingting; Duan, Zheng; Qian, Fulan

2014-07-18

Protein-protein interactions (PPIs) play key roles in most cellular processes, such as cell metabolism, immune response, endocrine function, DNA replication, and transcription regulation. PPI prediction is one of the most challenging problems in functional genomics. Although PPI data have been increasing because of the development of high-throughput technologies and computational methods, many problems are still far from being solved. In this study, a novel predictor was designed by using the Random Forest (RF) algorithm with the ensemble coding (EC) method. To reduce computational time, a feature selection method (DX) was adopted to rank the features and search the optimal feature combination. The DXEC method integrates many features and physicochemical/biochemical properties to predict PPIs. On the Gold Yeast dataset, the DXEC method achieves 67.2% overall precision, 80.74% recall, and 70.67% accuracy. On the Silver Yeast dataset, the DXEC method achieves 76.93% precision, 77.98% recall, and 77.27% accuracy. On the human dataset, the prediction accuracy reaches 80% for the DXEC-RF method. We extended the experiment to a bigger and more realistic dataset that maintains 50% recall on the Yeast All dataset and 80% recall on the Human All dataset. These results show that the DXEC method is suitable for performing PPI prediction. The prediction service of the DXEC-RF classifier is available at http://ailab.ahu.edu.cn:8087/ DXECPPI/index.jsp.

Predicting Functions of Proteins in Mouse Based on Weighted Protein-Protein Interaction Network and Protein Hybrid Properties

PubMed Central

Shi, Xiaohe; Lu, Wen-Cong; Cai, Yu-Dong; Chou, Kuo-Chen

2011-01-01

Background With the huge amount of uncharacterized protein sequences generated in the post-genomic age, it is highly desirable to develop effective computational methods for quickly and accurately predicting their functions. The information thus obtained would be very useful for both basic research and drug development in a timely manner. Methodology/Principal Findings Although many efforts have been made in this regard, most of them were based on either sequence similarity or protein-protein interaction (PPI) information. However, the former often fails to work if a query protein has no or very little sequence similarity to any function-known proteins, while the latter had similar problem if the relevant PPI information is not available. In view of this, a new approach is proposed by hybridizing the PPI information and the biochemical/physicochemical features of protein sequences. The overall first-order success rates by the new predictor for the functions of mouse proteins on training set and test set were 69.1% and 70.2%, respectively, and the success rate covered by the results of the top-4 order from a total of 24 orders was 65.2%. Conclusions/Significance The results indicate that the new approach is quite promising that may open a new avenue or direction for addressing the difficult and complicated problem. PMID:21283518

What Difference Does Patient and Public Involvement Make and What Are Its Pathways to Impact? Qualitative Study of Patients and Researchers from a Cohort of Randomised Clinical Trials

PubMed Central

Dudley, Louise; Gamble, Carrol; Preston, Jennifer; Buck, Deborah; Hanley, Bec; Williamson, Paula; Young, Bridget

2015-01-01

Background Patient and public involvement (PPI) is advocated in clinical trials yet evidence on how to optimise its impact is limited. We explored researchers' and PPI contributors' accounts of the impact of PPI within trials and factors likely to influence its impact. Methods Semi-structured qualitative interviews with researchers and PPI contributors accessed through a cohort of randomised clinical trials. Analysis of transcripts of audio-recorded interviews was informed by the principles of the constant comparative method, elements of content analysis and informant triangulation. Results We interviewed 21 chief investigators, 10 trial managers and 17 PPI contributors from 28 trials. The accounts of informants within the same trials were largely in agreement. Over half the informants indicted PPI had made a difference within a trial, through contributions that influenced either an aspect of a trial, or how researchers thought about a trial. According to informants, the opportunity for PPI to make a difference was influenced by two main factors: whether chief investigators had goals and plans for PPI and the quality of the relationship between the research team and the PPI contributors. Early involvement of PPI contributors and including them in responsive (e.g. advisory groups) and managerial (e.g. trial management groups) roles were more likely to achieve impact compared to late involvement and oversight roles (e.g. trial steering committees). Conclusion Those seeking to enhance PPI in trials should develop goals for PPI at an early stage that fits the needs of the trial, plan PPI implementation in accordance with these goals, invest in developing good relationships between PPI contributors and researchers, and favour responsive and managerial roles for contributors in preference to oversight-only roles. These features could be used by research funders in judging PPI in trial grant applications and to inform policies to optimise PPI within trials. PMID:26053063

Proton pump inhibitor-responsive esophageal eosinophilia: a historical perspective on a novel and evolving entity.

PubMed

Molina-Infante, Javier; Katzka, David A; Dellon, Evan S

2015-01-01

Eosinophilic esophagitis (EoE) is an emerging chronic esophageal disease, first described in 1993, with a steadily increasing incidence and prevalence in western countries. Over the 80's and early 90's, dense esophageal eosinophilia was mostly associated gastroesophageal reflux disease (GERD). For the next 15 years, EoE and GERD were rigidly considered separate entities: Esophageal eosinophilia with pathological acid exposure on pH monitoring or response to proton pump inhibitor (PPI) therapy was GERD, whereas normal pH monitoring or absence of response to PPIs was EoE. Updated guidelines in 2011 described a novel phenotype, proton pump inhibitor-responsive esophageal eosinophilia (PPI-REE), referring to patients who appear to have EoE clinically, but who achieve complete remission after PPI therapy. Currently, PPI-REE must be formally excluded before diagnosing EoE, since 30-40% of patients with suspected EoE are eventually diagnosed with PPI-REE.Interestingly, PPI-REE and EoE remain undistinguishable based on clinical, endoscopic, and histological findings, pH monitoring, and measurement of tissue markers and cytokines related to eosinophilic inflammation.This review article aims to revisit the relatively novel concept of PPI-REE from a historical perspective, given the strong belief that only GERD, as an acid peptic disorder, could respond to the acid suppressing ability of PPI therapy, is becoming outdated. Evolving evidence suggests that PPI-REE is genetically and phenotypically undistinguishable from EoE and PPI therapy alone can almost completely reverse allergic inflammation. As such, PPI-REE might constitute a subphenotype of EoE and PPI therapy may be the first therapeutic step and diet/ steroids may represent step up therapy. Possibly, the term PPI-REE will be soon replaced by PPI-responsive EoE. The mechanism as to why some patients respond to PPI therapy (PPI-REE) while others do not (EoE), remains to be elucidated.

Interaction of reelin and stress on immobility in the forced swim test but not dopamine-mediated locomotor hyperactivity or prepulse inhibition disruption: Relevance to psychotic and mood disorders.

PubMed

Notaras, Michael J; Vivian, Billie; Wilson, Carey; van den Buuse, Maarten

2017-07-13

Psychotic disorders, such as schizophrenia, as well as some mood disorders, such as bipolar disorder, have been suggested to share common biological risk factors. One such factor is reelin, a large extracellular matrix glycoprotein that regulates neuronal migration during development as well as numerous activity-dependent processes in the adult brain. The current study sought to evaluate whether a history of stress exposure interacts with endogenous reelin levels to modify behavioural endophenotypes of relevance to psychotic and mood disorders. Heterozygous Reeler Mice (HRM) and wildtype (WT) controls were treated with 50mg/L of corticosterone (CORT) in their drinking water from 6 to 9weeks of age, before undergoing behavioural testing in adulthood. We assessed methamphetamine-induced locomotor hyperactivity, prepulse inhibition (PPI) of acoustic startle, short-term spatial memory in the Y-maze, and depression-like behaviour in the Forced-Swim Test (FST). HRM genotype or CORT treatment did not affect methamphetamine-induced locomotor hyperactivity, a model of psychosis-like behaviour. At baseline, HRM showed decreased PPI at the commonly used 100msec interstimulus interval (ISI), but not at the 30msec ISI or following challenge with apomorphine. A history of CORT exposure potentiated immobility in the FST amongst HRM, but not WT mice. In the Y-maze, chronic CORT treatment decreased novel arm preference amongst HRM, reflecting reduced short-term spatial memory. These data confirm a significant role of endogenous reelin levels on stress-related behaviour, supporting a possible role in both bipolar disorder and schizophrenia. However, an interaction of reelin deficiency with dopaminergic regulation of psychosis-like behaviour remains unclear. Copyright © 2017 Elsevier B.V. All rights reserved.

Cheminformatics-aided discovery of small-molecule Protein-Protein Interaction (PPI) dual inhibitors of Tumor Necrosis Factor (TNF) and Receptor Activator of NF-κB Ligand (RANKL).

PubMed

Melagraki, Georgia; Ntougkos, Evangelos; Rinotas, Vagelis; Papaneophytou, Christos; Leonis, Georgios; Mavromoustakos, Thomas; Kontopidis, George; Douni, Eleni; Afantitis, Antreas; Kollias, George

2017-04-01

We present an in silico drug discovery pipeline developed and applied for the identification and virtual screening of small-molecule Protein-Protein Interaction (PPI) compounds that act as dual inhibitors of TNF and RANKL through the trimerization interface. The cheminformatics part of the pipeline was developed by combining structure-based with ligand-based modeling using the largest available set of known TNF inhibitors in the literature (2481 small molecules). To facilitate virtual screening, the consensus predictive model was made freely available at: http://enalos.insilicotox.com/TNFPubChem/. We thus generated a priority list of nine small molecules as candidates for direct TNF function inhibition. In vitro evaluation of these compounds led to the selection of two small molecules that act as potent direct inhibitors of TNF function, with IC50 values comparable to those of a previously-described direct inhibitor (SPD304), but with significantly reduced toxicity. These molecules were also identified as RANKL inhibitors and validated in vitro with respect to this second functionality. Direct binding of the two compounds was confirmed both for TNF and RANKL, as well as their ability to inhibit the biologically-active trimer forms. Molecular dynamics calculations were also carried out for the two small molecules in each protein to offer additional insight into the interactions that govern TNF and RANKL complex formation. To our knowledge, these compounds, namely T8 and T23, constitute the second and third published examples of dual small-molecule direct function inhibitors of TNF and RANKL, and could serve as lead compounds for the development of novel treatments for inflammatory and autoimmune diseases.

Protein-protein interaction network of gene expression in the hydrocortisone-treated keloid.

PubMed

Chen, Rui; Zhang, Zhiliang; Xue, Zhujia; Wang, Lin; Fu, Mingang; Lu, Yi; Bai, Ling; Zhang, Ping; Fan, Zhihong

2015-01-01

In order to explore the molecular mechanism of hydrocortisone in keloid tissue, the gene expression profiles of keloid samples treated with hydrocortisone were subjected to bioinformatics analysis. Firstly, the gene expression profiles (GSE7890) of five samples of keloid treated with hydrocortisone and five untreated keloid samples were downloaded from the Gene Expression Omnibus (GEO) database. Secondly, data were preprocessed using packages in R language and differentially expressed genes (DEGs) were screened using a significance analysis of microarrays (SAM) protocol. Thirdly, the DEGs were subjected to gene ontology (GO) function and KEGG pathway enrichment analysis. Finally, the interactions of DEGs in samples of keloid treated with hydrocortisone were explored in a human protein-protein interaction (PPI) network, and sub-modules of the DEGs interaction network were analyzed using Cytoscape software. Based on the analysis, 572 DEGs in the hydrocortisone-treated samples were screened; most of these were involved in the signal transduction and cell cycle. Furthermore, three critical genes in the module, including COL1A1, NID1, and PRELP, were screened in the PPI network analysis. These findings enhance understanding of the pathogenesis of the keloid and provide references for keloid therapy. © 2015 The International Society of Dermatology.

A novel non-contact radar sensor for affective and interactive analysis.

PubMed

Lin, Hong-Dun; Lee, Yen-Shien; Shih, Hsiang-Lan; Chuang, Bor-Nian

2013-01-01

Currently, many physiological signal sensing techniques have been applied for affective analysis in Human-Computer Interaction applications. Most known maturely developed sensing methods (EEG/ECG/EMG/Temperature/BP etc. al.) replied on contact way to obtain desired physiological information for further data analysis. However, those methods might cause some inconvenient and uncomfortable problems, and not easy to be used for affective analysis in interactive performing. To improve this issue, a novel technology based on low power radar technology (Nanosecond Pulse Near-field Sensing, NPNS) with 300 MHz radio-frequency was proposed to detect humans' pulse signal by the non-contact way for heartbeat signal extraction. In this paper, a modified nonlinear HRV calculated algorithm was also developed and applied on analyzing affective status using extracted Peak-to-Peak Interval (PPI) information from detected pulse signal. The proposed new affective analysis method is designed to continuously collect the humans' physiological signal, and validated in a preliminary experiment with sound, light and motion interactive performance. As a result, the mean bias between PPI (from NPNS) and RRI (from ECG) shows less than 1ms, and the correlation is over than 0.88, respectively.

Long-term kidney outcomes among users of proton pump inhibitors without intervening acute kidney injury.

PubMed

Xie, Yan; Bowe, Benjamin; Li, Tingting; Xian, Hong; Yan, Yan; Al-Aly, Ziyad

2017-06-01

Proton pump inhibitor (PPI) use is associated with an increased risk of acute kidney injury (AKI), incident chronic kidney disease (CKD), and progression to end-stage renal disease (ESRD). PPI-associated CKD is presumed to be mediated by intervening AKI. However, whether PPI use is associated with an increased risk of chronic renal outcomes in the absence of intervening AKI is unknown. To evaluate this we used the Department of Veterans Affairs national databases to build a cohort of 144,032 incident users of acid suppression therapy that included 125,596 PPI and 18,436 Histamine H2 receptor antagonist (H2 blockers) consumers. Over 5 years of follow-up in survival models, cohort participants were censored at the time of AKI occurrence. Compared with incident users of H2 blockers, incident users of PPIs had an increased risk of an estimated glomerular filtration rate (eGFR) under 60 ml/min/1.73m 2 (hazard ratio 1.19; 95% confidence interval 1.15-1.24), incident CKD (1.26; 1.20-1.33), eGFR decline over 30% (1.22; 1.16-1.28), and ESRD or eGFR decline over 50% (1.30; 1.15-1.48). Results were consistent in models that excluded participants with AKI either before chronic renal outcomes, during the time in the cohort, or before cohort entry. The proportion of PPI effect mediated by AKI was 44.7%, 45.47%, 46.00%, and 46.72% for incident eGFR under 60 ml/min/1.73m 2 , incident CKD, eGFR decline over 30%, and ESRD or over 50% decline in eGFR, respectively. Thus, PPI use is associated with increased risk of chronic renal outcomes in the absence of intervening AKI. Hence, reliance on antecedent AKI as warning sign to guard against the risk of CKD among PPI users is not sufficient as a sole mitigation strategy. Published by Elsevier Inc.

Randomized controlled trial of transoral incisionless fundoplication vs. proton pump inhibitors for treatment of gastroesophageal reflux disease.

PubMed

Witteman, Bart P L; Conchillo, Jose M; Rinsma, Nicolaas F; Betzel, Bark; Peeters, Andrea; Koek, Ger H; Stassen, Laurents P S; Bouvy, Nicole D

2015-04-01

Transoral incisionless fundoplication (TIF) was developed in an attempt to create a minimally invasive endoscopic procedure that mimics antireflux surgery. The objective of this trial was to evaluate effectiveness of TIF compared with proton pump inhibition in a population consisting of gastroesophageal reflux disease (GERD) patients controlled with proton pump inhibitors (PPIs) who opted for an endoscopic intervention over lifelong drug dependence. Patients with chronic GERD were randomized (2:1) for TIF or continuation of PPI therapy. American Society of Anesthesiologists >2, body mass index >35 kg/m(2), hiatal hernia >2 cm, and esophageal motility disorders were exclusion criteria. Primary outcome measure was GERD-related quality of life. Secondary outcome measures were esophageal acid exposure, number of reflux episodes, PPI usage, appearance of the gastroesophageal valve, and healing of reflux esophagitis. Crossover for the PPI group was allowed after 6 months. A total of 60 patients (TIF n=40, PPI n=20, mean body mass index 26 kg/m(2), 37 male) were included. At 6 months, GERD symptoms were more improved in the TIF group compared with the PPI group (P<0.001), with a similar improvement of distal esophageal acid exposure (P=0.228) compared with baseline. The pH normalization for TIF group and PPI group was 50% and 63%, respectively. All patients allocated for PPI treatment opted for crossover. At 12 months, quality of life remained improved after TIF compared with baseline (P<0.05), but no improvement in esophageal acid exposure compared with baseline was found (P=0.171) and normalization of pH was accomplished in only 29% in conjunction with deteriorated valve appearances at endoscopy and resumption of PPIs in 61%. Although TIF resulted in an improved GERD-related quality of life and produced a short-term improvement of the antireflux barrier in a selected group of GERD patients, no long-term objective reflux control was achieved.

High-Capacity Conductive Nanocellulose Paper Sheets for Electrochemically Controlled Extraction of DNA Oligomers

PubMed Central

Razaq, Aamir; Nyström, Gustav; Strømme, Maria; Mihranyan, Albert; Nyholm, Leif

2011-01-01

Highly porous polypyrrole (PPy)-nanocellulose paper sheets have been evaluated as inexpensive and disposable electrochemically controlled three-dimensional solid phase extraction materials. The composites, which had a total anion exchange capacity of about 1.1 mol kg−1, were used for extraction and subsequent release of negatively charged fluorophore tagged DNA oligomers via galvanostatic oxidation and reduction of a 30–50 nm conformal PPy layer on the cellulose substrate. The ion exchange capacity, which was, at least, two orders of magnitude higher than those previously reached in electrochemically controlled extraction, originated from the high surface area (i.e. 80 m2 g−1) of the porous composites and the thin PPy layer which ensured excellent access to the ion exchange material. This enabled the extractions to be carried out faster and with better control of the PPy charge than with previously employed approaches. Experiments in equimolar mixtures of (dT)6, (dT)20, and (dT)40 DNA oligomers showed that all oligomers could be extracted, and that the smallest oligomer was preferentially released with an efficiency of up to 40% during the reduction of the PPy layer. These results indicate that the present material is very promising for the development of inexpensive and efficient electrochemically controlled ion-exchange membranes for batch-wise extraction of biomolecules. PMID:22195031

In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networks.

PubMed

Folador, Edson Luiz; de Carvalho, Paulo Vinícius Sanches Daltro; Silva, Wanderson Marques; Ferreira, Rafaela Salgado; Silva, Artur; Gromiha, Michael; Ghosh, Preetam; Barh, Debmalya; Azevedo, Vasco; Röttger, Richard

2016-11-04

Corynebacterium pseudotuberculosis (Cp) is a gram-positive bacterium that is classified into equi and ovis serovars. The serovar ovis is the etiological agent of caseous lymphadenitis, a chronic infection affecting sheep and goats, causing economic losses due to carcass condemnation and decreased production of meat, wool, and milk. Current diagnosis or treatment protocols are not fully effective and, thus, require further research of Cp pathogenesis. Here, we mapped known protein-protein interactions (PPI) from various species to nine Cp strains to reconstruct parts of the potential Cp interactome and to identify potentially essential proteins serving as putative drug targets. On average, we predict 16,669 interactions for each of the nine strains (with 15,495 interactions shared among all strains). An in silico sanity check suggests that the potential networks were not formed by spurious interactions but have a strong biological bias. With the inferred Cp networks we identify 181 essential proteins, among which 41 are non-host homologous. The list of candidate interactions of the Cp strains lay the basis for developing novel hypotheses and designing according wet-lab studies. The non-host homologous essential proteins are attractive targets for therapeutic and diagnostic proposes. They allow for searching of small molecule inhibitors of binding interactions enabling modern drug discovery. Overall, the predicted Cp PPI networks form a valuable and versatile tool for researchers interested in Corynebacterium pseudotuberculosis.

Development and application of a recombination-based library versus library high- throughput yeast two-hybrid (RLL-Y2H) screening system.

PubMed

Yang, Fang; Lei, Yingying; Zhou, Meiling; Yao, Qili; Han, Yichao; Wu, Xiang; Zhong, Wanshun; Zhu, Chenghang; Xu, Weize; Tao, Ran; Chen, Xi; Lin, Da; Rahman, Khaista; Tyagi, Rohit; Habib, Zeshan; Xiao, Shaobo; Wang, Dang; Yu, Yang; Chen, Huanchun; Fu, Zhenfang; Cao, Gang

2018-02-16

Protein-protein interaction (PPI) network maintains proper function of all organisms. Simple high-throughput technologies are desperately needed to delineate the landscape of PPI networks. While recent state-of-the-art yeast two-hybrid (Y2H) systems improved screening efficiency, either individual colony isolation, library preparation arrays, gene barcoding or massive sequencing are still required. Here, we developed a recombination-based 'library vs library' Y2H system (RLL-Y2H), by which multi-library screening can be accomplished in a single pool without any individual treatment. This system is based on the phiC31 integrase-mediated integration between bait and prey plasmids. The integrated fragments were digested by MmeI and subjected to deep sequencing to decode the interaction matrix. We applied this system to decipher the trans-kingdom interactome between Mycobacterium tuberculosis and host cells and further identified Rv2427c interfering with the phagosome-lysosome fusion. This concept can also be applied to other systems to screen protein-RNA and protein-DNA interactions and delineate signaling landscape in cells.

Constructing an integrated gene similarity network for the identification of disease genes.

PubMed

Tian, Zhen; Guo, Maozu; Wang, Chunyu; Xing, LinLin; Wang, Lei; Zhang, Yin

2017-09-20

Discovering novel genes that are involved human diseases is a challenging task in biomedical research. In recent years, several computational approaches have been proposed to prioritize candidate disease genes. Most of these methods are mainly based on protein-protein interaction (PPI) networks. However, since these PPI networks contain false positives and only cover less half of known human genes, their reliability and coverage are very low. Therefore, it is highly necessary to fuse multiple genomic data to construct a credible gene similarity network and then infer disease genes on the whole genomic scale. We proposed a novel method, named RWRB, to infer causal genes of interested diseases. First, we construct five individual gene (protein) similarity networks based on multiple genomic data of human genes. Then, an integrated gene similarity network (IGSN) is reconstructed based on similarity network fusion (SNF) method. Finally, we employee the random walk with restart algorithm on the phenotype-gene bilayer network, which combines phenotype similarity network, IGSN as well as phenotype-gene association network, to prioritize candidate disease genes. We investigate the effectiveness of RWRB through leave-one-out cross-validation methods in inferring phenotype-gene relationships. Results show that RWRB is more accurate than state-of-the-art methods on most evaluation metrics. Further analysis shows that the success of RWRB is benefited from IGSN which has a wider coverage and higher reliability comparing with current PPI networks. Moreover, we conduct a comprehensive case study for Alzheimer's disease and predict some novel disease genes that supported by literature. RWRB is an effective and reliable algorithm in prioritizing candidate disease genes on the genomic scale. Software and supplementary information are available at http://nclab.hit.edu.cn/~tianzhen/RWRB/ .

Delayed-type hypersensitivity reactions induced by proton pump inhibitors: A clinical and in vitro T-cell reactivity study.

PubMed

Lin, C-Y; Wang, C-W; Hui, C-Y R; Chang, Y-C; Yang, C-H; Cheng, C-Y; Chen, W-W; Ke, W-M; Chung, W-H

2018-01-01

Proton pump inhibitors (PPIs) have been known to induce type I hypersensitivity reactions. However, severe delayed-type hypersensitivity reactions (DHR) induced by PPI, such as Stevens-Johnson syndrome (SJS), toxic epidermal necrolysis (TEN), or drug rash with eosinophilia and systemic symptoms (DRESS), are rarely reported. We conducted a study of a large series of PPI-related DHR, followed up their tolerability to alternative anti-ulcer agents, and investigated the T-cell reactivity to PPI in PPI-related DHR patients. We retrospectively analyzed patients with PPI-related DHR from multiple medical centers in Taiwan during the study period January 2003 to April 2016. We analyzed the causative PPI, clinical manifestations, organ involvement, treatment, and complications. We also followed up the potential risk of cross-hypersensitivity or tolerability to other PPI after their hypersensitivity episodes. Drug lymphocyte activation test (LAT) was conducted by measuring granulysin and interferon-γ to confirm the causalities. There were 69 cases of PPI-related DHR, including SJS/TEN (n=27) and DRESS (n=10). The LAT by measuring granulysin showed a sensitivity of 59.3% and specificity of 96.4%. Esomeprazole was the most commonly involved in PPI-related DHR (51%). Thirteen patients allergic to one kind of PPI could tolerate other structurally different PPI without cross-hypersensitivity reactions, whereas three patients developed cross-hypersensitivity reactions to alternative structurally similar PPI. The cross-reactivity to structurally similar PPI was also observed in LAT assay. PPIs have the potential to induce life-threatening DHR. In patients when PPI is necessary for treatment, switching to structurally different alternatives should be considered. © 2017 EAACI and John Wiley and Sons A/S. Published by John Wiley and Sons Ltd.

The role of emotion regulation in the relations between psychopathy factors and impulsive and premeditated aggression.

PubMed

Long, Katherine; Felton, Julia W; Lilienfeld, Scott O; Lejuez, Carl W

2014-10-01

Given the high rates of aggressive behavior among highly psychopathic individuals, much research has sought to clarify the nature of the relation between psychopathy and aggression. The present study examined relations between Fearless Dominance (PPI FD), Self-Centered Impulsivity (PPI SCI), and Coldheartedness (PPI CH) Factors of the Psychopathic Personality Inventory (PPI; Lilienfeld & Andrews, 1996) and aggression dimensions (premeditated and impulsive aggression) in a sample of substance users receiving inpatient treatment. At the univariate level, PPI FD traits were significantly and positively related to premeditated aggression, but were not significantly related to impulsive aggression. PPI SCI traits were positively related to both forms of aggression, whereas PPI CH was not significantly related to either aggression dimension. Emotion regulation difficulties, as measured by the Difficulties with Emotion Regulation Scale (DERS; Gratz & Roemer, 2004), were negatively related to PPI FD traits, positively related to PPI SCI traits, and negatively related to PPI CH traits. Both PPI SCI and PPI FD traits exerted significant indirect effects on impulsive aggression through the DERS. In contrast, the DERS did not mediate the relations between psychopathic traits and premeditated aggression. Results provide a more nuanced understanding of the psychopathy-aggression relations and suggest that difficulties with emotion regulation may be an important mediator of the relations between psychopathy factors and impulsive aggression. (PsycINFO Database Record (c) 2014 APA, all rights reserved).

The Role of Emotion Regulation in the Relations between Psychopathy Factors and Impulsive and Premeditated Aggression

PubMed Central

Long, Katherine; Felton, Julia W.; Lilienfeld, Scott O.; Lejuez, Carl W.

2014-01-01

Given the high rates of aggressive behavior among highly psychopathic individuals, much research has sought to clarify the nature of the relation between psychopathy and aggression. The present study examined relations between Fearless Dominance (PPI FD), Self-Centered Impulsivity (PPI SCI), and Coldheartedness (PPI CH) Factors of the Psychopathic Personality Inventory (PPI; Lilienfeld & Andrews, 1996) and aggression dimensions (premeditated and impulsive aggression) in a sample of substance users receiving inpatient treatment. At the univariate level, PPI FD traits were significantly and positively related to premeditated aggression, but were not significantly related to impulsive aggression. PPI SCI traits were positively related to both forms of aggression, whereas PPI CH was not significantly related to either aggression dimension. Emotion regulation difficulties, as measured by the Difficulties with Emotion Regulation Scale (DERS; Gratz & Roemer, 2004), were negatively related to PPI FD traits, positively related to PPI SCI traits, and negatively related to PPI CH traits. Both PPI SCI and PPI FD traits exerted significant indirect effects on impulsive aggression through the DERS. In contrast, the DERS did not mediate the relations between psychopathic traits and premeditated aggression. Results provide a more nuanced understanding of the psychopathy-aggression relations and suggest that difficulties with emotion regulation may be an important mediator of the relations between psychopathy factors and impulsive aggression. PMID:25198433

A Combined Molecular Dynamics and Experimental Study of Doped Polypyrrole.

PubMed

Fonner, John M; Schmidt, Christine E; Ren, Pengyu

2010-10-01

Polypyrrole (PPy) is a biocompatible, electrically conductive polymer that has great potential for battery, sensor, and neural implant applications. Its amorphous structure and insolubility, however, limit the experimental techniques available to study its structure and properties at the atomic level. Previous theoretical studies of PPy in bulk are also scarce. Using ab initio calculations, we have constructed a molecular mechanics force field of chloride-doped PPy (PPyCl) and undoped PPy. This model has been designed to integrate into the OPLS force field, and parameters are available for the Gromacs and TINKER software packages. Molecular dynamics (MD) simulations of bulk PPy and PPyCl have been performed using this force field, and the effects of chain packing and electrostatic scaling on the bulk polymer density have been investigated. The density of flotation of PPyCl films has been measured experimentally. Amorphous X-ray diffraction of PPyCl was obtained and correlated with atomic structures sampled from MD simulations. The force field reported here is foundational for bridging the gap between experimental measurements and theoretical calculations for PPy based materials.

A novel method to identify hub pathways of rheumatoid arthritis based on differential pathway networks.

PubMed

Wei, Shi-Tong; Sun, Yong-Hua; Zong, Shi-Hua

2017-09-01

The aim of the current study was to identify hub pathways of rheumatoid arthritis (RA) using a novel method based on differential pathway network (DPN) analysis. The present study proposed a DPN where protein‑protein interaction (PPI) network was integrated with pathway‑pathway interactions. Pathway data was obtained from background PPI network and the Reactome pathway database. Subsequently, pathway interactions were extracted from the pathway data by building randomized gene‑gene interactions and a weight value was assigned to each pathway interaction using Spearman correlation coefficient (SCC) to identify differential pathway interactions. Differential pathway interactions were visualized using Cytoscape to construct a DPN. Topological analysis was conducted to identify hub pathways that possessed the top 5% degree distribution of DPN. Modules of DPN were mined according to ClusterONE. A total of 855 pathways were selected to build pathway interactions. By filtrating pathway interactions of weight values >0.7, a DPN with 312 nodes and 791 edges was obtained. Topological degree analysis revealed 15 hub pathways, such as heparan sulfate/heparin‑glycosaminoglycan (HS‑GAG) degradation, HS‑GAG metabolism and keratan sulfate degradation for RA based on DPN. Furthermore, hub pathways were also important in modules, which validated the significance of hub pathways. In conclusion, the proposed method is a computationally efficient way to identify hub pathways of RA, which identified 15 hub pathways that may be potential biomarkers and provide insight to future investigation and treatment of RA.

Chemical polymerization and characterization of surfactant directed of polypyrrole-tannin-CTAB nanocomposites

NASA Astrophysics Data System (ADS)

Abdi, Mahnaz M.; Azli, Nur Farhana Waheeda Mohd; Lim, Hong Ngee; Tahir, Paridah Md; Razalli, Rawaida Liyana; Hoong, Yeoh Beng

2017-12-01

In this research, Tannin (TA) from Acacia mangium tree was used to modify polypyrrole (PPy) composite with enhanced physical and structural properties. Composite nanostructure preparation was done in the presence of cationic surfactant, cetyltrimethylammonium bromide (CTAB) to improve surface area and electron transferring of resulting polymer. The Fourier Transform InfraRed (FT-IR) spectrum showed the characteristics peaks of functional group of PPy, TA, and CTAB in the resulting composite indicating the incorporation of TA and CTAB into PPy structure. The spherical structure was observed for PPy/TA prepared in the presence of CTAB with higher porosity compared with the PPy/TA. Cyclic voltammograms of modified SPE electrode using Ppy/TA/CTAB showed enhanced current response compared with the electrode modified by only PPy or PPy/TA.

Patient and public involvement in the early stages of clinical trial development: a systematic cohort investigation

PubMed Central

Gamble, Carrol; Dudley, Louise; Allam, Alison; Bell, Philip; Goodare, Heather; Hanley, Bec; Preston, Jennifer; Walker, Alison; Williamson, Paula; Young, Bridget

2014-01-01

Background Randomised controlled trials (RCTs) are considered particularly likely to benefit from patient and public involvement (PPI). Decisions made by professional researchers at the outset may go on to have a significant impact on the potential for PPI contributions. Objective To increase knowledge of PPI within the early development of RCTs by systematically describing the reported level, nature and acceptability of proposed PPI to the funders. Methods Documentation from the outline application process for all RCTs that received funding from the Health Technology Assessment (HTA) Programme 2006–2010 was requested. For each application, data were extracted on trial characteristics, references to PPI in the development of the outline application and funding Board feedback, and plans for PPI in the full application and after the trial was funded. Results 110 applications were eligible with outline applications available for 90 (82%). The cohort covered a wide range of interventions and conditions. 54% (49/90) provided some information about PPI. 26 (28.9%) indicated PPI within the development of the outline application itself; 32 (35.6%) planned involvement in the full application and 43 (48%) once the trial was funded. Recruitment at diagnosis and surgical interventions were less likely to describe PPI. Blinded trials and trials in which participants may receive placebo only, more frequently described PPI activity. The HTA commissioning Board feedback rarely referred to PPI. Conclusions Incorporation of PPI within the development of the outline application or specification of plans for future involvement was low. Funder requests for applicants to provide information on PPI and justification for its absence should be welcomed but further research is needed to identify the impact of this on its contributions to research. Comments on PPI by reviewers should be directional rather than state that an increase is required. Challenges facing applicants in initiating PPI prior to funding need to be addressed. PMID:25056972

In-vitro biocompatibility and corrosion resistance of electrochemically assembled PPy/TNTA hybrid material for biomedical applications

NASA Astrophysics Data System (ADS)

Simi, V. S.; Satish, Aishwarya; Korrapati, Purna Sai; Rajendran, N.

2018-07-01

Nanostructured hybrid materials composed of inorganic and organic constituents of different chemistry and functionality have attracted wide range of biomedical applications. The uniform electrodeposition of polypyrrole into titania nanotube arrays was achieved by normal pulse voltammetry technique in lithium perchlorate electrolyte by varying the pulse period. The electrochemically assembled polypyrrole/titania nanotube arrays (PPy/TNTA) surface was characterized by structural characterizations including attenuated total reflectance -fourier transform infrared spectroscopy, Raman and X-ray photoelectron spectroscopy analysis. Morphological study carried out by high resolution scanning electron microscopy demonstrates the influence of varying pulse period in achieving the controlled deposition of polypyrrole into the nanotube frame work. Cyclic voltammetry study reveals the electroactive nature of the hybrid material. The contact angle measurements and In-vitro immersion studies in stimulated body fluid hanks' solution were carried out to evaluate the wettability and apatite forming ability of the developed hybrid material. The deposition of polypyrrole enhanced the corrosion resistance of TNTA as evidenced from the lower icorr value observed for PPy/TNTA. The corrosion protection behavior of the hybrid material revealed from the electrochemical impedance spectroscopic studies was clearly noticed from the increase in impedance and maximum phase angle values. Further In-vitro cell culture studies were carried out using MG63 osteoblast cells to evaluate the biocompatibility of the hybrid material. Noticeable improvement in corrosion protection and biocompatibility performance suggest the possible application of PPy/TNTA hybrid material for biomedical applications.

Proton Pump Inhibitors: Risk for Myopathy?

PubMed

Colmenares, Evan W; Pappas, Ashley L

2017-01-01

The purpose of this article is to describe the relationship between proton pump inhibitors (PPIs) and symptoms of myopathy based on case reports. A literature search was conducted in PubMed (1946 to June 2016) using MeSH terms proton pump inhibitors, omeprazole, esomeprazole, lansoprazole, dexlansoprazole, rabeprazole, pantoprazole, and muscular diseases. Additionally, a search was conducted in ToxNet and EMBASE using similar search criteria. The resulting articles were scanned to assess relevance to the review. Bibliographies of all relevant articles were evaluated for additional sources; 26 articles resulted from the search of PubMed, ToxNet, and EMBASE; articles that involved medications typically considered to have myalgia-like side effects (eg, statins), or included patients who presented with a confounding disease state (eg, Guillain-Barré) were excluded. In total, 11 case reports as well as a review of an adverse event reporting database that included 292 cases were evaluated. Association of PPI use and myopathy symptoms does not have a clear etiology. Overall, the available published data do not show a high risk of myopathy with PPI use but should be considered if a patient presents with myopathy symptoms and concurrent PPI use. A limited body of published data suggests that PPI use has been associated with myopathy-like symptoms without long-term effects following discontinuation. Although myopathy is a rare adverse effect observed with PPIs, it can be a serious side effect to be considered when starting a patient on acid suppression therapy.

Brand name and generic proton pump inhibitor prescriptions in the United States: insights from the national ambulatory medical care survey (2006-2010).

PubMed

Gawron, Andrew J; Feinglass, Joseph; Pandolfino, John E; Tan, Bruce K; Bove, Michiel J; Shintani-Smith, Stephanie

2015-01-01

Introduction. Proton pump inhibitors (PPI) are one of the most commonly prescribed medication classes with similar efficacy between brand name and generic PPI formulations. Aims. We determined demographic, clinical, and practice characteristics associated with brand name PPI prescriptions at ambulatory care visits in the United States. Methods. Observational cross sectional analysis using the National Ambulatory Medical Care Survey (NAMCS) of all adult (≥18 yrs of age) ambulatory care visits from 2006 to 2010. PPI prescriptions were identified by using the drug entry code as brand name only or generic available formulations. Descriptive statistics were reported in terms of unweighted patient visits and proportions of encounters with brand name PPI prescriptions. Global chi-square tests were used to compare visits with brand name PPI prescriptions versus generic PPI prescriptions for each measure. Poisson regression was used to determine the incidence rate ratio (IRR) for generic versus brand PPI prescribing. Results. A PPI was prescribed at 269.7 million adult ambulatory visits, based on 9,677 unweighted visits, of which 53% were brand name only prescriptions. In 2006, 76.0% of all PPI prescriptions had a brand name only formulation compared to 31.6% of PPI prescriptions in 2010. Visits by patients aged 25-44 years had the greatest proportion of brand name PPI formulations (57.9%). Academic medical centers and physician-owned practices had the greatest proportion of visits with brand name PPI prescriptions (58.9% and 55.6% of visits with a PPI prescription, resp.). There were no significant differences in terms of median income, patient insurance type, or metropolitan status when comparing the proportion of visits with brand name versus generic PPI prescriptions. Poisson regression results showed that practice ownership type was most strongly associated with the likelihood of receiving a brand name PPI over the entire study period. Compared to HMO visits, patient visits at academic medical centers (IRR 4.2, 95% CI 2.2-8.0), physician-owned practices (IRR 3.9, 95% CI 2.1-7.1), and community health centers (IRR 3.6, 95% CI 1.9-6.6) were all more likely to have brand name PPIs. Conclusion. PPI prescriptions with brand name only formulations are most strongly associated with physician practice type.

Directing Stem Cell Differentiation via Electrochemical Reversible Switching between Nanotubes and Nanotips of Polypyrrole Array.

PubMed

Wei, Yan; Mo, Xiaoju; Zhang, Pengchao; Li, Yingying; Liao, Jingwen; Li, Yongjun; Zhang, Jinxing; Ning, Chengyun; Wang, Shutao; Deng, Xuliang; Jiang, Lei

2017-06-27

Control of stem cell behaviors at solid biointerfaces is critical for stem-cell-based regeneration and generally achieved by engineering chemical composition, topography, and stiffness. However, the influence of dynamic stimuli at the nanoscale from solid biointerfaces on stem cell fate remains unclear. Herein, we show that electrochemical switching of a polypyrrole (Ppy) array between nanotubes and nanotips can alter surface adhesion, which can strongly influence mechanotransduction activation and guide differentiation of mesenchymal stem cells (MSCs). The Ppy array, prepared via template-free electrochemical polymerization, can be reversibly switched between highly adhesive hydrophobic nanotubes and poorly adhesive hydrophilic nanotips through an electrochemical oxidation/reduction process, resulting in dynamic attachment and detachment to MSCs at the nanoscale. Multicyclic attachment/detachment of the Ppy array to MSCs can activate intracellular mechanotransduction and osteogenic differentiation independent of surface stiffness and chemical induction. This smart surface, permitting transduction of nanoscaled dynamic physical inputs into biological outputs, provides an alternative to classical cell culture substrates for regulating stem cell fate commitment. This study represents a general strategy to explore nanoscaled interactions between stem cells and stimuli-responsive surfaces.

PPInterFinder--a mining tool for extracting causal relations on human proteins from literature.

PubMed

Raja, Kalpana; Subramani, Suresh; Natarajan, Jeyakumar

2013-01-01

One of the most common and challenging problem in biomedical text mining is to mine protein-protein interactions (PPIs) from MEDLINE abstracts and full-text research articles because PPIs play a major role in understanding the various biological processes and the impact of proteins in diseases. We implemented, PPInterFinder--a web-based text mining tool to extract human PPIs from biomedical literature. PPInterFinder uses relation keyword co-occurrences with protein names to extract information on PPIs from MEDLINE abstracts and consists of three phases. First, it identifies the relation keyword using a parser with Tregex and a relation keyword dictionary. Next, it automatically identifies the candidate PPI pairs with a set of rules related to PPI recognition. Finally, it extracts the relations by matching the sentence with a set of 11 specific patterns based on the syntactic nature of PPI pair. We find that PPInterFinder is capable of predicting PPIs with the accuracy of 66.05% on AIMED corpus and outperforms most of the existing systems. DATABASE URL: http://www.biomining-bu.in/ppinterfinder/

The two-factor model of psychopathic personality: evidence from the psychopathic personality inventory.

PubMed

Marcus, David K; Fulton, Jessica J; Edens, John F

2013-01-01

Psychopathy or psychopathic personality disorder represents a constellation of traits characterized by superficial charm, egocentricity, irresponsibility, fearlessness, persistent violation of social norms, and a lack of empathy, guilt, and remorse. Factor analyses of the Psychopathic Personality Inventory (PPI)typically yield two factors: Fearless Dominance (FD) and Self-Centered Impulsivity (SCI). Additionally, the Coldheartedness (CH) subscale typically does not load on either factor. The current paper includes a meta-analysis of studies that have examined theoretically important correlates of the two PPI factors and CH. Results suggest that (a) FD and SCI are orthogonal or weakly correlated, (b) each factor predicts distinct (and sometimes opposite) correlates, and (c) the FD factor is not highly correlated with most other measures of psychopathy. This pattern of results raises important questions about the relation between FD and SCI and the role of FD in conceptualizations of psychopathy. Our findings also indicate the need for future studies using the two-factor model of the PPI to conduct moderational analyses to examine potential interactions between FD and SCI in the prediction of important criterion measures.

PPInterFinder—a mining tool for extracting causal relations on human proteins from literature

PubMed Central

Raja, Kalpana; Subramani, Suresh; Natarajan, Jeyakumar

2013-01-01

One of the most common and challenging problem in biomedical text mining is to mine protein–protein interactions (PPIs) from MEDLINE abstracts and full-text research articles because PPIs play a major role in understanding the various biological processes and the impact of proteins in diseases. We implemented, PPInterFinder—a web-based text mining tool to extract human PPIs from biomedical literature. PPInterFinder uses relation keyword co-occurrences with protein names to extract information on PPIs from MEDLINE abstracts and consists of three phases. First, it identifies the relation keyword using a parser with Tregex and a relation keyword dictionary. Next, it automatically identifies the candidate PPI pairs with a set of rules related to PPI recognition. Finally, it extracts the relations by matching the sentence with a set of 11 specific patterns based on the syntactic nature of PPI pair. We find that PPInterFinder is capable of predicting PPIs with the accuracy of 66.05% on AIMED corpus and outperforms most of the existing systems. Database URL: http://www.biomining-bu.in/ppinterfinder/ PMID:23325628

Elucidating the Construct Validity of the Psychopathic Personality Inventory Triarchic Scales.

PubMed

Sellbom, Martin; Wygant, Dustin B; Drislane, Laura E

2015-01-01

This study sought to replicate and extend Hall and colleagues' (2014) work on developing and validating scales from the Psychopathic Personality Inventory (PPI) to index the triarchic psychopathy constructs of boldness, meanness, and disinhibition. This study also extended Hall et al.'s initial findings by including the PPI Revised (PPI-R). A community sample (n = 240) weighted toward subclinical psychopathy traits and a male prison sample (n = 160) were used for this study. Results indicated that PPI-Boldness, PPI-Meanness, and PPI-Disinhibition converged with other psychopathy, personality, and behavioral criteria in ways conceptually expected from the perspective of the triarchic psychopathy model, including showing very strong convergent and discriminant validity with their Triarchic Psychopathy Measure counterparts. These findings further enhance the utility of the PPI and PPI-R in measuring these constructs.

Ultrasonic vocalizations, predictability and sensorimotor gating in the rat

PubMed Central

Webber, Emily S.; Mankin, David E.; McGraw, Justin J.; Beckwith, Travis J.; Cromwell, Howard C.

2013-01-01

Prepulse inhibition (PPI) is a measure of sensorimotor gating in diverse groups of animals including humans. Emotional states can influence PPI in humans both in typical subjects and in individuals with mental illness. Little is known about emotional regulation during PPI in rodents. We used ultrasonic vocalization recording to monitor emotional states in rats during PPI testing. We altered the predictability of the PPI trials to examine any alterations in gating and emotional regulation. We also examined PPI in animals selectively bred for high or low levels of 50 kHz USV emission. Rats emitted high levels of 22 kHz calls consistently throughout the PPI session. USVs were sensitive to prepulses during the PPI session similar to startle. USV rate was sensitive to predictability among the different levels tested and across repeated experiences. Startle and inhibition of startle were not affected by predictability in a similar manner. No significant differences for PPI or startle were found related the different levels of predictability; however, there was a reduction in USV signals and an enhancement of PPI after repeated exposure. Animals selectively bred to emit high levels of USVs emitted significantly higher levels of USVs during the PPI session and a reduced ASR compared to the low and random selective lines. Overall, the results support the idea that PPI tests in rodents induce high levels of negative affect and that manipulating emotional styles of the animals alters the negative impact of the gating session as well as the intensity of the startle response. PMID:23850353

Assembling a protein-protein interaction map of the SSU processome from existing datasets.

PubMed

Lim, Young H; Charette, J Michael; Baserga, Susan J

2011-03-10

The small subunit (SSU) processome is a large ribonucleoprotein complex involved in small ribosomal subunit assembly. It consists of the U3 snoRNA and ∼72 proteins. While most of its components have been identified, the protein-protein interactions (PPIs) among them remain largely unknown, and thus the assembly, architecture and function of the SSU processome remains unclear. We queried PPI databases for SSU processome proteins to quantify the degree to which the three genome-wide high-throughput yeast two-hybrid (HT-Y2H) studies, the genome-wide protein fragment complementation assay (PCA) and the literature-curated (LC) datasets cover the SSU processome interactome. We find that coverage of the SSU processome PPI network is remarkably sparse. Two of the three HT-Y2H studies each account for four and six PPIs between only six of the 72 proteins, while the third study accounts for as little as one PPI and two proteins. The PCA dataset has the highest coverage among the genome-wide studies with 27 PPIs between 25 proteins. The LC dataset was the most extensive, accounting for 34 proteins and 38 PPIs, many of which were validated by independent methods, thereby further increasing their reliability. When the collected data were merged, we found that at least 70% of the predicted PPIs have yet to be determined and 26 proteins (36%) have no known partners. Since the SSU processome is conserved in all Eukaryotes, we also queried HT-Y2H datasets from six additional model organisms, but only four orthologues and three previously known interologous interactions were found. This provides a starting point for further work on SSU processome assembly, and spotlights the need for a more complete genome-wide Y2H analysis.

Assembling a Protein-Protein Interaction Map of the SSU Processome from Existing Datasets

PubMed Central

Baserga, Susan J.

2011-01-01

Background The small subunit (SSU) processome is a large ribonucleoprotein complex involved in small ribosomal subunit assembly. It consists of the U3 snoRNA and ∼72 proteins. While most of its components have been identified, the protein-protein interactions (PPIs) among them remain largely unknown, and thus the assembly, architecture and function of the SSU processome remains unclear. Methodology We queried PPI databases for SSU processome proteins to quantify the degree to which the three genome-wide high-throughput yeast two-hybrid (HT-Y2H) studies, the genome-wide protein fragment complementation assay (PCA) and the literature-curated (LC) datasets cover the SSU processome interactome. Conclusions We find that coverage of the SSU processome PPI network is remarkably sparse. Two of the three HT-Y2H studies each account for four and six PPIs between only six of the 72 proteins, while the third study accounts for as little as one PPI and two proteins. The PCA dataset has the highest coverage among the genome-wide studies with 27 PPIs between 25 proteins. The LC dataset was the most extensive, accounting for 34 proteins and 38 PPIs, many of which were validated by independent methods, thereby further increasing their reliability. When the collected data were merged, we found that at least 70% of the predicted PPIs have yet to be determined and 26 proteins (36%) have no known partners. Since the SSU processome is conserved in all Eukaryotes, we also queried HT-Y2H datasets from six additional model organisms, but only four orthologues and three previously known interologous interactions were found. This provides a starting point for further work on SSU processome assembly, and spotlights the need for a more complete genome-wide Y2H analysis. PMID:21423703

Querying graphs in protein-protein interactions networks using feedback vertex set.

PubMed

Blin, Guillaume; Sikora, Florian; Vialette, Stéphane

2010-01-01

Recent techniques increase rapidly the amount of our knowledge on interactions between proteins. The interpretation of these new information depends on our ability to retrieve known substructures in the data, the Protein-Protein Interactions (PPIs) networks. In an algorithmic point of view, it is an hard task since it often leads to NP-hard problems. To overcome this difficulty, many authors have provided tools for querying patterns with a restricted topology, i.e., paths or trees in PPI networks. Such restriction leads to the development of fixed parameter tractable (FPT) algorithms, which can be practicable for restricted sizes of queries. Unfortunately, Graph Homomorphism is a W[1]-hard problem, and hence, no FPT algorithm can be found when patterns are in the shape of general graphs. However, Dost et al. gave an algorithm (which is not implemented) to query graphs with a bounded treewidth in PPI networks (the treewidth of the query being involved in the time complexity). In this paper, we propose another algorithm for querying pattern in the shape of graphs, also based on dynamic programming and the color-coding technique. To transform graphs queries into trees without loss of informations, we use feedback vertex set coupled to a node duplication mechanism. Hence, our algorithm is FPT for querying graphs with a bounded size of their feedback vertex set. It gives an alternative to the treewidth parameter, which can be better or worst for a given query. We provide a python implementation which allows us to validate our implementation on real data. Especially, we retrieve some human queries in the shape of graphs into the fly PPI network.

Systems-level analysis of risk genes reveals the modular nature of schizophrenia.

PubMed

Liu, Jiewei; Li, Ming; Luo, Xiong-Jian; Su, Bing

2018-05-19

Schizophrenia (SCZ) is a complex mental disorder with high heritability. Genetic studies (especially recent genome-wide association studies) have identified many risk genes for schizophrenia. However, the physical interactions among the proteins encoded by schizophrenia risk genes remain elusive and it is not known whether the identified risk genes converge on common molecular networks or pathways. Here we systematically investigated the network characteristics of schizophrenia risk genes using the high-confidence protein-protein interactions (PPI) from the human interactome. We found that schizophrenia risk genes encode a densely interconnected PPI network (P = 4.15 × 10 -31 ). Compared with the background genes, the schizophrenia risk genes in the interactome have significantly higher degree (P = 5.39 × 10 -11 ), closeness centrality (P = 7.56 × 10 -11 ), betweeness centrality (P = 1.29 × 10 -11 ), clustering coefficient (P = 2.22 × 10 -2 ), and shorter average shortest path length (P = 7.56 × 10 -11 ). Based on the densely interconnected PPI network, we identified 48 hub genes and 4 modules formed by highly interconnected schizophrenia genes. We showed that the proteins encoded by schizophrenia hub genes have significantly more direct physical interactions. Gene ontology (GO) analysis revealed that cell adhesion, cell cycle, immune system response, and GABR-receptor complex categories were enriched in the modules formed by highly interconnected schizophrenia risk genes. Our study reveals that schizophrenia risk genes encode a densely interconnected molecular network and demonstrates the modular nature of schizophrenia. Copyright © 2018 Elsevier B.V. All rights reserved.

Gene expression profiles reveal key genes for early diagnosis and treatment of adamantinomatous craniopharyngioma.

PubMed

Yang, Jun; Hou, Ziming; Wang, Changjiang; Wang, Hao; Zhang, Hongbing

2018-04-23

Adamantinomatous craniopharyngioma (ACP) is an aggressive brain tumor that occurs predominantly in the pediatric population. Conventional diagnosis method and standard therapy cannot treat ACPs effectively. In this paper, we aimed to identify key genes for ACP early diagnosis and treatment. Datasets GSE94349 and GSE68015 were obtained from Gene Expression Omnibus database. Consensus clustering was applied to discover the gene clusters in the expression data of GSE94349 and functional enrichment analysis was performed on gene set in each cluster. The protein-protein interaction (PPI) network was built by the Search Tool for the Retrieval of Interacting Genes, and hubs were selected. Support vector machine (SVM) model was built based on the signature genes identified from enrichment analysis and PPI network. Dataset GSE94349 was used for training and testing, and GSE68015 was used for validation. Besides, RT-qPCR analysis was performed to analyze the expression of signature genes in ACP samples compared with normal controls. Seven gene clusters were discovered in the differentially expressed genes identified from GSE94349 dataset. Enrichment analysis of each cluster identified 25 pathways that highly associated with ACP. PPI network was built and 46 hubs were determined. Twenty-five pathway-related genes that overlapped with the hubs in PPI network were used as signatures to establish the SVM diagnosis model for ACP. The prediction accuracy of SVM model for training, testing, and validation data were 94, 85, and 74%, respectively. The expression of CDH1, CCL2, ITGA2, COL8A1, COL6A2, and COL6A3 were significantly upregulated in ACP tumor samples, while CAMK2A, RIMS1, NEFL, SYT1, and STX1A were significantly downregulated, which were consistent with the differentially expressed gene analysis. SVM model is a promising classification tool for screening and early diagnosis of ACP. The ACP-related pathways and signature genes will advance our knowledge of ACP pathogenesis and benefit the therapy improvement.

Predicting protein complexes from weighted protein-protein interaction graphs with a novel unsupervised methodology: Evolutionary enhanced Markov clustering.

PubMed

Theofilatos, Konstantinos; Pavlopoulou, Niki; Papasavvas, Christoforos; Likothanassis, Spiros; Dimitrakopoulos, Christos; Georgopoulos, Efstratios; Moschopoulos, Charalampos; Mavroudi, Seferina

2015-03-01

Proteins are considered to be the most important individual components of biological systems and they combine to form physical protein complexes which are responsible for certain molecular functions. Despite the large availability of protein-protein interaction (PPI) information, not much information is available about protein complexes. Experimental methods are limited in terms of time, efficiency, cost and performance constraints. Existing computational methods have provided encouraging preliminary results, but they phase certain disadvantages as they require parameter tuning, some of them cannot handle weighted PPI data and others do not allow a protein to participate in more than one protein complex. In the present paper, we propose a new fully unsupervised methodology for predicting protein complexes from weighted PPI graphs. The proposed methodology is called evolutionary enhanced Markov clustering (EE-MC) and it is a hybrid combination of an adaptive evolutionary algorithm and a state-of-the-art clustering algorithm named enhanced Markov clustering. EE-MC was compared with state-of-the-art methodologies when applied to datasets from the human and the yeast Saccharomyces cerevisiae organisms. Using public available datasets, EE-MC outperformed existing methodologies (in some datasets the separation metric was increased by 10-20%). Moreover, when applied to new human datasets its performance was encouraging in the prediction of protein complexes which consist of proteins with high functional similarity. In specific, 5737 protein complexes were predicted and 72.58% of them are enriched for at least one gene ontology (GO) function term. EE-MC is by design able to overcome intrinsic limitations of existing methodologies such as their inability to handle weighted PPI networks, their constraint to assign every protein in exactly one cluster and the difficulties they face concerning the parameter tuning. This fact was experimentally validated and moreover, new potentially true human protein complexes were suggested as candidates for further validation using experimental techniques. Copyright © 2015 Elsevier B.V. All rights reserved.

Reconfiguring the AR-TIF2 Protein–Protein Interaction HCS Assay in Prostate Cancer Cells and Characterizing the Hits from a LOPAC Screen

PubMed Central

Fancher, Ashley T.; Hua, Yun; Camarco, Daniel P.; Close, David A.; Strock, Christopher J.

2016-01-01

Abstract The continued activation of androgen receptor (AR) transcription and elevated expression of AR and transcriptional intermediary factor 2 (TIF2) coactivator observed in prostate cancer (CaP) recurrence and the development of castration-resistant CaP (CRPC) support a screening strategy for small-molecule inhibitors of AR-TIF2 protein–protein interactions (PPIs) to find new drug candidates. Small molecules can elicit tissue selective effects, because the cells of distinct tissues express different levels and cohorts of coregulatory proteins. We reconfigured the AR-TIF2 PPI biosensor (PPIB) assay in the PC-3 CaP cell line to determine whether AR modulators and hits from an AR-TIF2 PPIB screen conducted in U-2 OS cells would behave differently in the CaP cell background. Although we did not observe any significant differences in the compound responses between the assay performed in osteosarcoma and CaP cells, the U-2 OS AR-TIF2 PPIB assay would be more amenable to screening, because both the virus and cell culture demands are lower. We implemented a testing paradigm of counter-screens and secondary hit characterization assays that allowed us to identify and deprioritize hits that inhibited/disrupted AR-TIF2 PPIs and AR transcriptional activation (AR-TA) through antagonism of AR ligand binding or by non-specifically blocking nuclear receptor trafficking. Since AR-TIF2 PPI inhibitor/disruptor molecules act distally to AR ligand binding, they have the potential to modulate AR-TA in a cell-specific manner that is distinct from existing anti-androgen drugs, and to overcome the development of resistance to AR antagonism. We anticipate that the application of this testing paradigm to characterize the hits from an AR-TIF2 PPI high-content screening campaign will enable us to prioritize the AR-TIF2 PPI inhibitor/disruptor leads that have potential to be developed into novel therapeutics for CaP and CRPC. PMID:27606620

Identification of differentially expressed genes associated with the enhancement of X-ray susceptibility by RITA in a hypopharyngeal squamous cell carcinoma cell line (FaDu).

PubMed

Luan, Jinwei; Li, Xianglan; Guo, Rutao; Liu, Shanshan; Luo, Hongyu; You, Qingshan

2016-06-01

Next generation sequencing and bio-informatic analyses were conducted to investigate the mechanism of reactivation of p53 and induction of tumor cell apoptosis (RITA)-enhancing X-ray susceptibility in FaDu cells. The cDNA was isolated from FaDu cells treated with 0 X-ray, 8 Gy X-ray, or 8 Gy X-ray + RITA. Then, cDNA libraries were created and sequenced using next generation sequencing, and each assay was repeated twice. Subsequently, differentially expressed genes (DEGs) were identified using Cuffdiff in Cufflinks and their functions were predicted by pathway enrichment analyses. Genes that were constantly up- or down-regulated in 8 Gy X-ray-treated FaDu cells and 8 Gy X-ray + RITA-treated FaDu cells were obtained as RITA genes. Afterward, the protein-protein interaction (PPI) relationships were obtained from the STRING database and a PPI network was constructed using Cytoscape. Furthermore, ClueGO was used for pathway enrichment analysis of genes in the PPI network. Total 2,040 and 297 DEGs were identified in FaDu cells treated with 8 Gy X-ray or 8 Gy X-ray + RITA, respectively. PARP3 and NEIL1 were enriched in base excision repair, and CDK1 was enriched in p53 signaling pathway. RFC2 and EZH2 were identified as RITA genes. In the PPI network, many interaction relationships were identified (e.g., RFC2-CDK1, EZH2-CDK1 and PARP3-EZH2). ClueGO analysis showed that RFC2 and EZH2 were related to cell cycle. RFC2, EZH2, CDK1, PARP3 and NEIL1 may be associated, and together enhance the susceptibility of FaDu cells treated with RITA to the deleterious effects of X-ray.

Preparation of polypyrrole-embedded electrospun poly(lactic acid) nanofibrous scaffolds for nerve tissue engineering

PubMed Central

Zhou, Jun-feng; Wang, Yi-guo; Cheng, Liang; Wu, Zhao; Sun, Xiao-dan; Peng, Jiang

2016-01-01

Polypyrrole (PPy) is a biocompatible polymer with good conductivity. Studies combining PPy with electrospinning have been reported; however, the associated decrease in PPy conductivity has not yet been resolved. We embedded PPy into poly(lactic acid) (PLA) nanofibers via electrospinning and fabricated a PLA/PPy nanofibrous scaffold containing 15% PPy with sustained conductivity and aligned topography. There was good biocompatibility between the scaffold and human umbilical cord mesenchymal stem cells as well as Schwann cells. Additionally, the direction of cell elongation on the scaffold was parallel to the direction of fibers. Our findings suggest that the aligned PLA/PPy nanofibrous scaffold is a promising biomaterial for peripheral nerve regeneration. PMID:27904497

Sensorimotor Gating in Neurotensin-1 Receptor Null Mice

PubMed Central

Feifel, D.; Pang, Z.; Shilling, P.D.; Melendez, G.; Schreiber, R.; Button, D.

2009-01-01

BACKGROUND Converging evidence has implicated endogenous neurotensin (NT) in the pathophysiology of brain processes relevant to schizophrenia. Prepulse inhibition of the startle reflex (PPI) is a measure of sensorimotor gating and considered to be of strong relevance to neuropsychiatric disorders associated with psychosis and cognitive dysfunction. Mice genetically engineered to not express NT display deficits in PPI that model the PPI deficits seen in schizophrenia patients. NT1 receptors have been most strongly implicated in mediating the psychosis relevant effects of NT such as attenuating PPI deficits. To investigate the role of NT1 receptors in the regulation of PPI, we measured baseline PPI in wildtype (WT) and NT1 knockout (KO) mice. We also tested the effects of amphetamine and dizocilpine, a dopamine agonist and NMDA antagonist, respectively, that reduce PPI as well as the NT1 selective receptor agonist, PD149163, known to increase PPI in rats. METHODS Baseline PPI and acoustic startle response were measured in WT and NT1 knockout KO mice. After baseline testing, mice were tested again after receiving intraperatoneal (IP) saline or one of three doses of amphetamine (1.0, 3.0 and 10.0 mg/kg), dizocilpine (0.3, 1.0 and 3.0 mg/kg) and PD149163 (0.5, 2.0 and 6.0 mg/kg) on separate test days. RESULTS Baseline PPI and acoustic startle response in NT1 KO mice were not significantly different from NT1 WT mice. WT and KO mice exhibited similar responses to the PPI-disrupting effects of dizocilpine and amphetamine. PD149163 significantly facilitated PPI (P < 0.004) and decreased the acoustic startle response (P < 0.001) in WT but not NT1 KO mice. CONCLUSIONS The data does not support the regulation of baseline PPI or the PPI disruptive effects of amphetamine or dizocilpine by endogenous NT acting at the NT1 receptor, although they support the antipsychotic potential of pharmacological activation of NT1 receptors by NT1 agonists. PMID:19596359

Viral-templated gold/polypyrrole nanopeapods for an ammonia gas sensor

NASA Astrophysics Data System (ADS)

Yan, Yiran; Zhang, Miluo; Moon, Chung Hee; Su, Heng-Chia; Myung, Nosang V.; Haberer, Elaine D.

2016-08-01

One-dimensional gold/polypyrrole (Au/PPy) nanopeapods were fabricated using a viral template: M13 bacteriophage. The genetically modified filamentous virus displayed gold-binding peptides along its length, allowing selective attachment of gold nanoparticles (Au NPs) under ambient conditions. A PPy shell was electropolymerized on the viral-templated Au NP chains forming nanopeapod structures. The PPy shell morphology and thickness were controlled through electrodeposition potential and time, resulting in an ultra-thin conductive polymer shell of 17.4 ± 3.3 nm. A post-electrodeposition acid treatment was used to modify the electrical properties of these hybrid materials. The electrical resistance of the nanopeapods was monitored at each assembly step. Chemiresistive ammonia (NH3) gas sensors were developed from networks of the hybrid Au/PPy nanostructures. Room temperature sensing performance was evaluated from 5 to 50 ppmv and a mixture of reversible and irreversible chemiresistive behavior was observed. A sensitivity of 0.30%/ppmv was found for NH3 concentrations of 10 ppmv or less, and a lowest detection limit (LDL) of 0.007 ppmv was calculated. Furthermore, acid-treated devices exhibited an enhanced sensitivity of 1.26%/ppmv within the same concentration range and a calculated LDL of 0.005 ppmv.

Proton Pump Inhibitors in Gastroesophageal Reflux Disease: Friend or Foe.

PubMed

Gyawali, C Prakash

2017-09-01

Proton pump inhibitor (PPI) use in gastroesophageal reflux disease (GERD) has been redefined, in light of recent advances highlighting GERD phenotypes that respond to PPIs, and fresh revelations of potential risks of long-term PPI therapy. Erosive esophagitis predicts excellent response to PPI therapy, but non-erosive reflux disease (NERD) with abnormal reflux parameters on ambulatory reflux monitoring also demonstrates a similar response. In contrast, response is suboptimal in the absence of abnormal reflux parameters. In this setting, if an alternate appropriate indication for PPI therapy does not coexist, risks may outweigh benefits of PPI therapy. Adverse events from long-term PPI therapy continue to be reported, most based on association rather than cause-and-effect. Appropriate indications need to be established before embarking on long-term PPI therapy. Future research will define true risks of long-term PPI therapy, and develop alternate management options for acid peptic diseases.

Conventional versus robot-assisted laparoscopic Nissen fundoplication: a comparison of postoperative acid reflux parameters.

PubMed

Frazzoni, Marzio; Conigliaro, Rita; Colli, Giovanni; Melotti, Gianluigi

2012-06-01

Laparoscopic Nissen fundoplication (LNF) is a technically demanding surgical procedure designed to cure gastroesophageal reflux disease (GERD). It represents an alternative to life-long medical therapy and the only recommended treatment modality to overcome refractoriness to proton pump inhibitor (PPI) therapy. The recent development of robotic systems prompted evaluation of their use in antireflux surgery. Between 1997 and 2000, in a PPI-responsive series we found postoperative normalization of esophageal acid exposure time (EAET) in most but not all cases. Between 2007 and 2009, in a PPI-refractory series we found postoperative normalization of EAET in all cases. We decided to analyze retrospectively our prospectively collected data to evaluate whether differences other than the conventional or robot-assisted technique could justify postoperative differences in acid reflux parameters. Baseline demographic, endoscopic, and manometric parameters were compared between the two series of patients, as well as postoperative manometric and acid reflux parameters. There were no significant differences in the baseline demographic, endoscopic, and manometric characteristics between the two groups of patients. The median lower esophageal sphincter tone increased significantly, and the median EAET decreased significantly after conventional as well as after robot-assisted LNF. The median postoperative EAET was significantly lower in the robot-assisted (0.2%) than in the conventional LNF group (1%; P = 0.001). Abnormal EAET values were found in 6 of 44 (14%) and in 0 of 44 cases after conventional and robot-assisted LNF, respectively (P = 0.026). Robot-assisted LNF provided a significant gain in postoperative acid reflux parameters compared with the conventional technique. In a challenging clinical setting, such as PPI-refractoriness, in which the efficacy of endoscopic or pharmacological treatment modalities is only moderate, even a small therapeutic gain can be clinically relevant. In centers where robot-assisted LNF is available, it should be preferred to conventional LNF in PPI-refractory GERD.

Third-line rescue therapy with bismuth-containing quadruple regimen after failure of two treatments (with clarithromycin and levofloxacin) for H. pylori infection.

PubMed

Gisbert, J P; Perez-Aisa, A; Rodrigo, L; Molina-Infante, J; Modolell, I; Bermejo, F; Castro-Fernández, M; Antón, R; Sacristán, B; Cosme, A; Barrio, J; Harb, Y; Gonzalez-Barcenas, M; Fernandez-Bermejo, M; Algaba, A; Marín, A C; McNicholl, A G

2014-02-01

Helicobacter pylori eradication therapy with a proton pump inhibitor (PPI), clarithromycin, and amoxicillin fails in >20 % of cases. A rescue therapy with PPI-amoxicillin-levofloxacin still fails in >20 % of patients. To evaluate the efficacy and tolerability of a bismuth-containing quadruple regimen in patients with two consecutive eradication failures. Prospective multicenter study of patients in whom 1st treatment with PPI-clarithromycin-amoxicillin and 2nd with PPI-amoxicillin-levofloxacin had failed. A 3rd eradication regimen with a 7- to 14-day PPI (standard dose b.i.d.), bismuth subcitrate (120 mg q.i.d. or 240 mg b.i.d.), tetracycline (from 250 mg t.i.d. to 500 mg q.i.d.) and metronidazole (from 250 mg t.i.d. to 500 mg q.i.d.). Eradication was confirmed by (13)C-urea-breath-test 4-8 weeks after therapy. Compliance was determined through questioning and recovery of empty medication envelopes. Adverse effects were evaluated by means of a questionnaire. Two hundred patients (mean age 50 years, 55 % females, 20 % peptic ulcer/80 % uninvestigated-functional dyspepsia) were initially included, and two were lost to follow-up. In all, 97 % of patients complied with the protocol. Per-protocol and intention-to-treat eradication rates were 67 % (95 % CI 60-74 %) and 65 % (58-72 %). Adverse effects were reported in 22 % of patients, the most common being nausea (12 %), abdominal pain (11 %), metallic taste (8.5 %), and diarrhea (8 %), none of them severe. A bismuth-containing quadruple regimen is an acceptable third-line strategy and a safe alternative after two previous H. pylori eradication failures with standard clarithromycin- and levofloxacin-containing triple therapies.

The effect of endoscopic fundoplication and proton pump inhibitors on baseline impedance and heartburn severity in GERD patients.

PubMed

Rinsma, N F; Farré, R; Bouvy, N D; Masclee, A A M; Conchillo, J M

2015-02-01

Antireflux therapy may lead to recovery of impaired mucosal integrity in gastro-esophageal reflux disease (GERD) patients as reflected by an increase in baseline impedance. The study objective was to evaluate the effect of endoscopic fundoplication and proton pump inhibitor (PPI) PPI therapy on baseline impedance and heartburn severity in GERD patients. Forty-seven GERD patients randomized to endoscopic fundoplication (n = 32) or PPI therapy (n = 15), and 29 healthy controls were included. Before randomization and 6 months after treatment, baseline impedance was obtained during 24-h pH-impedance monitoring. Heartburn severity was evaluated using the GERD-HRQL questionnaire. Before treatment, baseline impedance in GERD patients was lower than in healthy controls (p < 0.001). Antireflux therapy increased baseline impedance (from 1498 [IQR 951-2472] to 2393 [IQR 1353-3027] Ω, p = 0.001), however it only led to a partial recovery when compared to healthy controls (2393 [IQR 1353-3027] vs 2983 [2335-3810] Ω, p < 0.01). The effect of both treatment options was not significantly different (p = 0.13) despite the increased number of non-acid reflux events in the PPI group. No correlation was found between baseline impedance and GERD symptoms before or after treatment. Reduction in acid reflux by endoscopic fundoplication or PPI therapy leads to an increase in baseline impedance in GERD patients, likely to reflect recovery of mucosal integrity. The impact of non-acid reflux events on esophageal mucosal integrity may be limited as no difference in the increase in baseline impedance was observed after both treatment options. The lack of association between impedance baseline and heartburn severity indicates that other factors may contribute to heartburn perception in GERD. © 2014 John Wiley & Sons Ltd.

A Novel Algorithm for Detecting Protein Complexes with the Breadth First Search

PubMed Central

Tang, Xiwei; Wang, Jianxin; Li, Min; He, Yiming; Pan, Yi

2014-01-01

Most biological processes are carried out by protein complexes. A substantial number of false positives of the protein-protein interaction (PPI) data can compromise the utility of the datasets for complexes reconstruction. In order to reduce the impact of such discrepancies, a number of data integration and affinity scoring schemes have been devised. The methods encode the reliabilities (confidence) of physical interactions between pairs of proteins. The challenge now is to identify novel and meaningful protein complexes from the weighted PPI network. To address this problem, a novel protein complex mining algorithm ClusterBFS (Cluster with Breadth-First Search) is proposed. Based on the weighted density, ClusterBFS detects protein complexes of the weighted network by the breadth first search algorithm, which originates from a given seed protein used as starting-point. The experimental results show that ClusterBFS performs significantly better than the other computational approaches in terms of the identification of protein complexes. PMID:24818139

Genetically Encoded Molecular Tension Probe for Tracing Protein-Protein Interactions in Mammalian Cells.

PubMed

Kim, Sung Bae; Nishihara, Ryo; Citterio, Daniel; Suzuki, Koji

2016-02-17

Optical imaging of protein-protein interactions (PPIs) facilitates comprehensive elucidation of intracellular molecular events. We demonstrate an optical measure for visualizing molecular tension triggered by any PPI in mammalian cells. Twenty-three kinds of candidate designs were fabricated, in which a full-length artificial luciferase (ALuc) was sandwiched between two model proteins of interest, e.g., FKBP and FRB. One of the designs greatly enhanced the bioluminescence in response to varying concentrations of rapamycin. It is confirmed with negative controls that the elevated bioluminescence is solely motivated from the molecular tension. The probe design was further modified toward eliminating the C-terminal end of ALuc and was found to improve signal-to-background ratios, named "a combinational probe". The utilities were elucidated with detailed substrate selectivity, bioluminescence imaging of live cells, and different PPI models. This study expands capabilities of luciferases as a tool for analyses of molecular dynamics and cell signaling in living subjects.

Decreased cerebellar-cerebral connectivity contributes to complex task performance

PubMed Central

Knops, André

2016-01-01

The cerebellum's role in nonmotor processes is now well accepted, but cerebellar interaction with cerebral targets is not well understood. Complex cognitive tasks activate cerebellar, parietal, and frontal regions, but the effective connectivity between these regions has never been tested. To this end, we used psycho-physiological interactions (PPI) analysis to test connectivity changes of cerebellar and parietal seed regions in complex (2-digit by 1-digit multiplication, e.g., 12 × 3) vs. simple (1-digit by 1-digit multiplication, e.g., 4 × 3) task conditions (“complex − simple”). For cerebellar seed regions (lobule VI, hemisphere and vermis), we found significantly decreased cerebellar-parietal, cerebellar-cingulate, and cerebellar-frontal connectivity in complex multiplication. For parietal seed regions (PFcm, PFop, PFm) we found significantly increased parietal-parietal and parietal-frontal connectivity in complex multiplication. These results suggest that decreased cerebellar-cerebral connectivity contributes to complex task performance. Interestingly, BOLD activity contrasts revealed partially overlapping parietal areas of increased BOLD activity but decreased cerebellar-parietal PPI connectivity. PMID:27334957

Features of Protein-Protein Interactions that Translate into Potent Inhibitors: Topology, Surface Area and Affinity

PubMed Central

Smith, Matthew C.; Gestwicki, Jason E.

2013-01-01

Protein-protein interactions (PPIs) control the assembly of multi-protein complexes and, thus, these contacts have enormous potential as drug targets. However, the field has produced a mix of both exciting success stories and frustrating challenges. Here, we review known examples and explore how the physical features of a PPI, such as its affinity, hotspots, off-rates, buried surface area and topology, may influence the chances of success in finding inhibitors. This analysis suggests that concise, tight binding PPIs are most amenable to inhibition. However, it is also clear that emerging technical methods are expanding the repertoire of “druggable” protein contacts and increasing the odds against difficult targets. In particular, natural product-like compound libraries, high throughput screens specifically designed for PPIs and approaches that favor discovery of allosteric inhibitors appear to be attractive routes. The first group of PPI inhibitors has entered clinical trials, further motivating the need to understand the challenges and opportunities in pursuing these types of targets. PMID:22831787

De novo designed library of linear helical peptides: an exploratory tool in the discovery of protein-protein interaction modulators.

PubMed

Bonache, M Ángeles; Balsera, Beatriz; López-Méndez, Blanca; Millet, Oscar; Brancaccio, Diego; Gómez-Monterrey, Isabel; Carotenuto, Alfonso; Pavone, Luigi M; Reille-Seroussi, Marie; Gagey-Eilstein, Nathalie; Vidal, Michel; de la Torre-Martinez, Roberto; Fernández-Carvajal, Asia; Ferrer-Montiel, Antonio; García-López, M Teresa; Martín-Martínez, Mercedes; de Vega, M Jesús Pérez; González-Muñiz, Rosario

2014-05-12

Protein-protein interactions (PPIs) have emerged as important targets for pharmaceutical intervention because of their essential role in numerous physiological and pathological processes, but screening efforts using small-molecules have led to very low hit rates. Linear peptides could represent a quick and effective approach to discover initial PPI hits, particularly if they have inherent ability to adopt specific peptide secondary structures. Here, we address this hypothesis through a linear helical peptide library, composed of four sublibraries, which was designed by theoretical predictions of helicity (Agadir software). The 13-mer peptides of this collection fixes either a combination of three aromatic or two aromatic and one aliphatic residues on one face of the helix (Ac-SSEEX(5)ARNX(9)AAX(12)N-NH2), since these are structural features quite common at PPIs interfaces. The 81 designed peptides were conveniently synthesized by parallel solid-phase methodologies, and the tendency of some representative library components to adopt the intended secondary structure was corroborated through CD and NMR experiments. As proof of concept in the search for PPI modulators, the usefulness of this library was verified on the widely studied p53-MDM2 interaction and on the communication between VEGF and its receptor Flt-1, two PPIs for which a hydrophobic α-helix is essential for the interaction. We have demonstrated here that, in both cases, selected peptides from the library, containing the right hydrophobic sequence of the hot-spot in one of the protein partners, are able to interact with the complementary protein. Moreover, we have discover some new, quite potent inhibitors of the VEGF-Flt-1 interaction, just by replacing one of the aromatic residues of the initial F(5)Y(9)Y(12) peptide by W, in agreement with previous results on related antiangiogenic peptides. Finally, the HTS evaluation of the full collection on thermoTRPs has led to a few antagonists of TRPV1 and TRPA1 channels, which open new avenues on the way to innovative modulators of these channels.

Patient and public involvement in the early stages of clinical trial development: a systematic cohort investigation.

PubMed

Gamble, Carrol; Dudley, Louise; Allam, Alison; Bell, Philip; Goodare, Heather; Hanley, Bec; Preston, Jennifer; Walker, Alison; Williamson, Paula; Young, Bridget

2014-07-23

Randomised controlled trials (RCTs) are considered particularly likely to benefit from patient and public involvement (PPI). Decisions made by professional researchers at the outset may go on to have a significant impact on the potential for PPI contributions. To increase knowledge of PPI within the early development of RCTs by systematically describing the reported level, nature and acceptability of proposed PPI to the funders. Documentation from the outline application process for all RCTs that received funding from the Health Technology Assessment (HTA) Programme 2006-2010 was requested. For each application, data were extracted on trial characteristics, references to PPI in the development of the outline application and funding Board feedback, and plans for PPI in the full application and after the trial was funded. 110 applications were eligible with outline applications available for 90 (82%). The cohort covered a wide range of interventions and conditions. 54% (49/90) provided some information about PPI. 26 (28.9%) indicated PPI within the development of the outline application itself; 32 (35.6%) planned involvement in the full application and 43 (48%) once the trial was funded. Recruitment at diagnosis and surgical interventions were less likely to describe PPI. Blinded trials and trials in which participants may receive placebo only, more frequently described PPI activity. The HTA commissioning Board feedback rarely referred to PPI. Incorporation of PPI within the development of the outline application or specification of plans for future involvement was low. Funder requests for applicants to provide information on PPI and justification for its absence should be welcomed but further research is needed to identify the impact of this on its contributions to research. Comments on PPI by reviewers should be directional rather than state that an increase is required. Challenges facing applicants in initiating PPI prior to funding need to be addressed. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

DCEUS-based focal parametric perfusion imaging of microvessel with single-pixel resolution and high contrast.

PubMed

Wang, Diya; Xiao, Mengnan; Hu, Hong; Zhang, Yu; Su, Zhe; Xu, Shanshan; Zong, Yujin; Wan, Mingxi

2018-03-01

This study aimed to develop a focal microvascular contrast-enhanced ultrasonic parametric perfusion imaging (PPI) scheme to overcome the tradeoff between the resolution, contrast, and accuracy of focal PPI in the tumor. Its resolution was limited by the low signal-to-clutter ratio (SCR) of time-intensity-curves (TICs) induced by multiple limitations, which deteriorated the accuracy and contrast of focal PPI. The scheme was verified by the in-vivo perfusion experiments. Single-pixel TICs were first extracted to ensure PPI with the highest resolution. The SCR of focal TICs in the tumor was improved using respiratory motion compensation combined with detrended fluctuation analysis. The entire and focal PPIs of six perfusion parameters were then accurately created after filtrating the valid TICs and targeted perfusion parameters. Compared with those of the conventional PPIs, the axial and lateral resolutions of focal PPIs were improved by 30.29% (p < .05) and 32.77% (p < .05), respectively; the average contrast and accuracy evaluated by SCR improved by 7.24 ± 4.90 dB (p < .05) and 5.18 ± 1.28 dB (p < .05), respectively. The edge, morphostructure, inhomogeneous hyper-enhanced distribution, and ring-like perfusion features in intratumoral microvessel were accurately distinguished and highlighted by the focal PPIs. The developed focal PPI can assist clinicians in making confirmed diagnoses and in providing appropriate therapeutic strategies for liver tumor. Copyright © 2017 Elsevier B.V. All rights reserved.

Synthesis of polypyrrole within the cell wall of yeast by redox-cycling of [Fe(CN)6](3-)/[Fe(CN)6](4-).

PubMed

Ramanavicius, Arunas; Andriukonis, Eivydas; Stirke, Arunas; Mikoliunaite, Lina; Balevicius, Zigmas; Ramanaviciene, Almira

2016-02-01

Yeast cells are often used as a model system in various experiments. Moreover, due to their high metabolic activity, yeast cells have a potential to be applied as elements in the design of biofuel cells and biosensors. However a wider application of yeast cells in electrochemical systems is limited due to high electric resistance of their cell wall. In order to reduce this problem we have polymerized conducting polymer polypyrrole (Ppy) directly in the cell wall and/or within periplasmic membrane. In this research the formation of Ppy was induced by [Fe(CN)6](3-)ions, which were generated from K4[Fe(CN)6], which was initially added to polymerization solution. The redox process was catalyzed by oxido-reductases, which are present in the plasma membrane of yeast cells. The formation of Ppy was confirmed by spectrophotometry and atomic force microscopy. It was confirmed that the conducting polymer polypyrrole was formed within periplasmic space and/or within the cell wall of yeast cells, which were incubated in solution containing pyrrole, glucose and [Fe(CN)6](4-). After 24h drying at room temperature we have observed that Ppy-modified yeast cell walls retained their initial spherical form. In contrast to Ppy-modified cells, the walls of unmodified yeast have wrinkled after 24h drying. The viability of yeast cells in the presence of different pyrrole concentrations has been evaluated. Copyright © 2015 Elsevier Inc. All rights reserved.

Investigation of candidate genes for osteoarthritis based on gene expression profiles.

PubMed

Dong, Shuanghai; Xia, Tian; Wang, Lei; Zhao, Qinghua; Tian, Jiwei

2016-12-01

To explore the mechanism of osteoarthritis (OA) and provide valid biological information for further investigation. Gene expression profile of GSE46750 was downloaded from Gene Expression Omnibus database. The Linear Models for Microarray Data (limma) package (Bioconductor project, http://www.bioconductor.org/packages/release/bioc/html/limma.html) was used to identify differentially expressed genes (DEGs) in inflamed OA samples. Gene Ontology function enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analysis of DEGs were performed based on Database for Annotation, Visualization and Integrated Discovery data, and protein-protein interaction (PPI) network was constructed based on the Search Tool for the Retrieval of Interacting Genes/Proteins database. Regulatory network was screened based on Encyclopedia of DNA Elements. Molecular Complex Detection was used for sub-network screening. Two sub-networks with highest node degree were integrated with transcriptional regulatory network and KEGG functional enrichment analysis was processed for 2 modules. In total, 401 up- and 196 down-regulated DEGs were obtained. Up-regulated DEGs were involved in inflammatory response, while down-regulated DEGs were involved in cell cycle. PPI network with 2392 protein interactions was constructed. Moreover, 10 genes including Interleukin 6 (IL6) and Aurora B kinase (AURKB) were found to be outstanding in PPI network. There are 214 up- and 8 down-regulated transcription factor (TF)-target pairs in the TF regulatory network. Module 1 had TFs including SPI1, PRDM1, and FOS, while module 2 contained FOSL1. The nodes in module 1 were enriched in chemokine signaling pathway, while the nodes in module 2 were mainly enriched in cell cycle. The screened DEGs including IL6, AGT, and AURKB might be potential biomarkers for gene therapy for OA by being regulated by TFs such as FOS and SPI1, and participating in the cell cycle and cytokine-cytokine receptor interaction pathway. Copyright © 2016 Turkish Association of Orthopaedics and Traumatology. Production and hosting by Elsevier B.V. All rights reserved.

Ultrasonic vocalizations, predictability and sensorimotor gating in the rat.

PubMed

Webber, Emily S; Mankin, David E; McGraw, Justin J; Beckwith, Travis J; Cromwell, Howard C

2013-09-15

Prepulse inhibition (PPI) is a measure of sensorimotor gating in diverse groups of animals including humans. Emotional states can influence PPI in humans both in typical subjects and in individuals with mental illness. Little is known about emotional regulation during PPI in rodents. We used ultrasonic vocalization recording to monitor emotional states in rats during PPI testing. We altered the predictability of the PPI trials to examine any alterations in gating and emotional regulation. We also examined PPI in animals selectively bred for high or low levels of 50kHz USV emission. Rats emitted high levels of 22kHz calls consistently throughout the PPI session. USVs were sensitive to prepulses during the PPI session similar to startle. USV rate was sensitive to predictability among the different levels tested and across repeated experiences. Startle and inhibition of startle were not affected by predictability in a similar manner. No significant differences for PPI or startle were found related to the different levels of predictability; however, there was a reduction in USV signals and an enhancement of PPI after repeated exposure. Animals selectively bred to emit high levels of USVs emitted significantly higher levels of USVs during the PPI session and a reduced ASR compared to the low and random selective lines. Overall, the results support the idea that PPI tests in rodents induce high levels of negative affect and that manipulating emotional styles of the animals alters the negative impact of the gating session as well as the intensity of the startle response. Copyright © 2013 Elsevier B.V. All rights reserved.

Management of Gastroesophageal Reflux Disease.

PubMed

Gyawali, C Prakash; Fass, Ronnie

2018-01-01

Management of gastroesophageal reflux disease (GERD) commonly starts with an empiric trial of proton pump inhibitor (PPI) therapy and complementary lifestyle measures, for patients without alarm symptoms. Optimization of therapy (improving compliance and timing of PPI doses), or increasing PPI dosage to twice daily in select circumstances, can reduce persistent symptoms. Patients with continued symptoms can be evaluated with endoscopy and tests of esophageal physiology, to better determine their disease phenotype and optimize treatment. Laparoscopic fundoplication, magnetic sphincter augmentation, and endoscopic therapies can benefit patients with well-characterized GERD. Patients with functional diseases that overlap with or mimic GERD can also be treated with neuromodulators (primarily antidepressants), or psychological interventions (psychotherapy, hypnotherapy, cognitive and behavioral therapy). Future approaches to treatment of GERD include potassium-competitive acid blockers, reflux-reducing agents, bile acid binders, injection of inert substances into the esophagogastric junction, and electrical stimulation of the lower esophageal sphincter. Copyright © 2018 AGA Institute. Published by Elsevier Inc. All rights reserved.

The Promiscuous Protein Binding Ability of Erythrosine B Studied by Metachromasy (Metachromasia)

PubMed Central

Ganesan, Lakshmi; Buchwald, Peter

2013-01-01

The present study aims to elucidate aspects of the protein binding ability of erythrosine B (ErB), a poly-iodinated xanthene dye and an FDA-approved food colorant (FD&C Red No. 3), which we have identified recently as a promiscuous inhibitor of protein–protein interactions (PPI) with a remarkably consistent median inhibitory concentration (IC50) in the 5–30 µM range. Because ErB exhibits metachromasy, i.e., color change upon binding to several proteins, we exploited this property to quantify its binding to proteins such as bovine serum albumin (BSA) and CD40L (CD154) and to determine the corresponding binding constants (Kd) and stoichiometry (nb) using spectrophotometric methods. Binding was reversible and the estimated affinities for both protein targets obtained here (Kd values of 14 and 20 µM for BSA and CD40L, respectively) were in good agreement with that expected from the protein–protein interaction (PPI) inhibitory activity of ErB. A stoichiometry greater than one was observed both for CD40L and BSA binding (nb of 5–6 and 8–9 for BSA and CD40L, respectively) indicating the possibility of nonspecific binding of the flat an rigid ErB molecule at multiple sites, which could explain the promiscuous PPI inhibitory activity if some of these overlap with the binding site of the protein partner and interfere with the binding. PMID:23456742

Reconstruction of the experimentally supported human protein interactome: what can we learn?

PubMed

Klapa, Maria I; Tsafou, Kalliopi; Theodoridis, Evangelos; Tsakalidis, Athanasios; Moschonas, Nicholas K

2013-10-02

Understanding the topology and dynamics of the human protein-protein interaction (PPI) network will significantly contribute to biomedical research, therefore its systematic reconstruction is required. Several meta-databases integrate source PPI datasets, but the protein node sets of their networks vary depending on the PPI data combined. Due to this inherent heterogeneity, the way in which the human PPI network expands via multiple dataset integration has not been comprehensively analyzed. We aim at assembling the human interactome in a global structured way and exploring it to gain insights of biological relevance. First, we defined the UniProtKB manually reviewed human "complete" proteome as the reference protein-node set and then we mined five major source PPI datasets for direct PPIs exclusively between the reference proteins. We updated the protein and publication identifiers and normalized all PPIs to the UniProt identifier level. The reconstructed interactome covers approximately 60% of the human proteome and has a scale-free structure. No apparent differentiating gene functional classification characteristics were identified for the unrepresented proteins. The source dataset integration augments the network mainly in PPIs. Polyubiquitin emerged as the highest-degree node, but the inclusion of most of its identified PPIs may be reconsidered. The high number (>300) of connections of the subsequent fifteen proteins correlates well with their essential biological role. According to the power-law network structure, the unrepresented proteins should mainly have up to four connections with equally poorly-connected interactors. Reconstructing the human interactome based on the a priori definition of the protein nodes enabled us to identify the currently included part of the human "complete" proteome, and discuss the role of the proteins within the network topology with respect to their function. As the network expansion has to comply with the scale-free theory, we suggest that the core of the human interactome has essentially emerged. Thus, it could be employed in systems biology and biomedical research, despite the considerable number of currently unrepresented proteins. The latter are probably involved in specialized physiological conditions, justifying the scarcity of related PPI information, and their identification can assist in designing relevant functional experiments and targeted text mining algorithms.

Contractor Past Performance Information (PPI) in Source Selection: A Comparison Study of Public and Private Sector

DTIC Science & Technology

2005-03-17

private sector . However, along the way, Government and private sector industry have begun to disagree about how PPI is collected and how PPI is used. Industry prefers a passive system of collecting delivery and quality data during contract performance, while the Federal Government uses both a passive system (similar to industry) as well as an active system of pulling PPI during contract performance. Industry uses PPI to establish and maintain a preferred vendor list from which to solicit bids, quotes, or proposals, while government uses PPI to assess

Effects of the PPy layer thickness on Co-PPy composite films

NASA Astrophysics Data System (ADS)

Haciismailoglu, Murside

2015-11-01

Co-PPy composite films were electrodeposited on ITO substrate from two different solutions potentiostatically. Firstly, the PPy layers with the thicknesses changing from 20 to 5000 nm were produced on ITO. Then Co was electrodeposited on these PPy/ITO substrates with a charge density of 1000 mC cm-2. The electrochemical properties were investigated by the current density-time transients and the variation of the elapsed time for the Co deposition depending on the PPy layer thickness. X-ray photoelectron (XPS) spectra indicated the presence of both Co metal and its oxides on the surface. The weak reflections of the Co3O4, CoO and hcp Co were detected by the X-ray diffraction (XRD) technique. According to scanning electron microscopy (SEM) images, the thickness of the PPy layer strongly affects the Co nucleation. The composite films with the PPy layer thinner than 200 nm and thicker than 2000 nm have an isotropic magnetic behavior due to the symmetrical crystal field. The composite films with the PPy layer thicknesses between 200 and 2000 nm have an anisotropic magnetic behavior attributable to the deterioration of this symmetrical crystal field by the PPy bubbles on the surface. All films are hard magnetic material, since the coercivities are larger than 125 Oe.

Molecular dysexpression in gastric cancer revealed by integrated analysis of transcriptome data.

PubMed

Li, Xiaomei; Dong, Weiwei; Qu, Xueling; Zhao, Huixia; Wang, Shuo; Hao, Yixin; Li, Qiuwen; Zhu, Jianhua; Ye, Min; Xiao, Wenhua

2017-05-01

Gastric cancer (GC) is often diagnosed in the advanced stages and is associated with a poor prognosis. Obtaining an in depth understanding of the molecular mechanisms of GC has lagged behind compared with other cancers. This study aimed to identify candidate biomarkers for GC. An integrated analysis of microarray datasets was performed to identify differentially expressed genes (DEGs) between GC and normal tissues. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were then performed to identify the functions of the DEGs. Furthermore, a protein-protein interaction (PPI) network of the DEGs was constructed. The expression levels of the DEGs were validated in human GC tissues using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). A set of 689 DEGs were identified in GC tissues, as compared with normal tissues, including 202 upregulated DEGs and 487 downregulated DEGs. The KEGG pathway analysis suggested that various pathways may play important roles in the pathology of GC, including pathways related to protein digestion and absorption, extracellular matrix-receptor interaction, and the metabolism of xenobiotics by cytochrome P450. The PPI network analysis indicated that the significant hub proteins consisted of SPP1, TOP2A and ARPC1B. RT-qPCR validation indicated that the expression levels of the top 10 most significantly dysexpressed genes were consistent with the illustration of the integrated analysis. The present study yielded a reference list of reliable DEGs, which represents a robust pool of candidates for further evaluation of GC pathogenesis and treatment.

Comparison of the gene expression profiles between gallstones and gallbladder polyps.

PubMed

Li, Quanfu; Ge, Xin; Xu, Xu; Zhong, Yonggang; Qie, Zengwang

2014-01-01

Gallstones and gallbladder polyps (GPs) are two major types of gallbladder diseases that share multiple common symptoms. However, their pathological mechanism remains largely unknown. The aim of our study is to identify gallstones and GPs related-genes and gain an insight into the underlying genetic basis of these diseases. We enrolled 7 patients with gallstones and 2 patients with GP for RNA-Seq and we conducted functional enrichment analysis and protein-protein interaction (PPI) networks analysis for identified differentially expressed genes (DEGs). RNA-Seq produced 41.7 million in gallstones and 32.1 million pairs in GPs. A total of 147 DEGs was identified between gallstones and GPs. We found GO terms for molecular functions significantly enriched in antigen binding (GO:0003823, P=5.9E-11), while for biological processes, the enriched GO terms were immune response (GO:0006955, P=2.6E-15), and for cellular component, the enriched GO terms were extracellular region (GO:0005576, P=2.7E-15). To further evaluate the biological significance for the DEGs, we also performed the KEGG pathway enrichment analysis. The most significant pathway in our KEGG analysis was Cytokine-cytokine receptor interaction (P=7.5E-06). PPI network analysis indicated that the significant hub proteins containing S100A9 (S100 calcium binding protein A9, Degree=94) and CR2 (complement component receptor 2, Degree=8). This present study suggests some promising genes and may provide a clue to the role of these genes playing in the development of gallstones and GPs.

Regulatory interactions between long noncoding RNA LINC00968 and miR-9-3p in non-small cell lung cancer: A bioinformatic analysis based on miRNA microarray, GEO and TCGA.

PubMed

Li, Dong-Yao; Chen, Wen-Jie; Shang, Jun; Chen, Gang; Li, Shi-Kang

2018-06-01

Long non-coding RNAs (lncRNAs) have been demonstrated to mediate carcinogenesis in various types of cancer. However, the regulatory role of lncRNA LINC00968 in lung adenocarcinoma remains unclear. The microRNA (miRNA) expression in LINC00968-overexpressing human lung adenocarcinoma A549 cells was detected using miRNA microarray analysis. miR-9-3p was selected for further analysis, and its expression was verified in the Gene Expression Omnibus (GEO) database. In addition, the regulatory axis of LINC00968 was validated using The Cancer Genome Atlas (TCGA) database. Results of the GEO database indicated miR-9-3p expression in lung adenocarcinoma was significantly higher compared with normal tissues. Functional enrichment analyses of the target genes of miR-9-3p indicated protein binding and the AMP-activated protein kinase pathway were the most enriched Gene Ontology and KEGG terms, respectively. Combining target genes with the correlated genes of LINC00968 and miR-9-3p, 120 objective genes were obtained, which were used to construct a protein-protein interaction (PPI) network. Cyclin A2 (CCNA2) was identified to have a vital role in the PPI network. Significant correlations were detected between LINC00968, miR-9-3p and CCNA2 in lung adenocarcinoma. The LINC00968/miR-9-3p/CCNA2 regulatory axis provides a new foundation for further evaluating the regulatory mechanisms of LINC00968 in lung adenocarcinoma.

Integrative Analysis of GWASs, Human Protein Interaction, and Gene Expression Identified Gene Modules Associated With BMDs

PubMed Central

He, Hao; Zhang, Lei; Li, Jian; Wang, Yu-Ping; Zhang, Ji-Gang; Shen, Jie; Guo, Yan-Fang

2014-01-01

Context: To date, few systems genetics studies in the bone field have been performed. We designed our study from a systems-level perspective by integrating genome-wide association studies (GWASs), human protein-protein interaction (PPI) network, and gene expression to identify gene modules contributing to osteoporosis risk. Methods: First we searched for modules significantly enriched with bone mineral density (BMD)-associated genes in human PPI network by using 2 large meta-analysis GWAS datasets through a dense module search algorithm. One included 7 individual GWAS samples (Meta7). The other was from the Genetic Factors for Osteoporosis Consortium (GEFOS2). One was assigned as a discovery dataset and the other as an evaluation dataset, and vice versa. Results: In total, 42 modules and 129 modules were identified significantly in both Meta7 and GEFOS2 datasets for femoral neck and spine BMD, respectively. There were 3340 modules identified for hip BMD only in Meta7. As candidate modules, they were assessed for the biological relevance to BMD by gene set enrichment analysis in 2 expression profiles generated from circulating monocytes in subjects with low versus high BMD values. Interestingly, there were 2 modules significantly enriched in monocytes from the low BMD group in both gene expression datasets (nominal P value <.05). Two modules had 16 nonredundant genes. Functional enrichment analysis revealed that both modules were enriched for genes involved in Wnt receptor signaling and osteoblast differentiation. Conclusion: We highlighted 2 modules and novel genes playing important roles in the regulation of bone mass, providing important clues for therapeutic approaches for osteoporosis. PMID:25119315

[Adherence with proton pump inhibitor therapy, by continuously taking nonsteroidal anti-inflammatory drugs].

PubMed

Pimanov, S I; Makarenko, E V; Dikareva, E A

2015-01-01

To estimate the impact of adherence with proton pump inhibitor (PPI) therapy on the incidence of nonsteroidal anti-inflammatory drug (NSAID)-induced gastropathy (NSAID gastropathy) in patients with rheumatoid arthritis (RA). PPI pharmacotherapy adherence was estimated using the Medication Adherence Questionnaire (MAQ) in 92 patients with RA, including 32 patients did not take a PPI and 60 used a PPI. The groups were matched for age, disease duration, and used NSAIDs. All those asked underwent video esophagogastroduodenoscopy. According to the data of MAQ survey, low, moderate, and high adherence subgroups could be identified among the patients treated with a PPI. NSAID gastropathy was detected in 43.8% of the patients taking no PPI, in 50% of those with low PPI treatment adherence, in 12.5% with moderate adherence, and in 4.5% with high adherence. In the patients with low adherence to PPI therapy, NSAID gastropathy was recorded 11 times more frequently than in those with high adherence (c2 = 7.77; p = 0.005). This condition occurred in 28.6% of the patients taking NSAID without preventively using a PPI in the absence of risk factors for NSAID gastropathy. Only 36.7% patients who had been recommended to use a PPI for the prevention of NSAID gastropathy strictly observed their doctor's directions. Low PPI pharmacotherapy adherence may serve as an additional risk factor for NSAID gastropathy in patients in whom preventive antisecretory therapy used in combination with NSAID is indicated.

Effects of proton pump inhibitors on lung cancer precise radiotherapy-induced radiation pneumonitis.

PubMed

Su, QiaoLi; Wang, Duoning; Yuan, Bo; Liu, Feng; Lei, Yi; Li, Shuangqing

2014-11-01

The objective of this study was to explore the effects of proton pump inhibitors (PPIs) on the development and prognosis of lung cancer precise radiotherapy-induced radiation pneumonitis. Clinical materials of 84 lung cancer patients who had radiation pneumonitis after precise radiotherapy were retrospectively analyzed, and the patients were divided into PPI group and control group, according to whether or not PPIs were applied. The development and prognosis of patients and the effects of different doses of PPI on patient condition from two groups were compared. There were 57 PPI cases in PPI group and 27 cases in control group. Basic characteristics of patients were not statistically different between the two groups; however, white blood cell count, oxygenation indexes, blood gas pH, and lung imaging index were significantly different (p < 0.05), indicating that radiation pneumonitis tended to be more severe in PPI group. As regards effects of PPI on prognosis of two groups, remission rate of radiation pneumonia in PPI group was significantly less than that of the control group. Among 57 cases in PPI group, there were 31 patients applied with PPI ≤ 1DDD and 31 patients applied with PPI > 1DDD. In comparison of the various parameters of patients, 7 days after being applied with different doses of PPI, there were no significant differences between the parameters of radiation pneumonitis. PPIs should be cautiously utilized to avoid the effects of lung cancer radiotherapy-induced radiation pneumonia.

Potential mechanism of corpus-predominant gastritis after PPI therapy in Helicobacter pylori-positive patients with GERD.

PubMed

Mukaisho, Ken-ichi; Hagiwara, Tadashi; Nakayama, Takahisa; Hattori, Takanori; Sugihara, Hiroyuki

2014-09-14

The long-term use of proton pump inhibitors (PPIs) exacerbates corpus atrophic gastritis in patients with Helicobacter pylori (H. pylori) infection. To identify a potential mechanism for this change, we discuss interactions between pH, bile acids, and H. pylori. Duodenogastric reflux, which includes bile, occurs in healthy individuals, and bile reflux is increased in patients with gastroesophageal reflux disease (GERD). Diluted human plasma and bile acids have been found to be significant chemoattractants and chemorepellents, respectively, for the bacillus H. pylori. Although only taurine conjugates, with a pKa of 1.8-1.9, are soluble in an acidic environment, glycine conjugates, with a pKa of 4.3-5.2, as well as taurine-conjugated bile acids are soluble in the presence of PPI therapy. Thus, the soluble bile acid concentrations in the gastric contents of patients with GERD after continuous PPI therapy are considerably higher than that in those with intact acid production. In the distal stomach, the high concentration of soluble bile acids is likely to act as a bactericide or chemorepellent for H. pylori. In contrast, the mucous layer in the proximal stomach has an optimal bile concentration that forms chemotactic gradients with plasma components required to direct H. pylori to the epithelial surface. H. pylori may then colonize in the stomach body rather than in the pyloric antrum, which may explain the occurrence of corpus-predominant gastritis after PPI therapy in H. pylori-positive patients with GERD.

Evidence of Probabilistic Behaviour in Protein Interaction Networks

DTIC Science & Technology

2008-01-31

Evidence of degree-weighted connectivity in nine PPI networks. a, Homo sapiens (human); b, Drosophila melanogaster (fruit fly); c-e, Saccharomyces...illustrates maps for the networks of Homo sapiens and Dro- sophila melanogaster, while maps for the remaining net- works are provided in Additional file 2. As...protein-protein interaction networks. a, Homo sapiens ; b, Drosophila melanogaster. Distances shown as average shortest path lengths L(k1, k2) between

Refractory gastroesophageal reflux disease

PubMed Central

Subramanian, Charumathi Raghu; Triadafilopoulos, George

2015-01-01

Gastroesophageal reflux disease (GERD) is a condition that develops when the reflux of stomach contents into the esophagus causes troublesome symptoms, esophageal injury, and/or complications. Use of proton pump inhibitors (PPI) remains the standard therapy for GERD and is effective in most patients. Those whose symptoms are refractory to PPIs should be evaluated further and other treatment options should be considered, according to individual patient characteristics. Response to PPIs could be total (no symptoms), partial (residual breakthrough symptoms), or absent (no change in symptoms). Patients experiencing complete response do not usually need further management. Patients with partial response can be treated surgically or by using emerging endoscopic therapies. Patients who exhibit no response to PPI need further evaluation to rule out other causes. PMID:25274499

The effects of the preferential 5-HT2A agonist psilocybin on prepulse inhibition of startle in healthy human volunteers depend on interstimulus interval.

PubMed

Vollenweider, Franz X; Csomor, Philipp A; Knappe, Bernhard; Geyer, Mark A; Quednow, Boris B

2007-09-01

Schizophrenia patients exhibit impairments in prepulse inhibition (PPI) of the startle response. Hallucinogenic 5-HT(2A) receptor agonists are used for animal models of schizophrenia because they mimic some symptoms of schizophrenia in humans and induce PPI deficits in animals. Nevertheless, one report indicates that the 5-HT(2A) receptor agonist psilocybin increases PPI in healthy humans. Hence, we investigated these inconsistent results by assessing the dose-dependent effects of psilocybin on PPI in healthy humans. Sixteen subjects each received placebo or 115, 215, and 315 microg/kg of psilocybin at 4-week intervals in a randomized and counterbalanced order. PPI at 30-, 60-, 120-, 240-, and 2000-ms interstimulus intervals (ISIs) was measured 90 and 165 min after drug intake, coinciding with the peak and post-peak effects of psilocybin. The effects of psilocybin on psychopathological core dimensions and sustained attention were assessed by the Altered States of Consciousness Rating Scale (5D-ASC) and the Frankfurt Attention Inventory (FAIR). Psilocybin dose-dependently reduced PPI at short (30 ms), had no effect at medium (60 ms), and increased PPI at long (120-2000 ms) ISIs, without affecting startle reactivity or habituation. Psilocybin dose-dependently impaired sustained attention and increased all 5D-ASC scores with exception of Auditory Alterations. Moreover, psilocybin-induced impairments in sustained attention performance were positively correlated with reduced PPI at the 30 ms ISI and not with the concomitant increases in PPI observed at long ISIs. These results confirm the psilocybin-induced increase in PPI at long ISIs and reveal that psilocybin also produces a decrease in PPI at short ISIs that is correlated with impaired attention and consistent with deficient PPI in schizophrenia.

Electrically controlled drug release from nanostructured polypyrrole coated on titanium

NASA Astrophysics Data System (ADS)

Sirivisoot, Sirinrath; Pareta, Rajesh; Webster, Thomas J.

2011-02-01

Previous studies have demonstrated that multi-walled carbon nanotubes grown out of anodized nanotubular titanium (MWNT-Ti) can be used as a sensing electrode for various biomedical applications; such sensors detected the redox reactions of certain molecules, specifically proteins deposited by osteoblasts during extracellular matrix bone formation. Since it is known that polypyrrole (PPy) can release drugs upon electrical stimulation, in this study antibiotics (penicillin/streptomycin, P/S) or an anti-inflammatory drug (dexamethasone, Dex), termed PPy[P/S] or PPy[Dex], respectively, were electrodeposited in PPy on titanium. The objective of the present study was to determine if such drugs can be released from PPy on demand and (by applying a voltage) control cellular behavior important for orthopedic applications. Results showed that PPy films possessed nanometer-scale roughness as analyzed by atomic force microscopy. X-ray photoelectron spectroscopy confirmed the presence of P/S and Dex encapsulated within the PPy films. Results from cyclic voltammetry showed that 80% of the drugs were released on demand when sweep voltages were applied for five cycles at a scan rate of 0.1 V s - 1. Furthermore, osteoblast (bone-forming cells) and fibroblast (fibrous tissue-forming cells) adhesion were determined on the PPy films. Results showed that PPy[Dex] enhanced osteoblast adhesion after 4 h of culture compared to plain Ti. PPy-Ti (with or without anionic drug doping) inhibited fibroblast adhesion compared to plain Ti. These in vitro results confirmed that electrodeposited PPy[P/S] and PPy[Dex] can release drugs on demand to potentially fight bacterial infection, reduce inflammation, promote bone growth or reduce fibroblast functions, further implicating the use of such materials as implant sensors.

Reflux parameters as modified by laparoscopic fundoplication in 40 patients with heartburn/regurgitation persisting despite PPI therapy: a study using impedance-pH monitoring.

PubMed

Frazzoni, Marzio; Conigliaro, Rita; Melotti, Gianluigi

2011-04-01

Patients with typical reflux symptoms (heartburn/regurgitation) persisting despite proton pump inhibitor (PPI) therapy are not uncommon. Impedance-pH monitoring detects gastroesophageal reflux at all pH levels and may establish if ongoing symptoms on PPI therapy are associated with acid/nonacid reflux. Laparoscopic fundoplication is a therapeutic option in such patients but reflux parameters on PPI therapy and after intervention and their relationship with symptom persistence/remission have been scarcely studied. The aim of this study was to assess reflux parameters and their relationship with symptoms before and after laparoscopic fundoplication, on and off PPI therapy, respectively, in patients with PPI-unresponsive heartburn/regurgitation and with a positive symptom-reflux association and/or abnormal reflux parameters detected on PPI therapy. Impedance-pH monitoring was performed on high-dose PPI therapy and 3 months after laparoscopic fundoplication, off PPI therapy, in 40 patients with PPI-unresponsive heartburn/regurgitation. Symptoms were scored by a validated questionnaire. Esophageal acid exposure time as well as the number of total and proximal reflux events and of acid and weakly acidic refluxes decreased significantly after surgery: normal values were found in 100, 77, 95, 92 and 65% of cases, respectively. Weakly alkaline refluxes increased significantly postoperatively but neither before nor after intervention were associated with symptoms. All patients reported total/subtotal remission of heartburn/regurgitation 3 months after surgery. Laparoscopic fundoplication improves acid and weakly acidic reflux parameters when compared with PPI therapy. This improvement justifies the very high post-surgical symptom remission rate that we observed. Prolonged follow-up is warranted but our findings strongly support the surgical option in PPI failures.

Proton Pump Inhibitor Initiation and Withdrawal affects Gut Microbiota and Readmission Risk in Cirrhosis.

PubMed

Bajaj, Jasmohan S; Acharya, Chathur; Fagan, Andrew; White, Melanie B; Gavis, Edith; Heuman, Douglas M; Hylemon, Phillip B; Fuchs, Michael; Puri, Puneet; Schubert, Mitchell L; Sanyal, Arun J; Sterling, Richard K; Stravitz, R Todd; Siddiqui, Mohammad S; Luketic, Velimir; Lee, Hannah; Sikaroodi, Masoumeh; Gillevet, Patrick M

2018-06-06

Cirrhosis is associated with gut microbial dysbiosis, high readmissions and proton pump inhibitor (PPI) overuse, which could be inter-linked. Our aim was to determine the effect of PPI use, initiation and withdrawl on gut microbiota and readmissions in cirrhosis. Four cohorts were enrolled. Readmissions study: Cirrhotic inpatients were followed throughout the hospitalization and 30/90-days post-discharge. PPI initiation, withdrawal/continuation patterns were analyzed between those with/without readmissions. Cross-sectional microbiota study: Cirrhotic outpatients and controls underwent stool microbiota analysis. Beneficial autochthonous and oral-origin taxa analysis vis-à-vis PPI use was performed. Longitudinal studies: Two cohorts of decompensated cirrhotic outpatients were enrolled. Patients on chronic unindicated PPI use were withdrawn for 14 days. Patients not on PPI were started on omeprazole for 14 days. Microbial analysis for oral-origin taxa was performed pre/post-intervention. Readmissions study: 343 inpatients (151 on admission PPI) were enrolled. 21 were withdrawn and 45 were initiated on PPI resulting in a PPI use increase of 21%. PPIs were associated with higher 30 (p = 0.002) and 90-day readmissions (p = 0.008) independent of comorbidities, medications, MELD and age. Cross-sectional microbiota: 137 cirrhotics (59 on PPI) and 45 controls (17 on PPI) were included. PPI users regardless of cirrhosis had higher oral-origin microbiota while cirrhotics on PPI had lower autochthonous taxa compared to the rest. Longitudinal studies: Fifteen decompensated cirrhotics tolerated omeprazole initiation with an increase in oral-origin microbial taxa compared to baseline. PPIs were withdrawn from an additional 15 outpatients, which resulted in a significant reduction of oral-origin taxa compared to baseline. PPIs modulate readmission risk and microbiota composition in cirrhosis, which responds to withdrawal. The systematic withdrawal and judicious use of PPIs is needed from a clinical and microbiological perspective in decompensated cirrhosis.

Cost Effectiveness of Gastroprotection with Proton Pump Inhibitors in Older Low-Dose Acetylsalicylic Acid Users in the Netherlands.

PubMed

Chau, Sek Hung; Sluiter, Reinier L; Kievit, Wietske; Wensing, Michel; Teichert, Martina; Hugtenburg, Jacqueline G

2017-05-01

The present study aimed to assess the cost effectiveness of concomitant proton pump inhibitor (PPI) treatment in low-dose acetylsalicylic acid (LDASA) users at risk of upper gastrointestinal (UGI) adverse effects as compared with no PPI co-medication with attention to the age-dependent influence of PPI-induced adverse effects. We used a Markov model to compare the strategy of PPI co-medication with no PPI co-medication in older LDASA users at risk of UGI adverse effects. As PPIs reduce the risk of UGI bleeding and dyspepsia, these risk factors were modelled together with PPI adverse effects for LDASA users 60-69, 70-79 (base case) and 80 years and older. Incremental cost-utility ratios (ICURs) were calculated as cost per quality-adjusted life-year (QALY) gained per age category. Furthermore, a budget impact analysis assessed the expected changes in expenditure of the Dutch healthcare system following the adoption of PPI co-treatment in all LDASA users potentially at risk of UGI adverse effects. PPI co-treatment of 70- to 79-year-old LDASA users, as compared with no PPI, resulted in incremental costs of €100.51 at incremental effects of 0.007 QALYs with an ICUR of €14,671/QALY. ICURs for 60- to 69-year-old LDASA users were €13,264/QALY and €64,121/QALY for patients 80 years and older. Initiation of PPI co-treatment for all Dutch LDASA users of 60 years and older at risk of UGI adverse effects but not prescribed a PPI (19%) would have cost €1,280,478 in the first year (year 2013 values). PPI co-medication in LDASA users at risk of UGI adverse effects is generally cost effective. However, this strategy becomes less cost effective with higher age, particularly in patients aged 80 years and older, mainly due to the increased risks of PPI-induced adverse effects.

Frequency of reporting on patient and public involvement (PPI) in research studies published in a general medical journal: a descriptive study.

PubMed

Price, Amy; Schroter, Sara; Snow, Rosamund; Hicks, Melissa; Harmston, Rebecca; Staniszewska, Sophie; Parker, Sam; Richards, Tessa

2018-03-23

While documented plans for patient and public involvement (PPI) in research are required in many grant applications, little is known about how frequently PPI occurs in practice. Low levels of reported PPI may mask actual activity due to limited PPI reporting requirements. This research analysed the frequency and types of reported PPI in the presence and absence of a journal requirement to include this information. A before and after comparison of PPI reported in research papers published in The BMJ before and 1 year after the introduction of a journal policy requiring authors to report if and how they involved patients and the public within their papers. Between 1 June 2013 and 31 May 2014, The BMJ published 189 research papers and 1 (0.5%) reported PPI activity. From 1 June 2015 to 31 May 2016, following the introduction of the policy, The BMJ published 152 research papers of which 16 (11%) reported PPI activity. Patients contributed to grant applications in addition to designing studies through to coauthorship and participation in study dissemination. Patient contributors were often not fully acknowledged; 6 of 17 (35%) papers acknowledged their contributions and 2 (12%) included them as coauthors. Infrequent reporting of PPI activity does not appear to be purely due to a failure of documentation. Reporting of PPI activity increased after the introduction of The BMJ 's policy, but activity both before and after was low and reporting was inconsistent in quality. Journals, funders and research institutions should collaborate to move us from the current situation where PPI is an optional extra to one where PPI is fully embedded in practice throughout the research process. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

A Fast Response Ammonia Sensor Based on Coaxial PPy-PAN Nanofiber Yarn.

PubMed

Liu, Penghong; Wu, Shaohua; Zhang, Yue; Zhang, Hongnan; Qin, Xiaohong

2016-06-23

Highly orientated polypyrrole (PPy)-coated polyacrylonitrile (PAN) (PPy-PAN) nanofiber yarn was prepared with an electrospinning technique and in-situ chemical polymerization. The morphology and chemical structure of PPy-PAN nanofiber yarn was characterized by scanning electron microscopy (SEM), field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), and fourier transform infrared spectroscopy (FTIR), which indicated that the PPy as the shell layer was homogeneously and uniformly polymerized on the surface of PAN nanofiber. The effects of different concentration of doping acid on the responses of PPy-PAN nanofiber yarn sensor were investigated. The electrical responses of the gas sensor based on the PPy-PAN nanofiber yarn to ammonia were investigated at room temperature. The nanoyarn sensor composed of uniaxially aligned PPy-PAN nanofibers with a one-dimensional structure exhibited a transient response, and the response time was less than 1 s. The excellent sensing properties mentioned above give rise to good potential application prospects in the field of ammonia sensor.

Asfotase-α improves bone growth, mineralization and strength in mouse models of neurofibromatosis type-1

PubMed Central

de la Croix Ndong, Jean; Makowski, Alexander James; Uppuganti, Sasidhar; Vignaux, Guillaume; Ono, Koichiro; Perrien, Daniel S.; Joubert, Simon; Baglio, Serena R.; Granchi, Donatella; Stevenson, David A.; Rios, Jonathan J.; Nyman, Jeffry S.; Elefteriou, Florent

2014-01-01

Mineralization of the skeleton depends on the balance between levels of pyrophosphate (PPi), an inhibitor of hydroxyapatite formation, and phosphate generated from PPi breakdown by alkaline phosphatase (ALP). We report here that ablation of Nf1, encoding the RAS/GTPase–activating protein neurofibromin, in bone–forming cells leads to supraphysiologic PPi accumulation, caused by a chronic ERK–dependent increase in genes promoting PPi synthesis and extracellular transport, namely Enpp1 and Ank. It also prevents BMP2–induced osteoprogenitor differentiation and, consequently, expression of ALP and PPi breakdown, further contributing to PPi accumulation. The short stature, impaired bone mineralization and strength in mice lacking Nf1 in osteochondroprogenitors or osteoblasts could be corrected by enzyme therapy aimed at reducing PPi concentration. These results establish neurofibromin as an essential regulator of bone mineralization, suggest that altered PPi homeostasis contributes to the skeletal dysplasiae associated with neurofibromatosis type-1 (NF1), and that some of the NF1 skeletal conditions might be preventable pharmacologically. PMID:24997609

Cost effectiveness in Canada of a multidrug prepackaged regimen (Hp-PAC)+ for Helicobacter pylori eradication.

PubMed

Agro, K; Blackhouse, G; Goeree, R; Willan, A R; Huang, J Q; Hunt, R H; O'Brien, B J

2001-01-01

To assess the cost effectiveness of a multidrug prepackaged regimen for Helicobacter pylori, the Hp-PAC (lansoprazole 30mg, clarithromycin 500 mg, amoxicillin 1 g, all twice daily), relative to alternative pharmacological strategies in the management of confirmed duodenal ulcer over a 1-year period from 2 perspectives: (i) a strict healthcare payer perspective (Ontario Ministry of Health) excluding the patient copayment; and (ii) a healthcare payer perspective including the patient copayment. A decision-analytical model was developed to estimate expected per patient costs [1998 Canadian dollars ($ Can)], weeks without ulcer and symptomatic ulcer recurrences for the Hp-PAC compared with: proton pump inhibitor (PPI)-clarithromycin-amoxicillin (PPI-CA), PPI-clarithromycin-metronidazole (PPI-CM), PPI-amoxicillin-metronidazole (PPI-AM) and ranitidine-bismuthmetronidazole-tetracycline (RAN-BMT). All PPI-based regimens had higher expected costs but better outcomes relative to RAN-BMT. From a strict healthcare payer perspective, PPI-CM ($Can 209) yielded lower expected costs than PPI-CA ($Can 221) and slightly lower costs than Hp-PAC ($Can 211). However, these 3 regimens all shared identical outcomes (51.2 weeks without ulcer). When the current Ontario, Canada, $Can 2 patient copayment was added to the dispensing fee, Hp-PAC yielded lower costs ($Can 214) than PPI-CM ($Can 216). From a strict healthcare payer perspective, Hp-PAC is weakly dominated by PPI-CM with an incremental cost effectiveness (relative to RAN-BMT) of $Can 5.77 per ulcer week averted. When the patient copayment is added to this perspective, Hp-PAC weakly dominates PPI-CM ($Can 5 per ulcer week averted). Regardless of perspective, Hp-PAC and PPI-CM differed by only $Can 2 per patient over 1 year and the expected time without ulcer was 51.2 weeks for both. More data on the clinical and statistical differences in H. pylori eradication with Hp-PAC and PPI-CM would be useful. This analysis does not in clude the possible advantage of Hp-PAC in terms of compliance and antibacterial resistance.

Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes

PubMed Central

Mazloom, Amin R.; Dannenfelser, Ruth; Clark, Neil R.; Grigoryan, Arsen V.; Linder, Kathryn M.; Cardozo, Timothy J.; Bond, Julia C.; Boran, Aislyn D. W.; Iyengar, Ravi; Malovannaya, Anna; Lanz, Rainer B.; Ma'ayan, Avi

2011-01-01

Coregulator proteins (CoRegs) are part of multi-protein complexes that transiently assemble with transcription factors and chromatin modifiers to regulate gene expression. In this study we analyzed data from 3,290 immuno-precipitations (IP) followed by mass spectrometry (MS) applied to human cell lines aimed at identifying CoRegs complexes. Using the semi-quantitative spectral counts, we scored binary protein-protein and domain-domain associations with several equations. Unlike previous applications, our methods scored prey-prey protein-protein interactions regardless of the baits used. We also predicted domain-domain interactions underlying predicted protein-protein interactions. The quality of predicted protein-protein and domain-domain interactions was evaluated using known binary interactions from the literature, whereas one protein-protein interaction, between STRN and CTTNBP2NL, was validated experimentally; and one domain-domain interaction, between the HEAT domain of PPP2R1A and the Pkinase domain of STK25, was validated using molecular docking simulations. The scoring schemes presented here recovered known, and predicted many new, complexes, protein-protein, and domain-domain interactions. The networks that resulted from the predictions are provided as a web-based interactive application at http://maayanlab.net/HT-IP-MS-2-PPI-DDI/. PMID:22219718

P-Finder: Reconstruction of Signaling Networks from Protein-Protein Interactions and GO Annotations.

PubMed

Young-Rae Cho; Yanan Xin; Speegle, Greg

2015-01-01

Because most complex genetic diseases are caused by defects of cell signaling, illuminating a signaling cascade is essential for understanding their mechanisms. We present three novel computational algorithms to reconstruct signaling networks between a starting protein and an ending protein using genome-wide protein-protein interaction (PPI) networks and gene ontology (GO) annotation data. A signaling network is represented as a directed acyclic graph in a merged form of multiple linear pathways. An advanced semantic similarity metric is applied for weighting PPIs as the preprocessing of all three methods. The first algorithm repeatedly extends the list of nodes based on path frequency towards an ending protein. The second algorithm repeatedly appends edges based on the occurrence of network motifs which indicate the link patterns more frequently appearing in a PPI network than in a random graph. The last algorithm uses the information propagation technique which iteratively updates edge orientations based on the path strength and merges the selected directed edges. Our experimental results demonstrate that the proposed algorithms achieve higher accuracy than previous methods when they are tested on well-studied pathways of S. cerevisiae. Furthermore, we introduce an interactive web application tool, called P-Finder, to visualize reconstructed signaling networks.

Struct2Net: a web service to predict protein–protein interactions using a structure-based approach

PubMed Central

Singh, Rohit; Park, Daniel; Xu, Jinbo; Hosur, Raghavendra; Berger, Bonnie

2010-01-01

Struct2Net is a web server for predicting interactions between arbitrary protein pairs using a structure-based approach. Prediction of protein–protein interactions (PPIs) is a central area of interest and successful prediction would provide leads for experiments and drug design; however, the experimental coverage of the PPI interactome remains inadequate. We believe that Struct2Net is the first community-wide resource to provide structure-based PPI predictions that go beyond homology modeling. Also, most web-resources for predicting PPIs currently rely on functional genomic data (e.g. GO annotation, gene expression, cellular localization, etc.). Our structure-based approach is independent of such methods and only requires the sequence information of the proteins being queried. The web service allows multiple querying options, aimed at maximizing flexibility. For the most commonly studied organisms (fly, human and yeast), predictions have been pre-computed and can be retrieved almost instantaneously. For proteins from other species, users have the option of getting a quick-but-approximate result (using orthology over pre-computed results) or having a full-blown computation performed. The web service is freely available at http://struct2net.csail.mit.edu. PMID:20513650

Counselors' Perspectives of Positive Psychology for the Treatment of Addiction: A Mixed Methods Pilot Study.

PubMed

Krentzman, Amy R; Barker, Stacey L

2016-01-01

Little is known about the use of positive psychology interventions (PPI) in addictions treatment. Questionnaires and interviews with alcohol and substance use disorder counselors explored theories of how PPIs might work, the degree to which they are used, and downsides. Results suggested that positive and pathology-based themes were attended in equal proportion, that substance abuse treatment should help clients develop a good life in recovery; that counselors already use PPI; and that PPI might counter negative cognitions and affect. Reservations for using PPI included relying on PPI exclusively and employing PPI indiscriminately without regard to client characteristics.

Counselors’ Perspectives of Positive Psychology for the Treatment of Addiction: A Mixed Methods Pilot Study

PubMed Central

Krentzman, Amy R.; Barker, Stacey L.

2016-01-01

Little is known about the use of positive psychology interventions (PPI) in addictions treatment. Questionnaires and interviews with alcohol and substance use disorder counselors explored theories of how PPIs might work, the degree to which they are used, and downsides. Results suggested that positive and pathology-based themes were attended in equal proportion, that substance abuse treatment should help clients develop a good life in recovery; that counselors already use PPI; and that PPI might counter negative cognitions and affect. Reservations for using PPI included relying on PPI exclusively and employing PPI indiscriminately without regard to client characteristics. PMID:27980355

Characterization of recombinant PPi-dependent 6-phosphofructokinases from Methylosinus trichosporium OB3b and Methylobacterium nodulans ORS 2060.

PubMed

Rozova, O N; Khmelenina, V N; Trotsenko, Y A

2012-03-01

The properties of the purified recombinant PPi-dependent 6-phosphofructokinases (PPi-PFKs) from the methanotroph Methylosinus trichosporium OB3b and rhizospheric phytosymbiont Methylobacterium nodulans ORS 2060 were determined. The dependence of activities of PPi-PFK-His(6)-tag from Ms. trichosporium OB3b (6 × 45 kDa) and PPi-PFK from Mb. nodulans ORS 2060 (4 × 43 kDa) on the concentrations of substrates of forward and reverse reactions conformed to Michaelis-Menten kinetics. Besides fructose-6-phosphate, the enzymes also phosphorylated sedoheptulose-7-phosphate. ADP or AMP (1 mM each) inhibited activity of the Ms. trichosporium PPi-PFK but did not affect the activity of the Mb. nodulans enzyme. Preference of PPi-PFKs to fructose-1,6-bisphosphate implied a predominant function of the enzymes in hexose phosphate synthesis in these bacteria. PPi-PFKs from the methylotrophs have low similarity of translated amino acid sequences (17% identity) and belong to different phylogenetic subgroups of type II 6-phosphofructokinases. The relationship of PPi-PFKs with microaerophilic character of Ms. trichosporium OB3b and adaptation of Mb. nodulans ORS 2060 to anaerobic phase of phytosymbiosis are discussed.

Three-dimensional graphene-polypyrrole hybrid electrochemical actuator

NASA Astrophysics Data System (ADS)

Liu, Jia; Wang, Zhi; Zhao, Yang; Cheng, Huhu; Hu, Chuangang; Jiang, Lan; Qu, Liangti

2012-11-01

The advancement of mechanical actuators benefits from the development of new structural materials with prominent properties. A novel three-dimensional (3D) hydrothermally converted graphene and polypyrrole (G-PPy) hybrid electrochemical actuator is presented, which is prepared via a convenient hydrothermal process, followed by in situ electropolymerization of pyrrole. The 3D pore-interconnected G-PPy pillar exhibits strong actuation responses superior to pure graphene and PPy film. In response to the low potentials of +/-0.8 V, the saturated strain of 3D G-PPy pillar can reach a record of 2.5%, which is more than 10 times higher than that of carbon nanotube film and about 3 times that of unitary graphene film under an applied potential of +/-1.2 V. Also, the 3D G-PPy actuator exhibits high actuation durability with high operating load as demonstrated by an 11 day continuous measurement. Finally, a proof-of-concept application of 3D G-PPy as smart filler for on/off switch is also demonstrated, which indicates the great potential of the 3D G-PPy structure developed in this study for advanced actuator systems.The advancement of mechanical actuators benefits from the development of new structural materials with prominent properties. A novel three-dimensional (3D) hydrothermally converted graphene and polypyrrole (G-PPy) hybrid electrochemical actuator is presented, which is prepared via a convenient hydrothermal process, followed by in situ electropolymerization of pyrrole. The 3D pore-interconnected G-PPy pillar exhibits strong actuation responses superior to pure graphene and PPy film. In response to the low potentials of +/-0.8 V, the saturated strain of 3D G-PPy pillar can reach a record of 2.5%, which is more than 10 times higher than that of carbon nanotube film and about 3 times that of unitary graphene film under an applied potential of +/-1.2 V. Also, the 3D G-PPy actuator exhibits high actuation durability with high operating load as demonstrated by an 11 day continuous measurement. Finally, a proof-of-concept application of 3D G-PPy as smart filler for on/off switch is also demonstrated, which indicates the great potential of the 3D G-PPy structure developed in this study for advanced actuator systems. Electronic supplementary information (ESI) available: Experimental setup for fabrication of G-PPy hybrid structure, and movie showing the on/off response of G-PPy filler. See DOI: 10.1039/c2nr32699j

PPi-dependent phosphofructotransferase (phosphofructokinase) activity in the mollicutes (mycoplasma) Acholeplasma laidlawii.

PubMed Central

Pollack, J D; Williams, M V

1986-01-01

A PPi-dependent phosphofructotransferase (PPi-fructose 6-phosphate 1-phosphotransferase, EC 2.7.1.90) which catalyzes the conversion of fructose 6 phosphate (F-6-P) to fructose 1,6-bisphosphate (F-1, 6-P2) was isolated from a cytoplasmic fraction of Acholeplasma laidlawii B-PG9 and partially purified (430-fold). PPi was required as the phosphate donor. ATP, dATP, CTP, dCTP, GTP, dGTP, UTP, dUTP, ITP, TTP, ADP, or Pi could not substitute for PPi. The PPi-dependent reaction (2.0 mM PPi) was not altered in the presence of any of these nucleotides (2.0 mM) or in the presence of smaller (less than or equal to 300 microM) amounts of fructose 2,6-bisphosphate, (NH4)2SO4, AMP, citrate, GDP, or phosphoenolpyruvate. Mg2+ and a pH of 7.4 were required for maximum activity. The partially purified enzyme in sucrose density gradient experiments had an approximate molecular weight of 74,000 and a sedimentation coefficient of 6.7. A second form of the enzyme (molecular weight, 37,000) was detected, although in relatively smaller amounts, by using Blue Sepharose matrix when performing electrophoresis experiments. The back reaction, F-1, 6-P2 to F-6-P, required Pi; arsenate could substitute for Pi, but not PPi or any other nucleotide tested. The computer-derived kinetic constants (+/- standard deviation) for the reaction in the PPi-driven direction of F-1, 6-P2 were as follows: v, 38.9 +/- 0.48 mM min-1; Ka(PPi), 0.11 +/- 0.04 mM; Kb(F-6-P), 0.65 +/- 0.15 mM; and Kia(PPi), 0.39 +/- 0.11 mM. A. laidlawii B-PG9 required PPi not only for the PPi-phosphofructotransferase reaction which we describe but also for purine nucleoside kinase activity. a dependency unknown in any other organism. In A. laidlawii B-PG9, the PPi requirement may be met by reactions in this organism already known to synthesize PPi (e.g., dUTPase and purine nucleobase phosphoribosyltransferases). In almost all other cells, the conversion of F-6-P to F-1,6-P2 is ATP dependent, and the reaction is generally considered to be the rate-limiting step of glycolysis. The ability of A. laidlawii B-PG9 and one other acholeplasma to use PPi instead of ATP as an energy source may offer these cytochrome-deficient organisms some metabolic advantage and may represent a conserved metabolic remnant of an earlier evolutionary process. PMID:3001032

Proton Pump Inhibitor Use and the Risk of Chronic Kidney Disease.

PubMed

Lazarus, Benjamin; Chen, Yuan; Wilson, Francis P; Sang, Yingying; Chang, Alex R; Coresh, Josef; Grams, Morgan E

2016-02-01

Proton pump inhibitors (PPIs) are among the most commonly used drugs worldwide and have been linked to acute interstitial nephritis. Less is known about the association between PPI use and chronic kidney disease (CKD). To quantify the association between PPI use and incident CKD in a population-based cohort. In total, 10,482 participants in the Atherosclerosis Risk in Communities study with an estimated glomerular filtration rate of at least 60 mL/min/1.73 m(2) were followed from a baseline visit between February 1, 1996, and January 30, 1999, to December 31, 2011. The data was analyzed from May 2015 to October 2015. The findings were replicated in an administrative cohort of 248,751 patients with an estimated glomerular filtration rate of at least 60 mL/min/1.73 m(2) from the Geisinger Health System. Self-reported PPI use in the Atherosclerosis Risk in Communities study or an outpatient PPI prescription in the Geisinger Health System replication cohort. Histamine2 (H2) receptor antagonist use was considered a negative control and active comparator. Incident CKD was defined using diagnostic codes at hospital discharge or death in the Atherosclerosis Risk in Communities Study, and by a sustained outpatient estimated glomerular filtration rate of less than 60 mL/min/1.73 m(2) in the Geisinger Health System replication cohort. Among 10,482 participants in the Atherosclerosis Risk in Communities study, the mean (SD) age was 63.0 (5.6) years, and 43.9% were male. Compared with nonusers, PPI users were more often of white race, obese, and taking antihypertensive medication. Proton pump inhibitor use was associated with incident CKD in unadjusted analysis (hazard ratio [HR], 1.45; 95% CI, 1.11-1.90); in analysis adjusted for demographic, socioeconomic, and clinical variables (HR, 1.50; 95% CI, 1.14-1.96); and in analysis with PPI ever use modeled as a time-varying variable (adjusted HR, 1.35; 95% CI, 1.17-1.55). The association persisted when baseline PPI users were compared directly with H2 receptor antagonist users (adjusted HR, 1.39; 95% CI, 1.01-1.91) and with propensity score-matched nonusers (HR, 1.76; 95% CI, 1.13-2.74). In the Geisinger Health System replication cohort, PPI use was associated with CKD in all analyses, including a time-varying new-user design (adjusted HR, 1.24; 95% CI, 1.20-1.28). Twice-daily PPI dosing (adjusted HR, 1.46; 95% CI, 1.28-1.67) was associated with a higher risk than once-daily dosing (adjusted HR, 1.15; 95% CI, 1.09-1.21). Proton pump inhibitor use is associated with a higher risk of incident CKD. Future research should evaluate whether limiting PPI use reduces the incidence of CKD.