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Sample records for functional tertiary interactions

  1. Cooperative Tertiary Interaction Network Guides RNA Folding

    Energy Technology Data Exchange (ETDEWEB)

    Behrouzi, Reza; Roh, Joon Ho; Kilburn, Duncan; Briber, R.M.; Woodson, Sarah A. (JHU); (Maryland)

    2013-04-08

    Noncoding RNAs form unique 3D structures, which perform many regulatory functions. To understand how RNAs fold uniquely despite a small number of tertiary interaction motifs, we mutated the major tertiary interactions in a group I ribozyme by single-base substitutions. The resulting perturbations to the folding energy landscape were measured using SAXS, ribozyme activity, hydroxyl radical footprinting, and native PAGE. Double- and triple-mutant cycles show that most tertiary interactions have a small effect on the stability of the native state. Instead, the formation of core and peripheral structural motifs is cooperatively linked in near-native folding intermediates, and this cooperativity depends on the native helix orientation. The emergence of a cooperative interaction network at an early stage of folding suppresses nonnative structures and guides the search for the native state. We suggest that cooperativity in noncoding RNAs arose from natural selection of architectures conducive to forming a unique, stable fold.

  2. Tertiary interactions within the ribosomal exit tunnel.

    Science.gov (United States)

    Kosolapov, Andrey; Deutsch, Carol

    2009-04-01

    Although tertiary folding of whole protein domains is prohibited by the cramped dimensions of the ribosomal tunnel, dynamic tertiary interactions may permit folding of small elementary units within the tunnel. To probe this possibility, we used a beta-hairpin and an alpha-helical hairpin from the cytosolic N terminus of a voltage-gated potassium channel and determined a probability of folding for each at defined locations inside and outside the tunnel. Minimalist tertiary structures can form near the exit port of the tunnel, a region that provides an entropic window for initial exploration of local peptide conformations. Tertiary subdomains of the nascent peptide fold sequentially, but not independently, during translation. These studies offer an approach for diagnosing the molecular basis for folding defects that lead to protein malfunction and provide insight into the role of the ribosome during early potassium channel biogenesis.

  3. RNA tertiary interactions in the large ribosomal subunit: The A-minor motif

    Energy Technology Data Exchange (ETDEWEB)

    Nissen, Poul; Ippolito, Joseph A.; Ban, Nenad; Moore, Peter B.; Steitz, Thomas A. (Yale University); (Yale University); (Yale Unversity)

    2009-10-07

    Analysis of the 2.4-{angstrom} resolution crystal structure of the large ribosomal subunit from Haloarcula marismortui reveals the existence of an abundant and ubiquitous structural motif that stabilizes RNA tertiary and quaternary structures. This motif is termed the A-minor motif, because it involves the insertion of the smooth, minor groove edges of adenines into the minor groove of neighboring helices, preferentially at C-G base pairs, where they form hydrogen bonds with one or both of the 2' OHs of those pairs. A-minor motifs stabilize contacts between RNA helices, interactions between loops and helices, and the conformations of junctions and tight turns. The interactions between the 3' terminal adenine of tRNAs bound in either the A site or the P site with 23S rRNA are examples of functionally significant A-minor interactions. The A-minor motif is by far the most abundant tertiary structure interaction in the large ribosomal subunit; 186 adenines in 23S and 5S rRNA participate, 68 of which are conserved. It may prove to be the universally most important long-range interaction in large RNA structures.

  4. Comparative sequence and structure analysis reveals the conservation and diversity of nucleotide positions and their associated tertiary interactions in the riboswitches.

    Directory of Open Access Journals (Sweden)

    Sri D Appasamy

    Full Text Available The tertiary motifs in complex RNA molecules play vital roles to either stabilize the formation of RNA 3D structure or to provide important biological functionality to the molecule. In order to better understand the roles of these tertiary motifs in riboswitches, we examined 11 representative riboswitch PDB structures for potential agreement of both motif occurrences and conservations. A total of 61 unique tertiary interactions were found in the reference structures. In addition to the expected common A-minor motifs and base-triples mainly involved in linking distant regions the riboswitch structures three highly conserved variants of A-minor interactions called G-minors were found in the SAM-I and FMN riboswitches where they appear to be involved in the recognition of the respective ligand's functional groups. From our structural survey as well as corresponding structure and sequence alignments, the agreement between motif occurrences and conservations are very prominent across the representative riboswitches. Our analysis provide evidence that some of these tertiary interactions are essential components to form the structure where their sequence positions are conserved despite a high degree of diversity in other parts of the respective riboswitches sequences. This is indicative of a vital role for these tertiary interactions in determining the specific biological function of riboswitch.

  5. Formation of Tertiary Interactions during rRNA GTPase Center Folding.

    Science.gov (United States)

    Rau, Michael J; Welty, Robb; Tom Stump, W; Hall, Kathleen B

    2015-08-28

    The 60-nt GTPase center (GAC) of 23S rRNA has a phylogenetically conserved secondary structure with two hairpin loops and a 3-way junction. It folds into an intricate tertiary structure upon addition of Mg(2+) ions, which is stabilized by the L11 protein in cocrystal structures. Here, we monitor the kinetics of its tertiary folding and Mg(2+)-dependent intermediate states by observing selected nucleobases that contribute specific interactions to the GAC tertiary structure in the cocrystals. The fluorescent nucleobase 2-aminopurine replaced three individual adenines, two of which make long-range stacking interactions and one that also forms hydrogen bonds. Each site reveals a unique response to Mg(2+) addition and temperature, reflecting its environmental change from secondary to tertiary structure. Stopped-flow fluorescence experiments revealed that kinetics of tertiary structure formation upon addition of MgCl2 are also site specific, with local conformational changes occurring from 5 ms to 4s and with global folding from 1 to 5s. Site-specific substitution with (15)N-nucleobases allowed observation of stable hydrogen bond formation by NMR experiments. Equilibrium titration experiments indicate that a stable folding intermediate is present at stoichiometric concentrations of Mg(2+) and suggest that there are two initial sites of Mg(2+) ion association.

  6. Observation of long-range tertiary interactions during ligand binding by the TPP riboswitch aptamer.

    Science.gov (United States)

    Duesterberg, Van K; Fischer-Hwang, Irena T; Perez, Christian F; Hogan, Daniel W; Block, Steven M

    2015-12-28

    The thiamine pyrophosphate (TPP) riboswitch is a cis-regulatory element in mRNA that modifies gene expression in response to TPP concentration. Its specificity is dependent upon conformational changes that take place within its aptamer domain. Here, the role of tertiary interactions in ligand binding was studied at the single-molecule level by combined force spectroscopy and Förster resonance energy transfer (smFRET), using an optical trap equipped for simultaneous smFRET. The 'Force-FRET' approach directly probes secondary and tertiary structural changes during folding, including events associated with binding. Concurrent transitions observed in smFRET signals and RNA extension revealed differences in helix-arm orientation between two previously-identified ligand-binding states that had been undetectable by spectroscopy alone. Our results show that the weaker binding state is able to bind to TPP, but is unable to form a tertiary docking interaction that completes the binding process. Long-range tertiary interactions stabilize global riboswitch structure and confer increased ligand specificity.

  7. Apolipoprotein E: isoform specific differences in tertiary structure and interaction with amyloid-β in human Alzheimer brain.

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    Phillip B Jones

    Full Text Available We applied a novel application of FLIM-FRET to in situ measurement and quantification of protein interactions to explore isoform specific differences in Aβ-ApoE interaction and ApoE tertiary conformation in senile plaques in human Alzheimer brain. ApoE3 interacts more closely with Aβ than ApoE4, but a greater proportion of Aβ molecules within plaques are decorated with ApoE4 than ApoE3, lending strong support to the hypothesis that isoform specific differences in ApoE are linked with Aβ deposition. We found an increased number of ApoE N-terminal fragments in ApoE4 plaques, consistent with the observation that ApoE4 is more easily cleaved than ApoE3. In addition, we measured a small but significant isoform specific difference in ApoE domain interaction. Based on our in situ data, supported by traditional biochemical data, we propose a pathway by which isoform specific conformational differences increase the level of cleavage at the hinge region of ApoE4, leading to a loss of ApoE function to mediate clearance of Aβ and thereby increase the risk of AD for carriers of the APOEε4 allele.

  8. Interactions to the fifth thropic level: secondary and tertiary parasitoi wasps show extraordinary efficiency in utilizing host resources

    NARCIS (Netherlands)

    Harvey, J.A.; Wagenaar, R.; Bezemer, T.M.

    2009-01-01

    Parasitoid wasps are highly efficient organisms at utilizing and assimilating limited resources from their hosts. This study explores interactions over three trophic levels, from the third (primary parasitoid) to the fourth (secondary parasitoid) and terminating in the fifth (tertiary parasitoid). H

  9. Interaction Of Calcium Phosphate Nanoparticles With Human Chorionic Gonadotropin Modifies Secondary And Tertiary Protein Structure

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    Al-Hakeim Hussein K

    2015-12-01

    Full Text Available Calcium phosphate nanoparticles (CaPNP have good biocompatibility and bioactivity inside human body. In this study, the interaction between CaPNP and human chorionic gonadotropin (hCG was analyzed to determine the changes in the protein structure in the presence of CaPNP and the quantity of protein adsorbed on the CaPNP surface. The results showed a significant adsorption of hCG on the CaPNP nanoparticle surface. The optimal fit was achieved using the Sips isotherm equation with a maximum adsorption capacity of 68.23 µg/mg. The thermodynamic parameters, including ∆H° and ∆G°, of the adsorption process are positive, whereas ∆S° is negative. The circular dichroism results of the adsorption of hCG on CaPNP showed the changes in its secondary structure; such changes include the decomposition of α-helix strand and the increase in β-pleated sheet and random coil percentages. Fluorescence study indicated minimal changes in the tertiary structure near the microenvironment of the aromatic amino acids such as tyrosine and phenyl alanine caused by the interaction forces between the CaPNP and hCG protein. The desorption process showed that the quantity of the hCG desorbed significantly increases as temperature increases, which indicates the weak forces between hCG and the surface.

  10. Phylogenetic Gaussian process model for the inference of functionally important regions in protein tertiary structures.

    Science.gov (United States)

    Huang, Yi-Fei; Golding, G Brian

    2014-01-01

    A critical question in biology is the identification of functionally important amino acid sites in proteins. Because functionally important sites are under stronger purifying selection, site-specific substitution rates tend to be lower than usual at these sites. A large number of phylogenetic models have been developed to estimate site-specific substitution rates in proteins and the extraordinarily low substitution rates have been used as evidence of function. Most of the existing tools, e.g. Rate4Site, assume that site-specific substitution rates are independent across sites. However, site-specific substitution rates may be strongly correlated in the protein tertiary structure, since functionally important sites tend to be clustered together to form functional patches. We have developed a new model, GP4Rate, which incorporates the Gaussian process model with the standard phylogenetic model to identify slowly evolved regions in protein tertiary structures. GP4Rate uses the Gaussian process to define a nonparametric prior distribution of site-specific substitution rates, which naturally captures the spatial correlation of substitution rates. Simulations suggest that GP4Rate can potentially estimate site-specific substitution rates with a much higher accuracy than Rate4Site and tends to report slowly evolved regions rather than individual sites. In addition, GP4Rate can estimate the strength of the spatial correlation of substitution rates from the data. By applying GP4Rate to a set of mammalian B7-1 genes, we found a highly conserved region which coincides with experimental evidence. GP4Rate may be a useful tool for the in silico prediction of functionally important regions in the proteins with known structures.

  11. Lateral interactions at functional monolayers

    NARCIS (Netherlands)

    Hsu, Shu Han

    2010-01-01

    Molecular nanostructures are important in the emerging field of nanoscience, because of the tunability of the properties of these structures. Nanostructures based on molecular interactions can be manipulated by selectively modifying specific functional groups while leaving the rest of the structures

  12. Assessment of drug-drug interactions among renal failure patients of nephrology ward in a south Indian tertiary care hospital

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    Mylapuram Rama

    2012-01-01

    Full Text Available Polypharmacy is common in drug prescriptions of chronic kidney disease patients. A study of the prescription patterns of drugs with potential interactions would be of interest to prevent drug related adverse events. A prospective observational study of six months (Dec 2009-May 2010 was carried out among the chronic kidney disease patients admitted to the nephrology ward of a South Indian tertiary care hospital. The pattern and rates of drug-drug interactions seen in the prescriptions of these patients was studied. Among the 205 prescriptions included, a total of 474 interactions were reported, making 2.7 interactions per prescription with incidence rates of 76.09%. Around 19.62% of interactions were of major severity. Most common interactions were found between ascorbic acid and cyanocobalamine (12.45%, clonidine and metoprolol (3.80% respectively. Hypo or hypertension (31.65%, decreased drug efficacy (29.11% and hypo or hyperglycemia (14.14%, were the most commonly reported clinical outcomes of the drug interactions. Cardiovascular drugs (calcium channel blockers and beta blockers; 52% constitute the major class of drugs involved in interactions. As most of the interactions had a delayed onset, long term follow-up is essential to predict the clinically significant outcomes of these interactions. Hence, drug interactions are commonly seen in the prescriptions of chronic kidney disease patients which can lead to serious adverse events if not detected early. Need for collaboration with a clinical pharmacist and electronic surveillance, which are absent in developing countries like India, is emphatic.

  13. A Highly Coupled Network of Tertiary Interactions in the SAM-I Riboswitch and Their Role in Regulatory Tuning.

    Science.gov (United States)

    Wostenberg, Christopher; Ceres, Pablo; Polaski, Jacob T; Batey, Robert T

    2015-11-06

    RNA folding in vivo is significantly influenced by transcription, which is not necessarily recapitulated by Mg(2+)-induced folding of the corresponding full-length RNA in vitro. Riboswitches that regulate gene expression at the transcriptional level are an ideal system for investigating this aspect of RNA folding as ligand-dependent termination is obligatorily co-transcriptional, providing a clear readout of the folding outcome. The folding of representative members of the SAM-I family of riboswitches has been extensively analyzed using approaches focusing almost exclusively upon Mg(2+) and/or S-adenosylmethionine (SAM)-induced folding of full-length transcripts of the ligand binding domain. To relate these findings to co-transcriptional regulatory activity, we have investigated a set of structure-guided mutations of conserved tertiary architectural elements of the ligand binding domain using an in vitro single-turnover transcriptional termination assay, complemented with phylogenetic analysis and isothermal titration calorimetry data. This analysis revealed a conserved internal loop adjacent to the SAM binding site that significantly affects ligand binding and regulatory activity. Conversely, most single point mutations throughout key conserved features in peripheral tertiary architecture supporting the SAM binding pocket have relatively little impact on riboswitch activity. Instead, a secondary structural element in the peripheral subdomain appears to be the key determinant in observed differences in regulatory properties across the SAM-I family. These data reveal a highly coupled network of tertiary interactions that promote high-fidelity co-transcriptional folding of the riboswitch but are only indirectly linked to regulatory tuning.

  14. Requirement for a conserved, tertiary interaction in the core of 23S ribosomal RNA

    DEFF Research Database (Denmark)

    Aagaard, C; Douthwaite, S

    1994-01-01

    A putative base-pairing interaction that determines the folding of the central region of 23S rRNA has been investigated by mutagenesis. Each of the possible base substitutions has been made at the phylogenetically covariant positions adenine-1262 (A1262) and U2017 in Escherichia coli 23S rRNA....... Every substitution that disrupts the potential for Watson-Crick base pairing between these positions reduces or abolishes the participation of 23S rRNA in protein synthesis. All mutant 23S rRNAs are assembled into 50S subunits, but the mutant subunits are less able to stably interact with 30S subunits...... to form translationally active ribosomes. The function of 23S rRNA is largely reestablished by introduction of an alternative G1262.C2017 or U1262.A2017 pair, although neither of these supports polysome formation quite as effectively as the wild-type pair. A 23S rRNA with a C1262.G2017 pair...

  15. Nitrile-functionalized tertiary amines as highly efficient and reversible SO2 absorbents.

    Science.gov (United States)

    Hong, Sung Yun; Kim, Heehwan; Kim, Young Jin; Jeong, Junkyo; Cheong, Minserk; Lee, Hyunjoo; Kim, Hoon Sik; Lee, Je Seung

    2014-01-15

    Three different types of nitrile-functionalized amines, including 3-(N,N-diethylamino)propionitrile (DEAPN), 3-(N,N-dibutylamino)propionitrile (DBAPN), and N-methyl-N,N-dipropionitrile amine (MADPN) were synthesized, and their SO2 absorption performances were evaluated and compared with those of hydroxy-functionalized amines such as N,N-diethyl-N-ethanol amine (DEEA), N,N-dibutyl-N-ethanol amine (DBEA), and N-methyl-N,N-diethanol amine (MDEA). Absorption-desorption cycle experiments clearly demonstrate that the nitrile-functionalized amines are more efficient than the hydroxy-functionalized amines in terms of absorption rate and regenerability. Computational calculations with DBEA and DBAPN revealed that DBEA bearing a hydroxyethyl group chemically interacts with SO2 through oxygen atom, forming an ionic compound with a covalently bound OSO2(-) group. On the contrary, DBAPN bearing a nitrile group physically interacts with SO2 through the nitrogen and the hydrogen atoms of the two methylene groups adjacent to the amino and nitrile functionalities. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. INCIDENCE OF POLYPHARMACY INDUCED DRUG INTERACTION IN A TERTIARY CARE HOSPITAL

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    Nimmy N. John*, R.H. Udupi and K.M. Binu

    2012-07-01

    Full Text Available Drug interaction represents a major problem in day- to- day practice. The incidence of adverse reactions increases almost exponentially as the number of drugs co prescribed rises, and this is in part due to interaction. Critically ill, chronically ill and elderly patients are particularly at risk of drug interactions due to polypharmacy as well as impaired homeostatic mechanisms. The study was aimed to assess polypharmacy and drug interaction in the prescriptions. The study was carried out by taking 200 prescriptions from different departments of our hospital and assessed the drug interaction through Micromedex and Drugs update. Polypharmacy was assessed using Prescribing indicators in WHO drug use indicators. Polypharmacy was observed in 85% of the prescriptions and drug interaction was observed in 58.5% of the prescriptions.

  17. The Prevalence and Symptoms Characteristic of Functional Constipation Using Rome III Diagnostic Criteria among Tertiary Education Students

    Science.gov (United States)

    2016-01-01

    Background and Aims Functional constipation is very common with heterogeneous symptoms that have substantial impact on patient quality of life as well as medical resources which are rarely reported as life-threatening. The aim of this study is to examine the prevalence and symptoms characteristic of functional constipation (FC) by using Rome III diagnostic criteria among tertiary education students with an intention to introduce treatment in the future. Methods Demographic, socio-economics characteristics and symptoms of FC using the Rome III criteria were sought using a questionnaire administered to Malaysian students in a tertiary education setting. Other data obtained were the general health status, lifestyle factors and anthropometric measurements. Using a simple random sampling method, a total of 1662 students were recruited in the study with a response rate of 95.0%. Sampled data are presented as frequency and percentage and stratified accordingly into categories for Chi-square analysis. Results The prevalence of functional constipation among the students was 16.2%, with a significantly higher prevalence among women (17.4%) than men (12.5%). Hard or lumpy stool, incomplete evacuation, anorectal obstruction and straining were reported as the commonest symptoms experienced. Type 3 was the most frequent stool consistency experienced among the constipated individuals (35.2%). Only 4.4% of individuals reported having less than three defecations per week. Using univariable analysis, FC was significantly associated with sex (odds ratio: 1.48, 95% CI: 1.06–2.06) and age group (odds ratio: 1.34, 95% CI: 1.01–1.79) with P value problem among tertiary education students (16.2%), with significantly more prevalence among the female respondents. Early detection of symptoms and further intervention studies focusing on treatment recommendation in improving the symptoms are essential. PMID:27997551

  18. Discovering functional interaction patterns in protein-protein interaction networks

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    Can Tolga

    2008-06-01

    Full Text Available Abstract Background In recent years, a considerable amount of research effort has been directed to the analysis of biological networks with the availability of genome-scale networks of genes and/or proteins of an increasing number of organisms. A protein-protein interaction (PPI network is a particular biological network which represents physical interactions between pairs of proteins of an organism. Major research on PPI networks has focused on understanding the topological organization of PPI networks, evolution of PPI networks and identification of conserved subnetworks across different species, discovery of modules of interaction, use of PPI networks for functional annotation of uncharacterized proteins, and improvement of the accuracy of currently available networks. Results In this article, we map known functional annotations of proteins onto a PPI network in order to identify frequently occurring interaction patterns in the functional space. We propose a new frequent pattern identification technique, PPISpan, adapted specifically for PPI networks from a well-known frequent subgraph identification method, gSpan. Existing module discovery techniques either look for specific clique-like highly interacting protein clusters or linear paths of interaction. However, our goal is different; instead of single clusters or pathways, we look for recurring functional interaction patterns in arbitrary topologies. We have applied PPISpan on PPI networks of Saccharomyces cerevisiae and identified a number of frequently occurring functional interaction patterns. Conclusion With the help of PPISpan, recurring functional interaction patterns in an organism's PPI network can be identified. Such an analysis offers a new perspective on the modular organization of PPI networks. The complete list of identified functional interaction patterns is available at http://bioserver.ceng.metu.edu.tr/PPISpan/.

  19. Structure-Function Relationships of a Tertiary Amine-Based Polycarboxybetaine.

    Science.gov (United States)

    Lee, Chen-Jung; Wu, Haiyan; Tang, Qiong; Cao, Bin; Wang, Huifeng; Cong, Hongbo; Zhe, Jiang; Xu, Fujian; Cheng, Gang

    2015-09-15

    Zwitterionic polycarboxybetaine (PCB) materials have attracted noticeable interest for biomedical applications, such as wound healing/tissue engineering, medical implants, and biosensors, due to their excellent antifouling properties and design flexibility. Antifouling materials with buffering capability are particularly useful for many biomedical applications. In this work, an integrated zwitterionic polymeric material, poly(2-((2-hydroxyethyl)(2-methacrylamidoethyl)ammonio)acetate) (PCBMAA-1T), was synthesized to carry desired properties (antifouling, switchability and buffering capability). A tertiary amine was used to replace quaternary ammonium as the cation to endow the materials with buffering capability under neutral pH. Through this study, a better understanding on the structure-property relationship of zwitterionic materials was obtained. The tertiary amine cation does not compromise antifouling properties of zwitterionic materials. The amount of adsorbed proteins on PCBMAA-1T polymer brushes is less than 0.8 ng/cm(2) for fibrinogen and 0.3 ng/cm(2) (detection limit of the surface plasmon resonance sensor) for both undiluted blood plasma and serum. It is found that the tertiary amine is favorable to obtain good lactone ring stability in switchable PCB materials. Titration study showed that PCBMAA-1T could resist pH changes under both acidic (pH 1-3) and neutral/basic (pH 7-9) conditions. To the best of our knowledge, such an all-in-one material has not been reported. We believe this material might be potentially used for a variety of applications, including tissue engineering, chronic wound healing and medical device coating.

  20. DRUG-DRUG INTERACTIONS IN PATIENTS DISTRESS FROM HYPERTENSION IN TERTIARY CARE HOSPITAL

    OpenAIRE

    Sowmya Boreda , Sagarika Addetla, Asha Sara Stephen

    2016-01-01

    Drug-Drug Interactions (DDIs) is an important issue and now it is also realized that many of them can be explained by change in the enzymes, which involve in metabolism that are present in and out of liver. Co-administration of some drugs act as enzyme inducers, whereas some are inhibitors of enzyme which results undesirable effects. Hypertension (HTN) is a most common cardiovascular disease which can be defined as “consistently elevated blood pressure (arterial) or average systol...

  1. Mathematics for Maths Anxious Tertiary Students: Integrating the cognitive and affective domains using interactive multimedia

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    Janet Taylor

    2011-04-01

    Full Text Available Today, commencing university students come from a diversity of backgrounds and have a broad range of abilities and attitudes. It is well known that attitudes towards mathematics, especially mathematics anxiety, can affect students’ performance to the extent that mathematics is often seen as a barrier to success by many. This paper reports on the design, development and evaluation of an interactive multimedia resource designed to explicitly address students’ beliefs and attitudes towards mathematics by following five characters as they progress through the highs and low of studying a preparatory mathematics course. The resource was built within two theoretical frameworks, one related to effective numeracy teaching (Marr and Helme 1991 and the other related to effective educational technology development (Laurillard 2002. Further, it uses a number of multimedia alternatives (video, audio, animations, diarying, interactive examples and self assessment to encourage students to feel part of a group, to reflect on their feelings and beliefs about mathematics, to expose students to authentic problem solving and generally build confidence through practice and self-assessment. Evaluation of the resource indicated that it encouraged students to value their own mathematical ability and helped to build confidence, while developing mathematical problem solving skills. The evaluation clearly demonstrated that it is possible to address the affective domain through multimedia initiatives and that this can complement the current focus on computer mediated communication as the primary method of addressing affective goals within the online environment.

  2. The Prevalence and Symptoms Characteristic of Functional Constipation Using Rome III Diagnostic Criteria among Tertiary Education Students.

    Science.gov (United States)

    Lim, Ying Jye; Rosita, Jamaluddin; Chieng, Jin Yu; Hazizi, Abu Saad

    2016-01-01

    Functional constipation is very common with heterogeneous symptoms that have substantial impact on patient quality of life as well as medical resources which are rarely reported as life-threatening. The aim of this study is to examine the prevalence and symptoms characteristic of functional constipation (FC) by using Rome III diagnostic criteria among tertiary education students with an intention to introduce treatment in the future. Demographic, socio-economics characteristics and symptoms of FC using the Rome III criteria were sought using a questionnaire administered to Malaysian students in a tertiary education setting. Other data obtained were the general health status, lifestyle factors and anthropometric measurements. Using a simple random sampling method, a total of 1662 students were recruited in the study with a response rate of 95.0%. Sampled data are presented as frequency and percentage and stratified accordingly into categories for Chi-square analysis. The prevalence of functional constipation among the students was 16.2%, with a significantly higher prevalence among women (17.4%) than men (12.5%). Hard or lumpy stool, incomplete evacuation, anorectal obstruction and straining were reported as the commonest symptoms experienced. Type 3 was the most frequent stool consistency experienced among the constipated individuals (35.2%). Only 4.4% of individuals reported having less than three defecations per week. Using univariable analysis, FC was significantly associated with sex (odds ratio: 1.48, 95% CI: 1.06-2.06) and age group (odds ratio: 1.34, 95% CI: 1.01-1.79) with P value < 0.05 significance level. In multivariate logistic regression analysis, only sex was found significantly associated with FC (adjusted odds ratio: 1.53, 95% CI: 1.08-2.17, P < 0.05). Based on the prevalence rate, constipation is a common problem among tertiary education students (16.2%), with significantly more prevalence among the female respondents. Early detection of symptoms

  3. An Investigation of Verticality in Tertiary Students’ Academic Writing Texts: A Systemic Functional Perspective

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    Vasemaca T. Ledua Alifereti

    2013-05-01

    Full Text Available This study, identifies, discusses and recommends specific linguistic features that can be explored by Non-Native English (NNE students studying at the University of the South Pacific (USP in Fiji to improve their academic writing texts. Firstly, the status of academic writing in relation to NNE speakers both globally and in Fiji is discussed. Secondly, two concepts ‘abstract and metaphorical’ mentioned to be lacking in USP student texts are described followed by an explanation of how the two concepts are acquired if viewed from three different perspectives. Thirdly, previous studies conducted that had explored the importance of building verticality in writing are presented. Although a number of studies have explored verticality, there are no records to show how it is represented in circumstantial elements. Next the Transitivity system which is the theoretical framework adopted by the study is discussed with a particular emphasis on Relational processes. It is claimed that abstract and metaphorical relations are made in Relational processes. Moreover, certain linguistic features closely associated with verticality are identified to elicit data. Additionally results are presented and discussed according to research questions asked. Findings prove that indeed circumstances are mostly incongruently realized in Relational clauses. In order to build verticality in tertiary students’ academic writing texts, one has to be able to understand abstract and metaphorical concepts and how they are linguistically realized in writing texts.Keywords: horizontal and vertical knowledge structures, abstract and metaphorical concepts, grammatical metaphor,  nominalization, rankshifted clauses

  4. Development and Function of Secondary and Tertiary Lymphoid Organs in the Small Intestine and the Colon

    Science.gov (United States)

    Buettner, Manuela; Lochner, Matthias

    2016-01-01

    The immune system of the gut has evolved a number of specific lymphoid structures that contribute to homeostasis in the face of microbial colonization and food-derived antigenic challenge. These lymphoid organs encompass Peyer’s patches (PP) in the small intestine and their colonic counterparts that develop in a programed fashion before birth. In addition, the gut harbors a network of lymphoid tissues that is commonly designated as solitary intestinal lymphoid tissues (SILT). In contrast to PP, SILT develop strictly after birth and consist of a dynamic continuum of structures ranging from small cryptopatches (CP) to large, mature isolated lymphoid follicles (ILF). Although the development of PP and SILT follow similar principles, such as an early clustering of lymphoid tissue inducer (LTi) cells and the requirement for lymphotoxin beta (LTβ) receptor-mediated signaling, the formation of CP and their further maturation into ILF is associated with additional intrinsic and environmental signals. Moreover, recent data also indicate that specific differences exist in the regulation of ILF formation between the small intestine and the colon. Importantly, intestinal inflammation in both mice and humans is associated with a strong expansion of the lymphoid network in the gut. Recent experiments in mice suggest that these structures, although they resemble large, mature ILF in appearance, may represent de novo-induced tertiary lymphoid organs (TLO). While, so far, it is not clear whether intestinal TLO contribute to the exacerbation of inflammatory pathology, it has been shown that ILF provide the critical microenvironment necessary for the induction of an effective host response upon infection with enteric bacterial pathogens. Regarding the importance of ILF for intestinal immunity, interfering with the development and maturation of these lymphoid tissues may offer novel means for manipulating the immune response during intestinal infection or inflammation. PMID

  5. ON THE INTERACTIVE FUNCTIONS OF TAG QUESTIONS

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Tag questions are a distinctive feature in spokenEnglish,but seldom used by the non-native speakers.Studies show that tags are employed by native speakersmainly to express their interactive and interpersonalmeaning.In this paper,the writer explores the natureof tag questions,mainly their interactive and inter-personal functions in daily coversation.Suggestionsare made with regard to the teaching of tags in theclassroom.

  6. Noncovalent Interactions in Density-Functional Theory

    CERN Document Server

    DiLabio, Gino A

    2014-01-01

    Non-covalent interactions are essential in the description of soft matter, including materials of technological importance and biological molecules. In density-functional theory, common approaches fail to describe dispersion forces, an essential component in noncovalent binding interactions. In the last decade, great progress has been made in the development of accurate and computationally-efficient methods to describe noncovalently bound systems within the framework of density-functional theory. In this review, we give an account of the field from a chemical and didactic perspective, describing different approaches to the calculation of dispersion energies and comparing their accuracy, complexity, popularity, and general availability. This review should be useful to the newcomer who wants to learn more about noncovalent interactions and the different methods available at present to describe them using density-functional theory.

  7. A cross-sectional study of cognitive functions and disability in schizophrenia from a tertiary care hospital in North India

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    Meha Jain

    2016-01-01

    Full Text Available Background: Cognitive functions are important predictors of day to day functioning. Cognitive functions are significantly affected in schizophrenia and various other psychiatric disorders. There are very few Indian studies studying the relationship between cognitive functions and disability. Aims and Objectives: The purpose of the present study was to assess the cognitive functions in stable patients of schizophrenia and compare them with normal controls and also to study the relationship between cognition and disability in these patients. Materials and Methods: Thirty stable patients of schizophrenia attending psychiatry outpatient clinic of a Tertiary Care Hospital of North India were included in the study. Thirty healthy volunteers with no psychiatric illness matched for age, gender, and education were also included cognitive functions were assessed using Brief Assessment of Cognition in Schizophrenia and disability was assessed using WHO Disability Assessment Schedule 2.0 (WHODAS 2.0. Results: Highly significant difference (P < 0.0001 was found between the cognitive functions of the schizophrenia group and healthy control group. The patients of schizophrenia had a maximum disability in the area of life activities followed by participation and cognition. There existed a significant negative correlation between cognition and mobility (r = −0.45, P < 0.05, getting along with people (r = −0.44, P < 0.05, life activities (r = −0.42, P < 0.05, participation (r = −0.39, P ≤ 0.05, and total scores on WHODAS 2.0 (r = −0.48, P ≤ 0.05. Conclusion: Cognitive functions are an important predictor of disability. Cognitive deficits exist even in the stable patients of schizophrenia which is significantly higher than the healthy group.

  8. Systemic Functional Linguistic Genre Pedagogy ((SFL GP) in a Tertiary EFL Writing Context in Indonesia

    Science.gov (United States)

    Emilia, Emi; Hamied, Fuad Abdul

    2015-01-01

    This article reports on the results of a study aiming to investigate whether systemic functional linguistic genre pedagogy (SFL GP) can help students develop their writing ability in English and the students' opinions about the teaching program using SFL GP. The study was conducted in one semester with 19 student teachers taking a writing course…

  9. Assessment of Functioning of RTI-STI Clinics associated with A Tertiary Care Centre, Jaipur

    Directory of Open Access Journals (Sweden)

    Priyanka Kapoor, Monika Rathore, Amita Kashyap, Abhinav Agrawal, Vaseem Naheed Baig

    2015-01-01

    Conclusion: More female reported to these clinics than male. Condoms provision was practiced most regularly. Other components of counselling and services were not practiced consistently. Partner treatment and revisits were particularly lacking. Consistent presence of counsellor at clinic is vital for functioning of clinics."

  10. Predicting loop-helix tertiary structural contacts in RNA pseudoknots.

    Science.gov (United States)

    Cao, Song; Giedroc, David P; Chen, Shi-Jie

    2010-03-01

    Tertiary interactions between loops and helical stems play critical roles in the biological function of many RNA pseudoknots. However, quantitative predictions for RNA tertiary interactions remain elusive. Here we report a statistical mechanical model for the prediction of noncanonical loop-stem base-pairing interactions in RNA pseudoknots. Central to the model is the evaluation of the conformational entropy for the pseudoknotted folds with defined loop-stem tertiary structural contacts. We develop an RNA virtual bond-based conformational model (Vfold model), which permits a rigorous computation of the conformational entropy for a given fold that contains loop-stem tertiary contacts. With the entropy parameters predicted from the Vfold model and the energy parameters for the tertiary contacts as inserted parameters, we can then predict the RNA folding thermodynamics, from which we can extract the tertiary contact thermodynamic parameters from theory-experimental comparisons. These comparisons reveal a contact enthalpy (DeltaH) of -14 kcal/mol and a contact entropy (DeltaS) of -38 cal/mol/K for a protonated C(+)*(G-C) base triple at pH 7.0, and (DeltaH = -7 kcal/mol, DeltaS = -19 cal/mol/K) for an unprotonated base triple. Tests of the model for a series of pseudoknots show good theory-experiment agreement. Based on the extracted energy parameters for the tertiary structural contacts, the model enables predictions for the structure, stability, and folding pathways for RNA pseudoknots with known or postulated loop-stem tertiary contacts from the nucleotide sequence alone.

  11. Study of Abnormal Liver Function Test during Pregnancy in a Tertiary Care Hospital in Chhattisgarh.

    Science.gov (United States)

    Mishra, Nalini; Mishra, V N; Thakur, Parineeta

    2016-10-01

    Abnormal liver function tests (LFTs) in pregnancy require proper interpretation in order to avoid pitfalls in the diagnosis. The underlying disorder can have a significant effect on the outcome of both mother and foetus. The present study was done with the objective to study the clinical profile, incidence and possible causes of derangements of liver function tests. Eighty pregnant women with abnormal liver dysfunction were studied prospectively. Women with chronic liver disease and drug-induced abnormal liver function test were excluded. All available LFTs including LDH were studied along with some more definitive tests to aid identification of underlying cause. Foetomaternal outcome was noted in all. The incidence of abnormal LFT was 0.9 %. 13/80 (16.75 %) women had liver disorder not specific to pregnancy, whereas 67/80 (83.25 %) women had pregnancy-specific liver dysfunction. Of these, 65(81.25 %) women with liver dysfunction had pre-eclampsia including 11 (13.75 %) with HELLP and six women with eclampsia. 48/65 (60 %) women had pre-eclampsia in the absence of HELLP syndrome or eclampsia. The mean value for bilirubin (mg %) in hypertensive disorders of pregnancy ranged from 1.64 to 3.8, between 5 and 10 for ICP and AFLP and >10 in infective hepatitis. Transaminases were highest in infective hepatitis, whereas alkaline phosphate was highest in ICP. Total 27 (33.75 %) women suffered from adverse outcome with four (5 %) maternal deaths and 23 (28.75 %) major maternal morbidities. 33/80 (41.25 %) women had intrauterine death. 26.25 % babies were small for date. Pregnancy-specific disorders are the leading cause of abnormal liver function test during pregnant state particularly in the third trimester. Pre-eclampsia-related disorder is the commonest. Gestational age of pregnancy and relative values of various liver function tests in different pregnancy-specific and pregnancy nonspecific disorders appear to be the best guide to clinch the diagnosis.

  12. [Effects study of standardized tertiary rehabilitation on promoting of the neurological functions in stroke patients with hemiplegia].

    Science.gov (United States)

    2006-10-10

    To investigate the effects of standardized tertiary rehabilitation (STR) on promotion of the neurological functions in stroke patients with hemiplegia. A large-sample, multi-center, randomized, controlled prospective study was conducted nationwide. 1209 stroke patients with hemiplegia, aged 40 - 80, within 11 d +/- 5 d after the onset, stabilized in vital life signs in the past one week, of 20 hospitals affiliated to medical colleges or of hospitals at the provincial level in mainland China were randomly allocated to one of the 2 baseline data-matched groups: control group (n = 599, 446 with cerebral infarction and 153 with cerebral hemorrhage) receiving routine intervention of internal medicine, and STR group (n = 610, 455 with cerebral infarction and 155 with cerebral hemorrhage), receiving routine intervention and STR including physical therapy and occupational therapy (OT) in addition. Evaluation was conducted by the time of enrollment, and by the ends of the first, third, and sixth months by the national clinical neurological function defects (CNFD) scoring. There were no significant differences in the baseline indexes between these 2 groups. The scores of CNFD at enrollment of the patients with cerebral infarction in the STR group was 21.55, not significantly different from that of the patients with cerebral infarction in the control group (22.16), however, the scores of these patients with cerebral infarction in the STR group by the ends of the first, third, and sixth months were 16.32, and 11.48, and 8.63 respectively, all significantly lower than those of the corresponding patients in the control group (18.95, 15.57, and 13.78 respectively, all P hemiplegia.

  13. SYSTEMIC FUNCTIONAL LINGUISTIC GENRE PEDAGOGY (SFL GP IN A TERTIARY EFL WRITING CONTEXT IN INDONESIA

    Directory of Open Access Journals (Sweden)

    Emi Emilia

    2015-07-01

    Full Text Available This article reports on the results of a study aiming to investigate whether systemic functional linguistic genre pedagogy (SFL GP can help students develop their writing ability in English and the students’ opinions about the teaching program using SFL GP. The study was conducted in one semester with 19 student teachers taking a writing course on argumentative texts, in the English Department at a state university in West Java, Indonesia. The texts in focus were Exposition, Discussion and Response to Literary Works, but in the interests of space, the article will centre around Exposition. The study used a qualitative case study research design with data collected from participant observations for 16 meetings, analysis of students’ texts collected over the program, and questionnaires distributed at the conclusion of the program. The results indicate that despite some aspects that still need improvement, SFL GP can generally help students develop their writing ability. Observation data show students’ writing skill improvement supported by students’ texts which depicts good control of the schematic structure and linguistic features of the texts in focus. Finally, questionnaire data reveal students’ consciousness of improved writing skill and positive responses to each activity in the program. Based on the results of the study, it is recommended that SFL GP be implemented in other contexts in Indonesia and other countries.

  14. Annexin-Phospholipid Interactions. Functional Implications

    Directory of Open Access Journals (Sweden)

    Javier Turnay

    2013-01-01

    Full Text Available Annexins constitute an evolutionary conserved multigene protein superfamily characterized by their ability to interact with biological membranes in a calcium dependent manner. They are expressed by all living organisms with the exception of certain unicellular organisms. The vertebrate annexin core is composed of four (eight in annexin A6 homologous domains of around 70 amino acids, with the overall shape of a slightly bent ring surrounding a central hydrophilic pore. Calcium- and phospholipid-binding sites are located on the convex side while the N-terminus links domains I and IV on the concave side. The N-terminus region shows great variability in length and amino acid sequence and it greatly influences protein stability and specific functions of annexins. These proteins interact mainly with acidic phospholipids, such as phosphatidylserine, but differences are found regarding their affinity for lipids and calcium requirements for the interaction. Annexins are involved in a wide range of intra- and extracellular biological processes in vitro, most of them directly related with the conserved ability to bind to phospholipid bilayers: membrane trafficking, membrane-cytoskeleton anchorage, ion channel activity and regulation, as well as antiinflammatory and anticoagulant activities. However, the in vivo physiological functions of annexins are just beginning to be established.

  15. Association Between Sedentary Lifestyle and Diastolic Dysfunction Among Outpatients With Normal Left Ventricular Systolic Function Presenting to a Tertiary Referral Center in the Middle East.

    Science.gov (United States)

    Matta, Stephanie; Chammas, Elie; Alraies, Chadi; Abchee, Antoine; AlJaroudi, Wael

    2016-05-01

    Sedentary lifestyle has become prevalent in our community. Recent data showed controversy on the effect of regular exercise on left ventricular compliance and myocardial relaxation. We sought to assess whether physical inactivity is an independent predictor of diastolic dysfunction in or community, after adjustment for several covariates. Consecutive outpatients presenting to the echocardiography laboratory between July 2013 and June 2014 were prospectively enrolled. Clinical variables were collected prospectively at enrollment. Patients were considered physically active if they exercised regularly ≥3× a week, ≥30 minutes each time. The primary endpoint was presence of diastolic dysfunction. The final cohort included 1356 patients (mean age [SD] 52.9 [17.4] years, 51.3% female). Compared with physically active patients, the 1009 (74.4%) physically inactive patients were older, more often female, and had more comorbidities and worse diastolic function (51.3% vs 38.3%; P < 0.001). On univariate analysis, physical inactivity was associated with 70% increased odds of having diastolic dysfunction (odds ratio: 1.70, 95% confidence interval: 1.32-2.18, P < 0.001). There was significant interaction between physical activity and left ventricular mass index (LVMI; P = 0.026). On multivariate analysis, patients who were physically inactive and had LVMI ≥ median had significantly higher odds of having diastolic dysfunction (odds ratio: 2.82, 95% confidence interval: 1.58-5.05, P < 0.001). In a large, prospectively enrolled cohort from a single tertiary center in the Middle East, physically inactive patients with increased LVMI had 2- to 3-fold increased odds of having diastolic dysfunction after multivariate adjustment. © 2016 Wiley Periodicals, Inc.

  16. Computing dispersion interactions in density functional theory

    Science.gov (United States)

    Cooper, V. R.; Kong, L.; Langreth, D. C.

    2010-02-01

    In this article techniques for including dispersion interactions within density functional theory are examined. In particular comparisons are made between four popular methods: dispersion corrected DFT, pseudopotential correction schemes, symmetry adapted perturbation theory, and a non-local density functional - the so called Rutgers-Chalmers van der Waals density functional (vdW-DF). The S22 benchmark data set is used to evaluate the relative accuracy of these methods and factors such as scalability and transferability are also discussed. We demonstrate that vdW-DF presents an excellent compromise between computational speed and accuracy and lends most easily to full scale application in solid materials. This claim is supported through a brief discussion of a recent large scale application to H2 in a prototype metal organic framework material (MOF), Zn2BDC2TED. The vdW-DF shows overwhelming promise for first-principles studies of physisorbed molecules in porous extended systems; thereby having broad applicability for studies as diverse as molecular adsorption and storage, battery technology, catalysis and gas separations.

  17. Tertiary education in Latvia today and tomorrow

    Directory of Open Access Journals (Sweden)

    Ludmila Panina

    2010-02-01

    Full Text Available The market economy principles are deeply implemented in the system of tertiary education in Latvia. The share of private sector and private funding is significantly big, as well as the variety of study programs. Nevertheless it is only one side of supply-demand dimension that might be seriously changed by economic crisis. The author draws tertiary sector development scenarios considering probable demographic, economical and political trends. The more efficient and effective interaction of tertiary and business sectors, the development oriented decentralisation of state macro economical and regional policy are the decisive success factors for sustainability both of the state and tertiary sector.

  18. A study of potential drug-drug interactions among critically ill patients at a tertiary care hospital

    Directory of Open Access Journals (Sweden)

    Manjeeta Gupta

    2016-08-01

    Conclusions: The present study showed high concomitant administration of potentially interacting drugs. The prevalence confirmed the association of age and polypharmacy. Vigilant prescribing approach is needed to prevent hazardous outcomes of pDDI. [Int J Basic Clin Pharmacol 2016; 5(4.000: 1281-1285

  19. Potential drug-drug interactions in medical intensive care unit of a tertiary care hospital in Pakistan.

    Science.gov (United States)

    Ismail, Mohammad; Khan, Farmanullah; Noor, Sidra; Haider, Iqbal; Haq, Inam-Ul; Ali, Zahid; Shah, Zahir; Hassam, Mohsin

    2016-10-01

    Background Patients admitted to intensive care unit (ICU) present with severe and life-threatening illnesses. Most of them suffer from various comorbidities. They usually receive complex pharmacotherapy with large number of medicines which increase the risk of drug-drug interactions (DDIs). Objective The present report aimed to investigate prevalence and levels of potential DDIs (pDDIs) in medical ICU. Methods Medications profiles of 416 patients were checked for pDDIs using Micromedex Drug-Reax(®). Prevalence, levels of severity and levels of documentation were reported. Results Of total 416 patients, 310 were exposed to pDDIs (overall prevalence = 74.5 %). Likewise, a prevalence rate of 13.9 % was recorded for contraindicated pDDIs, 52.2 % for major pDDI and 58.4 % for moderate pDDI. This study reported 740 interacting drug pairs that were presented in total 1686 pDDIs. Of 1686 pDDIs, 4.3 % were of contraindicated severity, 33.8 % of major severity and 49.6 % of moderate severity, whereas 45.5 % were of fair scientific evidence and 41.4 % of good scientific evidence. Conclusion In this study, pDDIs were found highly prevalent in ICU patients at a rate of 74.5 %. Most of the pDDIs had moderate severity; however, substantial number of interactions (38.1 %) had major and contraindicated severity.

  20. Probing of tertiary interactions in RNA: 2'-hydroxyl-base contacts between the RNase P RNA and pre-tRNA.

    Science.gov (United States)

    Pan, T; Loria, A; Zhong, K

    1995-01-01

    A general method has been developed to analyze all 2' hydroxyl groups involved in tertiary interactions in RNA in a single experiment. This method involves comparing the activity of populations of circularly permuted RNAs that contain or lack potential hydrogen-bond donors at each position. The 2' hydroxyls of the pre-tRNA substrate identified as potential hydrogen bond donors in intermolecular interactions with the ribozyme from eubacterial RNase P (P RNA) are located in the T stem and T loop, acceptor stem, and 3' CCA regions. To locate the hydrogen-bond acceptors for one of those 2' hydroxyls in the P RNA, a phylogenetically conserved adenosine was mutated to a guanosine. When this mutant P RNA was used, increased cleavage activity of a single circularly permuted substrate within the population was observed. The cleavage efficiency (kcat/Km) of a singly 2'-deoxy-substituted substrate at this position in the T stem was also determined. For the wild-type P RNA, the catalytic efficiency was significantly decreased compared with that of the all-ribo substrate, consistent with the notion that this 2' hydroxyl plays an important role. For the P RNA mutant, no additional effect was found upon 2'-deoxy substitution. We propose that this particular 2' hydroxyl in the pre-tRNA interacts specifically with this adenosine in the P RNA. This method should be useful in examining the role of 2' hydroxyl groups in other RNA-RNA and RNA-protein complexes. Images Fig. 2 Fig. 3 Fig. 4 PMID:8618931

  1. Interparticle Interactions and Self-Assembly of Functionalized Nanodiamonds.

    Science.gov (United States)

    Lai, Lin; Barnard, Amanda S

    2012-04-05

    Although unpassivated detonation nanodiamonds are known to form tightly bound (and sometimes ordered) superstructures, in most high performance applications the surface are deliberately functionalized, and this can profoundly alter the aggregation behavior. In the present study, we model the aggregation of functionalized nanodiamonds and show that functionalization greatly reduces the Coulombic interactions characteristic of unsaturated particles. Our results provide new insights into the interactions of functionalized nanoparticles.

  2. Bifunctional heterogeneous catalysis of silica-alumina-supported tertiary amines with controlled acid-base interactions for efficient 1,4-addition reactions.

    Science.gov (United States)

    Motokura, Ken; Tanaka, Satoka; Tada, Mizuki; Iwasawa, Yasuhiro

    2009-10-19

    We report the first tunable bifunctional surface of silica-alumina-supported tertiary amines (SA-NEt(2)) active for catalytic 1,4-addition reactions of nitroalkanes and thiols to electron-deficient alkenes. The 1,4-addition reaction of nitroalkanes to electron-deficient alkenes is one of the most useful carbon-carbon bond-forming reactions and applicable toward a wide range of organic syntheses. The reaction between nitroethane and methyl vinyl ketone scarcely proceeded with either SA or homogeneous amines, and a mixture of SA and amines showed very low catalytic activity. In addition, undesirable side reactions occurred in the case of a strong base like sodium ethoxide employed as a catalytic reagent. Only the present SA-supported amine (SA-NEt(2)) catalyst enabled selective formation of a double-alkylated product without promotions of side reactions such as an intramolecular cyclization reaction. The heterogeneous SA-NEt(2) catalyst was easily recovered from the reaction mixture by simple filtration and reusable with retention of its catalytic activity and selectivity. Furthermore, the SA-NEt(2) catalyst system was applicable to the addition reaction of other nitroalkanes and thiols to various electron-deficient alkenes. The solid-state magic-angle spinning (MAS) NMR spectroscopic analyses, including variable-contact-time (13)C cross-polarization (CP)/MAS NMR spectroscopy, revealed that acid-base interactions between surface acid sites and immobilized amines can be controlled by pretreatment of SA at different temperatures. The catalytic activities for these addition reactions were strongly affected by the surface acid-base interactions.

  3. Functionalized Carbon Nanotube-Polymer Composites and Interactions with Radiation

    Science.gov (United States)

    Barrera, Enrique V. (Inventor); Wilkins, Richard (Inventor); Shofner, Meisha (Inventor); Pulikkathara, Merlyn X. (Inventor); Vaidyanathan, Ranjii (Inventor)

    2014-01-01

    The present invention involves the interaction of radiation with functionalized carbon nanotubes that have been incorporated into various host materials, particularly polymeric ones. The present invention is directed to chemistries, methods, and apparatuses which exploit this type of radiation interaction, and to the materials which result from such interactions. The present invention is also directed toward the time dependent behavior of functionalized carbon nanotubes in such composite systems.

  4. From networks of protein interactions to networks of functional dependencies

    Directory of Open Access Journals (Sweden)

    Luciani Davide

    2012-05-01

    Full Text Available Abstract Background As protein-protein interactions connect proteins that participate in either the same or different functions, networks of interacting and functionally annotated proteins can be converted into process graphs of inter-dependent function nodes (each node corresponding to interacting proteins with the same functional annotation. However, as proteins have multiple annotations, the process graph is non-redundant, if only proteins participating directly in a given function are included in the related function node. Results Reasoning that topological features (e.g., clusters of highly inter-connected proteins might help approaching structured and non-redundant understanding of molecular function, an algorithm was developed that prioritizes inclusion of proteins into the function nodes that best overlap protein clusters. Specifically, the algorithm identifies function nodes (and their mutual relations, based on the topological analysis of a protein interaction network, which can be related to various biological domains, such as cellular components (e.g., peroxisome and cellular bud or biological processes (e.g., cell budding of the model organism S. cerevisiae. Conclusions The method we have described allows converting a protein interaction network into a non-redundant process graph of inter-dependent function nodes. The examples we have described show that the resulting graph allows researchers to formulate testable hypotheses about dependencies among functions and the underlying mechanisms.

  5. MRI in Optic Neuritis: Structure, Function, Interactions

    DEFF Research Database (Denmark)

    Fuglø, Dan

    2011-01-01

    resonance imaging (MRI), and the visual evoked potential (VEP) continues to show a delayed P100 indicating persistent demyelination. The explanation for this apparent discrepancy between structure and function could be due to either a redundancy in the visual pathways so that some degree of signal loss...... are low. Functional MRI (fMRI) is a non-invasive technique that can measure brain activity with a high spatial resolution. Recently, technical and methodological advancements have made it feasible to record VEPs and fMRI simultaneously and the relationship between averaged VEPs and averaged fMRI signals...... have been described. Still, to take full advantage of simultaneously recorded VEP-fMRI one would ideally want to track single-trial changes in the VEP and use this information in the fMRI analysis. In order to do this we examined 10 healthy volunteers with simultaneous VEP-fMRI. Different measures...

  6. Cytoskeleton, cytoskeletal interactions, and vascular endothelial function

    Directory of Open Access Journals (Sweden)

    Wang J

    2012-12-01

    Full Text Available Jingli Wang,1 Michael E Widlansky1,21Department of Medicine, Cardiovascular Medicine Division, 2Department of Pharmacology, Medical College of Wisconsin, Milwaukee, Wisconsin, USAAbstract: Far from being inert, the vascular endothelium is a critical regulator of vascular function. While the endothelium participates in autocrine, paracrine, and endocrine signaling, it also transduces mechanical signals from the cell surface involving key cell structural elements. In this review, we discuss the structure of the vascular endothelium and its relationship to traditional cardiovascular risk factors and clinical cardiovascular events. Further, we review the emerging evidence that cell structural elements, including the glycocalyx, intercellular junctions, and cytoskeleton elements, help the endothelium to communicate with its environment to regulate vascular function, including vessel permeability and signal transduction via nitric oxide bioavailability. Further work is necessary to better delineate the regulatory relationships between known key regulators of vascular function and endothelial cell structural elements.Keywords: endothelium, shear stress, eNOS, cardiovascular risk factors, glycocalyx

  7. Predictability of Genetic Interactions from Functional Gene Modules

    Directory of Open Access Journals (Sweden)

    Jonathan H. Young

    2017-02-01

    Full Text Available Characterizing genetic interactions is crucial to understanding cellular and organismal response to gene-level perturbations. Such knowledge can inform the selection of candidate disease therapy targets, yet experimentally determining whether genes interact is technically nontrivial and time-consuming. High-fidelity prediction of different classes of genetic interactions in multiple organisms would substantially alleviate this experimental burden. Under the hypothesis that functionally related genes tend to share common genetic interaction partners, we evaluate a computational approach to predict genetic interactions in Homo sapiens, Drosophila melanogaster, and Saccharomyces cerevisiae. By leveraging knowledge of functional relationships between genes, we cross-validate predictions on known genetic interactions and observe high predictive power of multiple classes of genetic interactions in all three organisms. Additionally, our method suggests high-confidence candidate interaction pairs that can be directly experimentally tested. A web application is provided for users to query genes for predicted novel genetic interaction partners. Finally, by subsampling the known yeast genetic interaction network, we found that novel genetic interactions are predictable even when knowledge of currently known interactions is minimal.

  8. Dispersion corrections to density functionals for water aromatic interactions.

    Science.gov (United States)

    Zimmerli, Urs; Parrinello, Michele; Koumoutsakos, Petros

    2004-02-08

    We investigate recently published methods for extending density functional theory to the description of long-range dispersive interactions. In all schemes an empirical correction consisting of a C6r(-6) term is introduced that is damped at short range. The coefficient C6 is calculated either from average molecular or atomic polarizabilities. We calculate geometry-dependent interaction energy profiles for the water benzene cluster and compare the results with second-order Møller-Plesset calculations. Our results indicate that the use of the B3LYP functional in combination with an appropriate mixing rule and damping function is recommended for the interaction of water with aromatics.

  9. The architecture of functional interaction networks in the retina.

    Science.gov (United States)

    Ganmor, Elad; Segev, Ronen; Schneidman, Elad

    2011-02-23

    Sensory information is represented in the brain by the joint activity of large groups of neurons. Recent studies have shown that, although the number of possible activity patterns and underlying interactions is exponentially large, pairwise-based models give a surprisingly accurate description of neural population activity patterns. We explored the architecture of maximum entropy models of the functional interaction networks underlying the response of large populations of retinal ganglion cells, in adult tiger salamander retina, responding to natural and artificial stimuli. We found that we can further simplify these pairwise models by neglecting weak interaction terms or by relying on a small set of interaction strengths. Comparing network interactions under different visual stimuli, we show the existence of local network motifs in the interaction map of the retina. Our results demonstrate that the underlying interaction map of the retina is sparse and dominated by local overlapping interaction modules.

  10. Unveiling protein functions through the dynamics of the interaction network.

    Directory of Open Access Journals (Sweden)

    Irene Sendiña-Nadal

    Full Text Available Protein interaction networks have become a tool to study biological processes, either for predicting molecular functions or for designing proper new drugs to regulate the main biological interactions. Furthermore, such networks are known to be organized in sub-networks of proteins contributing to the same cellular function. However, the protein function prediction is not accurate and each protein has traditionally been assigned to only one function by the network formalism. By considering the network of the physical interactions between proteins of the yeast together with a manual and single functional classification scheme, we introduce a method able to reveal important information on protein function, at both micro- and macro-scale. In particular, the inspection of the properties of oscillatory dynamics on top of the protein interaction network leads to the identification of misclassification problems in protein function assignments, as well as to unveil correct identification of protein functions. We also demonstrate that our approach can give a network representation of the meta-organization of biological processes by unraveling the interactions between different functional classes.

  11. Sequence Motifs in MADS Transcription Factors Responsible for Specificity and Diversification of Protein-Protein Interaction

    NARCIS (Netherlands)

    Dijk, van A.D.J.; Morabito, G.; Fiers, M.A.; Ham, van R.C.H.J.; Angenent, G.C.; Immink, R.G.H.

    2010-01-01

    Protein sequences encompass tertiary structures and contain information about specific molecular interactions, which in turn determine biological functions of proteins. Knowledge about how protein sequences define interaction specificity is largely missing, in particular for paralogous protein famil

  12. Interacting relativistic quantum dynamics for multi-time wave functions

    Directory of Open Access Journals (Sweden)

    Lienert Matthias

    2016-01-01

    Full Text Available In this paper, we report on recent progress about a rigorous and manifestly covariant interacting model for two Dirac particles in 1+1 dimensions [9, 10]. It is formulated using the multi-time formalism of Dirac, Tomonaga and Schwinger. The mechanism of interaction is a relativistic generalization of contact interactions, and it is achieved going beyond the usual functional-analytic Hamiltonian method.

  13. Interacting relativistic quantum dynamics for multi-time wave functions

    Science.gov (United States)

    Lienert, Matthias

    2016-11-01

    In this paper, we report on recent progress about a rigorous and manifestly covariant interacting model for two Dirac particles in 1+1 dimensions [9, 10]. It is formulated using the multi-time formalism of Dirac, Tomonaga and Schwinger. The mechanism of interaction is a relativistic generalization of contact interactions, and it is achieved going beyond the usual functional-analytic Hamiltonian method.

  14. The quenched generating functional for hadronic weak interactions

    NARCIS (Netherlands)

    Pallante, E.

    1999-01-01

    The ultraviolet behaviour of the generating functional for hadronic weak interactions with |ΔS| = 1, 2 is investigated to one loop for a generic number of flavours and in the quenched approximation. New quenched chiral logarithms generated by the weak interactions can be accounted for via a redefin

  15. Generalized Functional Linear Models With Semiparametric Single-Index Interactions

    KAUST Repository

    Li, Yehua

    2010-06-01

    We introduce a new class of functional generalized linear models, where the response is a scalar and some of the covariates are functional. We assume that the response depends on multiple covariates, a finite number of latent features in the functional predictor, and interaction between the two. To achieve parsimony, the interaction between the multiple covariates and the functional predictor is modeled semiparametrically with a single-index structure. We propose a two step estimation procedure based on local estimating equations, and investigate two situations: (a) when the basis functions are pre-determined, e.g., Fourier or wavelet basis functions and the functional features of interest are known; and (b) when the basis functions are data driven, such as with functional principal components. Asymptotic properties are developed. Notably, we show that when the functional features are data driven, the parameter estimates have an increased asymptotic variance, due to the estimation error of the basis functions. Our methods are illustrated with a simulation study and applied to an empirical data set, where a previously unknown interaction is detected. Technical proofs of our theoretical results are provided in the online supplemental materials.

  16. Identification and analysis of interactions between sea use functions

    NARCIS (Netherlands)

    Wal, van der J.T.; Quirijns, F.J.; Leopold, M.F.; Slijkerman, D.M.E.; Jongbloed, R.H.

    2009-01-01

    This report focuses on the interactions both positive and negative between offshore wind energy and the non-wind sea use functions.Some sea use functions can co-exist without substantial negative effects. Other combinations are problematic or even impossible and should be avoided. Therefore the inte

  17. Introduction: Links between Social Interaction and Executive Function

    Science.gov (United States)

    Lewis, Charlie; Carpendale, Jeremy I. M.

    2009-01-01

    The term executive function is used increasingly within developmental psychology and is often taken to refer to unfolding brain processes. We trace the origins of research on executive function to show that the link with social interaction has a long history. We suggest that a recent frenzy of research exploring methods for studying individual…

  18. Introduction: Links between Social Interaction and Executive Function

    Science.gov (United States)

    Lewis, Charlie; Carpendale, Jeremy I. M.

    2009-01-01

    The term executive function is used increasingly within developmental psychology and is often taken to refer to unfolding brain processes. We trace the origins of research on executive function to show that the link with social interaction has a long history. We suggest that a recent frenzy of research exploring methods for studying individual…

  19. Interaction corrections to the polarization function of graphene

    OpenAIRE

    2012-01-01

    The first-order interaction correction to the irreducible polarization function of pristine graphene is studied at arbitrary relation between momentum and frequency. The results are used to calculate the dielectric function and the dynamical conductivity of graphene beyond the standard random-phase approximation. The computed static dielectric constant compares favorably with recent experiments.

  20. Functional interaction between Lypd6 and nicotinic acetylcholine receptors

    DEFF Research Database (Denmark)

    Arvaniti, Maria; Jensen, Majbrit M; Soni, Neeraj;

    2016-01-01

    Nicotinic acetylcholine receptors (nAChRs) affect multiple physiological functions in the brain and their functions are modulated by regulatory proteins of the Lynx family. Here, we report for the first time a direct interaction of the Lynx protein LY6/PLAUR domain-containing 6 (Lypd6) with n...

  1. Interaction of pristine and functionalized carbon nanotubes with lipid membranes.

    Science.gov (United States)

    Baoukina, Svetlana; Monticelli, Luca; Tieleman, D Peter

    2013-10-10

    Carbon nanotubes are widely used in a growing number of applications. Their interactions with biological materials, cell membranes in particular, is of interest in applications including drug delivery and for understanding the toxicity of carbon nanotubes. We use extensive molecular dynamics simulations with the MARTINI model to study the interactions of model nanotubes of different thickness, length, and patterns of chemical modification with model membranes. In addition, we characterize the interactions of small bundles of carbon nanotubes with membrane models. Short pristine carbon nanotubes readily insert into membranes and adopt an orientation parallel to the plane of the membrane in the center of the membrane. Larger aggregates and functionalized nanotubes exhibit a range of possible interactions. The distribution and orientation of carbon nanotubes can be controlled by functionalizing the nanotubes. Free energy calculations provide thermodynamic insight into the preferred orientations of different nanotubes and quantify structural defects in the lipid matrix.

  2. Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data

    OpenAIRE

    Sourav Bandyopadhyay; Ryan Kelley; Krogan, Nevan J.; Trey Ideker

    2008-01-01

    Recently, a number of advanced screening technologies have allowed for the comprehensive quantification of aggravating and alleviating genetic interactions among gene pairs. In parallel, TAP-MS studies (tandem affinity purification followed by mass spectroscopy) have been successful at identifying physical protein interactions that can indicate proteins participating in the same molecular complex. Here, we propose a method for the joint learning of protein complexes and their functional relat...

  3. Efficient CO2 capture by tertiary amine-functionalized ionic liquids through Li+-stabilized zwitterionic adduct formation

    OpenAIRE

    Yang, Zhen-zhen; He, Liang-Nian

    2014-01-01

    Highly efficient CO2 absorption was realized through formation of zwitterionic adducts, combining synthetic strategies to ionic liquids (ILs) and coordination. The essence of our strategy is to make use of multidentate cation coordination between Li+ and an organic base. Also PEG-functionalized organic bases were employed to enhance the CO2-philicity. The ILs were reacted with CO2 to form the zwitterionic adduct. Coordination effects between various lithium salts and neutral ligands, as well ...

  4. Dynamic density functional theory with hydrodynamic interactions and fluctuations

    Energy Technology Data Exchange (ETDEWEB)

    Donev, Aleksandar, E-mail: donev@courant.nyu.edu; Vanden-Eijnden, Eric, E-mail: eve2@courant.nyu.edu [Courant Institute of Mathematical Sciences, New York University, New York, New York 10012 (United States)

    2014-06-21

    We derive a closed equation for the empirical concentration of colloidal particles in the presence of both hydrodynamic and direct interactions. The ensemble average of our functional Langevin equation reproduces known deterministic Dynamic Density Functional Theory (DDFT) [M. Rex and H. Löwen, “Dynamical density functional theory with hydrodynamic interactions and colloids in unstable traps,” Phys. Rev. Lett. 101(14), 148302 (2008)], and, at the same time, it also describes the microscopic fluctuations around the mean behavior. We suggest separating the ideal (non-interacting) contribution from additional corrections due to pairwise interactions. We find that, for an incompressible fluid and in the absence of direct interactions, the mean concentration follows Fick's law just as for uncorrelated walkers. At the same time, the nature of the stochastic terms in fluctuating DDFT is shown to be distinctly different for hydrodynamically-correlated and uncorrelated walkers. This leads to striking differences in the behavior of the fluctuations around Fick's law, even in the absence of pairwise interactions. We connect our own prior work [A. Donev, T. G. Fai, and E. Vanden-Eijnden, “A reversible mesoscopic model of diffusion in liquids: from giant fluctuations to Fick's law,” J. Stat. Mech.: Theory Exp. (2014) P04004] on fluctuating hydrodynamics of diffusion in liquids to the DDFT literature, and demonstrate that the fluid cannot easily be eliminated from consideration if one wants to describe the collective diffusion in colloidal suspensions.

  5. PREVALENCE OF PULMONARY FUNCTION DEFECTS IN PSORIASIS PATIENTS RECEIVING METHOTREXATE IN A TERTIARY CARE HOSPITAL IN TAMIL NADU, INDIA

    Directory of Open Access Journals (Sweden)

    Allwyn Vijay

    2015-10-01

    Full Text Available Methotrexate is an anti - metabolite widely used in malignancy, rheumatoid arthritis and refractory cases of psoriasis . 1 The value of low dose methotrexate is well established . 2 - 4 There are evidences of pulmonary function defects in patients on long term low dose methotrexate in rheumatoid arthritis patients. Because methotrexate is frequently used in patients suffering from conditions such as RA, dermatomyositis or sarcoidosis, which can be associated wi th interstitial lung disease, determining the exact role of methotrexate in the development of pulmonary complications in these patients seems to be difficult. Therefore, we conducted a cross - sectional study to analyse the findings found on chest x - rays, h igh resolution computed tomography (HRCT and pulmonary function tests (PFT in a cohort of patients without previous recognized interstitial lung disease who were taking methotrexate as a treatment for psoriatic arthritis, a condition not associated with pleuro pulmonary disease. RESULTS: In this study 154 patients from the outpatient department of psoriasis clinic of dermatology department of government general hospital, Chennai who were receiving methotrexate for psoriasis were screened. Out of which 30 patients who were eligible as per inclusion criteria were included in the study. In this study 9 patients showed normal radiology and pulmonary function test. 21 patients had pulmonary function abnormalities. In this study there were 13(43% patients with restrictive pulmonary function defect. Belzenegui . 14 et al reported 2 cases with mild restriction among 27 patients in a similar study. There were 10(33% patients with diffusion defect in this study. Belzenegui et al reported 2 cases among 27 patients in a similar study. There were 5(16% patients with small airway disease as suggested by decrease in mean mid expiratory flow. Belzenegui et al reported 5 cases among 27 patients in a similar study. There were 3(3% patients with

  6. Efficient CO2 capture by tertiary amine-functionalized ionic liquids through Li(+)-stabilized zwitterionic adduct formation.

    Science.gov (United States)

    Yang, Zhen-Zhen; He, Liang-Nian

    2014-01-01

    Highly efficient CO2 absorption was realized through formation of zwitterionic adducts, combining synthetic strategies to ionic liquids (ILs) and coordination. The essence of our strategy is to make use of multidentate cation coordination between Li(+) and an organic base. Also PEG-functionalized organic bases were employed to enhance the CO2-philicity. The ILs were reacted with CO2 to form the zwitterionic adduct. Coordination effects between various lithium salts and neutral ligands, as well as the CO2 capacity of the chelated ILs obtained were investigated. For example, the CO2 capacity of PEG150MeBu2N increased steadily from 0.10 to 0.66 (mol CO2 absorbed per mol of base) through the formation of zwitterionic adducts being stabilized by Li(+).

  7. Demonstrating Functional Interactive Language Teaching in the Nigerian Universities

    Science.gov (United States)

    Bello, Rachael O.; Oni-Buraimoh, Olawunmi O.

    2014-01-01

    Applied linguistics affords Linguists the opportunity of solving language related problems using various methods. In this paper, we x-ray the Nigerian University classroom situation in the teaching of the English language viz-a-viz the use of functional interactive method. Following Littlewood (1981) and Krashen (1982), we posit that the teaching…

  8. Can the hydrophilicity of functional monomers affect chemical interaction?

    Science.gov (United States)

    Feitosa, V P; Ogliari, F A; Van Meerbeek, B; Watson, T F; Yoshihara, K; Ogliari, A O; Sinhoreti, M A; Correr, A B; Cama, G; Sauro, S

    2014-02-01

    The number of carbon atoms and/or ester/polyether groups in spacer chains may influence the interaction of functional monomers with calcium and dentin. The present study assessed the chemical interaction and bond strength of 5 standard-synthesized phosphoric-acid ester functional monomers with different spacer chain characteristics, by atomic absorption spectroscopy (AAS), ATR-FTIR, thin-film x-ray diffraction (TF-XRD), scanning electron microscopy (SEM), and microtensile bond strength (μTBS). The tested functional monomers were 2-MEP (two-carbon spacer chain), 10-MDP (10-carbon), 12-MDDP (12-carbon), MTEP (more hydrophilic polyether spacer chain), and CAP-P (intermediate hydrophilicity ester spacer). The intensity of monomer-calcium salt formation measured by AAS differed in the order of 12-MDDP=10-MDP>CAP-P>MTEP>2-MEP. FTIR and SEM analyses of monomer-treated dentin surfaces showed resistance to rinsing for all monomer-dentin bonds, except with 2-MEP. TF-XRD confirmed the weaker interaction of 2-MEP. Highest µTBS was observed for 12-MDDP and 10-MDP. A shorter spacer chain (2-MEP) of phosphate functional monomers induced formation of unstable monomer-calcium salts, and lower chemical interaction and dentin bond strength. The presence of ester or ether groups within longer spacer carbon chains (CAP-P and MTEP) may affect the hydrophilicity, μTBS, and also the formation of monomer-calcium salts.

  9. Pomeron-Odderon Interactions: A Functional RG Flow Analysis

    CERN Document Server

    Vacca, Gian Paolo

    2016-01-01

    In the quest for an effective field theory which could help to understand some non perturbative feature of the QCD in the Regge limit, we consider a Reggeon Field Theory (RFT) for both Pomeron and Odderon interactions and perform an analysys of the critical theory using functional renormalization group techniques, unveiling a novel symmetry structure.

  10. Configuration interaction wave functions: A seniority number approach

    Energy Technology Data Exchange (ETDEWEB)

    Alcoba, Diego R. [Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and Instituto de Física de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Universitaria, 1428 Buenos Aires (Argentina); Torre, Alicia; Lain, Luis, E-mail: qfplapel@lg.ehu.es [Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Apdo. 644, E-48080 Bilbao (Spain); Massaccesi, Gustavo E. [Departamento de Ciencias Exactas, Ciclo Básico Común, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires (Argentina); Oña, Ofelia B. [Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas, Universidad Nacional de La Plata, CCT La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Diag. 113 y 64 (S/N), Sucursal 4, CC 16, 1900 La Plata (Argentina)

    2014-06-21

    This work deals with the configuration interaction method when an N-electron Hamiltonian is projected on Slater determinants which are classified according to their seniority number values. We study the spin features of the wave functions and the size of the matrices required to formulate states of any spin symmetry within this treatment. Correlation energies associated with the wave functions arising from the seniority-based configuration interaction procedure are determined for three types of molecular orbital basis: canonical molecular orbitals, natural orbitals, and the orbitals resulting from minimizing the expectation value of the N-electron seniority number operator. The performance of these bases is analyzed by means of numerical results obtained from selected N-electron systems of several spin symmetries. The comparison of the results highlights the efficiency of the molecular orbital basis which minimizes the mean value of the seniority number for a state, yielding energy values closer to those provided by the full configuration interaction procedure.

  11. Synthetic protein interactions reveal a functional map of the cell

    Science.gov (United States)

    Berry, Lisa K; Ólafsson, Guðjón; Ledesma-Fernández, Elena; Thorpe, Peter H

    2016-01-01

    To understand the function of eukaryotic cells, it is critical to understand the role of protein-protein interactions and protein localization. Currently, we do not know the importance of global protein localization nor do we understand to what extent the cell is permissive for new protein associations – a key requirement for the evolution of new protein functions. To answer this question, we fused every protein in the yeast Saccharomyces cerevisiae with a partner from each of the major cellular compartments and quantitatively assessed the effects upon growth. This analysis reveals that cells have a remarkable and unanticipated tolerance for forced protein associations, even if these associations lead to a proportion of the protein moving compartments within the cell. Furthermore, the interactions that do perturb growth provide a functional map of spatial protein regulation, identifying key regulatory complexes for the normal homeostasis of eukaryotic cells. DOI: http://dx.doi.org/10.7554/eLife.13053.001 PMID:27098839

  12. Allometric functional response model: body masses constrain interaction strengths.

    Science.gov (United States)

    Vucic-Pestic, Olivera; Rall, Björn C; Kalinkat, Gregor; Brose, Ulrich

    2010-01-01

    1. Functional responses quantify the per capita consumption rates of predators depending on prey density. The parameters of these nonlinear interaction strength models were recently used as successful proxies for predicting population dynamics, food-web topology and stability. 2. This study addressed systematic effects of predator and prey body masses on the functional response parameters handling time, instantaneous search coefficient (attack coefficient) and a scaling exponent converting type II into type III functional responses. To fully explore the possible combinations of predator and prey body masses, we studied the functional responses of 13 predator species (ground beetles and wolf spiders) on one small and one large prey resulting in 26 functional responses. 3. We found (i) a power-law decrease of handling time with predator mass with an exponent of -0.94; (ii) an increase of handling time with prey mass (power-law with an exponent of 0.83, but only three prey sizes were included); (iii) a hump-shaped relationship between instantaneous search coefficients and predator-prey body-mass ratios; and (iv) low scaling exponents for low predator-prey body mass ratios in contrast to high scaling exponents for high predator-prey body-mass ratios. 4. These scaling relationships suggest that nonlinear interaction strengths can be predicted by knowledge of predator and prey body masses. Our results imply that predators of intermediate size impose stronger per capita top-down interaction strengths on a prey than smaller or larger predators. Moreover, the stability of population and food-web dynamics should increase with increasing body-mass ratios in consequence of increases in the scaling exponents. 5. Integrating these scaling relationships into population models will allow predicting energy fluxes, food-web structures and the distribution of interaction strengths across food web links based on knowledge of the species' body masses.

  13. Functional interactions of DNA topoisomerases with a human replication origin.

    Science.gov (United States)

    Abdurashidova, Gulnara; Radulescu, Sorina; Sandoval, Oscar; Zahariev, Sotir; Danailov, Miltcho B; Demidovich, Alexander; Santamaria, Laura; Biamonti, Giuseppe; Riva, Silvano; Falaschi, Arturo

    2007-02-21

    The human DNA replication origin, located in the lamin B2 gene, interacts with the DNA topoisomerases I and II in a cell cycle-modulated manner. The topoisomerases interact in vivo and in vitro with precise bonds ahead of the start sites of bidirectional replication, within the pre-replicative complex region; topoisomerase I is bound in M, early G1 and G1/S border and topoisomerase II in M and the middle of G1. The Orc2 protein competes for the same sites of the origin bound by either topoisomerase in different moments of the cell cycle; furthermore, it interacts on the DNA with topoisomerase II during the assembly of the pre-replicative complex and with DNA-bound topoisomerase I at the G1/S border. Inhibition of topoisomerase I activity abolishes origin firing. Thus, the two topoisomerases are closely associated with the replicative complexes, and DNA topology plays an essential functional role in origin activation.

  14. Enhancing the functional content of eukaryotic protein interaction networks.

    Directory of Open Access Journals (Sweden)

    Gaurav Pandey

    Full Text Available Protein interaction networks are a promising type of data for studying complex biological systems. However, despite the rich information embedded in these networks, these networks face important data quality challenges of noise and incompleteness that adversely affect the results obtained from their analysis. Here, we apply a robust measure of local network structure called common neighborhood similarity (CNS to address these challenges. Although several CNS measures have been proposed in the literature, an understanding of their relative efficacies for the analysis of interaction networks has been lacking. We follow the framework of graph transformation to convert the given interaction network into a transformed network corresponding to a variety of CNS measures evaluated. The effectiveness of each measure is then estimated by comparing the quality of protein function predictions obtained from its corresponding transformed network with those from the original network. Using a large set of human and fly protein interactions, and a set of over 100 GO terms for both, we find that several of the transformed networks produce more accurate predictions than those obtained from the original network. In particular, the HC.cont measure and other continuous CNS measures perform well this task, especially for large networks. Further investigation reveals that the two major factors contributing to this improvement are the abilities of CNS measures to prune out noisy edges and enhance functional coherence in the transformed networks.

  15. Gene by neuroticism interaction and cognitive function among older adults.

    Science.gov (United States)

    Dar-Nimrod, Ilan; Chapman, Benjamin P; Robbins, John A; Porsteinsson, Anton; Mapstone, Mark; Duberstein, Paul R

    2012-11-01

    Both apolipoprotein E (ApoE) ε-4 allele(s) and elevated trait neuroticism, the tendency to experience distress, are associated with cognitive function among older adults. We predicted that neuroticism moderates the association between ApoE and cognitive function and also explored whether other personality dimensions (openness to experience, agreeableness, extraversion, and conscientiousness) affect the association between ApoE status and cognitive function. Five-hundred and ninety-seven older adults (mean age of 78 years) enrolled in the Ginkgo Evaluation of Memory study completed the NEO five-factor inventory of personality. Cognitive function was assessed via the cognitive portion of the Alzheimer's Disease Assessment Scale, and a blood sample for ApoE genotyping was drawn. As hypothesized, regression analysis indicated that neuroticism moderated the relationship between the presence of ApoE ε-4 and cognitive function. Individuals with high neuroticism scores had significantly lower scores on the cognitive portion of the Alzheimer's Disease Assessment Scale compared with individuals with low neuroticism scores, but this was true only among carriers of ApoE ε-4 (interaction effect β = 0.124, p = 0.028). There was scant evidence that other personality dimensions moderate the association between ApoE ε-4 and cognitive function. Cognitive function may be affected by ApoE and neuroticism acting in tandem. Research on the underlying physiological mechanisms by which neuroticism amplifies the effect of ApoE ε-4 is warranted. The study of genotype by phenotype interactions provides an important and useful direction for the study of cognitive function among older adults and for the development of novel prevention programs. Copyright © 2012 John Wiley & Sons, Ltd.

  16. Interactions of gut microbiota with functional food components and nutraceuticals.

    Science.gov (United States)

    Laparra, J M; Sanz, Y

    2010-03-01

    The human gut is populated by an array of bacterial species, which develop important metabolic and immune functions, with a marked effect on the nutritional and health status of the host. Dietary component also play beneficial roles beyond basic nutrition, leading to the development of the functional food concept and nutraceuticals. Prebiotics, polyunsaturated fatty acids (PUFAs) and phytochemicals are the most well characterized dietary bioactive compounds. The beneficial effects of prebiotics mainly relay on their influence on the gut microbiota composition and their ability to generate fermentation products (short-chain fatty acids) with diverse biological roles. PUFAs include the omega-3 and omega-6 fatty acids, whose balance may influence diverse aspects of immunity and metabolism. Moreover, interactions between PUFAs and components of the gut microbiota may also influence their biological roles. Phytochemicals are bioactive non-nutrient plant compounds, which have raised interest because of their potential effects as antioxidants, antiestrogenics, anti-inflammatory, immunomodulatory, and anticarcinogenics. However, the bioavailability and effects of polyphenols greatly depend on their transformation by components of the gut microbiota. Phytochemicals and their metabolic products may also inhibit pathogenic bacteria while stimulate the growth of beneficial bacteria, exerting prebiotic-like effects. Therefore, the intestinal microbiota is both a target for nutritional intervention and a factor influencing the biological activity of other food compounds acquired orally. This review focuses on the reciprocal interactions between the gut microbiota and functional food components, and the consequences of these interactions on human health. 2009 Elsevier Ltd. All rights reserved.

  17. Secondary-to-Tertiary Comparison through the Lens of Ways of Doing Mathematics in Relation to Functions: A Study in Collaboration with Teachers

    Science.gov (United States)

    Corriveau, Claudia

    2017-01-01

    This article addresses the issue of transition from secondary to post-secondary education through collaborative research with teachers from both levels. It takes into account implicit elements in this transition. Research on the transition in mathematics education tends to focus more on the tertiary level, studying difficulties encountered by…

  18. Preparation of a weak anion exchange/hydrophobic interaction dual-function mixed-mode chromatography stationary phase for protein separation using click chemistry.

    Science.gov (United States)

    Zhao, Kailou; Yang, Fan; Xia, Hongjun; Wang, Fei; Song, Qingguo; Bai, Quan

    2015-03-01

    In this study, 3-diethylamino-1-propyne was covalently bonded to the azide-silica by a click reaction to obtain a novel dual-function mixed-mode chromatography stationary phase for protein separation with a ligand containing tertiary amine and two ethyl groups capable of electrostatic and hydrophobic interaction functionalities, which can display hydrophobic interaction chromatography character in a high-salt-concentration mobile phase and weak anion exchange character in a low-salt-concentration mobile phase employed for protein separation. As a result, it can be employed to separate proteins with weak anion exchange and hydrophobic interaction modes, respectively. The resolution and selectivity of the stationary phase were evaluated in both hydrophobic interaction and ion exchange modes with standard proteins, respectively, which can be comparable to that of conventional weak anion exchange and hydrophobic interaction chromatography columns. Therefore, the synthesized weak anion exchange/hydrophobic interaction dual-function mixed-mode chromatography column can be used to replace two corresponding conventional weak anion exchange and hydrophobic interaction chromatography columns to separate proteins. Based on this mixed-mode chromatography stationary phase, a new off-line two-dimensional liquid chromatography technology using only a single dual-function mixed-mode chromatography column was developed. Nine kinds of tested proteins can be separated completely using the developed method within 2.0 h.

  19. Determining protein function and interaction from genome analysis

    Science.gov (United States)

    Eisenberg, David; Marcotte, Edward M.; Thompson, Michael J.; Pellegrini, Matteo; Yeates, Todd O.

    2004-08-03

    A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A' and B' have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A' and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links.

  20. Functional interaction between Lypd6 and nicotinic acetylcholine receptors

    DEFF Research Database (Denmark)

    Arvaniti, Maria; Jensen, Majbrit M; Soni, Neeraj;

    2016-01-01

    Nicotinic acetylcholine receptors (nAChRs) affect multiple physiological functions in the brain and their functions are modulated by regulatory proteins of the Lynx family. Here, we report for the first time a direct interaction of the Lynx protein LY6/PLAUR domain-containing 6 (Lypd6) with n......AChRs in human brain extracts, identifying Lypd6 as a novel regulator of nAChR function. Using protein cross-linking and affinity purification from human temporal cortical extracts, we demonstrate that Lypd6 is a synaptically enriched membrane-bound protein that binds to multiple nAChR subtypes in the human...... brain. Additionally, soluble recombinant Lypd6 protein attenuates nicotine-induced hippocampal inward currents in rat brain slices and decreases nicotine-induced extracellular signal-regulated kinase phosphorylation in PC12 cells, suggesting that binding of Lypd6 is sufficient to inhibit n...

  1. Holistic atlases of functional networks and interactions reveal reciprocal organizational architecture of cortical function.

    Science.gov (United States)

    Lv, Jinglei; Jiang, Xi; Li, Xiang; Zhu, Dajiang; Zhang, Shu; Zhao, Shijie; Chen, Hanbo; Zhang, Tuo; Hu, Xintao; Han, Junwei; Ye, Jieping; Guo, Lei; Liu, Tianming

    2015-04-01

    For decades, it has been largely unknown to what extent multiple functional networks spatially overlap/interact with each other and jointly realize the total cortical function. Here, by developing novel sparse representation of whole-brain fMRI signals and by using the recently publicly released large-scale Human Connectome Project high-quality fMRI data, we show that a number of reproducible and robust functional networks, including both task-evoked and resting state networks, are simultaneously distributed in distant neuroanatomic areas and substantially spatially overlapping with each other, thus forming an initial collection of holistic atlases of functional networks and interactions (HAFNIs). More interestingly, the HAFNIs revealed two distinct patterns of highly overlapped regions and highly specialized regions and exhibited that these two patterns of areas are reciprocally localized, revealing a novel organizational principle of cortical function.

  2. Distribution function approach to irreversible adsorption of interacting colloidal particles

    Science.gov (United States)

    Faraudo, Jordi; Bafaluy, Javier

    2000-01-01

    A statistical-mechanical description of the irreversible adsorption of interacting colloidal particles is developed. Our approach describes in a consistent way the interaction of particles from the bulk with adsorbed particles during the transport process towards the adsorbing surface. The macroscopic physical quantities corresponding to the actual process are expressed as averages over simpler auxiliary processes which proceed in the presence of a fixed number n of adsorbed particles. The adsorption rate verifies a generalized Langmuir equation, in which the kinetic resistance (the inverse of the kinetic coefficient) is expressed as the sum of a diffusional resistance and a resistance due to interaction with adsorbed particles during the transport process (blocking effect). Contrary to previous approaches, the blocking effect is not due to geometrical exclusion, instead it measures how the transport from the bulk is affected by the adsorbed particles. From the general expressions obtained, we have derived coverage expansions for the adsorption rate and the surface correlation function. The theory is applied to the case of colloidal particles interacting through DLVO potentials. This form of the kinetic coefficient is shown to be in agreement with recent experimental results, in which RSA fails.

  3. Twenty years of protein interaction studies for biological function deciphering.

    Science.gov (United States)

    Legrain, Pierre; Rain, Jean-Christophe

    2014-07-31

    Intensive methodological developments and technology innovation have been devoted to protein-protein interaction studies over 20years. Genetic indirect assays and sophisticated large scale biochemical analyses have jointly contributed to the elucidation of protein-protein interactions, still with a lot of drawbacks despite heavy investment in human resources and technologies. With the most recent developments in mass spectrometry and computational tools for studying protein content of complex samples, the initial goal of deciphering molecular bases of biological functions is now within reach. Here, we described the various steps of this process and gave examples of key milestones in this scientific story line. This article is part of a Special Issue entitled: 20years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini, Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez.

  4. Structural interaction and functional regulation of polycystin-2 by filamin.

    Directory of Open Access Journals (Sweden)

    Qian Wang

    Full Text Available Filamins are important actin cross-linking proteins implicated in scaffolding, membrane stabilization and signal transduction, through interaction with ion channels, receptors and signaling proteins. Here we report the physical and functional interaction between filamins and polycystin-2, a TRP-type cation channel mutated in 10-15% patients with autosomal dominant polycystic kidney disease. Yeast two-hybrid and GST pull-down experiments demonstrated that the C-termini of filamin isoforms A, B and C directly bind to both the intracellular N- and C-termini of polycystin-2. Reciprocal co-immunoprecipitation experiments showed that endogenous polycystin-2 and filamins are in the same complexes in renal epithelial cells and human melanoma A7 cells. We then examined the effect of filamin on polycystin-2 channel function by electrophysiology studies with a lipid bilayer reconstitution system and found that filamin-A substantially inhibits polycystin-2 channel activity. Our study indicates that filamins are important regulators of polycystin-2 channel function, and further links actin cytoskeletal dynamics to the regulation of this channel protein.

  5. Density functionals for the strong-interaction limit

    Science.gov (United States)

    Seidl, Michael; Perdew, John P.; Kurth, Stefan

    2000-07-01

    The strong-interaction limit of density-functional (DF) theory is simple and provides information required for an accurate resummation of DF perturbation theory. Here we derive the point-charge-plus-continuum (PC) model for that limit, and its gradient expansion. The exchange-correlation (xc) energy Exc[ρ]≡∫10dαWα[ρ] follows from the xc potential energies Wα at different interaction strengths α>=0 [but at fixed density ρ(r)]. For small α~0, the integrand Wα is obtained accurately from perturbation theory, but the perturbation expansion requires resummation for moderate and large α. For that purpose, we present density functionals for the coefficients in the asymptotic expansion Wα-->W∞+W'∞α-1/2 for α-->∞ in the PC model. WPC∞ arises from strict correlation, and W'PC∞ from zero-point vibration of the electrons around their strictly correlated distributions. The PC values for W∞ and W'∞ agree with those from a self-correlation-free meta-generalized gradient approximation, both for atoms and for atomization energies of molecules. We also (i) explain the difference between the PC cell and the exchange-correlation hole, (ii) present a density-functional measure of correlation strength, (iii) describe the electron localization and spin polarization energy in a highly stretched H2 molecule, and (iv) discuss the soft-plasmon instability of the low-density uniform electron gas.

  6. Co-evolution of quaternary organization and novel RNA tertiary interactions revealed in the crystal structure of a bacterial protein–RNA toxin–antitoxin system

    Science.gov (United States)

    Rao, Feng; Short, Francesca L.; Voss, Jarrod E.; Blower, Tim R.; Orme, Anastasia L.; Whittaker, Tom E.; Luisi, Ben F.; Salmond, George P. C.

    2015-01-01

    Genes encoding toxin–antitoxin (TA) systems are near ubiquitous in bacterial genomes and they play key roles in important aspects of bacterial physiology, including genomic stability, formation of persister cells under antibiotic stress, and resistance to phage infection. The CptIN locus from Eubacterium rectale is a member of the recently-discovered Type III class of TA systems, defined by a protein toxin suppressed by direct interaction with a structured RNA antitoxin. Here, we present the crystal structure of the CptIN protein–RNA complex to 2.2 Å resolution. The structure reveals a new heterotetrameric quaternary organization for the Type III TA class, and the RNA antitoxin bears a novel structural feature of an extended A-twist motif within the pseudoknot fold. The retention of a conserved ribonuclease active site as well as traits normally associated with TA systems, such as plasmid maintenance, implicates a wider functional role for Type III TA systems. We present evidence for the co-variation of the Type III component pair, highlighting a distinctive evolutionary process in which an enzyme and its substrate co-evolve. PMID:26350213

  7. Co-evolution of quaternary organization and novel RNA tertiary interactions revealed in the crystal structure of a bacterial protein-RNA toxin-antitoxin system.

    Science.gov (United States)

    Rao, Feng; Short, Francesca L; Voss, Jarrod E; Blower, Tim R; Orme, Anastasia L; Whittaker, Tom E; Luisi, Ben F; Salmond, George P C

    2015-10-30

    Genes encoding toxin-antitoxin (TA) systems are near ubiquitous in bacterial genomes and they play key roles in important aspects of bacterial physiology, including genomic stability, formation of persister cells under antibiotic stress, and resistance to phage infection. The CptIN locus from Eubacterium rectale is a member of the recently-discovered Type III class of TA systems, defined by a protein toxin suppressed by direct interaction with a structured RNA antitoxin. Here, we present the crystal structure of the CptIN protein-RNA complex to 2.2 Å resolution. The structure reveals a new heterotetrameric quaternary organization for the Type III TA class, and the RNA antitoxin bears a novel structural feature of an extended A-twist motif within the pseudoknot fold. The retention of a conserved ribonuclease active site as well as traits normally associated with TA systems, such as plasmid maintenance, implicates a wider functional role for Type III TA systems. We present evidence for the co-variation of the Type III component pair, highlighting a distinctive evolutionary process in which an enzyme and its substrate co-evolve.

  8. Dynein at the kinetochore: Timing, Interactions and Functions.

    Science.gov (United States)

    Bader, Jason R; Vaughan, Kevin T

    2010-05-01

    Kinetochores have been proposed to play multiple roles in mitotic chromosome alignment, including initial microtubule (MT) capture, monitoring MT attachments, prometaphase and anaphase chromosome movement and tension generation at metaphase. In addition, kinetochores are essential components of the spindle assembly checkpoint (SAC), and couple chromosome alignment with SAC silencing at metaphase. Although the molecular details of these activities remain under investigation, cytoplasmic dynein has been implicated in several aspects of MT and SAC regulation. Recent work clarifies the contribution of dynein to MT interactions and to events that drive anaphase onset. This review summarizes these studies and provides new models for dynein function. Copyright 2010 Elsevier Ltd. All rights reserved.

  9. Dynamical density functional theory with hydrodynamic interactions in confined geometries

    Science.gov (United States)

    Goddard, B. D.; Nold, A.; Kalliadasis, S.

    2016-12-01

    We study the dynamics of colloidal fluids in both unconfined geometries and when confined by a hard wall. Under minimal assumptions, we derive a dynamical density functional theory (DDFT) which includes hydrodynamic interactions (HI; bath-mediated forces). By using an efficient numerical scheme based on pseudospectral methods for integro-differential equations, we demonstrate its excellent agreement with the full underlying Langevin equations for systems of hard disks in partial confinement. We further use the derived DDFT formalism to elucidate the crucial effects of HI in confined systems.

  10. Functional interaction between Lypd6 and nicotinic acetylcholine receptors

    DEFF Research Database (Denmark)

    Arvaniti, Maria; Jensen, Majbrit M; Soni, Neeraj

    2016-01-01

    Nicotinic acetylcholine receptors (nAChRs) affect multiple physiological functions in the brain and their functions are modulated by regulatory proteins of the Lynx family. Here, we report for the first time a direct interaction of the Lynx protein LY6/PLAUR domain-containing 6 (Lypd6) with n...... brain. Additionally, soluble recombinant Lypd6 protein attenuates nicotine-induced hippocampal inward currents in rat brain slices and decreases nicotine-induced extracellular signal-regulated kinase phosphorylation in PC12 cells, suggesting that binding of Lypd6 is sufficient to inhibit n......AChR-mediated intracellular signaling. We further show that perinatal nicotine exposure in rats (4 mg/kg/day through minipumps to dams from embryonic day 7 to post-natal day 21) significantly increases Lypd6 protein levels in the hippocampus in adulthood, which did not occur after exposure to nicotine in adulthood only. Our...

  11. Code switching in student-student interaction; functions and reasons

    Directory of Open Access Journals (Sweden)

    Rita Amorim

    2012-01-01

    Full Text Available : Today’s students of English will communicate mostly with non-native speakers, in predominantly non-native speaking environments. English teachers know that if they are to realistically prepare students for international communication, they must focus on speaking activities that promote communicative competence and fluency. Presence of mother tongue in communicative exchanges is frequently detected by teachers in EFL classrooms. This study analyses student-student interaction during a group-work speaking activity, to uncover some of the reasons for code switching (CS. It also presents participants’ perspectives revealing mixed feelings towards this linguistic behaviour, which is sometimes intentional and sometimes unconscious. The aim of this paper is to illustrate how EFL students alternate between foreign language and native language to perform certain pragmatic functions and counter-balance for language deficiencies. It also considers the relationship between students’ language level and the functional character of their switches.

  12. Flotation of kaolinite with dodecyl tertiary amines

    Institute of Scientific and Technical Information of China (English)

    CAO Xue-feng; LIU Chang-miao; HU Yue-hua

    2009-01-01

    The flotation of kaolinite using a series of tertiary amines (N,N-dimethyl-dodecyl amine (DRN), N,N-diethyl-dodecyl amine (DEN), N,N-dipropyl-dodecyl amine (DPN) and N,N-dibenzyl-bodecyi amine (DBN)) was investigated. The results show that the maximum recoveries of kaolinite for DEN, DPN and DRN are 93%, 88% and 84%, respectively, but that of DBN is very low. On the basis of zeta potential and FT-IR spectra, the ionization of surface hydroxyl and isomorphic exchange of surface ions account for the charging mechanisms of kaolinite surface. The adsorption mechanism of tertiary amines on kaolinite surface is mainly electrostatic. The isoelectric point (IEP) of kaolinite increases from 3.4 to some more positive points after the interaction of kaolinite with the four tertiary amines. The FT-IR spectra of kaolinite change with the presence of some new sharp shapes belonging to the tertiary amines. The inductive electronic effects and space-steric effects of -CH_3, -C_2H_5, -C_3H_7 and -C_7H_7 bonding to N atom result in different collecting power of the four tertiary amines.

  13. Ecological interaction and phylogeny, studying functionality on composed networks

    Science.gov (United States)

    Cruz, Claudia P. T.; Fonseca, Carlos Roberto; Corso, Gilberto

    2012-02-01

    We study a class of composed networks that are formed by two tree networks, TP and TA, whose end points touch each other through a bipartite network BPA. We explore this network using a functional approach. We are interested in how much the topology, or the structure, of TX (X=A or P) determines the links of BPA. This composed structure is a useful model in evolutionary biology, where TP and TA are the phylogenetic trees of plants and animals that interact in an ecological community. We make use of ecological networks of dispersion of fruits, which are formed by frugivorous animals and plants with fruits; the animals, usually birds, eat fruits and disperse their seeds. We analyse how the phylogeny of TX determines or is correlated with BPA using a Monte Carlo approach. We use the phylogenetic distance among elements that interact with a given species to construct an index κ that quantifies the influence of TX over BPA. The algorithm is based on the assumption that interaction matrices that follows a phylogeny of TX have a total phylogenetic distance smaller than the average distance of an ensemble of Monte Carlo realisations. We find that the effect of phylogeny of animal species is more pronounced in the ecological matrix than plant phylogeny.

  14. Charge-Transfer Interactions in Organic Functional Materials

    Directory of Open Access Journals (Sweden)

    Bih-Yaw Jin

    2010-08-01

    Full Text Available Our goal in this review is three-fold. First, we provide an overview of a number of quantum-chemical methods that can abstract charge-transfer (CT information on the excited-state species of organic conjugated materials, which can then be exploited for the understanding and design of organic photodiodes and solar cells at the molecular level. We stress that the Composite-Molecule (CM model is useful for evaluating the electronic excited states and excitonic couplings of the organic molecules in the solid state. We start from a simple polyene dimer as an example to illustrate how interchain separation and chain size affect the intercahin interaction and the role of the charge transfer interaction in the excited state of the polyene dimers. With the basic knowledge from analysis of the polyene system, we then study more practical organic materials such as oligophenylenevinylenes (OPVn, oligothiophenes (OTn, and oligophenylenes (OPn. Finally, we apply this method to address the delocalization pathway (through-bond and/or through-space in the lowest excited state for cyclophanes by combining the charge-transfer contributions calculated on the cyclophanes and the corresponding hypothetical molecules with tethers removed. This review represents a step forward in the understanding of the nature of the charge-transfer interactions in the excited state of organic functional materials.

  15. Interaction between Functional Domains of Bacillus thuringiensis Insecticidal Crystal Proteins

    Science.gov (United States)

    Rang, Cécile; Vachon, Vincent; de Maagd, Ruud A.; Villalon, Mario; Schwartz, Jean-Louis; Bosch, Dirk; Frutos, Roger; Laprade, Raynald

    1999-01-01

    Interactions among the three structural domains of Bacillus thuringiensis Cry1 toxins were investigated by functional analysis of chimeric proteins. Hybrid genes were prepared by exchanging the regions coding for either domain I or domain III among Cry1Ab, Cry1Ac, Cry1C, and Cry1E. The activity of the purified trypsin-activated chimeric toxins was evaluated by testing their effects on the viability and plasma membrane permeability of Sf9 cells. Among the parental toxins, only Cry1C was active against these cells and only chimeras possessing domain II from Cry1C were functional. Combination of domain I from Cry1E with domains II and III from Cry1C, however, resulted in an inactive toxin, indicating that domain II from an active toxin is necessary, but not sufficient, for activity. Pores formed by chimeric toxins in which domain I was from Cry1Ab or Cry1Ac were slightly smaller than those formed by toxins in which domain I was from Cry1C. The properties of the pores formed by the chimeras are therefore likely to result from an interaction between domain I and domain II or III. Domain III appears to modulate the activity of the chimeric toxins: combination of domain III from Cry1Ab with domains I and II of Cry1C gave a protein which was more strongly active than Cry1C. PMID:10388684

  16. Tertiary Education in Portugal

    Science.gov (United States)

    OECD Publishing (NJ3), 2008

    2008-01-01

    Portugal's tertiary education sector has expanded significantly over the last 20 years, but participation and overall educational attainment levels remain below European standards and enrolment rates have begun to decline. The OECD review recommends that Portugal's national government should focus on strategic direction and leave higher education…

  17. Consumer diversity interacts with prey defenses to drive ecosystem function.

    Science.gov (United States)

    Rasher, Douglas B; Hoey, Andrew S; Hay, Mark E

    2013-06-01

    Prey traits linking consumer diversity to ecosystem function remain poorly understood. On tropical coral reefs, herbivores promote coral dominance by suppressing competing macroalgae, but the roles of herbivore identity and diversity, macroalgal defenses, and their interactions in affecting reef resilience and function are unclear. We studied adjacent pairs of no-take marine reserves and fished areas on reefs in Fiji and found that protected reefs supported 7-17x greater biomass, 2-3x higher species richness of herbivorous fishes, and 3-11x more live coral cover than did fished reefs. In contrast, macroalgae were 27-61x more abundant and 3-4x more species-rich on fished reefs. When we transplanted seven common macroalgae from fished reefs into reserves they were rapidly consumed, suggesting that rates of herbivory (ecosystem functioning) differed inside vs. outside reserves. We then video-recorded feeding activity on the same seven macroalgae when transplanted into reserves, and assessed the functional redundancy vs. complementarity of herbivorous fishes consuming these macroalgae. Of 29 species of larger herbivorous fishes on these reefs, only four species accounted for 97% of macroalgal consumption. Two unicornfish consumed a range of brown macroalgae, a parrotfish consumed multiple red algae, and a rabbitfish consumed a green alga, with almost no diet overlap among these groups. The two most chemically rich, allelopathic algae were each consumed by a single, but different, fish species. This striking complementarity resulted from herbivore species differing in their tolerances to macroalgal chemical and structural defenses. A model of assemblage diet breadth based on our feeding observations predicted that high browser diversity would be required for effective control of macroalgae on Fijian reefs. In support of this model, we observed strong negative relationships between herbivore diversity and macroalgal abundance and diversity across the six study reefs. Our

  18. INTERACTIVE VISUALIZATION OF PROBABILITY AND CUMULATIVE DENSITY FUNCTIONS

    KAUST Repository

    Potter, Kristin

    2012-01-01

    The probability density function (PDF), and its corresponding cumulative density function (CDF), provide direct statistical insight into the characterization of a random process or field. Typically displayed as a histogram, one can infer probabilities of the occurrence of particular events. When examining a field over some two-dimensional domain in which at each point a PDF of the function values is available, it is challenging to assess the global (stochastic) features present within the field. In this paper, we present a visualization system that allows the user to examine two-dimensional data sets in which PDF (or CDF) information is available at any position within the domain. The tool provides a contour display showing the normed difference between the PDFs and an ansatz PDF selected by the user and, furthermore, allows the user to interactively examine the PDF at any particular position. Canonical examples of the tool are provided to help guide the reader into the mapping of stochastic information to visual cues along with a description of the use of the tool for examining data generated from an uncertainty quantification exercise accomplished within the field of electrophysiology.

  19. Defining functional interactions during biogenesis of epithelial junctions

    Science.gov (United States)

    Erasmus, J. C.; Bruche, S.; Pizarro, L.; Maimari, N.; Pogglioli, T.; Tomlinson, C.; Lees, J.; Zalivina, I.; Wheeler, A.; Alberts, A.; Russo, A.; Braga, V. M. M.

    2016-01-01

    In spite of extensive recent progress, a comprehensive understanding of how actin cytoskeleton remodelling supports stable junctions remains to be established. Here we design a platform that integrates actin functions with optimized phenotypic clustering and identify new cytoskeletal proteins, their functional hierarchy and pathways that modulate E-cadherin adhesion. Depletion of EEF1A, an actin bundling protein, increases E-cadherin levels at junctions without a corresponding reinforcement of cell–cell contacts. This unexpected result reflects a more dynamic and mobile junctional actin in EEF1A-depleted cells. A partner for EEF1A in cadherin contact maintenance is the formin DIAPH2, which interacts with EEF1A. In contrast, depletion of either the endocytic regulator TRIP10 or the Rho GTPase activator VAV2 reduces E-cadherin levels at junctions. TRIP10 binds to and requires VAV2 function for its junctional localization. Overall, we present new conceptual insights on junction stabilization, which integrate known and novel pathways with impact for epithelial morphogenesis, homeostasis and diseases. PMID:27922008

  20. Functionalized anatomical models for EM-neuron Interaction modeling

    Science.gov (United States)

    Neufeld, Esra; Cassará, Antonino Mario; Montanaro, Hazael; Kuster, Niels; Kainz, Wolfgang

    2016-06-01

    The understanding of interactions between electromagnetic (EM) fields and nerves are crucial in contexts ranging from therapeutic neurostimulation to low frequency EM exposure safety. To properly consider the impact of in vivo induced field inhomogeneity on non-linear neuronal dynamics, coupled EM-neuronal dynamics modeling is required. For that purpose, novel functionalized computable human phantoms have been developed. Their implementation and the systematic verification of the integrated anisotropic quasi-static EM solver and neuronal dynamics modeling functionality, based on the method of manufactured solutions and numerical reference data, is described. Electric and magnetic stimulation of the ulnar and sciatic nerve were modeled to help understanding a range of controversial issues related to the magnitude and optimal determination of strength-duration (SD) time constants. The results indicate the importance of considering the stimulation-specific inhomogeneous field distributions (especially at tissue interfaces), realistic models of non-linear neuronal dynamics, very short pulses, and suitable SD extrapolation models. These results and the functionalized computable phantom will influence and support the development of safe and effective neuroprosthetic devices and novel electroceuticals. Furthermore they will assist the evaluation of existing low frequency exposure standards for the entire population under all exposure conditions.

  1. Interactive design of probability density functions for shape grammars

    KAUST Repository

    Dang, Minh

    2015-11-02

    A shape grammar defines a procedural shape space containing a variety of models of the same class, e.g. buildings, trees, furniture, airplanes, bikes, etc. We present a framework that enables a user to interactively design a probability density function (pdf) over such a shape space and to sample models according to the designed pdf. First, we propose a user interface that enables a user to quickly provide preference scores for selected shapes and suggest sampling strategies to decide which models to present to the user to evaluate. Second, we propose a novel kernel function to encode the similarity between two procedural models. Third, we propose a framework to interpolate user preference scores by combining multiple techniques: function factorization, Gaussian process regression, autorelevance detection, and l1 regularization. Fourth, we modify the original grammars to generate models with a pdf proportional to the user preference scores. Finally, we provide evaluations of our user interface and framework parameters and a comparison to other exploratory modeling techniques using modeling tasks in five example shape spaces: furniture, low-rise buildings, skyscrapers, airplanes, and vegetation.

  2. High-performance functional Renormalization Group calculations for interacting fermions

    Science.gov (United States)

    Lichtenstein, J.; Sánchez de la Peña, D.; Rohe, D.; Di Napoli, E.; Honerkamp, C.; Maier, S. A.

    2017-04-01

    We derive a novel computational scheme for functional Renormalization Group (fRG) calculations for interacting fermions on 2D lattices. The scheme is based on the exchange parametrization fRG for the two-fermion interaction, with additional insertions of truncated partitions of unity. These insertions decouple the fermionic propagators from the exchange propagators and lead to a separation of the underlying equations. We demonstrate that this separation is numerically advantageous and may pave the way for refined, large-scale computational investigations even in the case of complex multiband systems. Furthermore, on the basis of speedup data gained from our implementation, it is shown that this new variant facilitates efficient calculations on a large number of multi-core CPUs. We apply the scheme to the t ,t‧ Hubbard model on a square lattice to analyze the convergence of the results with the bond length of the truncation of the partition of unity. In most parameter areas, a fast convergence can be observed. Finally, we compare to previous results in order to relate our approach to other fRG studies.

  3. Functional interactions between steroid hormones and neurotrophin BDNF

    Institute of Scientific and Technical Information of China (English)

    Tadahiro; Numakawa; Daisaku; Yokomaku; Misty; Richards; Hiroaki; Hori; Naoki; Adachi; Hiroshi; Kunugi

    2010-01-01

    Brain-derived neurotrophic factor(BDNF),a critical neurotrophin,regulates many neuronal aspects including cell differentiation,cell survival,neurotransmission,and synaptic plasticity in the central nervous system(CNS) .Though BDNF has two types of receptors,high affinity tropomyosin-related kinase(Trk) B and low affinity p75 receptors,BDNF positively exerts its biological effects on neurons via activation of TrkB and of resultant intracellular signaling cascades including mitogenactivated protein kinase/extracellular signal-regulated protein kinase,phospholipase Cγ,and phosphoinositide 3-kinase pathways.Notably,it is possible that alteration in the expression and/or function of BDNF in the CNS is involved in the pathophysiology of various brain diseases such as stroke,Parkinson’s disease,Alzheimer’s disease,and mental disorders.On the other hand,glucocorticoids,stress-induced steroid hormones,also putatively contribute to the pathophysiology of depression.Interestingly,in addition to the reduction in BDNF levels due to increased glucocorticoid exposure,current reports demonstrate possible interactions between glucocorticoids and BDNF-mediated neuronal functions. Other steroid hormones,such as estrogen,are involved in not only sexual differentiation in the brain,but also numerous neuronal events including cell survival and synaptic plasticity.Furthermore,it is well known that estrogen plays a role in the pathophysiology of Parkinson’s disease,Alzheimer’s disease,and mental illness,while serving to regulate BDNF expression and/or function.Here,we present a broad overview of the current knowledge concerning the association between BDNF expression/function and steroid hormones(glucocorticoids and estrogen).

  4. A study on the interactions of doctors with medical representatives of pharmaceutical companies in a Tertiary Care Teaching Hospital of South India

    Directory of Open Access Journals (Sweden)

    Sandeep Kumar Gupta

    2016-01-01

    Full Text Available Background: The promotional activities by medical representatives (MRs of the pharmaceutical companies can impact the prescribing pattern of doctors. Hence, the interaction between doctors and the pharmaceutical industry is coming under increasing scrutiny. Objective: The primary objective was to assess the attitude of the doctors toward the interaction with the MRs of the pharmaceutical company. The secondary objective was to assess the awareness of the doctors about regulations governing their interaction with the pharmaceutical company. Materials and Methods: This was a cross-sectional study. This study was carried out using a pretested questionnaire containing 10 questions between June and September 2014. The doctors working in the Dhanalakshmi Srinivasan Medical College and Hospital, Perambalur (Tamil Nadu during the study period was included. Results: A total of 100 pretested questionnaires were distributed, and 81 doctors responded (response rate 81%. 37% doctors responded that they interacted with MR once a week whereas 25.9% told that they interact with MRs twice a month. About 69.1% doctors think that MR exaggerate the benefits of medicines and downplays the risks and contraindications of medicine(P = 0.000. 61.7% doctors think that MR has an impact on their prescribing (P = 0.000. 63% doctors stated that they had received promotional tools such as stationery items, drug sample, textbooks or journal reprints from MR in last 12 months (P = 0.0012. Unfortunately, 70.4% doctors have not read the guidelines about interacting with the pharmaceutical industry or its representative (P = 0.000. Conclusion: Rather than forbidding any connection between doctors and industry, it is better to establish ethical guidelines. The Medical Council of India code is a step in the right direction, but the majority of doctors in this study have not read the guidelines about interacting with the pharmaceutical industry or its representative.

  5. Beyond Flory theory: Distribution functions for interacting lattice trees

    Science.gov (United States)

    Rosa, Angelo; Everaers, Ralf

    2017-01-01

    While Flory theories [J. Isaacson and T. C. Lubensky, J. Physique Lett. 41, 469 (1980), 10.1051/jphyslet:019800041019046900; M. Daoud and J. F. Joanny, J. Physique 42, 1359 (1981), 10.1051/jphys:0198100420100135900; A. M. Gutin et al., Macromolecules 26, 1293 (1993), 10.1021/ma00058a016] provide an extremely useful framework for understanding the behavior of interacting, randomly branching polymers, the approach is inherently limited. Here we use a combination of scaling arguments and computer simulations to go beyond a Gaussian description. We analyze distribution functions for a wide variety of quantities characterizing the tree connectivities and conformations for the four different statistical ensembles, which we have studied numerically in [A. Rosa and R. Everaers, J. Phys. A: Math. Theor. 49, 345001 (2016), 10.1088/1751-8113/49/34/345001 and J. Chem. Phys. 145, 164906 (2016), 10.1063/1.4965827]: (a) ideal randomly branching polymers, (b) 2 d and 3 d melts of interacting randomly branching polymers, (c) 3 d self-avoiding trees with annealed connectivity, and (d) 3 d self-avoiding trees with quenched ideal connectivity. In particular, we investigate the distributions (i) pN(n ) of the weight, n , of branches cut from trees of mass N by severing randomly chosen bonds; (ii) pN(l ) of the contour distances, l , between monomers; (iii) pN(r ⃗) of spatial distances, r ⃗, between monomers, and (iv) pN(r ⃗|l ) of the end-to-end distance of paths of length l . Data for different tree sizes superimpose, when expressed as functions of suitably rescaled observables x ⃗=r ⃗/√{ } or x =l / . In particular, we observe a generalized Kramers relation for the branch weight distributions (i) and find that all the other distributions (ii-iv) are of Redner-des Cloizeaux type, q (x ⃗) =C |x| θexp(-(K|x |) t) . We propose a coherent framework, including generalized Fisher-Pincus relations, relating most of the RdC exponents to each other and to the contact and Flory

  6. Hepatitis C virus internal ribosome entry site RNA contains a tertiary structural element in a functional domain of stem–loop II

    Science.gov (United States)

    Lyons, Alita J.; Lytle, J. Robin; Gomez, Jordi; Robertson, Hugh D.

    2001-01-01

    The internal ribosome entry site (IRES) of hepatitis C virus (HCV) RNA contains >300 bases of highly conserved 5′-terminal sequence, most of it in the uncapped 5′-untranslated region (5′-UTR) upstream from the single AUG initiator triplet at which translation of the HCV polyprotein begins. Although progress has been made in defining singularities like the RNA pseudoknot near this AUG, the sequence and structural features of the HCV IRES which stimulate accurate and efficient initiation of protein synthesis are only partially defined. Here we report that a region further upstream from the AUG, stem–loop II of the HCV IRES, also contains an element of local tertiary structure which we have detected using RNase H cleavage and have mapped using the singular ability of two bases therein to undergo covalent intra-chain crosslinking stimulated by UV light. This pre-existing element maps to two non-contiguous stretches of the HCV IRES sequence, residues 53–68 and 103–117. Several earlier studies have shown that the correct sequence between bases 45 and 70 of the HCV IRES stem–loop II domain is required for initiation of protein synthesis. Because features of local tertiary structure like the one we report here are often associated with protein binding, we propose that the HCV stem–loop II element is directly involved in IRES action. PMID:11410661

  7. 14-3-3 phosphoprotein interaction networks – does isoform diversity present functional interaction specification?

    Directory of Open Access Journals (Sweden)

    Anna-Lisa ePaul

    2012-08-01

    Full Text Available The 14-3-3 proteins have emerged as major phosphoprotein interaction proteins and thereby constitute a key node in the Arabidopsis Interactome Map, a node through which a large number of important signals pass. Throughout their history of discovery and description, the 14-3-3s have been described as protein families and there has been some evidence that the different 14-3-3 family members within any organisms might carry isoform specific functions. However there has also been evidence for redundancy of 14-3-3 function, suggesting that the perceived 14-3-3 diversity may be the accumulation of neutral mutations over evolutionary time and as some 14-3-3 genes develop tissue or organ specific expression. This situation has led to a currently unresolved question – does 14-3-3 isoform sequence diversity indicate functional diversity at the biochemical or cellular level? We discuss here some of the key observations on both sides of the resulting debate, and present a set of contrastable observations to address the theory that sequence diversity does lead to functional diversity among 14-3-3 isoforms. The resulting model suggests strongly that there are indeed functional specificities in the 14-3-3s of Arabidopsis. The model further suggests that 14-3-3 diversity and specificity should enter into the discussion of 14-3-3 roles in signal transduction and be directly approached in experiments designed to address 14-3-3 functional roles. It is hoped that future studies involving 14-3-3s will continue to address specificity in experimental design and analysis.

  8. Bacterial degradation of tert-amyl alcohol proceeds via hemiterpene 2-methyl-3-buten-2-ol by employing the tertiary alcohol desaturase function of the Rieske nonheme mononuclear iron oxygenase MdpJ.

    Science.gov (United States)

    Schuster, Judith; Schäfer, Franziska; Hübler, Nora; Brandt, Anne; Rosell, Mònica; Härtig, Claus; Harms, Hauke; Müller, Roland H; Rohwerder, Thore

    2012-03-01

    Tertiary alcohols, such as tert-butyl alcohol (TBA) and tert-amyl alcohol (TAA) and higher homologues, are only slowly degraded microbially. The conversion of TBA seems to proceed via hydroxylation to 2-methylpropan-1,2-diol, which is further oxidized to 2-hydroxyisobutyric acid. By analogy, a branched pathway is expected for the degradation of TAA, as this molecule possesses several potential hydroxylation sites. In Aquincola tertiaricarbonis L108 and Methylibium petroleiphilum PM1, a likely candidate catalyst for hydroxylations is the putative tertiary alcohol monooxygenase MdpJ. However, by comparing metabolite accumulations in wild-type strains of L108 and PM1 and in two mdpJ knockout mutants of strain L108, we could clearly show that MdpJ is not hydroxylating TAA to diols but functions as a desaturase, resulting in the formation of the hemiterpene 2-methyl-3-buten-2-ol. The latter is further processed via the hemiterpenes prenol, prenal, and 3-methylcrotonic acid. Likewise, 3-methyl-3-pentanol is degraded via 3-methyl-1-penten-3-ol. Wild-type strain L108 and mdpJ knockout mutants formed isoamylene and isoprene from TAA and 2-methyl-3-buten-2-ol, respectively. It is likely that this dehydratase activity is catalyzed by a not-yet-characterized enzyme postulated for the isomerization of 2-methyl-3-buten-2-ol and prenol. The vitamin requirements of strain L108 growing on TAA and the occurrence of 3-methylcrotonic acid as a metabolite indicate that TAA and hemiterpene degradation are linked with the catabolic route of the amino acid leucine, including an involvement of the biotin-dependent 3-methylcrotonyl coenzyme A (3-methylcrotonyl-CoA) carboxylase LiuBD. Evolutionary aspects of favored desaturase versus hydroxylation pathways for TAA conversion and the possible role of MdpJ in the degradation of higher tertiary alcohols are discussed.

  9. Assessing the Use of YouTube Videos and Interactive Activities as a Critical Thinking Stimulator for Tertiary Students: An Action Research

    Science.gov (United States)

    June, Sethela; Yaacob, Aizan; Kheng, Yeoh Khar

    2014-01-01

    The purpose of this action research was to investigate the use of YouTube videos and interactive activities in stimulating critical thinking among students from a public university in Malaysia. There were 50 students of mixed background, comprised of local and foreign students who participated in this study which lasted for one semester. Data was…

  10. Study of potential drug interactions between prescribed drugs in geriatric patients attending outpatient department in a government tertiary care hospital in Maharashtra

    Directory of Open Access Journals (Sweden)

    Tushar Bhimrao Nishandar

    2016-08-01

    Conclusions: In the present study, PDIs were studied in geriatric population. Knowledge of the prevalence and predictors of clinically important PDIs will help physicians and pharmacists identify patients at higher risk of adverse drug interactions requiring more cautious pharmacotherapy. [Int J Basic Clin Pharmacol 2016; 5(4.000: 1569-1573

  11. Functional interactions between a glutamine synthetase promoter and MYB proteins.

    Science.gov (United States)

    Gómez-Maldonado, Josefa; Avila, Concepción; Torre, Fernando; Cañas, Rafael; Cánovas, Francisco M; Campbell, Malcolm M

    2004-08-01

    In Scots pine (Pinus sylvestris), ammonium assimilation is catalysed by glutamine synthetase (GS) [EC 6.3.1.2], which is encoded by two genes, PsGS1a and PsGS1b. PsGS1b is expressed in the vascular tissue throughout the plant body, where it is believed to play a role in recycling ammonium released by various facets of metabolism. The mechanisms that may underpin the transcriptional regulation of PsGS1b were explored. The PsGS1b promoter contains a region that is enriched in previously characterized cis-acting elements, known as AC elements. Pine nuclear proteins bound these AC element-rich regions in a tissue-specific manner. As previous experiments had shown that R2R3-MYB transcription factors could interact with AC elements, the capacity of the AC elements in the PsGS1b promoter to interact with MYB proteins was examined. Two MYB proteins from loblolly pine (Pinus taeda), PtMYB1 and PtMYB4, bound to the PsGS1b promoter were able to activate transcription from this promoter in yeast, arabidopsis and pine cells. Immunolocalization experiments revealed that the two MYB proteins were most abundant in cells previously shown to accumulate PsGS1b transcripts. Immunoprecipitation analysis and supershift electrophoretic mobility shift assays implicated these same two proteins in the formation of complexes between pine nuclear extracts and the PsGS1b promoter. Given that these MYB proteins were previously shown to have the capacity to activate gene expression related to lignin biosynthesis, we hypothesize that they may function to co-regulate lignification, a process that places significant demands on nitrogen recycling, and GS, the major enzyme involved in the nitrogen recycling pathway.

  12. Interaction between functional health literacy, patient activation, and glycemic control

    Directory of Open Access Journals (Sweden)

    Woodard LD

    2014-07-01

    Full Text Available LeChauncy D Woodard, Cassie R Landrum, Amber B Amspoker, David Ramsey, Aanand D Naik Veterans Affairs Health Services Research and Development Center for Innovations in Quality, Effectiveness and Safety, Michael E DeBakey Veterans Affairs Medical Center, and Section of Health Services Research, Department of Medicine, Baylor College of Medicine, Houston, TX, USA Background: Functional health literacy (FHL and patient activation can impact diabetes control through enhanced diabetes self-management. Less is known about the combined effect of these characteristics on diabetes outcomes. Using brief, validated measures, we examined the interaction between FHL and patient activation in predicting glycosylated hemoglobin (HbA1c control among a cohort of multimorbid diabetic patients.Methods: We administered a survey via mail to 387 diabetic patients with coexisting ­hypertension and ischemic heart disease who received outpatient care at one regional VA medical center between November 2010 and December 2010. We identified patients with the study conditions using the International Classification of Diseases-Ninth Revision-Clinical ­Modification (ICD-9-CM diagnoses codes and Current Procedure Terminology (CPT ­procedures codes. Surveys were returned by 195 (50.4% patients. We determined patient activation levels based on participant responses to the 13-item Patient Activation Measure and FHL levels using the single-item screening question, “How confident are you filling out medical forms by yourself?” We reviewed patient medical records to assess glycemic control. We used multiple logistic regression to examine whether activation and FHL were individually or jointly related to HbA1c control.Results: Neither patient activation nor FHL was independently related to glycemic control in the unadjusted main effects model; however, the interaction between the two was significantly associated with glycemic control (odds ratio 1.05 [95% confidence

  13. The Thermal Stability of Tertiary Pyridine Resin for the Application to Multi-functional Reprocessing Process - Adv.-ORIENT Cycle Development

    Energy Technology Data Exchange (ETDEWEB)

    Sato, Yoshihiko; Okada, K.; Akiyoshi, M.; Matsunaga, T. [AIST Tsukuba Central 5, Higashi 1-1-1, Tsukuba, Ibaraki 305-8565 (Japan); Suzuki, T. [Tokyo Tech (Japan); Koyama, S.; Ozawa, M. [Japan Atomic Energy Agency - JAEA (Japan)

    2009-06-15

    As part of 'Adv.-ORIENT' (Advanced Optimization by Recycling Instructive Elements) cycle technologies which aim to develop new fuel cycle based on FBR (Fast Breeder Reactor), the fundamental thermochemical properties of tertiary pyridine resin (TPR) and its mixtures with methanol/HCl and HNO{sub 3} were investigated and heating tests on gram scale with TPR/methanol/HNO{sub 3} were carried out in order to evaluate the thermal stability of TPR and to determine the conditions necessary to avoid runaway reactions. It was found that TPR with HCl was thermally stable. Evident thermal decomposition peaks were identified with TPR in the presence of concentrated HNO{sub 3}. No specific effect was observed for methanol involving. However, it was considered that the rapidly exothermic reaction can be controlled by heating temperature. (authors)

  14. The functional renormalization group for interacting quantum systems with spin-orbit interaction

    Energy Technology Data Exchange (ETDEWEB)

    Grap, Stephan Michael [RWTH Aachen (Germany). Inst. fuer Theorie der Statistischen Physik

    2013-07-15

    We studied the influence of spin-orbit interaction (SOI) in interacting low dimensional quantum systems at zero temperature within the framework of the functional renormalization group (fRG). Among the several types of spin-orbit interaction the so-called Rashba spin-orbit interaction is especially intriguing for future spintronic applications as it may be tuned via external electric fields. We investigated its effect on the low energy physics of an interacting quantum wire in an applied Zeeman field which is modeled as a generalization of the extended Hubbard model. To this end we performed a renormalization group study of the two particle interaction, including the SOI and the Zeeman field exactly on the single particle level. Considering the resulting two band model, we formulated the RG equations for the two particle vertex keeping the full band structure as well as the non trivial momentum dependence of the low energy two particle scattering processes. In order to solve these equations numerically we defined criteria that allowed us to classify whether a given set of initial conditions flows towards the strongly coupled regime. We found regions in the models parameter space where a weak coupling method as the fRG is applicable and it is possible to calculate additional quantities of interest. Furthermore we analyzed the effect of the Rashba SOI on the properties of an interacting multi level quantum dot coupled to two semi in nite leads. Of special interest was the interplay with a Zeeman field and its orientation with respect to the SOI term. We found a renormalization of the spin-orbit energy which is an experimental quantity used to asses SOI effects in transport measurements, as well as renormalized effective g factors used to describe the Zeeman field dependence. In particular in asymmetrically coupled systems the large parameter space allows for rich physics which we studied by means of the linear conductance obtained via the generalized Landauer

  15. Sleep and pain: interaction of two vital functions.

    Science.gov (United States)

    Roehrs, Timothy; Roth, Thomas

    2005-03-01

    Disturbed sleep is a key complaint of people experiencing acute and chronic pain. These two vital functions, sleep and pain, interact in complex ways that ultimately impact the biological and behavioral capacity of the individual. Polysomnographic studies of patients experiencing acute pain during postoperative recovery show shortened and fragmented sleep with reduced amounts of slow wave and rapid eye movement (REM) sleep, and the recovery is accompanied by normalization of sleep. Objective assessments of sleep in patients with various chronic pain conditions have been less definitive with some studies showing fragmented and shortened sleep and others showing normal sleep. Although daytime fatigue is a frequent complaint associated with complaints of pain-related disturbed sleep, objective assessments of daytime sleepiness reveal minimally elevated levels of sleepiness and emphasize the importance of distinguishing sleepiness and fatigue. The pain-sleep nexus has been modeled in healthy pain-free subjects and the studies have demonstrated the bidirectionality of the sleep-pain relation. Given this bidirectionality, treatment must focus on alleviation of both the pain and sleep disturbance. Few of the treatment studies have done such, and as a result no clear consensus on treatment approaches, much less on differential etiology-based treatment strategies, has emerged.

  16. Functional Roles of the Interaction of APP and Lipoprotein Receptors

    Science.gov (United States)

    Pohlkamp, Theresa; Wasser, Catherine R.; Herz, Joachim

    2017-01-01

    The biological fates of the key initiator of Alzheimer’s disease (AD), the amyloid precursor protein (APP), and a family of lipoprotein receptors, the low-density lipoprotein (LDL) receptor-related proteins (LRPs) and their molecular roles in the neurodegenerative disease process are inseparably interwoven. Not only does APP bind tightly to the extracellular domains (ECDs) of several members of the LRP group, their intracellular portions are also connected through scaffolds like the one established by FE65 proteins and through interactions with adaptor proteins such as X11/Mint and Dab1. Moreover, the ECDs of APP and LRPs share common ligands, most notably Reelin, a regulator of neuronal migration during embryonic development and modulator of synaptic transmission in the adult brain, and Agrin, another signaling protein which is essential for the formation and maintenance of the neuromuscular junction (NMJ) and which likely also has critical, though at this time less well defined, roles for the regulation of central synapses. Furthermore, the major independent risk factors for AD, Apolipoprotein (Apo) E and ApoJ/Clusterin, are lipoprotein ligands for LRPs. Receptors and ligands mutually influence their intracellular trafficking and thereby the functions and abilities of neurons and the blood-brain-barrier to turn over and remove the pathological product of APP, the amyloid-β peptide. This article will review and summarize the molecular mechanisms that are shared by APP and LRPs and discuss their relative contributions to AD.

  17. Thermoplastic starch/wood composites: interfacial interactions and functional properties.

    Science.gov (United States)

    Müller, Péter; Renner, Károly; Móczó, János; Fekete, Erika; Pukánszky, Béla

    2014-02-15

    Thermoplastic starch (TPS)/wood composites were prepared from starch plasticized with 36 wt% glycerol. The components were homogenized by dry-blending, extruded and injection molded to tensile bars. Tensile properties, structure, deformation, water adsorption and shrinkage were determined as a function of wood content, which changed between 0 and 40 vol% in 7 steps. The modification of TPS with wood particles improves several properties considerably. Stiffness and strength increases, and the effect is stronger for fibers with larger aspect ratio. Wood fibers reinforce TPS considerably due to poor matrix properties and strong interfacial interactions, the latter resulting in the decreased mobility of starch molecules and in the fracture of large wood particles during deformation. Strong interfacial adhesion leads to smaller water absorption than predicted from additivity, but water uptake remains relatively large even in the presence of wood particles. The shrinkage of injection molded TPS parts is very large, around 10%, and dimensional changes occur on a very long timescale of several hundred hours. Shrinkage decreases to a low level already at 15-20 vol% wood content rendering the composites good dimensional stability.

  18. The importance of species identity and interactions for multifunctionality depends on how ecosystem functions are valued.

    Science.gov (United States)

    Slade, Eleanor M; Kirwan, Laura; Bell, Thomas; Philipson, Christopher D; Lewis, Owen T; Roslin, Tomas

    2017-10-01

    Studies investigating how biodiversity affects ecosystem functioning increasingly focus on multiple functions measured simultaneously ("multifunctionality"). However, few such studies assess the role of species interactions, particularly under alternative environmental scenarios, despite interactions being key to ecosystem functioning. Here we address five questions of central importance to ecosystem multifunctionality using a terrestrial animal system. (1) Does the contribution of individual species differ for different ecosystem functions? (2) Do inter-species interactions affect the delivery of single functions and multiple functions? (3) Does the community composition that maximizes individual functions also maximize multifunctionality? (4) Is the functional role of individual species, and the effect of interspecific interactions, modified by changing environmental conditions? (5) How do these roles and interactions change under varying scenarios where ecosystem services are weighted to reflect different societal preferences? We manipulated species' relative abundance in dung beetle communities and measured 16 functions contributing to dung decomposition, plant productivity, nutrient recycling, reduction of greenhouse gases, and microbial activity. Using the multivariate diversity-interactions framework, we assessed how changes in species identity, composition, and interspecific interactions affected these functions in combination with an environmental driver (increased precipitation). This allowed us to identify key species and interactions across multiple functions. We then developed a desirability function approach to examine how individual species and species mixtures contribute to a desired state of overall ecosystem functioning. Species contributed unequally to individual functions, and to multifunctionality, and individual functions were maximized by different community compositions. Moreover, the species and interactions important for maintaining

  19. A probabilistic framework to predict protein function from interaction data integrated with semantic knowledge

    Directory of Open Access Journals (Sweden)

    Ramanathan Murali

    2008-09-01

    Full Text Available Abstract Background The functional characterization of newly discovered proteins has been a challenge in the post-genomic era. Protein-protein interactions provide insights into the functional analysis because the function of unknown proteins can be postulated on the basis of their interaction evidence with known proteins. The protein-protein interaction data sets have been enriched by high-throughput experimental methods. However, the functional analysis using the interaction data has a limitation in accuracy because of the presence of the false positive data experimentally generated and the interactions that are a lack of functional linkage. Results Protein-protein interaction data can be integrated with the functional knowledge existing in the Gene Ontology (GO database. We apply similarity measures to assess the functional similarity between interacting proteins. We present a probabilistic framework for predicting functions of unknown proteins based on the functional similarity. We use the leave-one-out cross validation to compare the performance. The experimental results demonstrate that our algorithm performs better than other competing methods in terms of prediction accuracy. In particular, it handles the high false positive rates of current interaction data well. Conclusion The experimentally determined protein-protein interactions are erroneous to uncover the functional associations among proteins. The performance of function prediction for uncharacterized proteins can be enhanced by the integration of multiple data sources available.

  20. Density functional theory calculations on dipeptide gallic acid interaction

    Science.gov (United States)

    Madhan, B.; Parthasarathi, R.; Subramanian, V.; Raghava Rao, J.; Nair, Balachandran Unni; Ramasami, T.

    2003-02-01

    In the present investigation, an attempt has been made to study the interaction of dipeptides with gallic acid, using Becke3 parameter Lee Yang Parr (B3LYP) method employing 3-21G*, 6-31G* and 6-31+G* basis sets. The interaction energies of the dipeptide-gallic acid complexes are in the range of -5 to -18 kcal/mol depending on the mode of intermolecular complexation. Calculated molecular electrostatic potential (MESP) for the various intermolecular complexes revealed the electrostatic nature of the interaction. Qualitative estimations based on chemical hardness and chemical potential demonstrated fractional electron transfer from dipeptide to gallic acid.

  1. The early development of executive function and its relation to social interaction: A brief review

    Directory of Open Access Journals (Sweden)

    Yusuke eMoriguchi

    2014-04-01

    Full Text Available Executive function (EF refers to the ability to execute appropriate actions and to inhibit inappropriate actions for the attainment of a specific goal. Research has shown that this ability develops rapidly during the preschool years. Recently, it has been proposed that research on executive function should consider the importance of social interaction. In this article, recent evidence regarding the early development of executive function and its relation to social interaction has been reviewed. Research consistently showed that social interaction can influence executive function skills in young children. However, the development of executive function may facilitate the cognitive skills that are important for social interaction. Taken together, there might be functional dependency between the development of executive function and social interaction.

  2. An Interactive Exercise To Learn Eukaryotic Cell Structure and Organelle Function.

    Science.gov (United States)

    Klionsky, Daniel J.; Tomashek, John J.

    1999-01-01

    Describes a cooperative, interactive problem-solving exercise for studying eukaryotic cell structure and function. Highlights the dynamic aspects of movement through the cell. Contains 15 references. (WRM)

  3. Semantic integration to identify overlapping functional modules in protein interaction networks

    Directory of Open Access Journals (Sweden)

    Ramanathan Murali

    2007-07-01

    Full Text Available Abstract Background The systematic analysis of protein-protein interactions can enable a better understanding of cellular organization, processes and functions. Functional modules can be identified from the protein interaction networks derived from experimental data sets. However, these analyses are challenging because of the presence of unreliable interactions and the complex connectivity of the network. The integration of protein-protein interactions with the data from other sources can be leveraged for improving the effectiveness of functional module detection algorithms. Results We have developed novel metrics, called semantic similarity and semantic interactivity, which use Gene Ontology (GO annotations to measure the reliability of protein-protein interactions. The protein interaction networks can be converted into a weighted graph representation by assigning the reliability values to each interaction as a weight. We presented a flow-based modularization algorithm to efficiently identify overlapping modules in the weighted interaction networks. The experimental results show that the semantic similarity and semantic interactivity of interacting pairs were positively correlated with functional co-occurrence. The effectiveness of the algorithm for identifying modules was evaluated using functional categories from the MIPS database. We demonstrated that our algorithm had higher accuracy compared to other competing approaches. Conclusion The integration of protein interaction networks with GO annotation data and the capability of detecting overlapping modules substantially improve the accuracy of module identification.

  4. Functional interactivity in social media: an examination of Chinese health care organizations' microblog profiles.

    Science.gov (United States)

    Jiang, Shaohai

    2017-09-08

    Social media hold enormous potentials as a communication tool for health care due to its interactive nature. However, prior research mainly focused on contingency interactivity of social media, by examining messages sent from health care organizations to audiences, while little is known about functional interactivity, which refers to social media's presence of functions for facilitating communication between users and its interface. That is, how health care organizations use interactive features on social media to communicate with the public. Thus, with a general basis of the functional interactivity framework proposed by Waters et al. (Engaging stakeholders through social networking: how nonprofit organizations are using Facebook. Pub Relat Rev 2009;35:102-106), the current study investigated three aspects of functional interactivity in microblogging, and its subsequent effects. Specifically, this study analyzed 500 Chinese hospitals' profiles on Sina Weibo, the most popular microblogging platform in China. The results showed that the most common functional interactivity feature was organization disclosure, followed by information dissemination, and audience involvement. These interactive features all positively predicted the number of followers. Also, Chinese private hospitals scored significantly higher than public hospitals to use interactive features offered by social media. The findings of this study provide important implications for health care organizations to understand new communicative functions available on social media, incorporate more functions into their profiles and thus provide audiences with greater opportunity to interact with them via social media. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  5. Direct Estimation of the Surface Location of Immobilized Functional Groups for Concerted Catalysis Using a Probe Molecule.

    Science.gov (United States)

    Noda, Hiroto; Motokura, Ken; Wakabayashi, Yusuke; Sasaki, Kaori; Tajiri, Hiroo; Miyaji, Akimitsu; Yamaguchi, Sho; Baba, Toshihide

    2016-04-04

    The location of active sites during concerted catalysis by a metal complex and tertiary amine on a SiO2 surface is discussed based on the interaction between the functionalized SiO2 surface and a probe molecule, p-formyl phenylboronic acid. The interactions of the probe molecule with the surface functionalities, diamine ligand, and tertiary amine, were analyzed by FT-IR and solid-state (13)C and (11)B MAS NMR. For the catalyst exhibiting high 1,4-addition activity, the diamine ligand and tertiary amine base exist in closer proximity than in the catalyst with low activity.

  6. Interactions of phenolic compounds with globular proteins and their effects on food-related functional properties

    NARCIS (Netherlands)

    Prigent, S.V.E.

    2005-01-01

    In order to modulate the functional properties of food proteins, the interactions between globular proteins and the monomeric phenolic, caffeoylquinic acid (CQA, chlorogenic acid), and the oligomeric phenolics, procyanidins, were characterized and investigated for their effect on protein functional

  7. Engineering of Droplet Manipulation in Tertiary Junction Microfluidic Channels

    Science.gov (United States)

    2017-06-30

    in silico investigation of path selection by a single droplet inside a tertiary junction microchannel using oil-in-water as a model system. The...droplet was generated at a T-junction inside a microfluidic chip and its flow behaviour as a function of droplet size, streamline position, viscosity...investigation of path selection by a single droplet inside a tertiary- junction microchannel using oil-in-water as a model system. The droplet was generated at

  8. Functional features and protein network of human sperm-egg interaction.

    Science.gov (United States)

    Sabetian, Soudabeh; Shamsir, Mohd Shahir; Abu Naser, Mohammed

    2014-12-01

    Elucidation of the sperm-egg interaction at the molecular level is one of the unresolved problems in sexual reproduction, and understanding the molecular mechanism is crucial in solving problems in infertility and failed in vitro fertilization (IVF). Many molecular interactions in the form of protein-protein interactions (PPIs) mediate the sperm-egg membrane interaction. Due to the complexity of the problem such as difficulties in analyzing in vivo membrane PPIs, many efforts have failed to comprehensively elucidate the fusion mechanism and the molecular interactions that mediate sperm-egg membrane fusion. The main purpose of this study was to reveal possible protein interactions and associated molecular function during sperm-egg interaction using a protein interaction network approach. Different databases have been used to construct the human sperm-egg interaction network. The constructed network revealed new interactions. These included CD151 and CD9 in human oocyte that interact with CD49 in sperm, and CD49 and ITGA4 in sperm that interact with CD63 and CD81, respectively, in the oocyte. These results showed that the different integrins in sperm may be involved in human sperm-egg interaction. It was also suggested that sperm ADAM2 plays a role as a protein candidate involved in sperm-egg membrane interaction by interacting with CD9 in the oocyte. Interleukin-4 receptor activity, receptor signaling protein tyrosine kinase activity, and manganese ion transmembrane transport activity are the major molecular functions in sperm-egg interaction protein network. The disease association analysis indicated that sperm-egg interaction defects are also reflected in other disease networks such as cardiovascular, hematological, and breast cancer diseases. By analyzing the network, we identified the major molecular functions and disease association genes in sperm-egg interaction protein. Further experimental studies will be required to confirm the significance of these new

  9. Airborne Bacterial interactions: functions out of thin air?

    Directory of Open Access Journals (Sweden)

    Bianca eAUDRAIN

    2015-12-01

    Full Text Available Bacteria produce and release a large diversity of small molecules including organic and inorganic volatile compounds, hereafter referred to as BVCs. Whereas BVCs were often only considered as wasted metabolic by-product sometimes perceived by animal olfactory systems, it is increasingly clear that they can also mediate cross-kingdom interactions with fungi, plants and animals. Recently, in vitro studies also reported the impact of BVCs on bacterial biology through modulation of antibiotic resistance, biofilm formation and virulence. Here, we review BVCs influence on bacterial adaptation to their environment and discuss the biological relevance of recently reported inter- and intra-species bacterial interactions mediated by BVCs.

  10. Three-dimensional tertiary structure of yeast phenylalanine transfer RNA

    Science.gov (United States)

    Kim, S. H.; Sussman, J. L.; Suddath, F. L.; Quigley, G. J.; Mcpherson, A.; Wang, A. H. J.; Seeman, N. C.; Rich, A.

    1974-01-01

    Results of an analysis and interpretation of a 3-A electron density map of yeast phenylalanine transfer RNA. Some earlier detailed assignments of nucleotide residues to electron density peaks are found to be in error, even though the overall tracing of the backbone conformation of yeast phenylalanine transfer RNA was generally correct. A new, more comprehensive interpretation is made which makes it possible to define the tertiary interactions in the molecule. The new interpretation makes it possible to visualize a number of tertiary interactions which not only explain the structural role of most of the bases which are constant in transfer RNAs, but also makes it possible to understand in a direct and simple fashion the chemical modification data on transfer RNA. In addition, this pattern of tertiary interactions provides a basis for understanding the general three-dimensional folding of all transfer RNA molecules.

  11. Interaction between asthma and lung function growth in early life

    DEFF Research Database (Denmark)

    Bisgaard, Hans; Jensen, Signe Marie; Bønnelykke, Klaus

    2012-01-01

    The causal direction between asthma and lung function deficit is unknown, but important for the focus of preventive measures and research into the origins of asthma.......The causal direction between asthma and lung function deficit is unknown, but important for the focus of preventive measures and research into the origins of asthma....

  12. Superparamagnetic bead interactions with functionalized surfaces characterized by an immunomicroarray

    DEFF Research Database (Denmark)

    Skottrup, Peter Durand; Hansen, Mikkel Fougt; Moresco, Jacob Lange;

    2010-01-01

    SiO2 performed better than polyethylene glycol-modified surfaces Two beads, Masterbeads and M-280 beads, were found to give superior results compared with other bead types. Antibody/ antigen interactions, Illustrated by C-reactive protein, were best performed with Masterbeads The results provide...

  13. Interactions between acid- and base-functionalized surfaces

    NARCIS (Netherlands)

    Giesbers, M.; Kleijn, J.M.; Cohen Stuart, M.A.

    2002-01-01

    In this paper we present an AFM force study on interactions between chemically modified surfaces. Surfaces with terminal groups of either NH2 or COOH were obtained by chemisorption of a silane-based compound (3-amino-propyltriethoxysilane) on silica or a thiol compound (11-mercapto undecanoic acid)

  14. HEXADECAPOLE INTERACTING BOSON APPROXIMATION STRUCTURE FUNCTIONS IN NEODYMIUM ISOTOPES

    NARCIS (Netherlands)

    PERRINO, R; BLASI, N; BORDEWIJK, JA; DELEO, R; HARAKEH, MN; DEJAGER, CW; MICHELETTI, S; PIGNANELLI, M; SANDOR, RKJ; DEVRIES, H; VANDERWERF, SY; WESSELING, J

    1993-01-01

    Low-lying hexadecapole states in stable even-even neodymium isotopes have been investigated by means of inelastic electron scattering. Transition charge densities were extracted in a Fourier-Bessel analysis of the form factors. The analysis of the experimental results within the interacting sdg-boso

  15. On the interaction of Linguistic Typology and Functional Grammar

    DEFF Research Database (Denmark)

    Rijkhoff, J.

    2002-01-01

    empirical research in a wide variety of languages as practiced in the context of linguistic typology and one particular theory, Simon Dik's theory of Functional Grammar. In my view, the relationship between Functional Grammar and linguistic typology is an excellent example of the fruitful combination...... of theory driven data collection and data driven hypothesis formation. Furthermore, typological facts do not only serve to confirm the theory of Functional Grammar, but they also serve as a heuristics for an extension of the theory.Research conducted within the wider theoretical framework of Dik......'s Functional Grammar has resulted in important contributions to linguistic typology, and, vice versa, empirical facts from a wide variety of languages have significantly improved the theory of Functional Grammar, especially regarding its typological adequacy. This article discusses the following contributions...

  16. Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.

    Science.gov (United States)

    Nabieva, Elena; Jim, Kam; Agarwal, Amit; Chazelle, Bernard; Singh, Mona

    2005-06-01

    Determining protein function is one of the most important problems in the post-genomic era. For the typical proteome, there are no functional annotations for one-third or more of its proteins. Recent high-throughput experiments have determined proteome-scale protein physical interaction maps for several organisms. These physical interactions are complemented by an abundance of data about other types of functional relationships between proteins, including genetic interactions, knowledge about co-expression and shared evolutionary history. Taken together, these pairwise linkages can be used to build whole-proteome protein interaction maps. We develop a network-flow based algorithm, FunctionalFlow, that exploits the underlying structure of protein interaction maps in order to predict protein function. In cross-validation testing on the yeast proteome, we show that FunctionalFlow has improved performance over previous methods in predicting the function of proteins with few (or no) annotated protein neighbors. By comparing several methods that use protein interaction maps to predict protein function, we demonstrate that FunctionalFlow performs well because it takes advantage of both network topology and some measure of locality. Finally, we show that performance can be improved substantially as we consider multiple data sources and use them to create weighted interaction networks. http://compbio.cs.princeton.edu/function

  17. Distinct functional interactions between actin isoforms and nonsarcomeric myosins.

    Directory of Open Access Journals (Sweden)

    Mirco Müller

    Full Text Available Despite their near sequence identity, actin isoforms cannot completely replace each other in vivo and show marked differences in their tissue-specific and subcellular localization. Little is known about isoform-specific differences in their interactions with myosin motors and other actin-binding proteins. Mammalian cytoplasmic β- and γ-actin interact with nonsarcomeric conventional myosins such as the members of the nonmuscle myosin-2 family and myosin-7A. These interactions support a wide range of cellular processes including cytokinesis, maintenance of cell polarity, cell adhesion, migration, and mechano-electrical transduction. To elucidate differences in the ability of isoactins to bind and stimulate the enzymatic activity of individual myosin isoforms, we characterized the interactions of human skeletal muscle α-actin, cytoplasmic β-actin, and cytoplasmic γ-actin with human myosin-7A and nonmuscle myosins-2A, -2B and -2C1. In the case of nonmuscle myosins-2A and -2B, the interaction with either cytoplasmic actin isoform results in 4-fold greater stimulation of myosin ATPase activity than was observed in the presence of α-skeletal muscle actin. Nonmuscle myosin-2C1 is most potently activated by β-actin and myosin-7A by γ-actin. Our results indicate that β- and γ-actin isoforms contribute to the modulation of nonmuscle myosin-2 and myosin-7A activity and thereby to the spatial and temporal regulation of cytoskeletal dynamics. FRET-based analyses show efficient copolymerization abilities for the actin isoforms in vitro. Experiments with hybrid actin filaments show that the extent of actomyosin coupling efficiency can be regulated by the isoform composition of actin filaments.

  18. Characteristics of Interactional Management Functions in Group Oral by Japanese Learners of English

    Science.gov (United States)

    Negishi, Junko

    2010-01-01

    This study attempted to investigate the characteristics of interaction dynamics in a group oral interaction carried out by Japanese learners of English. The relationship between the participants' language development and interactional management functions (IMFs) was also explored. Oral performance tests in a paired or a small group have recently…

  19. The Statics Dielectric Function and Interaction Potential In Strong Coupling With AdS/CFT

    CERN Document Server

    Liu, Lian; Liu, Hui

    2013-01-01

    In this paper, we studied the static dielectric function and interaction potential in strong coupling limit with AdS/CFT correspondence. The dielectric function is depressed compared with that in weak coupling. The interaction potential then presents a weaker screening characteristics in strong coupling, which indicates a smaller Debye mass compared with weak coupling.

  20. A MATLAB Function for Plotting Phase Planes Interactively

    OpenAIRE

    Forsman, Krister

    1992-01-01

    A MATLAB-function serving as a sort of graphical interface to the MATLAB ODE-solver ode45 is presented. The main use of it is to facilitate phase plane analysis of nonlinear 2-D systems via simulation. The numerical integration of the system is mouse-operated via the ginput-function. After each choice of initial value a simulation is made and plotted in the phase plane.

  1. Atom interaction propensities of oxygenated chemical functions in crystal packings

    Directory of Open Access Journals (Sweden)

    Christian Jelsch

    2017-03-01

    Full Text Available The crystal contacts of several families of hydrocarbon compounds substituted with one or several types of oxygenated chemical groups were analyzed statistically using the Hirshfeld surface methodology. The propensity of contacts to occur between two chemical types is described with the contact enrichment descriptor. The systematic large enrichment ratios of some interactions like the O—H...O hydrogen bonds suggests that these contacts are a driving force in the crystal packing formation. The same statement holds for the weaker C—H...O hydrogen bonds in ethers, esters and ketones, in the absence of polar H atoms. The over-represented contacts in crystals of oxygenated hydrocarbons are generally of two types: electrostatic attractions (hydrogen bonds and hydrophobic interactions. While Cl...O interactions are generally avoided, in a minority of chloro-oxygenated hydrocarbons, significant halogen bonding does occur. General tendencies can often be derived for many contact types, but outlier compounds are instructive as they display peculiar or rare features. The methodology also allows the detection of outliers which can be structures with errors. For instance, a significant number of hydroxylated molecules displaying over-represented non-favorable oxygen–oxygen contacts turned out to have wrongly oriented hydroxyl groups. Beyond crystal packings with a single molecule in the asymmetric unit, the behavior of water in monohydrate compounds and of crystals with Z′ = 2 (dimers are also investigated. It was found in several cases that, in the presence of several oxygenated chemical groups, cross-interactions between different chemical groups (e.g. water/alcohols; alcohols/phenols are often favored in the crystal packings. While some trends in accordance with common chemical principles are retrieved, some unexpected results can however appear. For example, in crystals of alcohol–phenol compounds, the strong O—H...O hydrogen bonds between

  2. The role of transforming growth factor beta in tertiary dentinogenesis

    Directory of Open Access Journals (Sweden)

    Tetiana Haniastuti

    2008-03-01

    Full Text Available The most visible repair response to pulp injury is the deposition of a tertiary dentin matrix over the dentinal tubules of the primary or secondary dentin. Tertiary dentin is distinguished as reactionary and reparative dentin, depending on the severity of the initiating response and the conditions under which the newly deposited dentin matrix was elaborated. Transforming growth factor beta (TGF-b superfamily is a large group of growth factors that serve important roles in regulating cell growth, differentiation, and function. Members of this superfamily have been implicated in the repair process of the dental tissue after injury. Although numerous studies have proved that those bioactive molecules carry out an important role in the formation of tertiary dentin, comprehensive report regarding that phenomenon is not yet available. This review article aimed to summarize the role of TGF-b on tertiary dentinogenesis during the progression of a carious lesion.

  3. The strange history of B functions or how theoretical chemists and mathematicians do (not) interact

    CERN Document Server

    Weniger, Ernst Joachim

    2008-01-01

    $B$ functions are a class of relatively complicated exponentially decaying basis functions. Since the molecular multicenter integrals of the much simpler Slater-type functions are notoriously difficult, it is not at all obvious why $B$ functions should offer any advantages. However, $B$ functions have Fourier transforms of exceptional simplicity, which greatly simplifies many of their molecular multicenter integrals. This article discusses the historical development of $B$ functions from the perspective of the interaction between mathematics and theoretical chemistry, which traditionally has not been very good. Nevertheless, future progress in theoretical chemistry depends very much on a fertile interaction with neighboring disciplines.

  4. QCD Green's Functions and Phases of Strongly-Interacting Matter

    Directory of Open Access Journals (Sweden)

    Schaefer B.J.

    2011-04-01

    Full Text Available After presenting a brief summary of functional approaches to QCD at vanishing temperatures and densities the application of QCD Green's functions at non-vanishing temperature and vanishing density is discussed. It is pointed out in which way the infrared behavior of the gluon propagator reflects the (de-confinement transition. Numerical results for the quark propagator are given thereby verifying the relation between (de--confinement and dynamical chiral symmetry breaking (restoration. Last but not least some results of Dyson-Schwinger equations for the color-superconducting phase at large densities are shown.

  5. Unique interaction pattern for a functionally biased ghrelin receptor agonist

    DEFF Research Database (Denmark)

    Sivertsen, Bjørn Behrens; Lang, Manja; Frimurer, Thomas M.

    2011-01-01

    /13) pathway. The recognition pattern of wFw-Isn-NH(2) with the ghrelin receptor also differed significantly from that of all previously characterized unbiased agonists. Most importantly, wFw-Isn-NH(2) was not dependent on GluIII:09 (Glu3.33), which otherwise is an obligatory TM III anchor point residue...... orientation as compared with, for example, the wFw peptide agonists. It is concluded that the novel peptide-mimetic ligand wFw-Isn-NH(2) is a biased ghrelin receptor agonist and that the selective signaling pattern presumably is due to its unique receptor recognition pattern lacking interaction with key...

  6. Organization of circadian functions: interaction with the body.

    NARCIS (Netherlands)

    Buijs, R.M.; Scheer, F.A.; Kreier, F.; Yi, C.; Bos, N.; Goncharuk, V.D.; Kalsbeek, A

    2006-01-01

    The hypothalamus integrates information from the brain and the body; this activity is essential for survival of the individual (adaptation to the environment) and the species (reproduction). As a result, countless functions are regulated by neuroendocrine and autonomic hypothalamic processes in conc

  7. Superparamagnetic bead interactions with functionalized surfaces characterized by an immunomicroarray

    DEFF Research Database (Denmark)

    Skottrup, Peter Durand; Hansen, Mikkel Fougt; Moresco, Jacob Lange

    2010-01-01

    Magneto-resistive sensors capable of detecting superparamagnetic micro-/nano-sized beads are promising alternatives to standard diagnostic assays based on absorbance or fluorescence and streptavidin-functionalized beads are widely used as an integral part of these sensors. Here we have developed ...

  8. Organization of circadian functions: interaction with the body.

    NARCIS (Netherlands)

    Buijs, R.M.; Scheer, F.A.; Kreier, F.; Yi, C.; Bos, N.; Goncharuk, V.D.; Kalsbeek, A

    2006-01-01

    The hypothalamus integrates information from the brain and the body; this activity is essential for survival of the individual (adaptation to the environment) and the species (reproduction). As a result, countless functions are regulated by neuroendocrine and autonomic hypothalamic processes in

  9. Functional Neuroimaging of Appetite and Gut–Brain Interactions

    NARCIS (Netherlands)

    Smeets, P.A.M.; Preissl, Hubert

    2016-01-01

    Ultimately, eating decisions are made in the brain, based on the integration
    of multiple neural and hormonal signals. Since the early 1990s the use of
    functional
    neuroimaging techniques has continued to increase. Their application
    in the study of the regulation of food intake and gut

  10. Gene-environment interaction and male reproductive function

    DEFF Research Database (Denmark)

    Axelsson, Jonatan; Bonde, Jens Peter; Giwercman, Yvonne L;

    2010-01-01

    As genetic factors can hardly explain the changes taking place during short time spans, environmental and lifestyle-related factors have been suggested as the causes of time-related deterioration of male reproductive function. However, considering the strong heterogeneity of male fecundity between...... that specific genotypes may confer a larger risk of male reproductive disorders following certain exposures. This paper presents a critical review of animal and human evidence on how genes may modify environmental effects on male reproductive function. Some examples have been found that support this mechanism...... of reproduction, namely environmental and lifestyle factors as the cause of sperm DNA damage. It remains to be investigated to what extent such genetic changes, by natural conception or through the use of assisted reproductive techniques, are transmitted to the next generation, thereby causing increased morbidity...

  11. The molecular understanding of interfacial interactions of functionalized graphene and chitosan

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Hong-ping, E-mail: zhp1006@126.com [Engineering Research Center of Biomass Materials, Ministry of Education, School of Materials Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010 (China); Luo, Xue-gang, E-mail: lxg@swust.edu.cn [Engineering Research Center of Biomass Materials, Ministry of Education, School of Materials Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010 (China); Lin, Xiao-yan, E-mail: linxiaoyan@swust.edu.cn [Engineering Research Center of Biomass Materials, Ministry of Education, School of Materials Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010 (China); Lu, Xiong, E-mail: luxiong@home.swjtu.edu.cn [Key Laboratory of Advanced Technologies of Materials, Ministry of Education, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031 (China); Tang, Youhong, E-mail: youhong.tang@flinders.edu.au [Centre for NanoScale Science and Technology and School of Computer Science, Engineering and Mathematics, Flinders University, South Australia 5042 (Australia)

    2016-01-01

    Graphical abstract: The type of the functional groups can be used to modulating interactions between graphene sheet and chitosan. - Highlights: • Investigate interfacial interactions between chitosan and functionalized graphene by DFT. • Observe covalent linkages between COOH-modified graphene and chitosan units. • Multi-functionalized graphene regulates the interfacial interactions with chitosan. • It is useful for guiding the preparation of graphene/chitosan composites. - Abstract: Graphene-reinforced chitosan scaffolds have been extensively studied for several years as promising hard tissue replacements. However, the interfacial interactions between graphene and chitosan are strongly related to the solubility, processability, and mechanical properties of graphene-reinforced chitosan (G–C) composites. The functionalization of graphene is regarded as the most effective way to improve the abovementioned properties of the G–C composite. In this study, the interfacial interactions between chitosan and functionalized graphene sheets with carboxylization (COOH-), amination (NH{sub 2}-), and hydroxylation (OH-) groups were systematically studied at the electronic level using the method of ab initio simulations based on quantum mechanics theory and the observations were compared with reported experimental results. The covalent linkages between COOH-modified graphene and the chitosan units were demonstrated and the combination of multi-functionalization on graphene could regulate the interfacial interactions between graphene and the chitosan. The interfacial interactions between chitosan and properly functionalized graphene are critical for the preparation of G–C-based composites for tissue engineering scaffolds and other applications.

  12. Range-separated meta-GGA functional designed for noncovalent interactions

    CERN Document Server

    Modrzejewski, Marcin; Szczęśniak, Małgorzata M

    2014-01-01

    The accuracy of applying density functional theory to noncovalent interactions is hindered by errors arising from low-density regions of interaction-induced change in the density gradient, error compensation between correlation and exchange functionals, and dispersion double counting. A new exchange-correlation functional designed for noncovalent interactions is proposed to address these problems. The functional consists of the range-separated PBEsol exchange considered in two variants, pure and hybrid, and the semilocal correlation functional of Modrzejewski et al. [J. Chem. Phys. 137, 204121 (2012)] designed with the constraint satisfaction technique to smoothly connect with a dispersion term. Two variants of dispersion correction are appended to the correlation functional: the atom-atom pairwise additive DFT-D3 model and the density-dependent many-body dispersion with self-consistent screening (MBD-rsSCS). From these building blocks a set of four functionals is created to systematically examine the role of...

  13. Cognitive, functional, and psychosocial outcome after severe traumatic brain injury: A cross-sectional study at a tertiary care trauma center

    Directory of Open Access Journals (Sweden)

    Sumit Sinha

    2013-01-01

    Full Text Available Background: Traumatic brain injury (TBI constitutes a significant public health problem. Objectives: To assess cognitive, functional, and psychosocial outcome in patients with severe TBI (STBI. Materials and Methods: A total of 77 survivors of STBI treated at our center were prospectively assessed in the outpatient department 1 year after the injury. These patients were assessed for cognitive, functional, and psychosocial outcome using cognitive outcome tests, dysfunctional analysis questionnaire, and personality trait inventory, respectively. Cognitive and functional outcome was graded as average and above average recovery (good recovery or below average recovery (poor recovery. Psychosocial outcome was assessed as average recovery (good recovery or mild impairment and severe impairment (poor to very poor recovery. Statistical analysis was done using Chi-square and Fisher′s exact tests. Results: The ability to learn new things was most affected aspect of cognitive function and only 1% of patients had good recovery in this domain. However, 44% had good outcome for simple memory. A total of 61% showed good recovery in several aspects of functional status. At the end of 1 year, 62.5% patients still remained unemployed. 45.4% patients had good recovery, while 37% had severe impairment for various personality traits and 40% of patients had impaired emotional stability, while 57% patients showed impaired recovery in depressive tendency. Conclusion: In this study 61% patients with STBI had good recovery in functional outcome and 45.4% in psychosocial outcome at 1 year follow-up. However, improvement in cognitive outcome was not so optimistic with the ability to learn new things being most affected.

  14. Pain symptoms and stooling patterns do not drive diagnostic costs for children with functional abdominal pain and irritable bowel syndrome in primary or tertiary care

    Science.gov (United States)

    The objectives of this study were to (1) compare the cost of medical evaluation for children with functional abdominal pain or irritable bowel syndrome brought to a pediatric gastroenterologist versus children who remained in the care of their pediatrician, (2) compare symptom characteristics for th...

  15. Interaction of poststroke voluntary effort and functional neuromuscular electrical stimulation.

    Science.gov (United States)

    Makowski, Nathaniel; Knutson, Jayme; Chae, John; Crago, Patrick

    2013-01-01

    Functional electrical stimulation (FES) may be able to augment functional arm and hand movement after stroke. Poststroke neuroprostheses that incorporate voluntary effort and FES to produce the desired movement must consider how forces generated by voluntary effort and FES combine, even in the same muscle, in order to provide an appropriate level of stimulation to elicit the desired assistive force. The goal of this study was to determine whether the force produced by voluntary effort and FES add together independently of effort or whether the increment in force depends on the level of voluntary effort. Isometric force matching tasks were performed under different combinations of voluntary effort and FES. Participants reached a steady level of force, and while attempting to maintain a constant effort level, FES was applied to augment the force. Results indicate that the increment in force produced by FES decreases as the level of initial voluntary effort increases. Potential mechanisms causing the change in force output are proposed, but the relative contribution of each mechanism is unknown.

  16. mGlu5 Receptor Functional Interactions and Addiction

    Directory of Open Access Journals (Sweden)

    Robyn eBrown

    2012-05-01

    Full Text Available The idea of ‘receptor mosaics’ suggests that proteins can form complex and dynamic networks, with respect to time and protein make up, which has the potential to make significant contributions to the diversity and specificity of GPCR signalling, particularly in neuropharmacology, where a few key receptors have been implicated in multiple neurological and psychiatric disorders such as addiction. Metabotropic glutamate type 5 receptors (mGlu5 have been shown to heterodimerise and form complexes with other GPCRs including adenosine A2A and dopamine D2 receptors. mGlu5-containing complexes are found in the striatum, a region of the brain known to be critical for mediating the rewarding and incentive motivational properties of drugs of abuse. Indeed, initial studies indicate a role for mGlu5-containing complexes in rewarding and conditioned effects of drugs, as well as drug-seeking behaviour. This is consistent with the substantial influence that mGlu5 complexes appear to have on striatal function, regulating both GABAergic output of striatopallidal neurons and glutamatergic input from corticostriatal afferents. Given their discrete localization, mGlu5-containing complexes represent a novel way in which to minimize the off-target effects and therefore provide us with an exciting therapeutic avenue for drug discovery efforts. Indeed, the therapeutic targeting of receptor mosaics in a tissue specific or temporal manner (for example, a sub-population of receptors in a ‘pathological state’ has the potential to dramatically reduce detrimental side effects that may otherwise impair vital brain function.

  17. Regulating social interactions: Developing a functional theory of collaboration

    Science.gov (United States)

    Borge, Marcela

    A role-playing intervention was developed and implemented in a fifth grade classroom. The goal of the intervention was to address serious problems that researchers have connected to dysfunctional collaborative interactions. These problems include an inability to: engage in important aspects of argumentation and communication, monitor and regulate group processes, and ensure equity in participation. To this end, a comprehensive theory of collaboration was presented to students through the use of four sociocognitive roles: mediation manager, collaboration manager, communication manager, and productivity manager. Each role came with a written guide that included specific goals and strategies related to the role. Metacognitive activities, including planning and reflection, were also used during class sessions to support students' understanding and role-use. Each of the students in the class was assigned one of the roles to manage during a two part collaborative science project. Students took quizzes on the roles and provided verbal and written feedback about their role-use and metacognitive activities. Students from one of the video-recorded groups were also interviewed after the intervention. Analyses of data from video sessions, quizzes, and interviews supported three important findings: (1) students were able to learn goals, and strategies for all of the roles, even though they only managed a single role, (2) students demonstrated the ability to take the information they learned and put it into practice, and (3) when students employed the roles while their group was working, members of the group accepted the role-use. These findings related to the learning and utilization of the roles are important because they: (1) imply that the intervention was successful at developing students' knowledge of the theory of collaboration that the roles represented, (2) indicate that students used this knowledge to monitor and regulate behaviors in an authentic context, and (3

  18. Preferential Interaction of Na+ over K+ to Carboxylate-functionalized Silver Nanoparticles

    Science.gov (United States)

    Elucidating mechanistic interactions between specific ions (Na+/ K+) and nanoparticle surfaces to alter particle stability in polar media has received little attention. We investigated relative preferential binding of Na+ and K+ to carboxylate-functionalized silver nanoparticles ...

  19. Adaptability of protein structures to enable functional interactions and evolutionary implications.

    Science.gov (United States)

    Haliloglu, Turkan; Bahar, Ivet

    2015-12-01

    Several studies in recent years have drawn attention to the ability of proteins to adapt to intermolecular interactions by conformational changes along structure-encoded collective modes of motions. These so-called soft modes, primarily driven by entropic effects, facilitate, if not enable, functional interactions. They represent excursions on the conformational space along principal low-ascent directions/paths away from the original free energy minimum, and they are accessible to the protein even before protein-protein/ligand interactions. An emerging concept from these studies is the evolution of structures or modular domains to favor such modes of motion that will be recruited or integrated for enabling functional interactions. Structural dynamics, including the allosteric switches in conformation that are often stabilized upon formation of complexes and multimeric assemblies, emerge as key properties that are evolutionarily maintained to accomplish biological activities, consistent with the paradigm sequence→structure→dynamics→function where 'dynamics' bridges structure and function.

  20. Kopitiam: Modular Incremental Interactive Full Functional Static Verification of Java Code

    DEFF Research Database (Denmark)

    Mehnert, Hannes

    2011-01-01

    WearedevelopingKopitiam,atooltointeractivelyprovefull functional correctness of Java programs using separation logic by inter- acting with the interactive theorem prover Coq. Kopitiam is an Eclipse plugin, enabling seamless integration into the workflow of a developer. Kopitiam enables a user to ...

  1. Functional Integral Approach to the Transition Temperature of Attractive Interacting Bose Gas in Traps

    Institute of Scientific and Technical Information of China (English)

    HU Guang-Xi; DAI Xian-Xi

    2004-01-01

    The functional integral approach (FIA) is introduced to study the transition temperature of an imperfect Bose gas in traps.An interacting model in quantum statistical mechanics is presented.With the model we study a Bose gas with attractive interaction trapped in an external potential.We obtain the result that the transition temperature of a trapped Bose gas will slightly shift upwards owing to the attractive interacting force.Successful application of the FIA to Bose systems is demonstrated.

  2. A Table of Third and Fourth Order Feynman Diagrams of the Interacting Fermion Green's Function

    CERN Document Server

    Mathar, R J

    2005-01-01

    The Feynman diagrams of the Green's function expansion of fermions interacting with a non-relativistic 2-body interaction are displayed in first, second and third order of the interaction as 2, 10 and 74 diagrams, respectively. A name convention for the diagrams is proposed and then used to tabulate the 706 diagrams of fourth order. The Hartree-Fock approximation summons up 2, 8, 40 and 224 of them, respectively.

  3. Interactions between Temperament, Stress, and Immune Function in Cattle

    Directory of Open Access Journals (Sweden)

    N. C. Burdick

    2011-01-01

    Full Text Available The detrimental effects caused by stressors encountered by animals during routine handling can pose economic problems for the livestock industry due to increased costs ultimately borne by the producer and the consumer. Stress adversely affects key physiological processes of the reproductive and immune systems. In recent years stress responsiveness has been associated with cattle behavior, specifically temperament. Cattle with more excitable temperaments, as measured by chute score, pen score, and exit velocity (flight speed, exhibit greater basal concentrations of glucocorticoids and catecholamines. Similar to stressed cattle, more temperamental cattle (i.e., cattle exhibiting greater exit velocity or pen and chute scores have poorer growth performance, carcass characteristics, and immune responses. Thus, understanding the interrelationship of stress and temperament can help in the development of selection and management practices that reduce the negative influence of temperament on growth and productivity of cattle. This paper discusses the relationship between stress and temperament and the developing evidence of an effect of temperament on immune function of cattle that have been handled or restrained. Specifically, the paper discusses different methodologies used to measure temperament, including chute score, pen score, and exit velocity, and discusses the reaction of cattle to different stressors including handling and restraint.

  4. Bisphenol A Interaction With Brain Development and Functions

    Directory of Open Access Journals (Sweden)

    P. Negri-Cesi

    2015-06-01

    Full Text Available Brain development is an organized, but constantly adaptive, process in which genetic and epigenetic signals allow neurons to differentiate, to migrate, and to develop correct connections. Gender specific prenatal sex hormone milieu participates in the dimorphic development of many neuronal networks. Environmental cues may interfere with these developmental programs, producing adverse outcomes. Bisphenol A (BPA, an estrogenic/antiandrogenic endocrine disruptor widely diffused in the environment, produces adverse effects at levels below the acceptable daily intake. This review analyzes the recent literature on the consequences of perinatal exposure to BPA environmental doses on the development of a dimorphic brain. The BPA interference with the development and function of the neuroendocrine hypothalamus and of the nuclei controlling energy balance, and with the hippocampal memory processing is also discussed. The detrimental action of BPA appears complex, involving different hormonal and epigenetic pathways activated, often in a dimorphic way, within clearcut susceptibility windows. To date, discrepancies in experimental approaches and in related outcomes make unfeasible to translate the available information into clear dose–response models for human risk assessment. Evaluation of BPA brain levels in relation to the appearance of adverse effects in future basic studies will certainly give better definition of the warning threshold for human health.

  5. A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling

    DEFF Research Database (Denmark)

    Blagoev, B.; Kratchmarova, I.; Ong, S.E.

    2003-01-01

    Mass spectrometry-based proteomics can reveal protein-protein interactions on a large scale, but it has been difficult to separate background binding from functionally important interactions and still preserve weak binders. To investigate the epidermal growth factor receptor (EGFR) pathway, we...

  6. Virtual-Reality-Based Social Interaction Training for Children with High-Functioning Autism

    Science.gov (United States)

    Ke, Fengfeng; Im, Tami

    2013-01-01

    Employing the multiple-baseline across-subjects design, the authors examined the implementation and potential effect of a virtual-reality-based social interaction program on the interaction and communication performance of children with high functioning autism. The data were collected via behavior observation and analysis, questionnaires, and…

  7. Virtual-Reality-Based Social Interaction Training for Children with High-Functioning Autism

    Science.gov (United States)

    Ke, Fengfeng; Im, Tami

    2013-01-01

    Employing the multiple-baseline across-subjects design, the authors examined the implementation and potential effect of a virtual-reality-based social interaction program on the interaction and communication performance of children with high functioning autism. The data were collected via behavior observation and analysis, questionnaires, and…

  8. Morphology predicts species' functional roles and their degree of specialization in plant–frugivore interactions

    Science.gov (United States)

    Dehling, D. Matthias; Schaefer, H. Martin; Böhning-Gaese, Katrin; Schleuning, Matthias

    2016-01-01

    Species' functional roles in key ecosystem processes such as predation, pollination or seed dispersal are determined by the resource use of consumer species. An interaction between resource and consumer species usually requires trait matching (e.g. a congruence in the morphologies of interaction partners). Species' morphology should therefore determine species' functional roles in ecological processes mediated by mutualistic or antagonistic interactions. We tested this assumption for Neotropical plant–bird mutualisms. We used a new analytical framework that assesses a species's functional role based on the analysis of the traits of its interaction partners in a multidimensional trait space. We employed this framework to test (i) whether there is correspondence between the morphology of bird species and their functional roles and (ii) whether morphologically specialized birds fulfil specialized functional roles. We found that morphological differences between bird species reflected their functional differences: (i) bird species with different morphologies foraged on distinct sets of plant species and (ii) morphologically distinct bird species fulfilled specialized functional roles. These findings encourage further assessments of species' functional roles through the analysis of their interaction partners, and the proposed analytical framework facilitates a wide range of novel analyses for network and community ecology. PMID:26817779

  9. Atom-light interactions in quasi-1D nanostructures: a Green's function perspective

    CERN Document Server

    Asenjo-Garcia, A; Chang, D E; Kimble, H J

    2016-01-01

    Based on a formalism that describes atom-light interactions in terms of the classical electromagnetic Green's function, we study the optical response of atoms and other quantum emitters coupled to one-dimensional photonic structures, such as cavities, waveguides, and photonic crystals. We demonstrate a clear mapping between the transmission spectra and the local Green's function that allows to identify signatures of dispersive and dissipative interactions between atoms, gaining insight into recent experiments.

  10. Density functional theory analysis of the impact of steric interaction on the function of switchable polarity solvents.

    Science.gov (United States)

    McNally, Joshua S; Noll, Bruce; Orme, Christopher J; Wilson, Aaron D

    2015-06-01

    A density functional theory (DFT) analysis has been performed to explore the impact of steric interactions on the function of switchable polarity solvents (SPS) and their implications on a quantitative structure-activity relationship (QSAR) model previously proposed for SPS. An X-ray crystal structure of the N,N-dimethylcyclohexylammonium bicarbonate (Hdmcha) salt has been solved as an asymmetric unit containing two cation/anion pairs, with a hydrogen bonding interaction observed between the bicarbonate anions, as well as between the cation and anion in each pair. DFT calculations provide an optimized structure of Hdmcha that closely resembles experimental data and reproduces the cation/anion interaction with the inclusion of a dielectric field. Relaxed potential energy surface (PES) scans have been performed on Hdmcha-based computational model compounds, differing in the size of functional group bonded to the nitrogen center, to assess the steric impact of the group on the relative energy and structural properties of the compound. Results suggest that both the length and amount of branching associated with the substituent impact the energetic limitations on rotation of the group along the N-R bond and NC-R bond, and disrupt the energy minimized position of the hydrogen bonded bicarbonate group. The largest interaction resulted from functional groups that featured five bonds between the ammonium proton and a proton on a functional group with the freedom of rotation to form a pseudo six membered ring which included both protons.

  11. Metal-Free α-C(sp3–H Functionalized Oxidative Cyclization of Tertiary N,N-Diaryl Amino Alcohols: Theoretical Approach for Mechanistic Pathway

    Directory of Open Access Journals (Sweden)

    Zakir Ullah

    2017-03-01

    Full Text Available The mechanistic pathway of TEMPO/I2-mediated oxidative cyclization of N,N-diaryl amino alcohols 1 was investigated. Based on direct empirical experiments, three key intermediates (aminium radical cation 3, α-aminoalkyl radical 4, and iminium 5, four types of reactive species (radical TEMPO, cationic TEMPO, TEMPO-I, and iodo radical, and three types of pathways ((1 SET/PCET mechanism; (2 HAT/1,6-H transfer mechanism; (3 ionic mechanism were assumed. Under the assumption, nine free energy diagrams were acquired through density functional theory calculations. From the comparison of solution-phase free energy, some possible mechanisms were excluded, and then the chosen plausible mechanisms were concretized using the more stable intermediate 7.

  12. Postnatal iron overload destroys NA-DA functional interactions.

    Science.gov (United States)

    Fredriksson, A; Archer, T

    2007-02-01

    C57/BL6 mice were administered either postnatal iron (Fe(2+) 7.5 mg/kg, on postnatal days 10-12) or vehicle, followed by administration of either DSP4 (50 mg/kg, s.c., 30 min after injection of zimeldine, 20 mg/kg, s.c.) or vehicle (saline) at 63 days of age. Three weeks later, iron/vehicle treated, DSP4/vehicle treated mice were injected with either a low dose of MPTP (2 x 20 mg/kg, with a 24-hr interval between injections) or vehicle. Behaviour testing took place a further three weeks (spontaneous behaviour and L-Dopa induced) and two weeks (clonidine-L-Dopa induced) later. Postnatal iron administration exacerbated the bradykinesia induced by MPTP and virtually abolished all spontaneous motor activity in NA-denervated mice that were MPTP-treated. Postnatal iron administration reduced markedly the restoration of motor activity by suprathreshold L-Dopa (20 mg/kg) following a 60-min habituation to the test chambers. Pretreatment with DSP4 effectively eliminated the restorative effect of L-Dopa in the MPTP mice. The synergistic effects of co-administration of clinidine (1 mg/kg) with a subthreshold dose of L-Dopa (5 mg/kg) in elevating the motor activity of MPTP mice were reduced markedly by postnatal iron administration, as well as by pretreatment with DSP4. NA-denervation by DSP4, after postnatal iron treatment, totally abolished the activity-elevating effects of the alpha-adrenoceptor agonist + DA-precursor combination in MPTP mice, and virtually eliminated these effects in saline (non-MPTP) mice. Postnatal iron administration caused enduring higher levels of total iron content in all the groups with an increased level in mice treated with DSP4 followed by MPTP. These divergent findings confirm the direct influence of NA innervation upon dopaminergic functional expression and indicate a permanent vulnerability both in the noradrenergic and dopaminergic pathways following the postnatal infliction of an iron overload.

  13. Tertiary Artefactness at the Interface

    DEFF Research Database (Denmark)

    Bertelsen, Olav Wedege

    2006-01-01

    specifically, I look into Wartofsky's account on the history of perception, and the function of art in this. The potential of this account in relation to human-computer interaction is to place experience and culture as first order aspects to be integrated with the traditional foci on cognition and work...... arrangement design....

  14. Know your neighbor: Microbiota and host epithelial cells interact locally to control intestinal function and physiology.

    Science.gov (United States)

    Sommer, Felix; Bäckhed, Fredrik

    2016-05-01

    Interactions between the host and its associated microbiota differ spatially and the local cross talk determines organ function and physiology. Animals and their organs are not uniform but contain several functional and cellular compartments and gradients. In the intestinal tract, different parts of the gut carry out different functions, tissue structure varies accordingly, epithelial cells are differentially distributed and gradients exist for several physicochemical parameters such as nutrients, pH, or oxygen. Consequently, the microbiota composition also differs along the length of the gut, but also between lumen and mucosa of the same intestinal segment, and even along the crypt-villus axis in the epithelium. Thus, host-microbiota interactions are highly site-specific and the local cross talk determines intestinal function and physiology. Here we review recent advances in our understanding of site-specific host-microbiota interactions and discuss their functional relevance for host physiology.

  15. Protein function prediction using neighbor relativity in protein-protein interaction network.

    Science.gov (United States)

    Moosavi, Sobhan; Rahgozar, Masoud; Rahimi, Amir

    2013-04-01

    There is a large gap between the number of discovered proteins and the number of functionally annotated ones. Due to the high cost of determining protein function by wet-lab research, function prediction has become a major task for computational biology and bioinformatics. Some researches utilize the proteins interaction information to predict function for un-annotated proteins. In this paper, we propose a novel approach called "Neighbor Relativity Coefficient" (NRC) based on interaction network topology which estimates the functional similarity between two proteins. NRC is calculated for each pair of proteins based on their graph-based features including distance, common neighbors and the number of paths between them. In order to ascribe function to an un-annotated protein, NRC estimates a weight for each neighbor to transfer its annotation to the unknown protein. Finally, the unknown protein will be annotated by the top score transferred functions. We also investigate the effect of using different coefficients for various types of functions. The proposed method has been evaluated on Saccharomyces cerevisiae and Homo sapiens interaction networks. The performance analysis demonstrates that NRC yields better results in comparison with previous protein function prediction approaches that utilize interaction network. Copyright © 2012 Elsevier Ltd. All rights reserved.

  16. Loop A Is Critical for the Functional Interaction of Two Beta vulgaris PIP Aquaporins

    Science.gov (United States)

    Jozefkowicz, Cintia; Rosi, Pablo; Sigaut, Lorena; Soto, Gabriela; Pietrasanta, Lía Isabel; Amodeo, Gabriela; Alleva, Karina

    2013-01-01

    Research done in the last years strongly support the hypothesis that PIP aquaporin can form heterooligomeric assemblies, specially combining PIP2 monomers with PIP1 monomers. Nevertheless, the structural elements involved in the ruling of homo versus heterooligomeric organization are not completely elucidated. In this work we unveil some features of monomer-monomer interaction in Beta vulgaris PIP aquaporins. Our results show that while BvPIP2;2 is able to interact with BvPIP1;1, BvPIP2;1 shows no functional interaction. The lack of functional interaction between BvPIP2;1 and BvPIP1;1 was further corroborated by dose-response curves of water permeability due to aquaporin activity exposed to different acidic conditions. We also found that BvPIP2;1 is unable to translocate BvPIP1;1-ECFP from an intracellular position to the plasma membrane when co-expressed, as BvPIP2;2 does. Moreover we postulate that the first extracellular loop (loop A) of BvPIP2;1, could be relevant for the functional interaction with BvPIP1;1. Thus, we investigate BvPIP2;1 loop A at an atomic level by Molecular Dynamics Simulation (MDS) and by direct mutagenesis. We found that, within the tetramer, each loop A presents a dissimilar behavior. Besides, BvPIP2;1 loop A mutants restore functional interaction with BvPIP1;1. This work is a contribution to unravel how PIP2 and PIP1 interact to form functional heterooligomeric assemblies. We postulate that BvPIP2;1 loop A is relevant for the lack of functional interaction with BvPIP1;1 and that the monomer composition of PIP assemblies determines their functional properties. PMID:23483963

  17. Casimir interaction energies for magneto-electric \\delta-function plates

    CERN Document Server

    Milton, Kimball A; Schaden, Martin; Shajesh, K V

    2013-01-01

    We present boundary conditions for the electromagnetic fields on a \\delta-function plate, having both electric and magnetic properties, sandwiched between two magneto-electric semi-infinite half spaces. The optical properties for an isolated \\delta-function plate are shown to be independent of the longitudinal material properties of the plate. The Casimir-Polder energy between an isotropically polarizable atom and a magneto-electric \\delta-function plate is attractive for a purely electric \\delta-function plate, repulsive for a purely magnetic \\delta-function plate, and vanishes for the simultaneous perfect conductor limit of both electric and magnetic properties of the \\delta-function plate. The interaction energy between two identical \\delta-function plates is always attractive. It can be attractive or repulsive when the plates have electric and magnetic properties interchanged and reproduces Boyer's result for the interaction energy between perfectly conducting electric and magnetic plates. The change in t...

  18. Specialized functional diversity and interactions of the Na,K-ATPase

    Directory of Open Access Journals (Sweden)

    Igor I. Krivoi

    2016-05-01

    Full Text Available Na,K-ATPase is a protein ubiquitously expressed in the plasma membrane of all animal cells and vitally essential for their functions. A specialized functional diversity of the Na,K-ATPase isozymes is provided by molecular heterogeneity, distinct subcellular localizations and functional interactions with molecular environment. Studies over the last decades clearly demonstrated complex and isoform-specific reciprocal functional interactions between the Na,K-ATPase and neighboring proteins and lipids. These interactions are enabled by a spatially restricted ion homeostasis, direct protein-protein/lipid interactions and protein kinase signaling pathways. In addition to its ‘classical’ function in ion translocation, the Na,K-ATPase is now considered as one of the most important signaling molecules in neuronal, epithelial, skeletal, cardiac and vascular tissues. Accordingly, the Na,K-ATPase forms specialized sub-cellular multimolecular microdomains which act as receptors to circulating endogenous cardiotonic steroids triggering a number of signaling pathways. Changes in these endogenous cardiotonic steroid levels and initiated signaling responses have significant adaptive values for tissues and whole organisms under numerous physiological and pathophysiological conditions. This review discusses recent progress in the studies of functional interactions between the Na,K-ATPase and molecular microenvironment, the Na,K-ATPase-dependent signaling pathways and their significance for diversity of cell function.

  19. Quantitative evaluation of interaction force between functional groups in protein and polymer brush surfaces.

    Science.gov (United States)

    Sakata, Sho; Inoue, Yuuki; Ishihara, Kazuhiko

    2014-03-18

    To understand interactions between polymer surfaces and different functional groups in proteins, interaction forces were quantitatively evaluated by force-versus-distance curve measurements using atomic force microscopy with a functional-group-functionalized cantilever. Various polymer brush surfaces were systematically prepared by surface-initiated atom transfer radical polymerization as well-defined model surfaces to understand protein adsorption behavior. The polymer brush layers consisted of phosphorylcholine groups (zwitterionic/hydrophilic), trimethylammonium groups (cationic/hydrophilic), sulfonate groups (anionic/hydrophilic), hydroxyl groups (nonionic/hydrophilic), and n-butyl groups (nonionic/hydrophobic) in their side chains. The interaction forces between these polymer brush surfaces and different functional groups (carboxyl groups, amino groups, and methyl groups, which are typical functional groups existing in proteins) were quantitatively evaluated by force-versus-distance curve measurements using atomic force microscopy with a functional-group-functionalized cantilever. Furthermore, the amount of adsorbed protein on the polymer brush surfaces was quantified by surface plasmon resonance using albumin with a negative net charge and lysozyme with a positive net charge under physiological conditions. The amount of proteins adsorbed on the polymer brush surfaces corresponded to the interaction forces generated between the functional groups on the cantilever and the polymer brush surfaces. The weakest interaction force and least amount of protein adsorbed were observed in the case of the polymer brush surface with phosphorylcholine groups in the side chain. On the other hand, positive and negative surfaces generated strong forces against the oppositely charged functional groups. In addition, they showed significant adsorption with albumin and lysozyme, respectively. These results indicated that the interaction force at the functional group level might be

  20. Atom-light interactions in quasi-one-dimensional nanostructures: A Green's-function perspective

    Science.gov (United States)

    Asenjo-Garcia, A.; Hood, J. D.; Chang, D. E.; Kimble, H. J.

    2017-03-01

    Based on a formalism that describes atom-light interactions in terms of the classical electromagnetic Green's function, we study the optical response of atoms and other quantum emitters coupled to one-dimensional photonic structures, such as cavities, waveguides, and photonic crystals. We demonstrate a clear mapping between the transmission spectra and the local Green's function, identifying signatures of dispersive and dissipative interactions between atoms. We also demonstrate the applicability of our analysis to problems involving three-level atoms, such as electromagnetically induced transparency. Finally we examine recent experiments, and anticipate future observations of atom-atom interactions in photonic band gaps.

  1. Study on Interaction Between Two Parallel Plates with Iteration Method in Functional Theory

    Institute of Scientific and Technical Information of China (English)

    Ming Zhou; Zheng-wu Wang; Zu-min Xu

    2008-01-01

    By introducing the functional theory into the calculation of electric double layer (EDL) interaction,the interaction energies of two parallel plates were calculated respectively at low,moderate,and high potentials. Compared with the results of two existing methods,Debye-Hiickel and Langmuir methods,which are appli- cable just to the critical potentials and perform poorly in the intermediate potential,the functional approach not only has much simpler expression of the EDL interaction energy,but also performs well in the entire range of potentials.

  2. NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology.

    Science.gov (United States)

    Wei, Qing; Khan, Ishita K; Ding, Ziyun; Yerneni, Satwica; Kihara, Daisuke

    2017-03-20

    The number of genomics and proteomics experiments is growing rapidly, producing an ever-increasing amount of data that are awaiting functional interpretation. A number of function prediction algorithms were developed and improved to enable fast and automatic function annotation. With the well-defined structure and manual curation, Gene Ontology (GO) is the most frequently used vocabulary for representing gene functions. To understand relationship and similarity between GO annotations of genes, it is important to have a convenient pipeline that quantifies and visualizes the GO function analyses in a systematic fashion. NaviGO is a web-based tool for interactive visualization, retrieval, and computation of functional similarity and associations of GO terms and genes. Similarity of GO terms and gene functions is quantified with six different scores including protein-protein interaction and context based association scores we have developed in our previous works. Interactive navigation of the GO function space provides intuitive and effective real-time visualization of functional groupings of GO terms and genes as well as statistical analysis of enriched functions. We developed NaviGO, which visualizes and analyses functional similarity and associations of GO terms and genes. The NaviGO webserver is freely available at: http://kiharalab.org/web/navigo .

  3. Automated calculation of anharmonic vibrational contributions to first hyperpolarizabilities: quadratic response functions from vibrational configuration interaction wave functions.

    Science.gov (United States)

    Hansen, Mikkel Bo; Christiansen, Ove; Hättig, Christof

    2009-10-21

    Quadratic response functions are derived and implemented for a vibrational configuration interaction state. Combined electronic and vibrational quadratic response functions are derived using Born-Oppenheimer vibronic product wave functions. Computational tractable expressions are derived for determining the total quadratic response contribution as a sum of contributions involving both electronic and vibrational linear and quadratic response functions. In the general frequency-dependent case this includes a new and more troublesome type of electronic linear response function. Pilot calculations for the FH, H(2)O, CH(2)O, and pyrrole molecules demonstrate the importance of vibrational contributions for accurate comparison to experiment and that the vibrational contributions in some cases can be very large. The calculation of transition properties between vibrational states is combined with sum-over-states expressions for analysis purposes. On the basis of this some simple analysis methods are suggested. Also, a preliminary study of the effect of finite lifetimes on quadratic response functions is presented.

  4. The Changes of Energy Interactions between Nucleus Function and Mitochondria Functions Causing Transmutation of Chronic Inflammation into Cancer Metabolism.

    Science.gov (United States)

    Ponizovskiy, Michail R

    2016-01-01

    Interactions between nucleus and mitochondria functions induce the mechanism of maintenance stability of cellular internal energy according to the first law of thermodynamics in able-bodied cells and changes the mechanisms of maintenance stability of cellular internal energy creating a transition stationary state of ablebodied cells into quasi-stationary pathologic states of acute inflammation transiting then into chronic inflammation and then transmuting into cancer metabolism. The mechanisms' influences of intruding etiologic pathologic agents (microbe, virus, etc.) lead to these changes of energy interactions between nucleus and mitochondria functions causing general acute inflammation, then passing into local chronic inflammation, and reversing into cancer metabolism transmutation. Interactions between biochemical processes and biophysical processes of cellular capacitors' operations create a supplementary mechanism of maintenance stability of cellular internal energy in the norm and in pathology. Discussion of some scientific works eliminates doubts of the authors of these works.

  5. Improving functional modules discovery by enriching interaction networks with gene profiles

    KAUST Repository

    Salem, Saeed

    2013-05-01

    Recent advances in proteomic and transcriptomic technologies resulted in the accumulation of vast amount of high-throughput data that span multiple biological processes and characteristics in different organisms. Much of the data come in the form of interaction networks and mRNA expression arrays. An important task in systems biology is functional modules discovery where the goal is to uncover well-connected sub-networks (modules). These discovered modules help to unravel the underlying mechanisms of the observed biological processes. While most of the existing module discovery methods use only the interaction data, in this work we propose, CLARM, which discovers biological modules by incorporating gene profiles data with protein-protein interaction networks. We demonstrate the effectiveness of CLARM on Yeast and Human interaction datasets, and gene expression and molecular function profiles. Experiments on these real datasets show that the CLARM approach is competitive to well established functional module discovery methods.

  6. One- and many-electron self-interaction error in local and global hybrid functionals

    Science.gov (United States)

    Schmidt, Tobias; Kümmel, Stephan

    2016-04-01

    Electronic self-interaction poses a fundamental challenge in density-functional theory. It greatly limits, e.g., the physical interpretation of eigenvalues as electron removal energies. We here investigate whether local hybrid functionals that are designed to be free from one-electron self-interaction lead to occupied Kohn-Sham eigenvalues and orbitals that approximate photoemission observables well. We compare the local hybrid results to the ones from global hybrid functionals that only partially counteract the self-interaction, and to the results that are obtained with a Perdew-Zunger-type self-interaction correction. Furthermore, we check whether being nominally free from one-electron self-interaction translates into a reduced many-electron self-interaction error. Our findings show that this is not the case for the local hybrid functionals that we studied: In practice they are similar to global hybrids in many respects, despite being formally superior. This finding indicates that there is a conceptual difference between the Perdew-Zunger way and the local hybrid way of translating the one-electron condition to a many-electron system. We also point out and solve some difficulties that occur when using local hybrid functionals in combination with pseudopotentials.

  7. Investigating the relationship among transformational leadership, interpersonal interaction and mentoring functions.

    Science.gov (United States)

    Huang, Ching-Yuan; Weng, Rhay-Hung; Chen, Yi-Ting

    2016-08-01

    This study aims to ascertain the relationship between transformational leadership, interpersonal interaction and mentoring functions among new staff nurses. Mentoring functions could improve the job performance of new nurses, provide them with support and thus reduce their turnover rate. A cross-sectional study was employed. A questionnaire survey was carried out to collect data among a sample of new nurses from three hospitals in Taiwan. After gathering a total of 306 valid surveys, multiple regression analysis was applied to test the hypothesis. Inspirational motivation, idealised influence and individualised consideration had positive correlations with the overall mentoring function, but intellectual stimulation showed a positive association only with career development function. Perceived similarity and interaction frequency also had positive correlations with mentoring functions. When the shift overlap rate exceeded 80%, mentoring function showed a negative result. The transformational leadership of mentors would improve the mentoring functions among new staff nurses. Perceived similarity and interaction frequency between mentees and mentors also had positive correlations with mentoring functions. It is crucial for hospitals to redesign their leadership training and motivation programmes to enhance the transformational leadership of mentors. Furthermore, nursing managers should promote interaction between new staff nurses and their mentors; however, the shift overlap rate should not be too high. © 2016 John Wiley & Sons Ltd.

  8. Data-driven analysis of functional brain interactions during free listening to music and speech.

    Science.gov (United States)

    Fang, Jun; Hu, Xintao; Han, Junwei; Jiang, Xi; Zhu, Dajiang; Guo, Lei; Liu, Tianming

    2015-06-01

    Natural stimulus functional magnetic resonance imaging (N-fMRI) such as fMRI acquired when participants were watching video streams or listening to audio streams has been increasingly used to investigate functional mechanisms of the human brain in recent years. One of the fundamental challenges in functional brain mapping based on N-fMRI is to model the brain's functional responses to continuous, naturalistic and dynamic natural stimuli. To address this challenge, in this paper we present a data-driven approach to exploring functional interactions in the human brain during free listening to music and speech streams. Specifically, we model the brain responses using N-fMRI by measuring the functional interactions on large-scale brain networks with intrinsically established structural correspondence, and perform music and speech classification tasks to guide the systematic identification of consistent and discriminative functional interactions when multiple subjects were listening music and speech in multiple categories. The underlying premise is that the functional interactions derived from N-fMRI data of multiple subjects should exhibit both consistency and discriminability. Our experimental results show that a variety of brain systems including attention, memory, auditory/language, emotion, and action networks are among the most relevant brain systems involved in classic music, pop music and speech differentiation. Our study provides an alternative approach to investigating the human brain's mechanism in comprehension of complex natural music and speech.

  9. The Interaction of Functional and Dysfunctional Emotions during Balance Beam Performance

    Science.gov (United States)

    Cottyn, Jorge; De Clercq, Dirk; Crombez, Geert; Lenoir, Matthieu

    2012-01-01

    The interaction between functional and dysfunctional emotions, as one of the major tenets of the Individual Zones of Optimal Functioning (IZOF) model (Hanin, 2000), was studied in a sport specific setting. Fourteen female gymnasts performed three attempts of a compulsory balance beam routine at three different heights. Heart rate and self-report…

  10. An Analysis of the Correspondence between Imagined Interaction Attributes and Functions

    Science.gov (United States)

    Bodie, Graham D.; Honeycutt, James M.; Vickery, Andrea J.

    2013-01-01

    Imagined interaction (II) theory has been productive for communication and social cognition scholarship. There is, however, a yet untested assumption within II theory that the 8 attributes are related to all 6 functions and that II functions can be compared and contrasted in terms of II attributes. In addition, there is little research exploring…

  11. How Socioeconomic Status, Executive Functioning and Verbal Interactions Contribute to Early Academic Achievement in Chinese Children

    Science.gov (United States)

    Chung, Kevin K. H.; Liu, Hongyun; McBride, Catherine; Wong, Anita M. -Y.; Lo, Jason C. M.

    2017-01-01

    The present study investigated the relative importance of executive functioning, parent-child verbal interactions, phonological awareness and visual skills on reading and mathematics for Chinese children from low-versus middle-socio economic status (SES) backgrounds. A total of 199 kindergarten children were assessed on executive functioning,…

  12. The Interaction of Functional and Dysfunctional Emotions during Balance Beam Performance

    Science.gov (United States)

    Cottyn, Jorge; De Clercq, Dirk; Crombez, Geert; Lenoir, Matthieu

    2012-01-01

    The interaction between functional and dysfunctional emotions, as one of the major tenets of the Individual Zones of Optimal Functioning (IZOF) model (Hanin, 2000), was studied in a sport specific setting. Fourteen female gymnasts performed three attempts of a compulsory balance beam routine at three different heights. Heart rate and self-report…

  13. Widely predicting specific protein functions based on protein-protein interaction data and gene expression profile

    Institute of Scientific and Technical Information of China (English)

    GAO Lei; LI Xia; GUO Zheng; ZHU MingZhu; LI YanHui; RAO ShaoQi

    2007-01-01

    GESTs (gene expression similarity and taxonomy similarity), a gene functional prediction approach previously proposed by us, is based on gene expression similarity and concept similarity of functional classes defined in Gene Ontology (GO). In this paper, we extend this method to protein-protein interaction data by introducing several methods to filter the neighbors in protein interaction networks for a protein of unknown function(s). Unlike other conventional methods, the proposed approach automatically selects the most appropriate functional classes as specific as possible during the learning process, and calls on genes annotated to nearby classes to support the predictions to some small-sized specific classes in GO. Based on the yeast protein-protein interaction information from MIPS and a dataset of gene expression profiles, we assess the performances of our approach for predicting protein functions to "biology process" by three measures particularly designed for functional classes organized in GO. Results show that our method is powerful for widely predicting gene functions with very specific functional terms. Based on the GO database published in December 2004, we predict some proteins whose functions were unknown at that time, and some of the predictions have been confirmed by the new SGD annotation data published in April, 2006.

  14. Widely predicting specific protein functions based on protein-protein interaction data and gene expression profile

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    GESTs (gene expression similarity and taxonomy similarity), a gene functional prediction approach previously proposed by us, is based on gene expression similarity and concept similarity of functional classes defined in Gene Ontology (GO). In this paper, we extend this method to protein-protein interac-tion data by introducing several methods to filter the neighbors in protein interaction networks for a protein of unknown function(s). Unlike other conventional methods, the proposed approach automati-cally selects the most appropriate functional classes as specific as possible during the learning proc-ess, and calls on genes annotated to nearby classes to support the predictions to some small-sized specific classes in GO. Based on the yeast protein-protein interaction information from MIPS and a dataset of gene expression profiles, we assess the performances of our approach for predicting protein functions to “biology process” by three measures particularly designed for functional classes organ-ized in GO. Results show that our method is powerful for widely predicting gene functions with very specific functional terms. Based on the GO database published in December 2004, we predict some proteins whose functions were unknown at that time, and some of the predictions have been confirmed by the new SGD annotation data published in April, 2006.

  15. Benzoyl peroxide (BPO)-promoted oxidative trifluoromethylation of tertiary amines with trimethyl(trifluoromethyl)silane.

    Science.gov (United States)

    Chu, Lingling; Qing, Feng-Ling

    2010-09-14

    The benzoyl peroxide (BPO)-promoted oxidative functionalization of tertiary amines under transition-metal-free reaction conditions was developed. Various 1-trifluoromethylated tetrahydroisoquinoline derivatives were prepared by employing this method. It constitutes the first example of direct trifluoromethylation of tertiary amines.

  16. Who Has to Pay for Their Education? Evidence from European Tertiary Education

    Science.gov (United States)

    Lim, Gieyoung; Kim, Chong-Uk

    2013-01-01

    In this article, we investigate a positive tertiary education externality in 18 European countries. Using a simple Cobb-Douglas-type production function with constant returns to scale, we find that there are positive spillover effects from tertiary education in European countries. According to our model prediction, on average, 72,000 new employed…

  17. STAT3-Interacting Proteins as Modulators of Transcription Factor Function: Implications to Targeted Cancer Therapy.

    Science.gov (United States)

    Yeh, Jennifer E; Frank, David A

    2016-04-19

    The oncogenic transcription factor STAT3 is inappropriately activated in multiple hematopoietic and solid malignancies, in which it drives the expression of genes involved in cell proliferation, differentiation, survival, and angiogenesis. Thus far, strategies to inhibit the function of STAT3 have focused on blocking the function of its activating kinases or sequestering its DNA binding ability. A less well-explored aspect of STAT3 function is its interaction with other proteins, which can modulate the oncogenic activity of STAT3 via its subcellular localization, DNA binding ability, and recruitment of transcriptional machinery. Herein we summarize what is currently known about STAT3-interacting proteins and describe the utility of a proteomics-based approach for successfully identifying and characterizing novel STAT3-interacting proteins that affect STAT3 transcriptional activity and oncogenic function.

  18. Multiple genetic interaction experiments provide complementary information useful for gene function prediction.

    Directory of Open Access Journals (Sweden)

    Magali Michaut

    Full Text Available Genetic interactions help map biological processes and their functional relationships. A genetic interaction is defined as a deviation from the expected phenotype when combining multiple genetic mutations. In Saccharomyces cerevisiae, most genetic interactions are measured under a single phenotype - growth rate in standard laboratory conditions. Recently genetic interactions have been collected under different phenotypic readouts and experimental conditions. How different are these networks and what can we learn from their differences? We conducted a systematic analysis of quantitative genetic interaction networks in yeast performed under different experimental conditions. We find that networks obtained using different phenotypic readouts, in different conditions and from different laboratories overlap less than expected and provide significant unique information. To exploit this information, we develop a novel method to combine individual genetic interaction data sets and show that the resulting network improves gene function prediction performance, demonstrating that individual networks provide complementary information. Our results support the notion that using diverse phenotypic readouts and experimental conditions will substantially increase the amount of gene function information produced by genetic interaction screens.

  19. Functional organization and its implication in evolution of the human protein-protein interaction network

    Directory of Open Access Journals (Sweden)

    Zhao Yiqiang

    2012-04-01

    Full Text Available Abstract Background Based on the distinguishing properties of protein-protein interaction networks such as power-law degree distribution and modularity structure, several stochastic models for the evolution of these networks have been purposed, motivated by the idea that a validated model should reproduce similar topological properties of the empirical network. However, being able to capture topological properties does not necessarily mean it correctly reproduces how networks emerge and evolve. More importantly, there is already evidence suggesting functional organization and significance of these networks. The current stochastic models of evolution, however, grow the network without consideration for biological function and natural selection. Results To test whether protein interaction networks are functionally organized and their impacts on the evolution of these networks, we analyzed their evolution at both the topological and functional level. We find that the human network is shown to be functionally organized, and its function evolves with the topological properties of the network. Our analysis suggests that function most likely affects local modularity of the network. Consistently, we further found that the topological unit is also the functional unit of the network. Conclusion We have demonstrated functional organization of a protein interaction network. Given our observations, we suggest that its significance should not be overlooked when studying network evolution.

  20. Buckets and Fire: Metaphors in Tertiary Teaching

    Science.gov (United States)

    Emerson, Lisa; Mansvelt, Juliana

    2015-01-01

    This paper examines New Zealand tertiary teachers' use of metaphor and their attitudes to the consumer metaphor in relation to teaching. Based on interviews with 16 tertiary teachers, this study shows that although teachers believe the consumer metaphor is accepted by students, tertiary institutions and policy makers, and that it has affected…

  1. A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling

    DEFF Research Database (Denmark)

    Blagoev, B.; Kratchmarova, I.; Ong, S.E.

    2003-01-01

    Mass spectrometry-based proteomics can reveal protein-protein interactions on a large scale, but it has been difficult to separate background binding from functionally important interactions and still preserve weak binders. To investigate the epidermal growth factor receptor (EGFR) pathway, we...... and Src homologous and collagen (Shc) protein. We identified 228 proteins, of which 28 were selectively enriched upon stimulation. EGFR and Shc, which interact directly with the bait, had large differential ratios. Many signaling molecules specifically formed complexes with the activated EGFR-Shc, as did...... plectin, epiplakin, cytokeratin networks, histone H3, the glycosylphosphatidylinositol (GPI)-anchored molecule CD59, and two novel proteins. SILAC combined with modification-based affinity purification is a useful approach to detect specific and functional protein-protein interactions....

  2. Detection of Sugar-Lectin Interactions by Multivalent Dendritic Sugar Functionalized Single-Walled Carbon Nanotubes

    CERN Document Server

    Vasu, K S; Bagul, R S; Jayaraman, N; Sood, A K; 10.1063/1.4739793

    2012-01-01

    We show that single walled carbon nanotubes (SWNT) decorated with sugar functionalized poly (propyl ether imine) (PETIM) dendrimer is a very sensitive platform to quantitatively detect carbohydrate recognizing proteins, namely, lectins. The changes in electrical conductivity of SWNT in field effect transistor device due to carbohydrate - protein interactions form the basis of present study. The mannose sugar attached PETIM dendrimers undergo charge - transfer interactions with the SWNT. The changes in the conductance of the dendritic sugar functionalized SWNT after addition of lectins in varying concentrations were found to follow the Langmuir type isotherm, giving the concanavalin A (Con A) - mannose affinity constant to be 8.5 x 106 M-1. The increase in the device conductance observed after adding 10 nM of Con A is same as after adding 20 \\muM of a non - specific lectin peanut agglutinin, showing the high specificity of the Con A - mannose interactions. The specificity of sugar-lectin interactions was chara...

  3. Using compound similarity and functional domain composition for prediction of drug-target interaction networks.

    Science.gov (United States)

    Chen, Lei; He, Zhi-Song; Huang, Tao; Cai, Yu-Dong

    2010-11-01

    Study of interactions between drugs and target proteins is an essential step in genomic drug discovery. It is very hard to determine the compound-protein interactions or drug-target interactions by experiment alone. As supplementary, effective prediction model using machine learning or data mining methods can provide much help. In this study, a prediction method based on Nearest Neighbor Algorithm and a novel metric, which was obtained by combining compound similarity and functional domain composition, was proposed. The target proteins were divided into the following groups: enzymes, ion channels, G protein-coupled receptors, and nuclear receptors. As a result, four predictors with the optimal parameters were established. The overall prediction accuracies, evaluated by jackknife cross-validation test, for four groups of target proteins are 90.23%, 94.74%, 97.80%, and 97.51%, respectively, indicating that compound similarity and functional domain composition are very effective to predict drug-target interaction networks.

  4. Obtaining control of cell surface functionalizations via Pre-targeting and Supramolecular host guest interactions.

    Science.gov (United States)

    Rood, Mark T M; Spa, Silvia J; Welling, Mick M; Ten Hove, Jan Bart; van Willigen, Danny M; Buckle, Tessa; Velders, Aldrik H; van Leeuwen, Fijs W B

    2017-01-06

    The use of mammalian cells for therapeutic applications is finding its way into modern medicine. However, modification or "training" of cells to make them suitable for a specific application remains complex. By envisioning a chemical toolbox that enables specific, but straight-forward and generic cellular functionalization, we investigated how membrane-receptor (pre)targeting could be combined with supramolecular host-guest interactions based on β-cyclodextrin (CD) and adamantane (Ad). The feasibility of this approach was studied in cells with membranous overexpression of the chemokine receptor 4 (CXCR4). By combining specific targeting of CXCR4, using an adamantane (Ad)-functionalized Ac-TZ14011 peptide (guest; KD = 56 nM), with multivalent host molecules that entailed fluorescent β-CD-Poly(isobutylene-alt-maleic-anhydride)-polymers with different fluorescent colors and number of functionalities, host-guest cell-surface modifications could be studied in detail. A second set of Ad-functionalized entities enabled introduction of additional surface functionalities. In addition, the attraction between CD and Ad could be used to drive cell-cell interactions. Combined we have shown that supramolecular interactions, that are based on specific targeting of an overexpressed membrane-receptor, allow specific and stable, yet reversible, surface functionalization of viable cells and how this approach can be used to influence the interaction between cells and their surroundings.

  5. Interactions between Histamine H3 and Dopamine D2 Receptors and the Implications for Striatal Function

    OpenAIRE

    Ferrada, Carla; Ferré, Sergi; Casadó, Vicent; Cortés, Antonio; Justinova, Zuzana; Barnes, Chanel; Canela, Enric I.; Goldberg, Steven R.; Leurs, Rob; Lluis, Carme; Franco, Rafael

    2008-01-01

    The striatum contains a high density of histamine H3 receptors, but their role in striatal function is poorly understood. Previous studies have demonstrated antagonistic interactions between striatal H3 and dopamine D1 receptors at the biochemical level, while contradictory results have been reported about interactions between striatal H3 and dopamine D2 receptors. In the present study, by using reserpinized mice, we demonstrate the existence of behaviorally significant antagonistic postsynap...

  6. Benchmarking Fermi orbital self-interaction corrected density functional theory on molecules

    CERN Document Server

    Hahn, Torsten; Kortus, Jens; Pederson, Mark R

    2015-01-01

    The correction of the self-interaction error (SIE) that is inherent to all standard density functional theory (DFT) calculations is an object of increasing interest. In this article we apply the very recently developed Fermi-orbital based approach for the self-interaction correction (FOSIC) to a set of different molecular systems. Our study covers systems ranging from simple diatomic to large organic molecules. We focus our analysis on the direct estimation of the ionization potential from orbital eigenvalues.

  7. Evolution of domain-peptide interactions to coadapt specificity and affinity to functional diversity.

    Science.gov (United States)

    Kelil, Abdellali; Levy, Emmanuel D; Michnick, Stephen W

    2016-07-05

    Evolution of complexity in eukaryotic proteomes has arisen, in part, through emergence of modular independently folded domains mediating protein interactions via binding to short linear peptides in proteins. Over 30 years, structural properties and sequence preferences of these peptides have been extensively characterized. Less successful, however, were efforts to establish relationships between physicochemical properties and functions of domain-peptide interactions. To our knowledge, we have devised the first strategy to exhaustively explore the binding specificity of protein domain-peptide interactions. We applied the strategy to SH3 domains to determine the properties of their binding peptides starting from various experimental data. The strategy identified the majority (∼70%) of experimentally determined SH3 binding sites. We discovered mutual relationships among binding specificity, binding affinity, and structural properties and evolution of linear peptides. Remarkably, we found that these properties are also related to functional diversity, defined by depth of proteins within hierarchies of gene ontologies. Our results revealed that linear peptides evolved to coadapt specificity and affinity to functional diversity of domain-peptide interactions. Thus, domain-peptide interactions follow human-constructed gene ontologies, which suggest that our understanding of biological process hierarchies reflect the way chemical and thermodynamic properties of linear peptides and their interaction networks, in general, have evolved.

  8. Functional Ecological Gene Networks to Reveal the Changes Among Microbial Interactions Under Elevated Carbon Dioxide Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Ye; Zhou, Jizhong; Luo, Feng; He, Zhili; Tu, Qichao; Zhi, Xiaoyang

    2010-05-17

    Biodiversity and its responses to environmental changes is a central issue in ecology, and for society. Almost all microbial biodiversity researches focus on species richness and abundance but ignore the interactions among different microbial species/populations. However, determining the interactions and their relationships to environmental changes in microbial communities is a grand challenge, primarily due to the lack of information on the network structure among different microbial species/populations. Here, a novel random matrix theory (RMT)-based conceptual framework for identifying functional ecological gene networks (fEGNs) is developed with the high throughput functional gene array hybridization data from the grassland microbial communities in a long-term FACE (Free Air CO2 Enrichment) experiment. Both fEGNs under elevated CO2 (eCO2) and ambient CO2 (aCO2) possessed general characteristics of many complex systems such as scale-free, small-world, modular and hierarchical. However, the topological structure of the fEGNs is distinctly different between eCO2 and aCO2, suggesting that eCO2 dramatically altered the interactions among different microbial functional groups/populations. In addition, the changes in network structure were significantly correlated with soil carbon and nitrogen dynamics, and plant productivity, indicating the potential importance of network interactions in ecosystem functioning. Elucidating network interactions in microbial communities and their responses to environmental changes are fundamentally important for research in microbial ecology, systems microbiology, and global change.

  9. AtPID: the overall hierarchical functional protein interaction network interface and analytic platform for Arabidopsis.

    Science.gov (United States)

    Li, Peng; Zang, Weidong; Li, Yuhua; Xu, Feng; Wang, Jigang; Shi, Tieliu

    2011-01-01

    Protein interactions are involved in important cellular functions and biological processes that are the fundamentals of all life activities. With improvements in experimental techniques and progress in research, the overall protein interaction network frameworks of several model organisms have been created through data collection and integration. However, most of the networks processed only show simple relationships without boundary, weight or direction, which do not truly reflect the biological reality. In vivo, different types of protein interactions, such as the assembly of protein complexes or phosphorylation, often have their specific functions and qualifications. Ignorance of these features will bring much bias to the network analysis and application. Therefore, we annotate the Arabidopsis proteins in the AtPID database with further information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways. The latest updated AtPID database is available at http://www.megabionet.org/atpid/.

  10. Benchmarks for electronically excited states: Time-dependent density functional theory and density functional theory based multireference configuration interaction

    DEFF Research Database (Denmark)

    Silva-Junior, Mario R.; Schreiber, Marko; Sauer, Stephan P. A.;

    2008-01-01

    Time-dependent density functional theory (TD-DFT) and DFT-based multireference configuration interaction (DFT/MRCI) calculations are reported for a recently proposed benchmark set of 28 medium-sized organic molecules. Vertical excitation energies, oscillator strengths, and excited-state dipole...... moments are computed using the same geometries (MP2/6-31G*) and basis set (TZVP) as in our previous ab initio benchmark study on electronically excited states. The results from TD-DFT (with the functionals BP86, B3LYP, and BHLYP) and from DFT/MRCI are compared against the previous high-level ab initio...

  11. Group I Metabotropic Glutamate Receptor Interacting Proteins: Fine-Tuning Receptor Functions in Health and Disease.

    Science.gov (United States)

    Kalinowska, Magdalena; Francesconi, Anna

    2016-01-01

    Group I metabotropic glutamate receptors mediate slow excitatory neurotransmission in the central nervous system and are critical to activity-dependent synaptic plasticity, a cellular substrate of learning and memory. Dysregulated receptor signaling is implicated in neuropsychiatric conditions ranging from neurodevelopmental to neurodegenerative disorders. Importantly, group I metabotropic glutamate receptor signaling functions can be modulated by interacting proteins that mediate receptor trafficking, expression and coupling efficiency to signaling effectors. These interactions afford cell- or pathway-specific modulation to fine-tune receptor function, thus representing a potential target for pharmacological interventions in pathological conditions.

  12. Lattice Green's Function for Infinite Square Lattice in the Second Nearest-Neighbour Interaction Approximation

    Institute of Scientific and Technical Information of China (English)

    FAN Hong-Yi; LIN Jing-Xian

    2001-01-01

    In dealing with the square lattice model,we replace the traditionally needed Born-Von Karmann periodic boundary condition with additional Hamiltonian terms to make up a ring lattice.In doing so,the lattice Green's function of an infinite square lattice in the second nearest-neighbour interaction approximation can be derived by means of the matrix Green's function method.It is shown that the density of states may change when the second nearest-neighbour interaction is turned on.``

  13. Complementary and alternative medicine (CAM) use in children with functional abdominal pain (FAP) and irritable bowel syndrome (IBS) differs in tertiary vs. primary care and is related to mother's view of child disability

    Science.gov (United States)

    We sought to determine if CAM use was greater in children in tertiary vs. primary care, and whether child or parent report of pain characteristics, and/or child and mother's psychological characteristics differed between those who did/did not use CAM. We identified children 7-10 years of age with FA...

  14. Fine-granularity functional interaction signatures for characterization of brain conditions.

    Science.gov (United States)

    Hu, Xintao; Zhu, Dajiang; Lv, Peili; Li, Kaiming; Han, Junwei; Wang, Lihong; Shen, Dinggang; Guo, Lei; Liu, Tianming

    2013-07-01

    In the human brain, functional activity occurs at multiple spatial scales. Current studies on functional brain networks and their alterations in brain diseases via resting-state functional magnetic resonance imaging (rs-fMRI) are generally either at local scale (regionally confined analysis and inter-regional functional connectivity analysis) or at global scale (graph theoretic analysis). In contrast, inferring functional interaction at fine-granularity sub-network scale has not been adequately explored yet. Here our hypothesis is that functional interaction measured at fine-granularity sub-network scale can provide new insight into the neural mechanisms of neurological and psychological conditions, thus offering complementary information for healthy and diseased population classification. In this paper, we derived fine-granularity functional interaction (FGFI) signatures in subjects with Mild Cognitive Impairment (MCI) and Schizophrenia by diffusion tensor imaging (DTI) and rs-fMRI, and used patient-control classification experiments to evaluate the distinctiveness of the derived FGFI features. Our experimental results have shown that the FGFI features alone can achieve comparable classification performance compared with the commonly used inter-regional connectivity features. However, the classification performance can be substantially improved when FGFI features and inter-regional connectivity features are integrated, suggesting the complementary information achieved from the FGFI signatures.

  15. Growing functional modules from a seed protein via integration of protein interaction and gene expression data

    Directory of Open Access Journals (Sweden)

    Dimitrakopoulou Konstantina

    2007-10-01

    Full Text Available Abstract Background Nowadays modern biology aims at unravelling the strands of complex biological structures such as the protein-protein interaction (PPI networks. A key concept in the organization of PPI networks is the existence of dense subnetworks (functional modules in them. In recent approaches clustering algorithms were applied at these networks and the resulting subnetworks were evaluated by estimating the coverage of well-established protein complexes they contained. However, most of these algorithms elaborate on an unweighted graph structure which in turn fails to elevate those interactions that would contribute to the construction of biologically more valid and coherent functional modules. Results In the current study, we present a method that corroborates the integration of protein interaction and microarray data via the discovery of biologically valid functional modules. Initially the gene expression information is overlaid as weights onto the PPI network and the enriched PPI graph allows us to exploit its topological aspects, while simultaneously highlights enhanced functional association in specific pairs of proteins. Then we present an algorithm that unveils the functional modules of the weighted graph by expanding a kernel protein set, which originates from a given 'seed' protein used as starting-point. Conclusion The integrated data and the concept of our approach provide reliable functional modules. We give proofs based on yeast data that our method manages to give accurate results in terms both of structural coherency, as well as functional consistency.

  16. Topological invariants for interacting topological insulators. II. Breakdown of single-particle Green's function formalism

    Science.gov (United States)

    He, Yuan-Yao; Wu, Han-Qing; Meng, Zi Yang; Lu, Zhong-Yi

    2016-05-01

    Topological phase transitions in free fermion systems can be characterized by the closing of single-particle gap and the change in topological invariants. However, in the presence of electronic interactions, topological phase transitions can be more complicated. In paper I of this series [Phys. Rev. B 93, 195163 (2016), 10.1103/PhysRevB.93.195163], we have proposed an efficient scheme to evaluate the topological invariants based on the single-particle Green's function formalism. Here, in paper II, we demonstrate several interaction-driven topological phase transitions (TPTs) in two-dimensional (2D) interacting topological insulators (TIs) via large-scale quantum Monte Carlo (QMC) simulations, based on the scheme of evaluating topological invariants presented in paper I. Across these transitions, the defining symmetries of the TIs have been neither explicitly nor spontaneously broken. In the first two models, the topological invariants calculated from the Green's function formalism succeed in characterizing the topologically distinct phases and identifying interaction-driven TPTs. However, in the other two models, we find that the single-particle gap does not close and the topological invariants constructed from the single-particle Green's function acquire no change across the TPTs. Unexpected breakdown of the Green's function formalism in constructing the topological invariants is thus discovered. We thence classify the topological phase transitions in interacting TIs into two categories in practical computation: Those that have noninteracting correspondence can be characterized successfully by the topological invariants constructed from the Green's functions, while for the others that do not have noninteracting correspondence, the Green's function formalism experiences a breakdown, but more interesting and exciting phenomena, such as emergent collective critical modes at the transition, arise. Discussion on the success and breakdown of topological invariants

  17. The electrokinetic characterization of gold nanoparticles, functionalized with cationic functional groups, and its' interaction with DNA.

    Science.gov (United States)

    Lazarus, Geraldine Genevive; Revaprasadu, Neerish; López-Viota, Julián; Singh, Moganavelli

    2014-09-01

    Gold nanoparticles have attracted strong biomedical interest for drug delivery due to their low toxic nature, surface plasmon resonance and capability of increasing the stability of the payload. However, gene transfection represents another important biological application. Considering that cellular barriers keep enclosed their secret to deliver genes using nanoparticles, an important step can be achieved by studying the functionalization of nanoparticles with DNA. In the present contribution the synthesis of nanoparticles consisting of a gold core coated with one or more layers of amino acid (l-lysine), and cationic polyelectrolytes (poly-ethyleneimine and poly-l-lysine) is reported. All nanoparticles were subjected to dynamic light scattering, electrophoretic mobility measurements, UV-vis optical spectrophotometry analysis and transmission electron microscopy imaging. In addition, the adsorption of DNA plasmid (pSGS) with linear and supercoiled configurations was studied for those gold nanoparticles under the most suitable surface modifications. Preliminary results showed that the gold nanoparticles functionalized with poly-ethyleneimine and poly-l-lysine, respectively, and bound to linear DNA configurations, present in absolute value a higher electrophoretic mobility irrespective of the pH of the media, compared to the supercoiled and nicked configuration. The findings from this study suggest that poly-ethyleneimine and poly-l-lysine functionalized gold nanoparticles are biocompatible and may be promising in the chemical design and future optimization of nanostructures for biomedical applications such as gene and drug delivery.

  18. Optimizing Scoring Function of Protein-Nucleic Acid Interactions with Both Affinity and Specificity

    Science.gov (United States)

    Yan, Zhiqiang; Wang, Jin

    2013-01-01

    Protein-nucleic acid (protein-DNA and protein-RNA) recognition is fundamental to the regulation of gene expression. Determination of the structures of the protein-nucleic acid recognition and insight into their interactions at molecular level are vital to understanding the regulation function. Recently, quantitative computational approach has been becoming an alternative of experimental technique for predicting the structures and interactions of biomolecular recognition. However, the progress of protein-nucleic acid structure prediction, especially protein-RNA, is far behind that of the protein-ligand and protein-protein structure predictions due to the lack of reliable and accurate scoring function for quantifying the protein-nucleic acid interactions. In this work, we developed an accurate scoring function (named as SPA-PN, SPecificity and Affinity of the Protein-Nucleic acid interactions) for protein-nucleic acid interactions by incorporating both the specificity and affinity into the optimization strategy. Specificity and affinity are two requirements of highly efficient and specific biomolecular recognition. Previous quantitative descriptions of the biomolecular interactions considered the affinity, but often ignored the specificity owing to the challenge of specificity quantification. We applied our concept of intrinsic specificity to connect the conventional specificity, which circumvents the challenge of specificity quantification. In addition to the affinity optimization, we incorporated the quantified intrinsic specificity into the optimization strategy of SPA-PN. The testing results and comparisons with other scoring functions validated that SPA-PN performs well on both the prediction of binding affinity and identification of native conformation. In terms of its performance, SPA-PN can be widely used to predict the protein-nucleic acid structures and quantify their interactions. PMID:24098651

  19. Influence and interaction indexes for pseudo-Boolean functions: a unified least squares approach

    CERN Document Server

    Marichal, Jean-Luc

    2012-01-01

    The Banzhaf power and interaction indexes for a pseudo-Boolean function (or a cooperative game) appear naturally as leading coefficients in the standard least squares approximation of the function by a pseudo-Boolean function of a specified degree. We first observe that this property still holds if we consider approximations by pseudo-Boolean functions depending only on specified variables. We then show that the Banzhaf influence index can also be obtained from the latter approximation problem. Considering certain weighted versions of this approximation problem, we introduce a class of weighted Banzhaf influence indexes, analyze their most important properties, and point out similarities between the weighted Banzhaf influence index and the corresponding weighted Banzhaf interaction index.

  20. MRIVIEW: An interactive computational tool for investigation of brain structure and function

    Energy Technology Data Exchange (ETDEWEB)

    Ranken, D.; George, J.

    1993-12-31

    MRIVIEW is a software system which uses image processing and visualization to provide neuroscience researchers with an integrated environment for combining functional and anatomical information. Key features of the software include semi-automated segmentation of volumetric head data and an interactive coordinate reconciliation method which utilizes surface visualization. The current system is a precursor to a computational brain atlas. We describe features this atlas will incorporate, including methods under development for visualizing brain functional data obtained from several different research modalities.

  1. Interaction of copernicium with gold: Assessment of applicability of simple density functional theories

    CERN Document Server

    Zaitsevskii, Andréi V

    2012-01-01

    Interactions of Cn (element 112) atoms with small Au clusters are studied using accurate ab initio scalar relativistic coupled cluster method for correlation treatment and two-component relativistic density functional theory (RDFT) to account for spin-dependent relativistic effect. The results demonstrate the failure of RDFT with simple generalized-gradient and hybrid functionals in describing Cn--Au bonds in complex systems.

  2. Scheme for Direct Measurement of the Wigner Function via Resonant Interaction

    Institute of Scientific and Technical Information of China (English)

    ZHENG Shi-Biao

    2008-01-01

    We propose a scheme for direct measurement of the Wigner function for a cavity mode. In the scheme the cavity field resonantly interacts with an atomic ensemble. Under certain conditions, the state of the cavity mode is transferred to the atomic system. After a displacement the measurement of the parity of the atomic excitation number directly yields the Wigner function of the initial state of the cavity mode.

  3. Defining the functional domain of programmed cell death 10 through its interactions with phosphatidylinositol-3,4,5-trisphosphate.

    Directory of Open Access Journals (Sweden)

    Christopher F Dibble

    Full Text Available Cerebral cavernous malformations (CCM are vascular abnormalities of the central nervous system predisposing blood vessels to leakage, leading to hemorrhagic stroke. Three genes, Krit1 (CCM1, OSM (CCM2, and PDCD10 (CCM3 are involved in CCM development. PDCD10 binds specifically to PtdIns(3,4,5P3 and OSM. Using threading analysis and multi-template modeling, we constructed a three-dimensional model of PDCD10. PDCD10 appears to be a six-helical-bundle protein formed by two heptad-repeat-hairpin structures (alpha1-3 and alpha4-6 sharing the closest 3D homology with the bacterial phosphate transporter, PhoU. We identified a stretch of five lysines forming an amphipathic helix, a potential PtdIns(3,4,5P3 binding site, in the alpha5 helix. We generated a recombinant wild-type (WT and three PDCD10 mutants that have two (Delta2KA, three (Delta3KA, and five (Delta5KA K to A mutations. Delta2KA and Delta3KA mutants hypothetically lack binding residues to PtdIns(3,4,5P3 at the beginning and the end of predicted helix, while Delta5KA completely lacks all predicted binding residues. The WT, Delta2KA, and Delta3KA mutants maintain their binding to PtdIns(3,4,5P3. Only the Delta5KA abolishes binding to PtdIns(3,4,5P3. Both Delta5KA and WT show similar secondary and tertiary structures; however, Delta5KA does not bind to OSM. When WT and Delta5KA are co-expressed with membrane-bound constitutively-active PI3 kinase (p110-CAAX, the majority of the WT is co-localized with p110-CAAX at the plasma membrane where PtdIns(3,4,5P3 is presumably abundant. In contrast, the Delta5KA remains in the cytoplasm and is not present in the plasma membrane. Combining computational modeling and biological data, we propose that the CCM protein complex functions in the PI3K signaling pathway through the interaction between PDCD10 and PtdIns(3,4,5P3.

  4. Specific interaction with cardiolipin triggers functional activation of Dynamin-Related Protein 1.

    Directory of Open Access Journals (Sweden)

    Itsasne Bustillo-Zabalbeitia

    Full Text Available Dynamin-Related Protein 1 (Drp1, a large GTPase of the dynamin superfamily, is required for mitochondrial fission in healthy and apoptotic cells. Drp1 activation is a complex process that involves translocation from the cytosol to the mitochondrial outer membrane (MOM and assembly into rings/spirals at the MOM, leading to membrane constriction/division. Similar to dynamins, Drp1 contains GTPase (G, bundle signaling element (BSE and stalk domains. However, instead of the lipid-interacting Pleckstrin Homology (PH domain present in the dynamins, Drp1 contains the so-called B insert or variable domain that has been suggested to play an important role in Drp1 regulation. Different proteins have been implicated in Drp1 recruitment to the MOM, although how MOM-localized Drp1 acquires its fully functional status remains poorly understood. We found that Drp1 can interact with pure lipid bilayers enriched in the mitochondrion-specific phospholipid cardiolipin (CL. Building on our previous study, we now explore the specificity and functional consequences of this interaction. We show that a four lysine module located within the B insert of Drp1 interacts preferentially with CL over other anionic lipids. This interaction dramatically enhances Drp1 oligomerization and assembly-stimulated GTP hydrolysis. Our results add significantly to a growing body of evidence indicating that CL is an important regulator of many essential mitochondrial functions.

  5. Functional interaction of nicotinic acetylcholine receptors and Na+/K+ ATPase from Locusta migratoria manilensis (Meyen).

    Science.gov (United States)

    Bao, Haibo; Sun, Huahua; Xiao, Youxin; Zhang, Yixi; Wang, Xin; Xu, Xiaoyong; Liu, Zewen; Fang, Jichao; Li, Zhong

    2015-03-06

    Associated proteins are important for the correct functioning of nicotinic acetylcholine receptors (nAChRs). In the present study, a neonicotinoid-agarose affinity column was used to isolate related proteins from a solubilized membrane preparation from the nervous system of Locusta migratoria manilensis (Meyen). 1530 peptides were identified and most of them were involved in the membranous structure, molecular interaction and cellular communication. Among these peptides, Na(+)/K(+) ATPase had the highest MASCOT score and were involved in the molecular interaction, which suggested that Na(+)/K(+) ATPase and nAChRs might have strong and stable interactions in insect central nervous system. In the present study, functional interactions between nAChRs and Na(+)/K(+) ATPase were examined by heterologous expression in Xenopus oocytes. The results showed that the activated nAChRs increased pump currents of Na(+)/K(+) ATPase, which did not require current flow through open nAChRs. In turn, Na(+)/K(+) ATPase significantly increased agonist sensitivities of nAChRs in a pump activity-independent manner and reduced the maximum current (Imax) of nAChRs. These findings provide novel insights concerning the functional interactions between insect nAChRs and Na(+)/K(+) ATPase.

  6. The interactive effect of social pain and executive functioning on aggression: an fMRI experiment.

    Science.gov (United States)

    Chester, David S; Eisenberger, Naomi I; Pond, Richard S; Richman, Stephanie B; Bushman, Brad J; Dewall, C Nathan

    2014-05-01

    Social rejection often increases aggression, but the neural mechanisms underlying this effect remain unclear. This experiment tested whether neural activity in the dorsal anterior cingulate cortex (dACC) and anterior insula in response to social rejection predicted greater subsequent aggression. Additionally, it tested whether executive functioning moderated this relationship. Participants completed a behavioral measure of executive functioning, experienced social rejection while undergoing functional magnetic resonance imaging and then completed a task in which they could aggress against a person who rejected them using noise blasts . We found that dACC activation and executive functioning interacted to predict aggression. Specifically, participants with low executive functioning showed a positive association between dACC activation and aggression, whereas individuals with high executive functioning showed a negative association. Similar results were found for the left anterior insula. These findings suggest that social pain can increase or decrease aggression, depending on an individual's regulatory capability.

  7. Partition and Correlation Functions of a Freely Crossed Network Using Ising Model-Type Interactions

    CERN Document Server

    Saito, Akira

    2016-01-01

    We set out to determine the partition and correlation functions of a network under the assumption that its elements are freely connected, with an Ising model-type interaction energy associated with each connection. The partition function is obtained from all combinations of loops on the free network, while the correlation function between two elements is obtained based on all combinations of routes between these points, as well as all loops on the network. These functions allow measurement of the dynamics over the whole of any network, regardless of its form. Furthermore, even as parts are added to the network, the partition and correlation functions can still be obtained. As an example, we obtain the partition and correlation functions in a crystal system under the repeated addition of fixed parts.

  8. Interaction between Palladium Nanoparticles and Surface-Modified Carbon Nanotubes: Role of Surface Functionalities

    DEFF Research Database (Denmark)

    Zhang, Bingsen; Shao, Lidong; Zhang, Wei;

    2014-01-01

    It is crucial to accurately describe the interaction between the surface functionality and the supported metal catalyst because it directly determines the activity and selectivity of a catalytic reaction. It is, however, challenging with a metal-carbon catalytic system owing to the ultrafine feat...

  9. The molecular understanding of interfacial interactions of functionalized graphene and chitosan

    Science.gov (United States)

    Zhang, Hong-ping; Luo, Xue-gang; Lin, Xiao-yan; Lu, Xiong; Tang, Youhong

    2016-01-01

    Graphene-reinforced chitosan scaffolds have been extensively studied for several years as promising hard tissue replacements. However, the interfacial interactions between graphene and chitosan are strongly related to the solubility, processability, and mechanical properties of graphene-reinforced chitosan (G-C) composites. The functionalization of graphene is regarded as the most effective way to improve the abovementioned properties of the G-C composite. In this study, the interfacial interactions between chitosan and functionalized graphene sheets with carboxylization (COOH-), amination (NH2-), and hydroxylation (OH-) groups were systematically studied at the electronic level using the method of ab initio simulations based on quantum mechanics theory and the observations were compared with reported experimental results. The covalent linkages between COOH-modified graphene and the chitosan units were demonstrated and the combination of multi-functionalization on graphene could regulate the interfacial interactions between graphene and the chitosan. The interfacial interactions between chitosan and properly functionalized graphene are critical for the preparation of G-C-based composites for tissue engineering scaffolds and other applications.

  10. Interactive Effects between Maternal Parenting and Negative Emotionality on Social Functioning among Very Young Chinese Children

    Science.gov (United States)

    Ren, Lixin; Zhang, Xiao; Zhou, Ning; Ng, Mei Lee

    2017-01-01

    Research Findings: This study examined how child negative emotionality interacted with mothers' self-reported parenting in predicting different aspects of social functioning among very young Chinese children. A total of 109 Chinese nursery children in Hong Kong participated with their parents. Maternal supportive and aversive parenting practices…

  11. Interactions between Levels of Attention Ability and Levels of Bilingualism in Children's Executive Functioning

    Science.gov (United States)

    Sorge, Geoff B.; Toplak, Maggie E.; Bialystok, Ellen

    2017-01-01

    Attention difficulty is associated with poor performance on executive functioning (EF) tasks, yet EF is enhanced in bilingual children. However, no research to date has investigated the possible interaction between bilingualism and attention ability in children to determine the consequences for EF when both are present. We assessed a sample of…

  12. Sparse representation of higher-order functional interaction patterns in task-based FMRI data.

    Science.gov (United States)

    Zhang, Shu; Li, Xiang; Lv, Jinglei; Jiang, Xi; Zhu, Dajiang; Chen, Hanbo; Zhang, Tuo; Guo, Lei; Liu, Tianming

    2013-01-01

    Traditional task-based fMRI activation detection methods, e.g., the widely used general linear model (GLM), assume that the brain's hemodynamic responses follow the block-based or event-related stimulus paradigm. Typically, these activation detections are performed voxel-wise independently, and then are usually followed by statistical corrections. Despite remarkable successes and wide adoption of these methods, it remains largely unknown how functional brain regions interact with each other within specific networks during task performance blocks and in the baseline. In this paper, we present a novel algorithmic pipeline to statistically infer and sparsely represent higher-order functional interaction patterns within the working memory network during task performance and in the baseline. Specifically, a collection of higher-order interactions are inferred via the greedy equivalence search (GES) algorithm for both task and baseline blocks. In the next stage, an effective online dictionary learning algorithm is utilized for sparse representation of the inferred higher-order interaction patterns. Application of this framework on a working memory task-based fMRI data reveals interesting and meaningful distributions of the learned sparse dictionary atoms in task and baseline blocks. In comparison with traditional voxel-wise activation detection and recent pair-wise functional connectivity analysis, our framework offers a new methodology for representation and exploration of higher-order functional activities in the brain.

  13. Social Interaction Style of Children and Adolescents with High-Functioning Autism Spectrum Disorder

    Science.gov (United States)

    Scheeren, Anke M.; Koot, Hans M.; Begeer, Sander

    2012-01-01

    Qualitative differences in social interaction style exist "within" the autism spectrum. In this study we examined whether these differences are associated with (1) the severity of autistic symptoms and comorbid disruptive behavior problems, (2) the child's psycho-social health, and (3) executive functioning and perspective taking skills. The…

  14. Specificity and functional interaction of the polymerase complex proteins of human and avian metapneumoviruses

    NARCIS (Netherlands)

    M.T. de Graaf (Marieke); S. Herfst (Sander); E.J.A. Schrauwen (Eefje); Y. Choi (Ying); B.G. van den Hoogen (Bernadette); A.D.M.E. Osterhaus (Albert); R.A.M. Fouchier (Ron)

    2008-01-01

    textabstractHuman metapneumovirus (HMPV) and avian metapneumovirus (AMPV) have a similar genome organization and protein composition, but a different host range. AMPV subgroup C (AMPV-C) is more closely relaled to HMPV than other AMPVs. To investigate the specificity and functional interaction of th

  15. Interaction between food components, intestinal microbiota and intestinal mucosa as a function of intestinal health

    NARCIS (Netherlands)

    Venema, K.; Sandt, H. van de

    2003-01-01

    Interaction between food components, intestinal microbiota and intestinal mucosa was studied as a function of intestinal health. A microbiota was found to be important for the onset and progression of inflammatory diseases. Studies revealed a prominent effect of micro-organisms on the gene expressio

  16. Mapping Functional Brain Development: Building a Social Brain through Interactive Specialization

    Science.gov (United States)

    Johnson, Mark H.; Grossmann, Tobias; Kadosh, Kathrin Cohen

    2009-01-01

    The authors review a viewpoint on human functional brain development, interactive specialization (IS), and its application to the emerging network of cortical regions referred to as the "social brain." They advance the IS view in 2 new ways. First, they extend IS into a domain to which it has not previously been applied--the emergence of social…

  17. Identifying functional modules in protein-protein interaction networks: An integrated exact approach

    NARCIS (Netherlands)

    Dittrich, M.; Klau, G.W.; Rosenwald, A.; Dandekar, T.; et al, not CWI

    2008-01-01

    Motivation: With the exponential growth of expression and protein-protein interaction (PPI) data, the frontier of research in system biology shifts more and more to the integrated analysis of these large datasets. Of particular interest is the identification of functional modules in PPI networks, sh

  18. Interactive Effects between Maternal Parenting and Negative Emotionality on Social Functioning among Very Young Chinese Children

    Science.gov (United States)

    Ren, Lixin; Zhang, Xiao; Zhou, Ning; Ng, Mei Lee

    2017-01-01

    Research Findings: This study examined how child negative emotionality interacted with mothers' self-reported parenting in predicting different aspects of social functioning among very young Chinese children. A total of 109 Chinese nursery children in Hong Kong participated with their parents. Maternal supportive and aversive parenting practices…

  19. Interactions between Levels of Attention Ability and Levels of Bilingualism in Children's Executive Functioning

    Science.gov (United States)

    Sorge, Geoff B.; Toplak, Maggie E.; Bialystok, Ellen

    2017-01-01

    Attention difficulty is associated with poor performance on executive functioning (EF) tasks, yet EF is enhanced in bilingual children. However, no research to date has investigated the possible interaction between bilingualism and attention ability in children to determine the consequences for EF when both are present. We assessed a sample of…

  20. Twenty weeks of home-based interactive training of children with cerebral palsy improves functional abilities

    DEFF Research Database (Denmark)

    Lorentzen, Jakob; Greve, Line Z; Kliim-Due, Mette

    2015-01-01

    BACKGROUND: Home-based training is becoming ever more important with increasing demands on the public health systems. We investigated whether individualized and supervised interactive home-based training delivered through the internet improves functional abilities in children with cerebral palsy...

  1. A molecular dynamics study on the interaction between epoxy and functionalized graphene sheets

    DEFF Research Database (Denmark)

    Melro, Liliana Sofia S. F. P.; Pyrz, Ryszard; Jensen, Lars Rosgaard

    2016-01-01

    The interaction between graphene and epoxy resin was studied using molecular dynamics simulations. The interfacial shear strength and pull out force were calculated for functionalised graphene layers (carboxyl, carbonyl, and hydroxyl) and epoxy composites interfaces. The influence of functional...... and epoxy resin increases....

  2. Functional phylogenetic analysis of LGI proteins identifies an interaction motif crucial for myelination.

    Science.gov (United States)

    Kegel, Linde; Jaegle, Martine; Driegen, Siska; Aunin, Eerik; Leslie, Kris; Fukata, Yuko; Watanabe, Masahiko; Fukata, Masaki; Meijer, Dies

    2014-04-01

    The cellular interactions that drive the formation and maintenance of the insulating myelin sheath around axons are only partially understood. Leucine-rich glioma-inactivated (LGI) proteins play important roles in nervous system development and mutations in their genes have been associated with epilepsy and amyelination. Their function involves interactions with ADAM22 and ADAM23 cell surface receptors, possibly in apposing membranes, thus attenuating cellular interactions. LGI4-ADAM22 interactions are required for axonal sorting and myelination in the developing peripheral nervous system (PNS). Functional analysis revealed that, despite their high homology and affinity for ADAM22, LGI proteins are functionally distinct. To dissect the key residues in LGI proteins required for coordinating axonal sorting and myelination in the developing PNS, we adopted a phylogenetic and computational approach and demonstrate that the mechanism of action of LGI4 depends on a cluster of three amino acids on the outer surface of the LGI4 protein, thus providing a structural basis for the mechanistic differences in LGI protein function in nervous system development and evolution.

  3. Data Equivalency of an Interactive Voice Response System for Home Assessment of Back Pain and Function

    Directory of Open Access Journals (Sweden)

    William S Shaw

    2007-01-01

    Full Text Available BACKGROUND: Interactive voice response (IVR systems that collect survey data using automated, push-button telephone responses may be useful to monitor patients’ pain and function at home; however, its equivalency to other data collection methods has not been studied.

  4. Nanometer arrays of functional light harvesting antenna complexes by nanoimprint lithography and host-guest interactions

    NARCIS (Netherlands)

    Escalante, Maryana; Zhao, Yiping; Ludden, Manon J.W.; Vermeij, Rolf; Olsen, John D.; Berenschot, Erwin; Hunter, C. Neil; Huskens, Jurriaan; Subramaniam, Vinod; Otto, Cees

    2008-01-01

    We show an approach based on a combination of site-directed mutagenesis, NIL and multivalent host−guest interactions for the realization of engineered ordered functional arrays of purified components of the photosynthetic system, the membrane-bound LH2 complex. In addition to micrometer-scale patter

  5. White matter microstructure of attentional networks predicts attention and consciousness functional interactions.

    Science.gov (United States)

    Chica, Ana B; Thiebaut de Schotten, Michel; Bartolomeo, Paolo; Paz-Alonso, Pedro M

    2017-09-13

    Attention is considered as one of the pre-requisites of conscious perception. Phasic alerting and exogenous orienting improve conscious perception of near-threshold information through segregated brain networks. Using a multimodal neuroimaging approach, combining data from functional MRI (fMRI) and diffusion-weighted imaging (DWI), we investigated the influence of white matter properties of the ventral branch of superior longitudinal fasciculus (SLF III) in functional interactions between attentional systems and conscious perception. Results revealed that (1) reduced integrity of the left hemisphere SLF III was predictive of the neural interactions observed between exogenous orienting and conscious perception, and (2) increased integrity of the left hemisphere SLF III was predictive of the neural interactions observed between phasic alerting and conscious perception. Our results combining fMRI and DWI data demonstrate that structural properties of the white matter organization determine attentional modulations over conscious perception.

  6. Capacitance, charge dynamics, and electrolyte-surface interactions in functionalized carbide-derived carbon electrodes

    Directory of Open Access Journals (Sweden)

    Boris Dyatkin

    2015-12-01

    Full Text Available This study analyzed the dynamics of ionic liquid electrolyte inside of defunctionalized, hydrogenated, and aminated pores of carbide-derived carbon supercapacitor electrodes. The approach tailors surface functionalities and tunes nanoporous structures to decouple the influence of pore wall composition on capacitance, ionic resistance, and long-term cyclability. Quasi-elastic neutron scattering probes the self-diffusion properties and electrode-ion interactions of electrolyte molecules confined in functionalized pores. Room-temperature ionic liquid interactions in confined pores are strongest when the hydrogen-containing groups are present on the surface. This property translates into higher capacitance and greater ion transport through pores during electrochemical cycling. Unlike hydrogenated pores, aminated pores do not favorably interact with ionic liquid ions and, subsequently, are outperformed by defunctionalized surfaces.

  7. Functional interactions within 23S rRNA involving the peptidyltransferase center

    DEFF Research Database (Denmark)

    Douthwaite, S

    1992-01-01

    A molecular genetic approach has been employed to investigate functional interactions within 23S rRNA. Each of the three base substitutions at guanine 2032 has been made. The 2032A mutation confers resistance to the antibiotics chloramphenicol and clindamycin, which interact with the 23S r...... that also confer antibiotic resistance. Both the domain II deletion and the 2057A mutation relieve the hypersensitive effect of the 2032A mutation, producing an erythromycin-resistant phenotype; in addition, the combination of the 2032A and 2057A mutations confers a higher level of chloramphenicol...... and chloramphenicol. Introduction of the domain II deletion into these double-mutation constructs gives rise to erythromycin resistance. The results are interpreted as indicating that position 2032 interacts with the peptidyltransferase loop and that there is a functional connection between domains II and V....

  8. STRUCTURAL FUNCTIONAL MODEL OF ACADEMIC STAFF INTERACTION WITHIN A UNIVERSITY COMPLEX

    Directory of Open Access Journals (Sweden)

    N. V. Silkina

    2015-03-01

    Full Text Available The research analyzes the possibility of coordinated activity of academic staff affiliated to secondary and higher educational institutions within a university complex. The applied methods integrate the analysis of regulatory documents and cooperation expertise of academic staff along with general modeling methods based on the structural and functional approach. The research outcomes reveal the spheres and types of academic staff interaction at various educational levels; the principles and conditions of the interaction in question being defined. The authors demonstrate a structural functional model, determining the organizational and professional aspects, as well as the results of academic staff interaction within the university complex. Implementation of the given model can facilitate the effective integration of split-level educational organizations into the university complex structure.

  9. Exchange-Correlation Effects for Noncovalent Interactions in Density Functional Theory.

    Science.gov (United States)

    Otero-de-la-Roza, A; DiLabio, Gino A; Johnson, Erin R

    2016-07-12

    In this article, we develop an understanding of how errors from exchange-correlation functionals affect the modeling of noncovalent interactions in dispersion-corrected density-functional theory. Computed CCSD(T) reference binding energies for a collection of small-molecule clusters are decomposed via a molecular many-body expansion and are used to benchmark density-functional approximations, including the effect of semilocal approximation, exact-exchange admixture, and range separation. Three sources of error are identified. Repulsion error arises from the choice of semilocal functional approximation. This error affects intermolecular repulsions and is present in all n-body exchange-repulsion energies with a sign that alternates with the order n of the interaction. Delocalization error is independent of the choice of semilocal functional but does depend on the exact exchange fraction. Delocalization error misrepresents the induction energies, leading to overbinding in all induction n-body terms, and underestimates the electrostatic contribution to the 2-body energies. Deformation error affects only monomer relaxation (deformation) energies and behaves similarly to bond-dissociation energy errors. Delocalization and deformation errors affect systems with significant intermolecular orbital interactions (e.g., hydrogen- and halogen-bonded systems), whereas repulsion error is ubiquitous. Many-body errors from the underlying exchange-correlation functional greatly exceed in general the magnitude of the many-body dispersion energy term. A functional built to accurately model noncovalent interactions must contain a dispersion correction, semilocal exchange, and correlation components that minimize the repulsion error independently and must also incorporate exact exchange in such a way that delocalization error is absent.

  10. First generation TREN dendrimers functionalized with naphthyl and/or dansyl units. Ground and excited state electronic interactions and protonation effects.

    Science.gov (United States)

    Passaniti, Paolo; Maestri, Mauro; Ceroni, Paola; Bergamini, Giacomo; Vögtle, Fritz; Fakhrnabavi, Hassan; Lukin, Oleg

    2007-04-01

    We report the photophysical properties (absorption and emission spectra, quantum yield, and lifetime) of five dendrimers of first generation based on a TREN (tris(2-aminoethyl)amine) skeleton functionalized at the periphery with naphthyl and/or 5-dimethylamino-1-naphthalenesulfonamide (hereafter called dansyl) chromophores. Each dendrimer comprises one tertiary amine unit in the core and three branches carrying a sulfonimido unit at the periphery, each one substituted by two identical or different moieties. In particular, TD6 and TN6 contain dansyl (D) or naphthyl (N) units, respectively, while TD3B3, TN3B3 and TN3D3 contain dansyl, naphthyl or benzyl (B) units at the periphery. The spectroscopic behaviour of these dendrimers has been investigated in acetonitrile solution and compared with that of reference compounds. For all dendrimers the absorption bands are red shifted compared to those of monomeric naphthyl and dansyl reference compounds. Moreover, the intense naphthyl and dansyl fluorescence is greatly quenched because of strong interactions between the two aromatic moieties linked by a sulfonimido unit. Protonation of the amine units of the dendrimers by addition of CF(3)SO(3)H (triflic) acid causes a decrease in intensity of the luminescence and a change in the shape of the emission bands. The shapes of the titration curves depend on the dendrimer, but in any case the effect of acid can be fully reversed by successive addition of base (tributylamine). The obtained results reveal that among the intradendrimer interactions the most important one is that taking place (via mesomeric interaction) between the various chromophores and a pair of sulfonimido groups.

  11. Finding finer functions for partially characterized proteins by protein-protein interaction networks

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Based on high-throughput data, numerous algorithms have been designed to find functions of novel proteins. However, the effectiveness of such algorithms is currently limited by some fundamental factors, including (1) the low a-priori probability of novel proteins participating in a detailed function; (2) the huge false data present in high-throughput datasets; (3) the incomplete data coverage of functional classes; (4) the abundant but heterogeneous negative samples for training the algorithms; and (5) the lack of detailed functional knowledge for training algorithms. Here, for partially characterized proteins, we suggest an approach to finding their finer functions based on protein interaction sub-networks or gene expression patterns, defined in function-specific subspaces. The proposed approach can lessen the above-mentioned problems by properly defining the prediction range and functionally filtering the noisy data, and thus can efficiently find proteins' novel functions. For thousands of yeast and human proteins partially characterized, it is able to reliably find their finer functions (e.g., the translational functions) with more than 90% precision. The predicted finer functions are highly valuable both for guiding the follow-up wet-lab validation and for providing the necessary data for training algorithms to learn other proteins.

  12. Prediction of Protein-protein Interactions on the Basis of Evolutionary Conservation of Protein Functions

    Directory of Open Access Journals (Sweden)

    Ekaterina Kotelnikova

    2007-01-01

    Full Text Available Motivation: Although a great deal of progress is being made in the development of fast and reliable experimental techniques to extract genome-wide networks of protein-protein and protein-DNA interactions, the sequencing of new genomes proceeds at an even faster rate. That is why there is a considerable need for reliable methods of in-silico prediction of protein interaction based solely on sequence similarity information and known interactions from well-studied organisms. This problem can be solved if a dependency exists between sequence similarity and the conservation of the proteins’ functions.Results: In this paper, we introduce a novel probabilistic method for prediction of protein-protein interactions using a new empirical probabilistic formula describing the loss of interactions between homologous proteins during the course of evolution. This formula describes an evolutional process quite similar to the process of the Earth’s population growth. In addition, our method favors predictions confi rmed by several interacting pairs over predictions coming from a single interacting pair. Our approach is useful in working with “noisy” data such as those coming from high-throughput experiments. We have generated predictions for fi ve “model” organisms: H. sapiens, D. melanogaster, C. elegans, A. thaliana, and S. cerevisiae and evaluated the quality of these predictions.

  13. A Fortran program to calculate the matrix elements of the Coulomb interaction involving hydrogenic wave functions

    Science.gov (United States)

    Sarkadi, L.

    2017-03-01

    The program MTRXCOUL [1] calculates the matrix elements of the Coulomb interaction between a charged particle and an atomic electron, ∫ ψf∗ (r) | R - r | - 1ψi(r) d r. Bound-free transitions are considered, and non-relativistic hydrogenic wave functions are used. In this revised version a bug discovered in the F3Y CPC Program Library (PL) subprogram [2] is fixed. Furthermore, the COULCC CPC PL subprogram [3] applied for the calculations of the radial wave functions of the free states and the Bessel functions is replaced by the CPC PL subprogram DCOUL [4].

  14. Mapping functional brain development: Building a social brain through interactive specialization.

    Science.gov (United States)

    Johnson, Mark H; Grossmann, Tobias; Cohen Kadosh, Kathrin

    2009-01-01

    The authors review a viewpoint on human functional brain development, interactive specialization (IS), and its application to the emerging network of cortical regions referred to as the social brain. They advance the IS view in 2 new ways. First, they extend IS into a domain to which it has not previously been applied--the emergence of social cognition and mentalizing computations in the brain. Second, they extend the implications of the IS view from the emergence of specialized functions within a cortical region to a focus on how different cortical regions with complementary functions become orchestrated into networks during human postnatal development.

  15. A novel functional module detection algorithm for protein-protein interaction networks

    Directory of Open Access Journals (Sweden)

    Zhang Aidong

    2006-12-01

    Full Text Available Abstract Background The sparse connectivity of protein-protein interaction data sets makes identification of functional modules challenging. The purpose of this study is to critically evaluate a novel clustering technique for clustering and detecting functional modules in protein-protein interaction networks, termed STM. Results STM selects representative proteins for each cluster and iteratively refines clusters based on a combination of the signal transduced and graph topology. STM is found to be effective at detecting clusters with a diverse range of interaction structures that are significant on measures of biological relevance. The STM approach is compared to six competing approaches including the maximum clique, quasi-clique, minimum cut, betweeness cut and Markov Clustering (MCL algorithms. The clusters obtained by each technique are compared for enrichment of biological function. STM generates larger clusters and the clusters identified have p-values that are approximately 125-fold better than the other methods on biological function. An important strength of STM is that the percentage of proteins that are discarded to create clusters is much lower than the other approaches. Conclusion STM outperforms competing approaches and is capable of effectively detecting both densely and sparsely connected, biologically relevant functional modules with fewer discards.

  16. Thick-target transmission method for excitation functions of interaction cross sections

    CERN Document Server

    Aikawa, M; Imai, S

    2016-01-01

    We propose a method, called as thick-target transmission (T3) method, to obtain an excitation function of interaction cross sections. In an ordinal experiment to measure the excitation function of interaction cross sections by the transmission method, we need to change the beam energy for each cross section. In the T3 method, the excitation function is derived from the beam attenuations measured at the targets of different thicknesses without changing the beam energy. The advantage of the T3 method is the simplicity and availability for radioactive beams. To confirm the availability, we perform a simulation for the 12C+27Al system with the PHITS code instead of actual experiments. Our results have large uncertainties but well reproduce the tendency of the experimental data.

  17. The function of communities in protein interaction networks at multiple scales

    Directory of Open Access Journals (Sweden)

    Jones Nick S

    2010-07-01

    Full Text Available Abstract Background If biology is modular then clusters, or communities, of proteins derived using only protein interaction network structure should define protein modules with similar biological roles. We investigate the link between biological modules and network communities in yeast and its relationship to the scale at which we probe the network. Results Our results demonstrate that the functional homogeneity of communities depends on the scale selected, and that almost all proteins lie in a functionally homogeneous community at some scale. We judge functional homogeneity using a novel test and three independent characterizations of protein function, and find a high degree of overlap between these measures. We show that a high mean clustering coefficient of a community can be used to identify those that are functionally homogeneous. By tracing the community membership of a protein through multiple scales we demonstrate how our approach could be useful to biologists focusing on a particular protein. Conclusions We show that there is no one scale of interest in the community structure of the yeast protein interaction network, but we can identify the range of resolution parameters that yield the most functionally coherent communities, and predict which communities are most likely to be functionally homogeneous.

  18. Protein-protein interaction network-based detection of functionally similar proteins within species.

    Science.gov (United States)

    Song, Baoxing; Wang, Fen; Guo, Yang; Sang, Qing; Liu, Min; Li, Dengyun; Fang, Wei; Zhang, Deli

    2012-07-01

    Although functionally similar proteins across species have been widely studied, functionally similar proteins within species showing low sequence similarity have not been examined in detail. Identification of these proteins is of significant importance for understanding biological functions, evolution of protein families, progression of co-evolution, and convergent evolution and others which cannot be obtained by detection of functionally similar proteins across species. Here, we explored a method of detecting functionally similar proteins within species based on graph theory. After denoting protein-protein interaction networks using graphs, we split the graphs into subgraphs using the 1-hop method. Proteins with functional similarities in a species were detected using a method of modified shortest path to compare these subgraphs and to find the eligible optimal results. Using seven protein-protein interaction networks and this method, some functionally similar proteins with low sequence similarity that cannot detected by sequence alignment were identified. By analyzing the results, we found that, sometimes, it is difficult to separate homologous from convergent evolution. Evaluation of the performance of our method by gene ontology term overlap showed that the precision of our method was excellent. Copyright © 2012 Wiley Periodicals, Inc.

  19. Scoring protein relationships in functional interaction networks predicted from sequence data.

    Directory of Open Access Journals (Sweden)

    Gaston K Mazandu

    Full Text Available UNLABELLED: The abundance of diverse biological data from various sources constitutes a rich source of knowledge, which has the power to advance our understanding of organisms. This requires computational methods in order to integrate and exploit these data effectively and elucidate local and genome wide functional connections between protein pairs, thus enabling functional inferences for uncharacterized proteins. These biological data are primarily in the form of sequences, which determine functions, although functional properties of a protein can often be predicted from just the domains it contains. Thus, protein sequences and domains can be used to predict protein pair-wise functional relationships, and thus contribute to the function prediction process of uncharacterized proteins in order to ensure that knowledge is gained from sequencing efforts. In this work, we introduce information-theoretic based approaches to score protein-protein functional interaction pairs predicted from protein sequence similarity and conserved protein signature matches. The proposed schemes are effective for data-driven scoring of connections between protein pairs. We applied these schemes to the Mycobacterium tuberculosis proteome to produce a homology-based functional network of the organism with a high confidence and coverage. We use the network for predicting functions of uncharacterised proteins. AVAILABILITY: Protein pair-wise functional relationship scores for Mycobacterium tuberculosis strain CDC1551 sequence data and python scripts to compute these scores are available at http://web.cbio.uct.ac.za/~gmazandu/scoringschemes.

  20. A nonorthogonal state-interaction approach for matrix product state wave functions

    CERN Document Server

    Knecht, Stefan; Autschbach, Jochen; Reiher, Markus

    2016-01-01

    We present a state-interaction approach for matrix product state (MPS) wave functions in a nonorthogonal molecular orbital basis. Our approach allows us to calculate for example transition and spin-orbit coupling matrix elements between arbitrary electronic states provided that they share the same one-electron basis functions and active orbital space, respectively. The key element is the transformation of the MPS wave functions of different states from a nonorthogonal to a biorthonormal molecular orbital basis representation exploiting a sequence of non-unitary transformations following a proposal by Malmqvist (Int. J. Quantum Chem. 30, 479 (1986)). This is well-known for traditional wave-function parametrizations but has not yet been exploited for MPS wave functions.

  1. New parameterization of Skyrme's interaction for regularized multi-reference energy density functional calculations

    CERN Document Server

    Washiyama, K; Avez, B; Bender, M; Heenen, P -H; Hellemans, V

    2012-01-01

    [Background] Symmetry restoration and configuration mixing in the spirit of the generator coordinate method based on energy density functionals have become widely used techniques in low-energy nuclear structure physics. Recently, it has been pointed out that these techniques are ill-defined for standard Skyrme functionals, and a regularization procedure has been proposed to remove the resulting spuriosities from such calculations. This procedure imposes an integer power of the density for the density dependent terms of the functional. At present, only dated parameterizations of the Skyrme interaction fulfill this condition. [Purpose] To construct a set of parameterizations of the Skyrme energy density functional for multi-reference energy density functional calculations with regularization using the state-of-the-art fitting protocols. [Method] The parameterizations were adjusted to reproduce ground state properties of a selected set of doubly magic nuclei and properties of nuclear matter. Subsequently, these ...

  2. Interactions of human hemoglobin with charged ligand-functionalized iron oxide nanoparticles and effect of counterions

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Goutam, E-mail: ghoshg@yahoo.com [UGC-DAE Consortium for Scientific Research, Mumbai Centre (India); Panicker, Lata [Bhabha Atomic Research Centre, Solid State Physics Division (India)

    2014-12-15

    Human hemoglobin is an important metalloprotein. It has tetrameric structure with each subunit containing a ‘heme’ group which carries oxygen and carbon dioxide in blood. In this work, we have investigated the interactions of human hemoglobin (Hb) with charged ligand-functionalized iron oxide nanoparticles and the effect of counterions, in aqueous medium. Several techniques like DLS and ζ-potential measurements, UV–vis, fluorescence, and CD spectroscopy have been used to characterize the interaction. The nanoparticle size was measured to be in the range of 20–30 nm. Our results indicated the binding of Hb with both positively as well as negatively charged ligand-functionalized iron oxide nanoparticles in neutral aqueous medium which was driven by the electrostatic and the hydrophobic interactions. The electrostatic binding interaction was not seen in phosphate buffer at pH 7.4. We have also observed that the ‘heme’ groups of Hb remained unaffected on binding with charged nanoparticles, suggesting the utility of the charged ligand-functionalized nanoparticles in biomedical applications.

  3. Conformational transitions and interactions underlying the function of membrane embedded receptor protein kinases.

    Science.gov (United States)

    Bocharov, Eduard V; Sharonov, Georgy V; Bocharova, Olga V; Pavlov, Konstantin V

    2017-01-25

    Among membrane receptors, the single-span receptor protein kinases occupy a broad but specific functional niche determined by distinctive features of the underlying transmembrane signaling mechanisms that are briefly overviewed on the basis of some of the most representative examples, followed by a more detailed discussion of several hierarchical levels of organization and interactions involved. All these levels, including single-molecule interactions (e.g., dimerization, liganding, chemical modifications), local processes (e.g. lipid membrane perturbations, cytoskeletal interactions), and larger scale phenomena (e.g., effects of membrane surface shape or electrochemical potential gradients) appear to be closely integrated to achieve the observed diversity of the receptor functioning. Different species of receptor protein kinases meet their specific functional demands through different structural features defining their responses to stimulation, but certain common patterns exist. Signaling by receptor protein kinases is typically associated with the receptor dimerization and clustering, ligand-induced rearrangements of receptor domains through allosteric conformational transitions with involvement of lipids, release of the sequestered lipids, restriction of receptor diffusion, cytoskeleton and membrane shape remodeling. Understanding of complexity and continuity of the signaling processes can help identifying currently neglected opportunities for influencing the receptor signaling with potential therapeutic implications. This article is part of a Special Issue entitled: Interactions between membrane receptors in cellular membranes edited by Kalina Hristova.

  4. Proteomic analysis of FUS interacting proteins provides insights into FUS function and its role in ALS.

    Science.gov (United States)

    Kamelgarn, Marisa; Chen, Jing; Kuang, Lisha; Arenas, Alexandra; Zhai, Jianjun; Zhu, Haining; Gal, Jozsef

    2016-10-01

    Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease. Mutations in the Fused in Sarcoma/Translocated in Liposarcoma (FUS/TLS) gene cause a subset of familial ALS cases and are also implicated in sporadic ALS. FUS is typically localized to the nucleus. The ALS-related FUS mutations cause cytoplasmic mis-localization and the formation of stress granule-like structures. Abnormal cytoplasmic FUS localization was also found in a subset of frontotemporal dementia (FTLD) cases without FUS mutations. To better understand the function of FUS, we performed wild-type and mutant FUS pull-downs followed by proteomic identification of the interacting proteins. The FUS interacting partners we identified are involved in multiple pathways, including chromosomal organization, transcription, RNA splicing, RNA transport, localized translation, and stress response. FUS interacted with hnRNPA1 and Matrin-3, RNA binding proteins whose mutations were also reported to cause familial ALS, suggesting that hnRNPA1 and Matrin-3 may play common pathogenic roles with FUS. The FUS interactions displayed varied RNA dependence. Numerous FUS interacting partners that we identified are components of exosomes. We found that FUS itself was present in exosomes, suggesting that the secretion of FUS might contribute to the cell-to-cell spreading of FUS pathology. FUS interacting proteins were sequestered into the cytoplasmic mutant FUS inclusions that could lead to their mis-regulation or loss of function, contributing to ALS pathogenesis. Our results provide insights into the physiological functions of FUS as well as important pathways where mutant FUS can interfere with cellular processes and potentially contribute to the pathogenesis of ALS.

  5. A molecular dynamics study on the interaction between epoxy and functionalized graphene sheets

    Science.gov (United States)

    Melro, L. S.; Pyrz, R.; Jensen, L. R.

    2016-07-01

    The interaction between graphene and epoxy resin was studied using molecular dynamics simulations. The interfacial shear strength and pull out force were calculated for functionalised graphene layers (carboxyl, carbonyl, and hydroxyl) and epoxy composites interfaces. The influence of functional groups, as well as their distribution and coverage density on the graphene sheets were also analysed through the determination of the Young's modulus. Functionalisation proved to be detrimental to the mechanical properties, nonetheless according to interfacial studies the interaction between graphene and epoxy resin increases.

  6. Dynamic circadian protein-protein interaction networks predict temporal organization of cellular functions.

    Directory of Open Access Journals (Sweden)

    Thomas Wallach

    2013-03-01

    Full Text Available Essentially all biological processes depend on protein-protein interactions (PPIs. Timing of such interactions is crucial for regulatory function. Although circadian (~24-hour clocks constitute fundamental cellular timing mechanisms regulating important physiological processes, PPI dynamics on this timescale are largely unknown. Here, we identified 109 novel PPIs among circadian clock proteins via a yeast-two-hybrid approach. Among them, the interaction of protein phosphatase 1 and CLOCK/BMAL1 was found to result in BMAL1 destabilization. We constructed a dynamic circadian PPI network predicting the PPI timing using circadian expression data. Systematic circadian phenotyping (RNAi and overexpression suggests a crucial role for components involved in dynamic interactions. Systems analysis of a global dynamic network in liver revealed that interacting proteins are expressed at similar times likely to restrict regulatory interactions to specific phases. Moreover, we predict that circadian PPIs dynamically connect many important cellular processes (signal transduction, cell cycle, etc. contributing to temporal organization of cellular physiology in an unprecedented manner.

  7. Polynomial scaling approximations and dynamic correlation corrections to doubly occupied configuration interaction wave functions.

    Science.gov (United States)

    Van Raemdonck, Mario; Alcoba, Diego R; Poelmans, Ward; De Baerdemacker, Stijn; Torre, Alicia; Lain, Luis; Massaccesi, Gustavo E; Van Neck, Dimitri; Bultinck, Patrick

    2015-09-14

    A class of polynomial scaling methods that approximate Doubly Occupied Configuration Interaction (DOCI) wave functions and improve the description of dynamic correlation is introduced. The accuracy of the resulting wave functions is analysed by comparing energies and studying the overlap between the newly developed methods and full configuration interaction wave functions, showing that a low energy does not necessarily entail a good approximation of the exact wave function. Due to the dependence of DOCI wave functions on the single-particle basis chosen, several orbital optimisation algorithms are introduced. An energy-based algorithm using the simulated annealing method is used as a benchmark. As a computationally more affordable alternative, a seniority number minimising algorithm is developed and compared to the energy based one revealing that the seniority minimising orbital set performs well. Given a well-chosen orbital basis, it is shown that the newly developed DOCI based wave functions are especially suitable for the computationally efficient description of static correlation and to lesser extent dynamic correlation.

  8. Increasing metagenomic resolution of microbiome interactions through functional phylogenomics and bacterial sub-communities

    Directory of Open Access Journals (Sweden)

    Angélica eCibrián-Jaramillo

    2016-02-01

    Full Text Available The genomic composition of the microbiome and its relationship with the environment is an exciting open question in biology. Metagenomics is a useful tool in the discovery of previously unknown taxa, but its use to understand the functional and ecological capacities of the microbiome is limited until taxonomy and function are understood in the context of the community. We suggest that this can be achieved using a combined functional phylogenomics and co-culture-based experimental strategy that can increase our capacity to measure sub-community interactions. Functional phylogenomics can identify and partition the genome such that hidden gene functions and gene clusters with unique evolutionary signals are revealed. We can test these phylogenomic predictions using an experimental model based on sub-community populations that represent a subset of the diversity directly obtained from environmental samples. These populations increase the detection of mechanisms that drive functional forces in the assembly of the microbiome, in particular the role of metabolites from keystone taxa in community interactions. Our combined approach leverages the potential of metagenomics to address biological questions from ecological systems.

  9. FunPred-1: protein function prediction from a protein interaction network using neighborhood analysis.

    Science.gov (United States)

    Saha, Sovan; Chatterjee, Piyali; Basu, Subhadip; Kundu, Mahantapas; Nasipuri, Mita

    2014-12-01

    Proteins are responsible for all biological activities in living organisms. Thanks to genome sequencing projects, large amounts of DNA and protein sequence data are now available, but the biological functions of many proteins are still not annotated in most cases. The unknown function of such non-annotated proteins may be inferred or deduced from their neighbors in a protein interaction network. In this paper, we propose two new methods to predict protein functions based on network neighborhood properties. FunPred 1.1 uses a combination of three simple-yet-effective scoring techniques: the neighborhood ratio, the protein path connectivity and the relative functional similarity. FunPred 1.2 applies a heuristic approach using the edge clustering coefficient to reduce the search space by identifying densely connected neighborhood regions. The overall accuracy achieved in FunPred 1.2 over 8 functional groups involving hetero-interactions in 650 yeast proteins is around 87%, which is higher than the accuracy with FunPred 1.1. It is also higher than the accuracy of many of the state-of-the-art protein function prediction methods described in the literature. The test datasets and the complete source code of the developed software are now freely available at http://code.google.com/p/cmaterbioinfo/ .

  10. Molecular Level Characterization of the Structure and Interactions in Peptide-Functionalized Metal-Organic Frameworks.

    Science.gov (United States)

    Todorova, Tanya K; Rozanska, Xavier; Gervais, Christel; Legrand, Alexandre; Ho, Linh N; Berruyer, Pierrick; Lesage, Anne; Emsley, Lyndon; Farrusseng, David; Canivet, Jérôme; Mellot-Draznieks, Caroline

    2016-11-07

    We use density functional theory, newly parameterized molecular dynamics simulations, and last generation (15) N dynamic nuclear polarization surface enhanced solid-state NMR spectroscopy (DNP SENS) to understand graft-host interactions and effects imposed by the metal-organic framework (MOF) host on peptide conformations in a peptide-functionalized MOF. Focusing on two grafts typified by MIL-68-proline (-Pro) and MIL-68-glycine-proline (-Gly-Pro), we identified the most likely peptide conformations adopted in the functionalized hybrid frameworks. We found that hydrogen bond interactions between the graft and the surface hydroxyl groups of the MOF are essential in determining the peptides conformation(s). DNP SENS methodology shows unprecedented signal enhancements when applied to these peptide-functionalized MOFs. The calculated chemical shifts of selected MIL-68-NH-Pro and MIL-68-NH-Gly-Pro conformations are in a good agreement with the experimentally obtained (15) N NMR signals. The study shows that the conformations of peptides when grafted in a MOF host are unlikely to be freely distributed, and conformational selection is directed by strong host-guest interactions. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Species interactions regulate the collapse of biodiversity and ecosystem function in tropical forest fragments.

    Science.gov (United States)

    Bregman, Tom P; Lees, Alexander C; Seddon, Nathalie; Macgregor, Hannah E A; Darski, Bianca; Aleixo, Alexandre; Bonsall, Michael B; Tobias, Joseph A

    2015-10-01

    Competitive interactions among species with similar ecological niches are known to regulate the assembly of biological communities. However, it is not clear whether such forms of competition can predict the collapse of communities and associated shifts in ecosystem function in the face of environmental change. Here, we use phylogenetic and functional trait data to test whether communities of two ecologically important guilds of tropical birds (frugivores and insectivores) are structured by species interactions in a fragmented Amazonian forest landscape. In both guilds, we found that forest patch size, quality, and degree of isolation influence the phylogenetic and functional trait structure of communities, with small, degraded, or isolated forest patches having an increased signature of competition (i.e., phylogenetic and functional trait overdispersion in relation to null models). These results suggest that local extinctions in the context of fragmentation are nonrandom, with a consistent bias toward more densely occupied regions of niche space. We conclude that the loss of biodiversity in fragmented landscapes is mediated by niche-based competitive interactions among species, with potentially far-reaching implications for key ecosystem processes, including seed dispersal and plant damage by phytophagous insects.

  12. Parkin functionally interacts with PGC-1α to preserve mitochondria and protect dopaminergic neurons.

    Science.gov (United States)

    Zheng, Lu; Bernard-Marissal, Nathalie; Moullan, Norman; D'Amico, Davide; Auwerx, Johan; Moore, Darren J; Knott, Graham; Aebischer, Patrick; Schneider, Bernard L

    2017-02-01

    To understand the cause of Parkinson's disease (PD), it is important to determine the functional interactions between factors linked to the disease. Parkin is associated with autosomal recessive early-onset PD, and controls the transcription of PGC-1α, a master regulator of mitochondrial biogenesis. These two factors functionally interact to regulate the turnover and quality of mitochondria, by increasing both mitophagic activity and mitochondria biogenesis. In cortical neurons, co-expressing PGC-1α and Parkin increases the number of mitochondria, enhances maximal respiration, and accelerates the recovery of the mitochondrial membrane potential following mitochondrial uncoupling. PGC-1α enhances Mfn2 transcription, but also leads to increased degradation of the Mfn2 protein, a key ubiquitylation target of Parkin on mitochondria. In vivo, Parkin has significant protective effects on the survival and function of nigral dopaminergic neurons in which the chronic expression of PGC-1α is induced. Ultrastructural analysis shows that these two factors together control the density of mitochondria and their interaction with the endoplasmic reticulum. These results highlight the combined effects of Parkin and PGC-1α in the maintenance of mitochondrial homeostasis in dopaminergic neurons. These two factors synergistically control the quality and function of mitochondria, which is important for the survival of neurons in Parkinson's disease. © The Authors 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  13. Emerging functions as host cell factors - an encyclopedia of annexin-pathogen interactions.

    Science.gov (United States)

    Kuehnl, Alexander; Musiol, Agnes; Raabe, Carsten A; Rescher, Ursula

    2016-10-01

    Emerging infectious diseases and drug-resistant infectious agents call for the development of innovative antimicrobial strategies. With pathogenicity now considered to arise from the complex and bi-directional interplay between a microbe and the host, host cell factor targeting has emerged as a promising approach that might overcome the limitations of classical antimicrobial drug development and could open up novel and efficient therapeutic strategies. Interaction with and modulation of host cell membranes is a recurrent theme in the host-microbe relationship. In this review, we provide an overview of what is currently known about the role of the Ca2+ dependent, membrane-binding annexin protein family in pathogen-host interactions, and discuss their emerging functions as host cell derived auxiliary proteins in microbe-host interactions and host cell targets.

  14. Dispersion-corrected density functional theory for aromatic interactions in complex systems.

    Science.gov (United States)

    Ehrlich, Stephan; Moellmann, Jonas; Grimme, Stefan

    2013-04-16

    Aromatic interactions play a key role in many chemical and biological systems. However, even if very simple models are chosen, the systems of interest are often too large to be handled with standard wave function theory (WFT). Although density functional theory (DFT) can easily treat systems of more than 200 atoms, standard semilocal (hybrid) density functional approximations fail to describe the London dispersion energy, a factor that is essential for accurate predictions of inter- and intramolecular noncovalent interactions. Therefore dispersion-corrected DFT provides a unique tool for the investigation and analysis of a wide range of complex aromatic systems. In this Account, we start with an analysis of the noncovalent interactions in simple model dimers of hexafluorobenzene (HFB) and benzene, with a focus on electrostatic and dispersion interactions. The minima for the parallel-displaced dimers of HFB/HFB and HFB/benzene can only be explained when taking into account all contributions to the interaction energy and not by electrostatics alone. By comparison of saturated and aromatic model complexes, we show that increased dispersion coefficients for sp(2)-hybridized carbon atoms play a major role in aromatic stacking. Modern dispersion-corrected DFT yields accurate results (about 5-10% error for the dimerization energy) for the relatively large porphyrin and coronene dimers, systems for which WFT can provide accurate reference data only with huge computational effort. In this example, it is also demonstrated that new nonlocal, density-dependent dispersion corrections and atom pairwise schemes mutually agree with each other. The dispersion energy is also important for the complex inter- and intramolecular interactions that arise in the molecular crystals of aromatic molecules. In studies of hexahelicene, dispersion-corrected DFT yields "the right answer for the right reason". By comparison, standard DFT calculations reproduce intramolecular distances quite

  15. A Partitioned Correlation Function Interaction approach for describing electron correlation in atoms

    CERN Document Server

    Verdebout, S; Jönsson, P; Gaigalas, G; Fischer, C Froese; Godefroid, M

    2013-01-01

    Traditional multiconfiguration Hartree-Fock (MCHF) and configuration interaction (CI) methods are based on a single orthonormal orbital basis (OB). For atoms with complicated shell structures, a large OB is needed to saturate all the electron correlation effects. The large OB leads to massive configuration state function (CSF) expansions that are difficult to handle. We show that it is possible to relax the orthonormality restriction on the OB and break down the originally large calculations to a set of smaller ones that can be run in parallel. Each calculation determines a partitioned correlation function (PCF) that accounts for a specific correlation effect. The PCFs are built on optimally localized orbital sets and are added to a zero-order multireference (MR) function to form a total wave function. The mixing coefficients of the PCFs are fixed from a small generalized eigenvalue problem. The required matrices are computed using a biorthonormal transformation technique. The new method, called partitioned c...

  16. [Functional role of dragonfly legs before and after hatching: reorganization of coordinating interactions].

    Science.gov (United States)

    Sviderskiĭ, V L; Plotnikova, S I; Gorelkin, V S; Severina, I Iu; Isavnina, I L

    2012-11-01

    The characteristics of a structure-functional organization of leg apparatus were examined in the dragonfly Aeshna grandis: larvae of the final stadium, which legs perform a locomotion function and adults (imago) rising on a wing, which legs lose a locomotion function and are used mainly for catching a prey in the air. It has been demonstrated that legs of the imago practically do not differ from those of the larva either in shape or in proportion of segments of the leg and all changes in the functional role of legs of the imago are implemented due to modifications of mechanisms of limb muscle control and an appropriate reorganization or coordinating interactions. As it is proved by the obtained data, this reorganization concerns mechanisms of the generation of motor commands as well as close coordination of the activity of wing and leg apparatus and some others. The abovementioned mechanisms are discussed.

  17. Evidence for Heterodimerization and Functional Interaction of the Angiotensin Type 2 Receptor and the Receptor MAS

    DEFF Research Database (Denmark)

    Leonhardt, Julia; Steckelings, Ulrike Muscha

    2017-01-01

    The angiotensin type 2 receptor (AT2R) and the receptor MAS are receptors of the protective arm of the renin-angiotensin system. They mediate strikingly similar actions. Moreover, in various studies, AT2R antagonists blocked the effects of MAS agonists and vice versa. Such cross-inhibition may...... indicate heterodimerization of these receptors. Therefore, this study investigated the molecular and functional interplay between MAS and the AT2R. Molecular interactions were assessed by fluorescence resonance energy transfer and by cross correlation spectroscopy in human embryonic kidney-293 cells...... transfected with vectors encoding fluorophore-tagged MAS or AT2R. Functional interaction of AT2R and MAS was studied in astrocytes with CX3C chemokine receptor-1 messenger RNA expression as readout. Coexpression of fluorophore-tagged AT2R and MAS resulted in a fluorescence resonance energy transfer efficiency...

  18. Exact out-of-time-ordered correlation functions for an interacting lattice fermion model

    Science.gov (United States)

    Tsuji, Naoto; Werner, Philipp; Ueda, Masahito

    2017-01-01

    Exact solutions for local equilibrium and nonequilibrium out-of-time-ordered correlation (OTOC) functions are obtained for a lattice fermion model with on-site interactions, namely, the Falicov-Kimball (FK) model, in the large dimensional and thermodynamic limit. Our approach is based on the nonequilibrium dynamical mean-field theory generalized to an extended Kadanoff-Baym contour. We find that the density-density OTOC is most enhanced at intermediate coupling around the metal-insulator phase transition. In the high-temperature limit, the OTOC remains nontrivially finite and interaction dependent, even though dynamical charge correlations probed by an ordinary response function are completely suppressed. We propose an experiment to measure OTOCs of fermionic lattice systems including the FK and Hubbard models in ultracold atomic systems.

  19. Task-specific rehabilitation of finger-hand function using interactive computer gaming.

    Science.gov (United States)

    Szturm, Tony; Peters, James F; Otto, Chris; Kapadia, Naaz; Desai, Ankur

    2008-11-01

    The present case study assessed the feasibility of using an interactive gaming system, coupled with the manipulation of common objects, as a form of repetitive, task-specific movement therapy. Three adults with moderate chronic motor impairments of the fingers and hand participated: one 36-year-old man with an incomplete cervical spinal cord injury, one 60-year-old man with a left cortical cerebro-vascular accident, and one 38-year-old woman with left hemiplegic cerebral palsy. Each subject received an intervention of 15 one-hour sessions, which consisted solely of interactive exercise gaming using a diverse range of objects. The objects provided graded and challenging training levels, which emulated the functional properties of objects used in daily life. This in turn produced positive effects on the recovery of active finger range of motion and hand function.

  20. The Van der Waals interaction of the hydrogen molecule an exact local energy density functional

    CERN Document Server

    Choy, T C

    1999-01-01

    We verify that the van der Waals interaction and hence all dispersion interactions for the hydrogen molecule given by: W''= -{A/R^6}-{B/R^8}-{C/R^10}- ..., in which R is the internuclear separation, are exactly soluble. The constants A=6.4990267..., B=124.3990835 ... and C=1135.2140398... (in Hartree units) first obtained approximately by Pauling and Beach (PB) [1] using a linear variational method, can be shown to be obtainable to any desired accuracy via our exact solution. In addition we shall show that a local energy density functional can be obtained, whose variational solution rederives the exact solution for this problem. This demonstrates explicitly that a static local density functional theory exists for this system. We conclude with remarks about generalising the method to other hydrogenic systems and also to helium.

  1. Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Ashwani Kumar

    2016-01-01

    Full Text Available As antibiotic resistance is increasingly becoming a public health concern, an improved understanding of the bacterial DNA damage response (DDR, which is commonly targeted by antibiotics, could be of tremendous therapeutic value. Although the genetic components of the bacterial DDR have been studied extensively in isolation, how the underlying biological pathways interact functionally remains unclear. Here, we address this by performing systematic, unbiased, quantitative synthetic genetic interaction (GI screens and uncover widespread changes in the GI network of the entire genomic integrity apparatus of Escherichia coli under standard and DNA-damaging growth conditions. The GI patterns of untreated cultures implicated two previously uncharacterized proteins (YhbQ and YqgF as nucleases, whereas reorganization of the GI network after DNA damage revealed DDR roles for both annotated and uncharacterized genes. Analyses of pan-bacterial conservation patterns suggest that DDR mechanisms and functional relationships are near universal, highlighting a modular and highly adaptive genomic stress response.

  2. Effect of taurine and potential interactions with caffeine on cardiovascular function.

    Science.gov (United States)

    Schaffer, Stephen W; Shimada, Kayoko; Jong, Chian Ju; Ito, Takashi; Azuma, Junichi; Takahashi, Kyoko

    2014-05-01

    The major impetus behind the rise in energy drink popularity among adults is their ability to heighten mental alertness, improve physical performance and supply energy. However, accompanying the exponential growth in energy drink usage have been recent case reports and analyses from the National Poison Data System, raising questions regarding the safety of energy drinks. Most of the safety concerns have centered on the effect of energy drinks on cardiovascular and central nervous system function. Although the effects of caffeine excess have been widely studied, little information is available on potential interactions between the other active ingredients of energy drinks and caffeine. One of the active ingredients often mentioned as a candidate for interactions with caffeine is the beta-amino acid, taurine. Although taurine is considered a conditionally essential nutrient for humans and is thought to play a key role in several human diseases, clinical studies evaluating the effects of taurine are limited. However, based on this review regarding possible interactions between caffeine and taurine, we conclude that taurine should neutralize several untoward effects of caffeine excess. In agreement with this conclusion, the European Union's Scientific Committee on Food published a report in March 2003 summarizing its investigation into potential interactions of the ingredients in energy drinks. At the cardiovascular level, they concluded that "if there are any interactions between caffeine and taurine, taurine might reduce the cardiovascular effects of caffeine." Although these interactions remain to be further examined in humans, the physiological functions of taurine appear to be inconsistent with the adverse cardiovascular symptoms associated with excessive consumption of caffeine-taurine containing beverages.

  3. Functional interaction of Parkinson's disease-associated LRRK2 with members of the dynamin GTPase superfamily

    Science.gov (United States)

    Stafa, Klodjan; Tsika, Elpida; Moser, Roger; Musso, Alessandra; Glauser, Liliane; Jones, Amy; Biskup, Saskia; Xiong, Yulan; Bandopadhyay, Rina; Dawson, Valina L.; Dawson, Ted M.; Moore, Darren J.

    2014-01-01

    Mutations in LRRK2 cause autosomal dominant Parkinson's disease (PD). LRRK2 encodes a multi-domain protein containing GTPase and kinase domains, and putative protein–protein interaction domains. Familial PD mutations alter the GTPase and kinase activity of LRRK2 in vitro. LRRK2 is suggested to regulate a number of cellular pathways although the underlying mechanisms are poorly understood. To explore such mechanisms, it has proved informative to identify LRRK2-interacting proteins, some of which serve as LRRK2 kinase substrates. Here, we identify common interactions of LRRK2 with members of the dynamin GTPase superfamily. LRRK2 interacts with dynamin 1–3 that mediate membrane scission in clathrin-mediated endocytosis and with dynamin-related proteins that mediate mitochondrial fission (Drp1) and fusion (mitofusins and OPA1). LRRK2 partially co-localizes with endosomal dynamin-1 or with mitofusins and OPA1 at mitochondrial membranes. The subcellular distribution and oligomeric complexes of dynamin GTPases are not altered by modulating LRRK2 in mouse brain, whereas mature OPA1 levels are reduced in G2019S PD brains. LRRK2 enhances mitofusin-1 GTP binding, whereas dynamin-1 and OPA1 serve as modest substrates of LRRK2-mediated phosphorylation in vitro. While dynamin GTPase orthologs are not required for LRRK2-induced toxicity in yeast, LRRK2 functionally interacts with dynamin-1 and mitofusin-1 in cultured neurons. LRRK2 attenuates neurite shortening induced by dynamin-1 by reducing its levels, whereas LRRK2 rescues impaired neurite outgrowth induced by mitofusin-1 potentially by reversing excessive mitochondrial fusion. Our study elucidates novel functional interactions of LRRK2 with dynamin-superfamily GTPases that implicate LRRK2 in the regulation of membrane dynamics important for endocytosis and mitochondrial morphology. PMID:24282027

  4. Topological and functional properties of the small GTPases protein interaction network.

    Directory of Open Access Journals (Sweden)

    Anna Delprato

    Full Text Available Small GTP binding proteins of the Ras superfamily (Ras, Rho, Rab, Arf, and Ran regulate key cellular processes such as signal transduction, cell proliferation, cell motility, and vesicle transport. A great deal of experimental evidence supports the existence of signaling cascades and feedback loops within and among the small GTPase subfamilies suggesting that these proteins function in a coordinated and cooperative manner. The interplay occurs largely through association with bi-partite regulatory and effector proteins but can also occur through the active form of the small GTPases themselves. In order to understand the connectivity of the small GTPases signaling routes, a systems-level approach that analyzes data describing direct and indirect interactions was used to construct the small GTPases protein interaction network. The data were curated from the Search Tool for the Retrieval of Interacting Genes (STRING database and include only experimentally validated interactions. The network method enables the conceptualization of the overall structure as well as the underlying organization of the protein-protein interactions. The interaction network described here is comprised of 778 nodes and 1943 edges and has a scale-free topology. Rac1, Cdc42, RhoA, and HRas are identified as the hubs. Ten sub-network motifs are also identified in this study with themes in apoptosis, cell growth/proliferation, vesicle traffic, cell adhesion/junction dynamics, the nicotinamide adenine dinucleotide phosphate (NADPH oxidase response, transcription regulation, receptor-mediated endocytosis, gene silencing, and growth factor signaling. Bottleneck proteins that bridge signaling paths and proteins that overlap in multiple small GTPase networks are described along with the functional annotation of all proteins in the network.

  5. Effects of Interactive Function Forms in a Self-Organized Critical Model Based on Neural Networks

    Institute of Scientific and Technical Information of China (English)

    ZHAO Xiao-Wei; ZHOU Li-Ming; CHEN Tian-Lun

    2003-01-01

    Based on the standard self-organizing map neural network model and an integrate-and-fire mechanism, we introduce a kind of coupled map lattice system to investigate scale-invariance behavior in the activity of model neural populations. We let the parameter β, which together with α represents the interactive strength between neurons, have different function forms, and we find the function forms and their parameters are very important to our model's avalanche dynamical behaviors, especially to the emergence of different avalanche behaviors in different areas of our system.

  6. Effects of Interactive Function Forms in a Self-Organized Critical Model Based on Neural Networks

    Institute of Scientific and Technical Information of China (English)

    ZHAOXiao-Wei; ZHOULi-Ming; CHENTian-Lun

    2003-01-01

    Based on the standard self-organizing map neural network model and an integrate-and-fire mechanism, we introduce a kind of coupled map lattice system to investigate scale-invariance behavior in the activity of model neural populations. We let the parameter β, which together with α represents the interactive strength between neurons, have different function forms, and we find the function forms and their parameters are very important to our model''s avalanche dynamical behaviors, especially to the emergence of different avalanche behaviors in different areas of our system.

  7. A functional interaction between ribosomal proteins S7 and S11 within the bacterial ribosome.

    Science.gov (United States)

    Robert, Francis; Brakier-Gingras, Léa

    2003-11-01

    In this study, we used site-directed mutagenesis to disrupt an interaction that had been detected between ribosomal proteins S7 and S11 in the crystal structure of the bacterial 30 S subunit. This interaction, which is located in the E site, connects the head of the 30 S subunit to the platform and is involved in the formation of the exit channel through which passes the 30 S-bound messenger RNA. Neither mutations in S7 nor mutations in S11 prevented the incorporation of the proteins into the 30 S subunits but they perturbed the function of the ribosome. In vivo assays showed that ribosomes with either mutated S7 or S11 were altered in the control of translational fidelity, having an increased capacity for frameshifting, readthrough of a nonsense codon and codon misreading. Toeprinting and filter-binding assays showed that 30 S subunits with either mutated S7 or S11 have an enhanced capacity to bind mRNA. The effects of the S7 and S11 mutations can be related to an increased flexibility of the head of the 30 S, to an opening of the mRNA exit channel and to a perturbation of the proposed allosteric coupling between the A and E sites. Altogether, our results demonstrate that S7 and S11 interact in a functional manner and support the notion that protein-protein interactions contribute to the dynamics of the ribosome.

  8. A functional interaction between ATF7 and TAF12 that is modulated by TAF4.

    Science.gov (United States)

    Hamard, Pierre-Jacques; Dalbies-Tran, Rozenn; Hauss, Charlotte; Davidson, Irwin; Kedinger, Claude; Chatton, Bruno

    2005-05-12

    The ATF7 proteins, which are members of the cyclic AMP responsive binding protein (CREB)/activating transcription factor (ATF) family of transcription factors, display quite versatile properties: they can interact with the adenovirus E1a oncoprotein, mediating part of its transcriptional activity; they heterodimerize with the Jun, Fos or related transcription factors, likely modulating their DNA-binding specificity; they also recruit to the promoter a stress-induced protein kinase (JNK2). In the present study, we investigate the functional relationships of ATF7 with hsTAF12 (formerly hsTAF(II)20/15), which has originally been identified as a component of the general transcription factor TFIID. We show that overexpression of hsTAF12 potentiates ATF7-induced transcriptional activation through direct interaction with ATF7, suggesting that TAF12 is a functional partner of ATF7. In support of this conclusion, chromatin immunoprecipitation experiments confirm the interaction of ATF7 with TAF12 on an ATF7-responsive promoter, in the absence of any artificial overexpression of both proteins. We also show that the TAF12-dependent transcriptional activation is competitively inhibited by TAF4. Although both TAF12 isoforms (TAF12-1 and -2, formerly TAF(II)20 and TAF(II)15) interact with the ATF7 activation region through their histone-fold domain, only the largest, hsTAF12-1, mediates transcriptional activation through its N-terminal region.

  9. Insect antimicrobial peptides show potentiating functional interactions against Gram-negative bacteria.

    Science.gov (United States)

    Rahnamaeian, Mohammad; Cytryńska, Małgorzata; Zdybicka-Barabas, Agnieszka; Dobslaff, Kristin; Wiesner, Jochen; Twyman, Richard M; Zuchner, Thole; Sadd, Ben M; Regoes, Roland R; Schmid-Hempel, Paul; Vilcinskas, Andreas

    2015-05-01

    Antimicrobial peptides (AMPs) and proteins are important components of innate immunity against pathogens in insects. The production of AMPs is costly owing to resource-based trade-offs, and strategies maximizing the efficacy of AMPs at low concentrations are therefore likely to be advantageous. Here, we show the potentiating functional interaction of co-occurring insect AMPs (the bumblebee linear peptides hymenoptaecin and abaecin) resulting in more potent antimicrobial effects at low concentrations. Abaecin displayed no detectable activity against Escherichia coli when tested alone at concentrations of up to 200 μM, whereas hymenoptaecin affected bacterial cell growth and viability but only at concentrations greater than 2 μM. In combination, as little as 1.25 μM abaecin enhanced the bactericidal effects of hymenoptaecin. To understand these potentiating functional interactions, we investigated their mechanisms of action using atomic force microscopy and fluorescence resonance energy transfer-based quenching assays. Abaecin was found to reduce the minimal inhibitory concentration of hymenoptaecin and to interact with the bacterial chaperone DnaK (an evolutionarily conserved central organizer of the bacterial chaperone network) when the membrane was compromised by hymenoptaecin. These naturally occurring potentiating interactions suggest that combinations of AMPs could be used therapeutically against Gram-negative bacterial pathogens that have acquired resistance to common antibiotics.

  10. Electromagnetic semitransparent $\\delta$-function plate: Casimir interaction energy between parallel infinitesimally thin plates

    CERN Document Server

    Parashar, Prachi; Shajesh, K V; Schaden, M

    2012-01-01

    We derive boundary conditions for electromagnetic fields on a $\\delta$-function plate. The optical properties of such a plate are shown to necessarily be anisotropic in that they only depend on the transverse properties of the plate. We unambiguously obtain the boundary conditions for a perfectly conducting $\\delta$-function plate in the limit of infinite dielectric response. We show that a material does not "optically vanish" in the thin-plate limit. The thin-plate limit of a plasma slab of thickness $d$ with plasma frequency $\\omega_p^2=\\zeta_p/d$ reduces to a $\\delta$-function plate for frequencies ($\\omega=i\\zeta$) satisfying $\\zeta d \\ll \\sqrt{\\zeta_p d} \\ll 1$. We show that the Casimir interaction energy between two parallel perfectly conducting $\\delta$-function plates is the same as that for parallel perfectly conducting slabs. Similarly, we show that the interaction energy between an atom and a perfect electrically conducting $\\delta$-function plate is the usual Casimir-Polder energy, which is verifi...

  11. Microstructural Characterization of Alloy 617 Crept into the Tertiary Regime

    Energy Technology Data Exchange (ETDEWEB)

    Lillo, Thomas Martin [Idaho National Laboratory; Wright, Richard Neil [Idaho National Laboratory

    2015-07-01

    The microstructure of Alloy 617 was characterized following creep tests interrupted at total creep strains ranging from 2-20%. A range of creep temperatures (750-1000oC) and initial creep stresses (10-145 MPa) produced creep test durations ranging from 1 to 5800 hours. Image analysis of optical photomicrographs on longitudinal sections of the gage length was used to document the fraction of creep porosity as a function of creep parameters. Creep porosity was negligible below tertiary creep strains of 10% and increased with tertiary creep strain, thereafter. For a given temperature and total creep strain, creep porosity increased with decreasing creep stress. Creep porosity increased linearly with duration of the creep experiment. TEM performed on the gage sections did not reveal significant creep cavity formation on grain boundaries at the sub-micron level. It was concluded that the onset of tertiary creep did not result from creep cavitation and more likely arose due to the formation of low energy dislocation substructures with increasing tertiary strain.

  12. Aerobic exercise interacts with neurotrophic factors to predict cognitive functioning in adolescents.

    Science.gov (United States)

    Lee, Tatia M C; Wong, Mark Lawrence; Lau, Benson Wui-Man; Lee, Jada Chia-Di; Yau, Suk-Yu; So, Kwok-Fai

    2014-01-01

    Recent findings have suggested that aerobic exercise may have a positive effect on brain functioning, in addition to its well-recognized beneficial effects on human physiology. This study confirmed the cognitive effects of aerobic exercise on the human brain. It also examined the relationships between exercise and the serum levels of neurotrophic factors (BDNF, IGI-1, and VEGF). A total of 91 healthy teens who exercised regularly participated in this study. A between-group design was adopted to compare cognitive functioning subserved by the frontal and temporal brain regions and the serum levels of neurotrophic factors between 45 regular exercisers and 46 matched controls. The exercisers performed significantly better than the controls on the frontal and temporal functioning parameters measured. This beneficial cognitive effect was region-specific because no such positive cognitive effect on task-tapping occipital functioning was observed. With respect to the serum levels of the neurotrophic factors, a negative correlation between neurotrophic factors (BDNF and VEGF) with frontal and medial-temporal lobe function was revealed. Furthermore, the levels of BDNF and VEGF interacted with exercise status in predicting frontal and temporal lobe function. This is the first report of the interaction effects of exercise and neurotrophic factors on cognitive functioning. Herein, we report preliminary evidence of the beneficial effects of regular aerobic exercise in improving cognitive functions in teens. These beneficial effects are region-specific and are associated with the serum levels of neurotrophic factors. Our findings lay the path for future studies looking at ways to translate these beneficial effects to therapeutic strategies for adolescents.

  13. BDNF genotype interacts with motor-function to influence rehabilitation responsiveness post-stroke

    Directory of Open Access Journals (Sweden)

    Christine T Shiner

    2016-05-01

    Full Text Available Background. Persistent motor impairment is common but highly heterogeneous post-stroke. Genetic polymorphisms, including those identified on the brain derived neurotrophic factor (BDNF and apolipoprotein E (APOE genes, may contribute to this variability by limiting the capacity for use-dependent neuroplasticity, and hence rehabilitation responsiveness.Objective. To determine whether BDNF and APOE genotypes influence motor improvement facilitated by post-stroke upper-limb rehabilitation. Methods. BDNF Val66Met and APOE isoform genotypes were determined using leukocyte DNA for 55 community-dwelling patients 2-123 months post-stroke. All patients completed a dose-matched upper-limb rehabilitation program of either Wii-based Movement Therapy or Constraint-induced Movement Therapy. Upper-limb motor-function was assessed pre- and post-therapy using a suite of functional measures. Results. Motor-function improved for all patients post-therapy, with no difference between therapy groups. In the pooled data, there was no significant effect of BDNF or APOE genotype on motor-function at baseline, or following the intervention. However, a significant interaction between the level of residual motor-function and BDNF genotype was identified (p=0.029, whereby post-therapy improvement was significantly less for Met allele carriers with moderate and high, but not low motor-function. There was no significant association between APOE genotype and therapy outcomes. Conclusions. This study identified a novel interaction between the BDNF Val66Met polymorphism, motor-function status and the magnitude of improvement with rehabilitation in chronic stroke. This polymorphism does not preclude, but may reduce, the magnitude of motor improvement with therapy, particularly for patients with higher but not lower residual motor-function. BDNF genotype should be considered in the design and interpretation of clinical trials.

  14. Calculation of the matrix elements of the Coulomb interaction involving relativistic hydrogenic wave functions

    Science.gov (United States)

    Sarkadi, L.

    2017-03-01

    The program MTRDCOUL [1] calculates the matrix elements of the Coulomb interaction between a charged particle and an atomic electron, ∫ ψf∗ (r) ∣ R - r∣-1ψi(r) d r. Bound-free transitions are considered, and relativistic hydrogenic wave functions are used. In this revised version a bug discovered in the F3Y CPC Program Library subprogram [2] is fixed.

  15. PTPN14 interacts with and negatively regulates the oncogenic function of YAP

    OpenAIRE

    Liu, X; Yang, N; Figel, SA; Wilson, KE; Morrison, CD; Gelman, IH; Zhang, J

    2012-01-01

    The Hippo signaling pathway regulates cellular proliferation and survival, thus exerting profound effects on normal cell fate and tumorigenesis. The pivotal effector of this pathway is YAP, a transcriptional co-activator amplified in mouse and human cancers where it promotes epithelial-to-mesenchymal transition and malignant transformation. Here, we report a novel regulatory mechanism for the YAP oncogenic function via direct interaction with non-receptor tyrosine phosphatase 14 (PTPN14) thro...

  16. Van Hove correlation functions in an interacting electron gas: Equation-of-motion approach

    Science.gov (United States)

    Schinner, Andreas; Bachlechner, Martina E.

    1992-10-01

    An extension of the classical van Hove correlation functions to a three-dimensional system of identical fermions is investigated, taking into account interaction effects. This is done within the framework of a Singwi-Tosi-Land-Sjölander-like static local-field approximation, combined with second-order effects of plasmon damping. As a main result the relaxation of the Fermi hole around an instantaneously removed electron is presented.

  17. Forging the Basis for Developing Protein-Ligand Interaction Scoring Functions.

    Science.gov (United States)

    Liu, Zhihai; Su, Minyi; Han, Li; Liu, Jie; Yang, Qifan; Li, Yan; Wang, Renxiao

    2017-02-21

    In structure-based drug design, scoring functions are widely used for fast evaluation of protein-ligand interactions. They are often applied in combination with molecular docking and de novo design methods. Since the early 1990s, a whole spectrum of protein-ligand interaction scoring functions have been developed. Regardless of their technical difference, scoring functions all need data sets combining protein-ligand complex structures and binding affinity data for parametrization and validation. However, data sets of this kind used to be rather limited in terms of size and quality. On the other hand, standard metrics for evaluating scoring function used to be ambiguous. Scoring functions are often tested in molecular docking or even virtual screening trials, which do not directly reflect the genuine quality of scoring functions. Collectively, these underlying obstacles have impeded the invention of more advanced scoring functions. In this Account, we describe our long-lasting efforts to overcome these obstacles, which involve two related projects. On the first project, we have created the PDBbind database. It is the first database that systematically annotates the protein-ligand complexes in the Protein Data Bank (PDB) with experimental binding data. This database has been updated annually since its first public release in 2004. The latest release (version 2016) provides binding data for 16 179 biomolecular complexes in PDB. Data sets provided by PDBbind have been applied to many computational and statistical studies on protein-ligand interaction and various subjects. In particular, it has become a major data resource for scoring function development. On the second project, we have established the Comparative Assessment of Scoring Functions (CASF) benchmark for scoring function evaluation. Our key idea is to decouple the "scoring" process from the "sampling" process, so scoring functions can be tested in a relatively pure context to reflect their quality. In our

  18. rpanel: Simple Interactive Controls for R Functions Using the tcltk Package

    Directory of Open Access Journals (Sweden)

    Adrian Bowman

    2007-01-01

    Full Text Available In a variety of settings it is extremely helpful to be able to apply R functions through buttons, sliders and other types of graphical control. This is particularly true in plotting activities where immediate communication between such controls and a graphical display allows the user to interact with a plot in a very effective manner. The tcltk package provides extensive tools for this and the aim of the rpanel package is to provide simple and well documented functions which make these facilities as accessible as possible. In addition, the operations which form the basis of communication within tcltk are managed in a way which allows users to write functions with a more standard form of parameter passing. This paper describes the basic design of the software and illustrates it on a variety of examples of interactive control of graphics. The tkrplot system is used to allow plots to be integrated with controls into a single panel. An example of the use of a graphical image, and the ability to interact with this, is also discussed.

  19. rpanel: Simple Interactive Controls for R Functions Using the tcltk Package

    Directory of Open Access Journals (Sweden)

    Gavin Alexander

    2006-01-01

    Full Text Available In a variety of settings it is extremely helpful to be able to apply R functions through buttons, sliders and other types of graphical control. This is particularly true in plotting activities where immediate communication between such controls and a graphical display allows the user to interact with a plot in a very effective manner. The tcltk package provides extensive tools for this and the aim of the rpanel package is to provide simple and well documented functions which make these facilities as accessible as possible. In addition, the operations which form the basis of communication within tcltk are managed in a way which allows users to write functions with a more standard form of parameter passing. This paper describes the basic design of the software and illustrates it on a variety of examples of interactive control of graphics. The tkrplot system is used to allow plots to be integrated with controls into a single panel. An example of the use of a graphical image, and the ability to interact with this, is also discussed.

  20. Habitat structure, trophic structure and ecosystem function: interactive effects in a bromeliad-insect community.

    Science.gov (United States)

    Srivastava, Diane S

    2006-09-01

    Although previous studies have shown that ecosystem functions are affected by either trophic structure or habitat structure, there has been little consideration of their combined effects. Such interactions may be particularly important in systems where habitat and trophic structure covary. I use the aquatic insects in bromeliads to examine the combined effects of trophic structure and habitat structure on a key ecosystem function: detrital processing. In Costa Rican bromeliads, trophic structure naturally covaries with both habitat complexity and habitat size, precluding any observational analysis of interactions between factors. I therefore designed mesocosms that allowed each factor to be manipulated separately. Increases in mesocosm complexity reduced predator (damselfly larva) efficiency, resulting in high detritivore abundances, indirectly increasing detrital processing rates. However, increased complexity also directly reduced the per capita foraging efficiency of the detritivores. Over short time periods, these trends effectively cancelled each other out in terms of detrital processing. Over longer time periods, more complex patterns emerged. Increases in mesocosm size also reduced both predator efficiency and detritivore efficiency, leading to no net effect on detrital processing. In many systems, ecosystem functions may be impacted by strong interactions between trophic structure and habitat structure, cautioning against examining either effect in isolation.

  1. Integration of the Multi-DOA Estimation Functionality to Human-Robot Interaction

    Directory of Open Access Journals (Sweden)

    Caleb Rascon

    2015-02-01

    Full Text Available Sound source localization is important in human interaction, such as in locating the origin of long-distance calls or facing other humans while in a conversation. It is of interest to apply such functionality to the core of human-robot interaction (HRI and investigate its benefits, if any. In this paper, we propose three strategies for how to integrate the functionality of multiple directions-of-arrival (multi-DOA estimation with a common scenario, in which the robot acts as a waiter while applying audio source localization. The proposed strategies are: a the robot locates calls from users at a relatively long distance; b the robot faces the user when taking the order; and c the robot announces whether the acoustic environment is not conducive to understanding a speech command (mainly where more than one user speaks at once. It was seen that users react favourably to the functionality, and that it even has a noticeable influence on the success of the interaction.

  2. Aberrant intra-salience network dynamic functional connectivity impairs large-scale network interactions in schizophrenia.

    Science.gov (United States)

    Wang, Xiangpeng; Zhang, Wenwen; Sun, Yujing; Hu, Min; Chen, Antao

    2016-12-01

    Aberrant functional interactions between several large-scale networks, especially the central executive network (CEN), the default mode network (DMN) and the salience network (SN), have been postulated as core pathophysiologic features of schizophrenia; however, the attributing factors of which remain unclear. The study employed resting-state fMRI with 77 participants (42 patients and 35 controls). We performed dynamic functional connectivity (DFC) and functional connectivity (FC) analyses to explore the connectivity patterns of these networks. Furthermore, we performed a structural equation model (SEM) analysis to explore the possible role of the SN in modulating network interactions. The results were as follows: (1) The inter-network connectivity showed decreased connectivity strength and increased time-varying instability in schizophrenia; (2) The SN manifested schizophrenic intra-network dysfunctions in both the FC and DFC patterns; (3) The connectivity properties of the SN were effective in discriminating controls from patients; (4) In patients, the dynamic intra-SN connectivity negatively predicted the inter-network FC, and this effect was mediated by intra-SN connectivity strength. These findings suggest that schizophrenia show systematic deficits in temporal stability of large-scale network connectivity. Furthermore, aberrant network interactions in schizophrenia could be attributed to instable intra-SN connectivity and the dysfunction of the SN may be an intrinsic biomarker of the disease. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Self-Consistent Density Functional Including Long-Range van der Waals Interactions

    Science.gov (United States)

    Ferri, Nicola; Distasio, Robert A., Jr.; Car, Roberto; Scheffler, Matthias; Tkatchenko, Alexandre

    2013-03-01

    Van der Waals (vdW) interactions are significant for a wide variety of systems, from noble-gas dimers to organic/inorganic interfaces. The long-range vdW energy is a tiny fraction (0.001%) of the total energy, hence it is typically assumed not to change electronic properties. Although the vdW-DF functional includes the effect of vdW energy on electronic structure, the influence of ``true'' long-range vdW interactions is difficult to assess since a significant part of vdW-DF energy arises from short distances. Here, we present a self-consistent (SC) implementation of the long-range Tkatchenko-Scheffler (TS) functional, including its extension to surfaces. The analysis of self-consistency for rare-gas dimers allows us to reconcile two different views on vdW interactions: (i) Feynman's view that claims changes in the electron density and (ii) atoms separated by infinite barrier. In agreement with previous work, we find negligible contribution from self-consistency in the structure and stability of vdW-bound complexes. However, a closer look at organic/inorganic interfaces reveals notable modification of energy levels when using the SC-TS vdW density functional.

  4. Iloprost induces tertiary dentin formation.

    Science.gov (United States)

    Limjeerajarus, Chalida Nakalekha; Chanarattanubol, Thichaporn; Trongkij, Panruethai; Rujiwanichkul, Mirantee; Pavasant, Prasit

    2014-11-01

    Prostacyclin (PGI2), a member of the prostaglandin family, can promote angiogenesis and cell proliferation. In this study, the effect of the application of a PGI2 analog (iloprost) on dentin repair was examined in vitro and in vivo. Iloprost significantly stimulated the expression of vascular endothelial growth factor and osteo-/odontogenic marker messenger RNA in human dental pulp cells (HDPCs) under osteoinductive conditions in vitro. In addition, iloprost enhanced HDPC alkaline phosphatase enzymatic activity and mineral deposition. An in vivo study was performed using a rat molar mechanical pulp exposure model. After 30 days, histologic analysis revealed that there was a dramatic tertiary dentin formation in the iloprost-treated group compared with the calcium hydroxide and the untreated control groups. Furthermore, vascular endothelial growth factor protein expression in dental pulp tissue was increased in the iloprost-treated group as determined by immunohistochemical staining. Taken together, the present study, for the first time, shows that iloprost induces the expression of osteo-/odontogenic markers in vitro and promotes angiogenic factor expression and enhances tertiary dentin formation in vivo. This implies the potential clinical usefulness of iloprost in vital pulp therapy. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  5. Tertiary hypothyroidism in a dog

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    Shiel Robert E

    2007-02-01

    Full Text Available A nine-year-old male entire Labrador was diagnosed with pituitary dependent hyperadrenocorticism. Following seven months of successful mitotane therapy, the dog presented with marked weight gain, seborrhoea and alopecia. Routine clinicopathological analyses revealed marked hypercholesterolaemia. Serum total and free thyroxine (T4 concentrations were below their respective reference ranges. Serum thyroid stimulating hormone (cTSH concentration was within reference range. TSH and thyrotropin releasing hormone (TRH response tests revealed adequate stimulation of total T4 in both, and cTSH in the latter test. Magnetic resonance imaging revealed a mass arising from the pituitary fossa, with suprasellar extension. A diagnosis of tertiary hypothyroidism was made. Following four weeks of levothyroxine therapy, circulating cholesterol concentration had declined, weight loss had ensued and dermatological abnormalities had improved. Euthanasia was performed four months later due to the development of neurological signs. A highly infiltrative pituitary adenoma, with effacement of the overlying hypothalamus was identified on post mortem examination. Tertiary hypothyroidism has not been previously reported in dogs.

  6. Hypervalent Nonbonded Interactions of a Divalent Sulfur Atom. Implications in Protein Architecture and the Functions

    Directory of Open Access Journals (Sweden)

    Noriyoshi Isozumi

    2012-06-01

    Full Text Available In organic molecules a divalent sulfur atom sometimes adopts weak coordination to a proximate heteroatom (X. Such hypervalent nonbonded S···X interactions can control the molecular structure and chemical reactivity of organic molecules, as well as their assembly and packing in the solid state. In the last decade, similar hypervalent interactions have been demonstrated by statistical database analysis to be present in protein structures. In this review, weak interactions between a divalent sulfur atom and an oxygen or nitrogen atom in proteins are highlighted with several examples. S···O interactions in proteins showed obviously different structural features from those in organic molecules (i.e., πO → σS* versus nO → σS* directionality. The difference was ascribed to the HOMO of the amide group, which expands in the vertical direction (πO rather than in the plane (nO. S···X interactions in four model proteins, phospholipase A2 (PLA2, ribonuclease A (RNase A, insulin, and lysozyme, have also been analyzed. The results suggested that S···X interactions would be important factors that control not only the three-dimensional structure of proteins but also their functions to some extent. Thus, S···X interactions will be useful tools for protein engineering and the ligand design.

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

    Science.gov (United States)

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

    2015-10-22

    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.

  8. Local network topology in human protein interaction data predicts functional association.

    Directory of Open Access Journals (Sweden)

    Hua Li

    Full Text Available The use of high-throughput techniques to generate large volumes of protein-protein interaction (PPI data has increased the need for methods that systematically and automatically suggest functional relationships among proteins. In a yeast PPI network, previous work has shown that the local connection topology, particularly for two proteins sharing an unusually large number of neighbors, can predict functional association. In this study we improved the prediction scheme by developing a new algorithm and applied it on a human PPI network to make a genome-wide functional inference. We used the new algorithm to measure and reduce the influence of hub proteins on detecting function-associated protein pairs. We used the annotations of the Gene Ontology (GO and the Kyoto Encyclopedia of Genes and Genomes (KEGG as benchmarks to compare and evaluate the function relevance. The application of our algorithms to human PPI data yielded 4,233 significant functional associations among 1,754 proteins. Further functional comparisons between them allowed us to assign 466 KEGG pathway annotations to 274 proteins and 123 GO annotations to 114 proteins with estimated false discovery rates of <21% for KEGG and <30% for GO. We clustered 1,729 proteins by their functional associations and made functional inferences from detailed analysis on one subcluster highly enriched in the TGF-beta signaling pathway (P<10(-50. Analysis of another four subclusters also suggested potential new players in six signaling pathways worthy of further experimental investigations. Our study gives clear insight into the common neighbor-based prediction scheme and provides a reliable method for large-scale functional annotation in this post-genomic era.

  9. Revealing complex function, process and pathway interactions with high-throughput expression and biological annotation data.

    Science.gov (United States)

    Singh, Nitesh Kumar; Ernst, Mathias; Liebscher, Volkmar; Fuellen, Georg; Taher, Leila

    2016-10-20

    The biological relationships both between and within the functions, processes and pathways that operate within complex biological systems are only poorly characterized, making the interpretation of large scale gene expression datasets extremely challenging. Here, we present an approach that integrates gene expression and biological annotation data to identify and describe the interactions between biological functions, processes and pathways that govern a phenotype of interest. The product is a global, interconnected network, not of genes but of functions, processes and pathways, that represents the biological relationships within the system. We validated our approach on two high-throughput expression datasets describing organismal and organ development. Our findings are well supported by the available literature, confirming that developmental processes and apoptosis play key roles in cell differentiation. Furthermore, our results suggest that processes related to pluripotency and lineage commitment, which are known to be critical for development, interact mainly indirectly, through genes implicated in more general biological processes. Moreover, we provide evidence that supports the relevance of cell spatial organization in the developing liver for proper liver function. Our strategy can be viewed as an abstraction that is useful to interpret high-throughput data and devise further experiments.

  10. Changes in the Functional Properties of Three Starches by Interaction with Lima Bean Proteins

    Directory of Open Access Journals (Sweden)

    Alejandra Huerta-Abrego

    2010-01-01

    Full Text Available The functional properties of starches determine their potential applications in food systems. These properties depend largely on granular and molecular structure and can be physically, chemically or enzymatically modified. One way of modifying starch functional properties is by interaction with other food components, such as proteins. Starch-protein interactions are frequent in plant foods, particularly cereals and legumes, which are formed mainly of starches and proteins. An evaluation has been done of changes in the functional properties of three native starches (corn, Zea mays L.; cassava, Manihot esculenta; and lima bean, Phaseolus lunatus L. when blended with lima bean protein concentrate. The gelatinization temperature of each blend increased compared to its corresponding native starch. The cassava starch/lima bean protein blend had the highest overall swelling power and water absorption capacity values at all temperatures. Maximum viscosity for each blend was higher than for the corresponding native starches. The blends of lima bean protein with cassava and corn starches did not exhibit syneresis. The lima bean starch/lima bean protein blend had the highest gel firmness values, followed by the blends with corn and cassava starches. The protein-starch mixtures are an alternative in the improvement of the starch functional properties which are useful in the development of nutritional products.

  11. Fluorometric estimation of amino acids interaction with colloidal suspension of FITC functionalized graphene oxide nanoparticles

    Science.gov (United States)

    Dave, Kashyap; Dhayal, Marshal

    2017-02-01

    A hydrosol approach developed to synthesize fluorescence quenched fluorescein isothiocyanate (FITC) functionalized colloidal suspension of graphene oxide nanoparticles (GONP). UV-vis spectroscopic measurements showed characteristic peak at 236 nm and 300 nm due to pi-pi* interaction in Cdbnd C and n-pi* transition in Cdbnd O bond of GONP, respectively. Attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectra showed reduced intensity of 1429 cm-1 IR band of GONP due to the electrostatic and pi-pi interactions of FITC with GONP in FITC-GONP. ATR-FTIR spectra of different amino acid co-functionalised FITC-GONP showed an increase in the FTIR band intensity at 1429 cm-1 which was significantly reduced due to electrostatic/pi-pi interactions of FITC with GONP in the absence of the amino acids. A peak at 1084 cm-1 in ATR-FTIR spectra appears which confirms the interaction between amine group of amino acids and sbnd COO- groups at GONP surface. The FITC interaction with GONP lead to fluorescence resonance energy transfers (FRET) and resulted in a liner decrease in the FITC fluorescence with an increase of GONP concentration. An increase in the reappearance of FITC fluorescence observed while the amino acid concentration was increased in co-functionalised FITC-GONP. The quantified amount of reappeared fluorescence of FITC in amino acid co-functionalised FITC-GONP depends on the concentration, polar and non-polar nature of amino acids. The reappearance of FITC from the surface of FITC-GONP with the addition of amino acid was found to be consistent with the organic substitute, size of amino acids and their functionalities. Therefore, FRET based method using FITC-GONP colloidal suspension may have potential application in determining the binding nature of biomolecules with GONP for biomedical applications.

  12. Engaging Heterogeneity: Tertiary Literacy in New Times.

    Science.gov (United States)

    Hirst, Elizabeth Wyshe

    The "massification" of higher education in Australia and the associated increasing student diversity have significant implications for tertiary education. In particular, students seem to be struggling with the demands of tertiary literacy with commentators claiming that literacy standards are in decline. The solution has been to provide study…

  13. Nodular tertiary syphilis in an immunocompetent patient*

    Science.gov (United States)

    Bittencourt, Maraya de Jesus Semblano; de Brito, Arival Cardoso; Nascimento, Bianca Angelina Macêdodo; Carvalho, Alessandra Haber; Drago, Marion Guimarães

    2016-01-01

    Acquired syphilis can be divided into primary, secondary, latent, and tertiary stages. About 25% of patients with untreated primary syphilis will develop late signs that generally occur after three to five years, with involvement of several organs. The authors present an immunocompetent female who developed a tertiary stage syphilis presenting with long-standing nodular plaques. PMID:27579755

  14. Understanding Secondary-Tertiary Transition in Mathematics

    Science.gov (United States)

    Clark, Megan; Lovric, Miroslav

    2009-01-01

    In Clark and Lovric ("Suggestion for a theoretical model for secondary-tertiary transition in mathematics", "Math. Educ. Res. J." 20(2) (2008), pp. 25-37) we began developing a model for the secondary-tertiary transition in mathematics, based on the anthropological notion of a rite of passage. We articulated several reasons why we believe that the…

  15. Direct calculation of the lattice Green function with arbitrary interactions for general crystals.

    Science.gov (United States)

    Yasi, Joseph A; Trinkle, Dallas R

    2012-06-01

    Efficient computation of lattice defect geometries such as point defects, dislocations, disconnections, grain boundaries, interfaces, and free surfaces requires accurate coupling of displacements near the defect to the long-range elastic strain. Flexible boundary condition methods embed a defect in infinite harmonic bulk through the lattice Green function. We demonstrate an efficient and accurate calculation of the lattice Green function from the force-constant matrix for general crystals with an arbitrary basis by extending a method for Bravais lattices. New terms appear due to the presence of optical modes and the possible loss of inversion symmetry. By separately treating poles and discontinuities in reciprocal space, numerical accuracy is controlled at all distances. We compute the lattice Green function for a two-dimensional model with broken symmetry to elucidate the role of different coupling terms. The algorithm is generally applicable in two and three dimensions to crystals with arbitrary number of atoms in the unit cell, symmetry, and interactions.

  16. Surface functionalization of SPR chip for specific molecular interaction analysis under flow condition

    Directory of Open Access Journals (Sweden)

    Tao Ma

    2017-03-01

    Full Text Available Surface functionalization of sensor chip for probe immobilization is crucial for the biosensing applications of surface plasmon resonance (SPR sensors. In this paper, we report a method circulating the dopamine aqueous solution to coat polydopamine film on sensing surface for surface functionalization of SPR chip. The polydopamine film with available thickness can be easily prepared by controlling the circulation time and the biorecognition elements can be immobilized on the polydopamine film for specific molecular interaction analysis. These operations are all performed under flow condition in the fluidic system, and have the advantages of easy implementation, less time consuming, and low cost, because the reagents and devices used in the operations are routinely applied in most laboratories. In this study, the specific absorption between the protein A probe immobilized on the sensing surface and human immunoglobulin G in the buffer is monitored based on this surface functionalization strategy to demonstrated its feasibility for SPR biosensing applications.

  17. Rosetta stone method for detecting protein function and protein-protein interactions from genome sequences

    Science.gov (United States)

    Eisenberg, David; Marcotte, Edward M.; Pellegrini, Matteo; Thompson, Michael J.; Yeates, Todd O.

    2002-10-15

    A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A' and B' have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A' and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links.

  18. An efficient method for the preparation of tertiary esters by palladium-catalyzed alkoxycarbonylation of aryl bromides.

    Science.gov (United States)

    Xin, Zhuo; Gøgsig, Thomas M; Lindhardt, Anders T; Skrydstrup, Troels

    2012-01-06

    The palladium-catalyzed alkoxycarbonylation of aryl bromides is described for the efficient preparation of tertiary esters. The protocol proved compatible with a wide variety of functionalized (hetero)aromatic bromides, as well as several different sterically hindered tertiary alcohols, affording the alkoxycarbonylated products in high yields. Finally, the formation of aromatic trityl esters is discussed. © 2011 American Chemical Society

  19. I-mfa domain proteins specifically interact with SERTA domain proteins and repress their transactivating functions.

    Science.gov (United States)

    Kusano, Shuichi; Shiimura, Yuki; Eizuru, Yoshito

    2011-09-01

    The I-mfa domain proteins I-mfa and HIC are considered to be candidate tumor suppressor genes and have been shown to be involved in transcriptional regulation. We show here that I-mfa and HIC specifically interact with SEI-1 through their C-terminal I-mfa domains in vivo. This interaction affects the intracellular localization of I-mfa and requires the region of SEI-1 between 30 and 90 amino acids, which includes its SERTA domain, and results in repression of its intrinsic transcriptional activity. I-mfa also decreases the levels of the SEI-1·DP-1 complex and endogenous Fbxw7 mRNA, the expression of which is coregulated by E2F·DP-1 and SEI-1 in an interaction-dependent manner in vitro. In addition, I-mfa also specifically interacts with other SERTA domain-containing proteins, including SEI-2, SEI-3, SERTAD3 and SERTAD4, through its I-mfa domain in vivo. This interaction also affects the intracellular localization of I-mfa and represses the intrinsic transcriptional activities of SEI-2 and SERTAD3, which are also involved in the E2F-dependent transcription. These data reveal for the first time that I-mfa domain proteins interact with SERTA domain proteins and negatively regulate their transcriptional activity. Because SEI-1, SEI-2 and SERTAD3, whose intrinsic transcriptional activities are repressed by I-mfa, are suggested to be oncogenes, I-mfa domain proteins may be involved in their oncogenic functions by negatively regulating their transcriptional activities.

  20. Functional Divergence of Hsp90 Genetic Interactions in Biofilm and Planktonic Cellular States.

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    Stephanie Diezmann

    Full Text Available Candida albicans is among the most prevalent opportunistic fungal pathogens. Its capacity to cause life-threatening bloodstream infections is associated with the ability to form biofilms, which are intrinsically drug resistant reservoirs for dispersal. A key regulator of biofilm drug resistance and dispersal is the molecular chaperone Hsp90, which stabilizes many signal transducers. We previously identified 226 C. albicans Hsp90 genetic interactors under planktonic conditions, of which 56 are involved in transcriptional regulation. Six of these transcriptional regulators have previously been implicated in biofilm formation, suggesting that Hsp90 genetic interactions identified in planktonic conditions may have functional significance in biofilms. Here, we explored the relationship between Hsp90 and five of these transcription factor genetic interactors: BCR1, MIG1, TEC1, TUP1, and UPC2. We deleted each transcription factor gene in an Hsp90 conditional expression strain, and assessed biofilm formation and morphogenesis. Strikingly, depletion of Hsp90 conferred no additional biofilm defect in the mutants. An interaction was observed in which deletion of BCR1 enhanced filamentation upon reduction of Hsp90 levels. Further, although Hsp90 modulates expression of TEC1, TUP1, and UPC2 in planktonic conditions, it has no impact in biofilms. Lastly, we probed for physical interactions between Hsp90 and Tup1, whose WD40 domain suggests that it might interact with Hsp90 directly. Hsp90 and Tup1 formed a stable complex, independent of temperature or developmental state. Our results illuminate a physical interaction between Hsp90 and a key transcriptional regulator of filamentation and biofilm formation, and suggest that Hsp90 has distinct genetic interactions in planktonic and biofilm cellular states.

  1. Norepinephrine versus dopamine and their interaction in modulating synaptic function in the prefrontal cortex.

    Science.gov (United States)

    Xing, Bo; Li, Yan-Chun; Gao, Wen-Jun

    2016-06-15

    Among the neuromodulators that regulate prefrontal cortical circuit function, the catecholamine transmitters norepinephrine (NE) and dopamine (DA) stand out as powerful players in working memory and attention. Perturbation of either NE or DA signaling is implicated in the pathogenesis of several neuropsychiatric disorders, including attention deficit hyperactivity disorder (ADHD), post-traumatic stress disorder (PTSD), schizophrenia, and drug addiction. Although the precise mechanisms employed by NE and DA to cooperatively control prefrontal functions are not fully understood, emerging research indicates that both transmitters regulate electrical and biochemical aspects of neuronal function by modulating convergent ionic and synaptic signaling in the prefrontal cortex (PFC). This review summarizes previous studies that investigated the effects of both NE and DA on excitatory and inhibitory transmissions in the prefrontal cortical circuitry. Specifically, we focus on the functional interaction between NE and DA in prefrontal cortical local circuitry, synaptic integration, signaling pathways, and receptor properties. Although it is clear that both NE and DA innervate the PFC extensively and modulate synaptic function by activating distinctly different receptor subtypes and signaling pathways, it remains unclear how these two systems coordinate their actions to optimize PFC function for appropriate behavior. Throughout this review, we provide perspectives and highlight several critical topics for future studies. This article is part of a Special Issue entitled SI: Noradrenergic System. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Compact wave function for bond dissociation and Van der Waals interactions: A natural amplitude assessment

    CERN Document Server

    Giesbertz, K J H

    2014-01-01

    Electron correlations in molecules can be divided in short range dynamical correlations, long range Van der Waals type interactions and near degeneracy static correlations. In this work we analyze how these three types of correlations can be incorporated in a simple wave function of restricted functional form consisting of an orbital product multiplied by a single correlation function $f(r_{12})$ depending on the interelectronic distance $r_{12}$. Since the three types of correlations mentioned lead to different signatures in terms of the natural orbital (NO) amplitudes in two-electron systems we make an analysis of the wave function in terms of the NO amplitudes for a model system of a diatomic molecule. In our numerical implementation we fully optimize the orbitals and the correlation function on a spatial grid without restrictions on their functional form. For the model system we can prove that none of the amplitudes vanishes and moreover that it displays a distinct sign pattern and a series of avoided cro...

  3. Three-dimensional reconstructions come to life--interactive 3D PDF animations in functional morphology.

    Directory of Open Access Journals (Sweden)

    Thomas van de Kamp

    Full Text Available Digital surface mesh models based on segmented datasets have become an integral part of studies on animal anatomy and functional morphology; usually, they are published as static images, movies or as interactive PDF files. We demonstrate the use of animated 3D models embedded in PDF documents, which combine the advantages of both movie and interactivity, based on the example of preserved Trigonopterus weevils. The method is particularly suitable to simulate joints with largely deterministic movements due to precise form closure. We illustrate the function of an individual screw-and-nut type hip joint and proceed to the complex movements of the entire insect attaining a defence position. This posture is achieved by a specific cascade of movements: Head and legs interlock mutually and with specific features of thorax and the first abdominal ventrite, presumably to increase the mechanical stability of the beetle and to maintain the defence position with minimal muscle activity. The deterministic interaction of accurately fitting body parts follows a defined sequence, which resembles a piece of engineering.

  4. Three-dimensional reconstructions come to life--interactive 3D PDF animations in functional morphology.

    Science.gov (United States)

    van de Kamp, Thomas; dos Santos Rolo, Tomy; Vagovič, Patrik; Baumbach, Tilo; Riedel, Alexander

    2014-01-01

    Digital surface mesh models based on segmented datasets have become an integral part of studies on animal anatomy and functional morphology; usually, they are published as static images, movies or as interactive PDF files. We demonstrate the use of animated 3D models embedded in PDF documents, which combine the advantages of both movie and interactivity, based on the example of preserved Trigonopterus weevils. The method is particularly suitable to simulate joints with largely deterministic movements due to precise form closure. We illustrate the function of an individual screw-and-nut type hip joint and proceed to the complex movements of the entire insect attaining a defence position. This posture is achieved by a specific cascade of movements: Head and legs interlock mutually and with specific features of thorax and the first abdominal ventrite, presumably to increase the mechanical stability of the beetle and to maintain the defence position with minimal muscle activity. The deterministic interaction of accurately fitting body parts follows a defined sequence, which resembles a piece of engineering.

  5. A fast iterative-clique percolation method for identifying functional modules in protein interaction networks

    Institute of Scientific and Technical Information of China (English)

    Penggang SUN; Lin GAO

    2009-01-01

    Accumulating evidence suggests that biological systems are composed of interacting, separable, functional modules-groups of vertices within which connections are dense but between which they are sparse. Identifying these modules is likely through capturing the biologically mean-ingful interactions. In recent years, many algorithms have been developed for detecting such structures. These al-gorithms, however, are computationally demanding, which limits their applications. In this paper, we propose a fast iterative-clique percolation method (ICPM) for identifying overlapping functional modules in protein-protein interac-tion (PPI) networks. Our method is based on clique percola-tion method (CPM), and it not only considers the degree of nodes to minimize the search space (the vertices in k-cliques must have the degree of k - 1 at least), but also converts k-cliques to (k - 1)-cliques. It finds k-cliques by append-ing one node to (k - 1)-cliques. By testing our method on PPI networks, our analysis of the yeast PPI network suggeststhat most of these modules have well-supported biological significance.

  6. Genetic identification of a network of factors that functionally interact with the nucleosome remodeling ATPase ISWI.

    Directory of Open Access Journals (Sweden)

    Giosalba Burgio

    2008-06-01

    Full Text Available Nucleosome remodeling and covalent modifications of histones play fundamental roles in chromatin structure and function. However, much remains to be learned about how the action of ATP-dependent chromatin remodeling factors and histone-modifying enzymes is coordinated to modulate chromatin organization and transcription. The evolutionarily conserved ATP-dependent chromatin-remodeling factor ISWI plays essential roles in chromosome organization, DNA replication, and transcription regulation. To gain insight into regulation and mechanism of action of ISWI, we conducted an unbiased genetic screen to identify factors with which it interacts in vivo. We found that ISWI interacts with a network of factors that escaped detection in previous biochemical analyses, including the Sin3A gene. The Sin3A protein and the histone deacetylase Rpd3 are part of a conserved histone deacetylase complex involved in transcriptional repression. ISWI and the Sin3A/Rpd3 complex co-localize at specific chromosome domains. Loss of ISWI activity causes a reduction in the binding of the Sin3A/Rpd3 complex to chromatin. Biochemical analysis showed that the ISWI physically interacts with the histone deacetylase activity of the Sin3A/Rpd3 complex. Consistent with these findings, the acetylation of histone H4 is altered when ISWI activity is perturbed in vivo. These findings suggest that ISWI associates with the Sin3A/Rpd3 complex to support its function in vivo.

  7. Yeast mitochondrial protein-protein interactions reveal diverse complexes and disease-relevant functional relationships.

    Science.gov (United States)

    Jin, Ke; Musso, Gabriel; Vlasblom, James; Jessulat, Matthew; Deineko, Viktor; Negroni, Jacopo; Mosca, Roberto; Malty, Ramy; Nguyen-Tran, Diem-Hang; Aoki, Hiroyuki; Minic, Zoran; Freywald, Tanya; Phanse, Sadhna; Xiang, Qian; Freywald, Andrew; Aloy, Patrick; Zhang, Zhaolei; Babu, Mohan

    2015-02-06

    Although detailed, focused, and mechanistic analyses of associations among mitochondrial proteins (MPs) have identified their importance in varied biological processes, a systematic understanding of how MPs function in concert both with one another and with extra-mitochondrial proteins remains incomplete. Consequently, many questions regarding the role of mitochondrial dysfunction in the development of human disease remain unanswered. To address this, we compiled all existing mitochondrial physical interaction data for over 1200 experimentally defined yeast MPs and, through bioinformatic analysis, identified hundreds of heteromeric MP complexes having extensive associations both within and outside the mitochondria. We provide support for these complexes through structure prediction analysis, morphological comparisons of deletion strains, and protein co-immunoprecipitation. The integration of these MP complexes with reported genetic interaction data reveals substantial crosstalk between MPs and non-MPs and identifies novel factors in endoplasmic reticulum-mitochondrial organization, membrane structure, and mitochondrial lipid homeostasis. More than one-third of these MP complexes are conserved in humans, with many containing members linked to clinical pathologies, enabling us to identify genes with putative disease function through guilt-by-association. Although still remaining incomplete, existing mitochondrial interaction data suggests that the relevant molecular machinery is modular, yet highly integrated with non-mitochondrial processes.

  8. Proteoliposomes as Tool for Assaying Membrane Transporter Functions and Interactions with Xenobiotics

    Directory of Open Access Journals (Sweden)

    Annamaria Tonazzi

    2013-09-01

    Full Text Available Proteoliposomes represent a suitable and up to date tool for studying membrane transporters which physiologically mediate absorption, excretion, trafficking and reabsorption of nutrients and metabolites. Using recently developed reconstitution strategies, transporters can be inserted in artificial bilayers with the same orientation as in the cell membranes and in the absence of other interfering molecular systems. These methodologies are very suitable for studying kinetic parameters and molecular mechanisms. After the first applications on mitochondrial transporters, in the last decade, proteoliposomes obtained with optimized methodologies have been used for studying plasma membrane transporters and defining their functional and kinetic properties and structure/function relationships. A lot of information has been obtained which has clarified and completed the knowledge on several transporters among which the OCTN sub-family members, transporters for neutral amino acid, B0AT1 and ASCT2, and others. Transporters can mediate absorption of substrate-like derivatives or drugs, improving their bioavailability or can interact with these compounds or other xenobiotics, leading to side/toxic effects. Therefore, proteoliposomes have recently been used for studying the interaction of some plasma membrane and mitochondrial transporters with toxic compounds, such as mercurials, H2O2 and some drugs. Several mechanisms have been defined and in some cases the amino acid residues responsible for the interaction have been identified. The data obtained indicate proteoliposomes as a novel and potentially important tool in drug discovery.

  9. On the role of inter-nucleosomal interactions and intrinsic nucleosome dynamics in chromatin function

    Directory of Open Access Journals (Sweden)

    Wladyslaw A. Krajewski

    2016-03-01

    Full Text Available Evidence is emerging that many diseases result from defects in gene functions, which, in turn, depend on the local chromatin environment of a gene. However, it still remains not fully clear how chromatin activity code is ‘translated’ to the particular ‘activating’ or ‘repressing’ chromatin structural transition. Commonly, chromatin remodeling in vitro was studied using mononucleosomes as a model. However, recent data suggest that structural reorganization of a single mononucleosome is not equal to remodeling of a nucleosome particle under multinucleosomal content – such as, interaction of nucleosomes via flexible histone termini could significantly alter the mode (and the resulting products of nucleosome structural transitions. It is becoming evident that a nucleosome array does not constitute just a ‘polymer’ of individual ‘canonical’ nucleosomes due to multiple inter-nucleosomal interactions which affect nucleosome dynamics and structure. It could be hypothesized, that inter-nucleosomal interactions could act in cooperation with nucleosome inherent dynamics to orchestrate DNA-based processes and promote formation and stabilization of highly-dynamic, accessible structure of a nucleosome array. In the proposed paper we would like to discuss the nucleosome dynamics within the chromatin fiber mainly as it pertains to the roles of the structural changes mediated by inter-nucleosomal interactions.

  10. Interaction of boron with graphite: A van der Waals density functional study

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Juan; Wang, Chen [Beijing Key Lab of Fine Ceramics, Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing 100084 (China); Liang, Tongxiang, E-mail: txliang@tsinghua.edu.cn [State Key Lab of New Ceramic and Fine Processing, Tsinghua University, Beijing 100084 (China); Lai, Wensheng [Advanced Material Laboratory, School of Materials Science & Engineering, Tsinghua University, Beijing, 100084 (China)

    2016-08-30

    Highlights: • A van der Waals density-functional approach is applied to study the interaction of boron with graphite. • VdW-DF functionals give fair agreement of crystal parameters with experiments. • The π electron approaches boron while adsorbing on graphite surface. • The hole introduced by boron mainly concentrates on boron and the nearest three carbon atoms. • PBE cannot describe the interstitial boron in graphite because of the ignoring binding of graphite sheets. - Abstract: Boron doping has been widely investigated to improve oxidation resistance of graphite. In this work the interaction of boron with graphite is investigated by a van der Waals density-functional approach (vdW-DF). The traditional density-functional theory (DFT) is well accounted for the binding in boron-substituted graphite. However, to investigate the boron atom on graphite surface and the interstitial impurities require use of a description of graphite interlayer binding. Traditional DFT cannot describe the vdW physics, for instance, GGA calculations show no relevant binding between graphite sheets. LDA shows some binding, but they fail to provide an accurate account of vdW forces. In this paper, we compare the calculation results of graphite lattice constant and cohesive energy by several functionals, it shows that vdW-DF such as two optimized functionals optB88-vdW and optB86b-vdW give much improved results than traditional DFT. The vdW-DF approach is then applied to study the interaction of boron with graphite. Boron adsorption, substitution, and intercalation are discussed in terms of structural parameters and electronic structures. When adsorbing on graphite surface, boron behaves as π electron acceptor. The π electron approaches boron atom because of more electropositive of boron than carbon. For substitution situation, the hole introduced by boron mainly concentrates on boron and the nearest three carbon atoms. The B-doped graphite system with the hole has less

  11. Using aqueous ammonia in hydroaminomethylation reactions: ruthenium-catalyzed synthesis of tertiary amines.

    Science.gov (United States)

    Wu, Lipeng; Fleischer, Ivana; Zhang, Min; Liu, Qiang; Franke, Robert; Jackstell, Ralf; Beller, Matthias

    2014-12-01

    The direct synthesis of tertiary amines from ammonia and olefins is presented. Using a combination of Ru3 (CO)12 and 2-phosphino-substituted imidazole ligand as catalyst system allows for hydroaminomethylation reactions of bulk aliphatic and functionalized olefins. Tertiary amines are obtained in an atom-efficient domino process in moderate to good isolated yields (45-76%) with excellent regioselectivities (n/iso up to 99:1).

  12. Interactions in 1-ethyl-3-methyl imidazolium tetracyanoborate ion pair: Spectroscopic and density functional study

    Energy Technology Data Exchange (ETDEWEB)

    Mao, James X.; Lee, Anita S.; Kitchin, John R.; Nulwala, Hunaid B.; Luebke, David R.; Damodaran, Krishnan

    2013-01-25

    Density Functional Theory is used to investigate a weakly coordinating room-temperature ionic liquid, 1-ethyl-3-methyl imidazolium tetracyanoborate ([Emim]{sup +}[TCB]{sup -}). Four locally stable conformers of the ion pair were located. Atoms-in-molecules (AIM) and electron density analysis indicated the existence of several hydrogen bonds. Further investigation through the Natural Bond Orbital (NBO) and Natural Energy Decomposition Analysis (NEDA) calculations provided insight into the origin of interactions in the [Emim]{sup +}[TCB]{sup -} ion pair. Strength of molecular interactions in the ionic liquid was correlated with frequency shifts of the characteristic vibrations of the ion pair. Harmonic vibrations of the ion pair were also compared with the experimental Raman and Infrared spectra. Vibrational frequencies were assigned by visualizing displacements of atoms around their equilibrium positions and through Potential Energy Distribution (PED) analysis.

  13. Specific features of 5S rRNA structure - its interactions with macromolecules and possible functions.

    Science.gov (United States)

    Smirnov, A V; Entelis, N S; Krasheninnikov, I A; Martin, R; Tarassov, I A

    2008-12-01

    Small non-coding RNAs are today a topic of great interest for molecular biologists because they can be regarded as relicts of a hypothetical "RNA world" which, apparently, preceded the modern stage of organic evolution on Earth. The small molecule of 5S rRNA (approximately 120 nucleotides) is a component of large ribosomal subunits of all living beings (5S rRNAs are not found only in mitoribosomes of fungi and metazoans). This molecule interacts with various protein factors and 23S (28S) rRNA. This review contains the accumulated data to date concerning 5S rRNA structure, interactions with other biological macromolecules, intracellular traffic, and functions in the cell.

  14. Density Functional Theory Study of the Interaction between Thymine and Luteolin

    Institute of Scientific and Technical Information of China (English)

    王晓岚; 蔡皖飞; 郑妍; 李来才; 田安民

    2012-01-01

    The density function B3LYP method has been used to optimize the geometries of the luteolin, thymine and lute- olin-thymine complexes at 6-31+G* basis. The vibrational frequencies have been studied at the same level to ana- lyze these seventeen complexes, respectively. Theories of atoms in molecules (AIM) and natural bond orbital (NBO) have been utilized to investigate the hydrogen bonds involved in all the systems. The interaction energies of the complexes corrected by basis set superposition error are between -93.00-76.69 kJ/mol. The calculating results indicate that strong hydrogen bonding interactions have been found in the luteolin-thymine complexes.

  15. Arabidopsis TWISTED DWARF1 functionally interacts with Auxin Exporter ABCB1 on the root plasma membrane

    DEFF Research Database (Denmark)

    Wang, Bangjun; Bailly, Aurélien; Zwiewka, Marta

    2013-01-01

    Plant architecture is influenced by the polar, cell-to-cell transport of auxin that is primarily provided and regulated by plasma membrane efflux catalysts of the PIN-FORMED and B family of ABC transporter (ABCB) classes. The latter were shown to require the functionality of the FK506 binding...... assays, we demonstrate a predominant lateral, mainly outward-facing, plasma membrane location for TWD1 in the root epidermis characterized by the lateral marker ABC transporter G36/PLEIOTROPIC DRUG-RESISTANCE8/PENETRATION3. At these epidermal plasma membrane domains, TWD1 colocalizes with nonpolar ABCB1....... In planta bioluminescence resonance energy transfer analysis was used to verify specific ABC transporter B1 (ABCB1)-TWD1 interaction. Our data support a model in which TWD1 promotes lateral ABCB-mediated auxin efflux via protein-protein interaction at the plasma membrane, minimizing reflux from the root...

  16. Solving the self-interaction problem in Kohn-Sham density functional theory: Application to atoms

    Science.gov (United States)

    Däne, M.; Gonis, A.; Nicholson, D. M.; Stocks, G. M.

    2015-04-01

    In previous work, we proposed a computational methodology that addresses the elimination of the self-interaction error from the Kohn-Sham formulation of the density functional theory. We demonstrated how the exchange potential can be obtained, and presented results of calculations for atomic systems up to Kr carried out within a Cartesian coordinate system. In this paper, we provide complete details of this self-interaction free method formulated in spherical coordinates based on the explicit equidensity basis ansatz. We prove analytically that derivatives obtained using this method satisfy the Virial theorem for spherical orbitals, where the problem can be reduced to one dimension. We present the results of calculations of ground-state energies of atomic systems throughout the periodic table carried out within the exchange-only mode.

  17. Interactions in 1-ethyl-3-methyl imidazolium tetracyanoborate ion pair: Spectroscopic and density functional study

    Energy Technology Data Exchange (ETDEWEB)

    Mao, James X; Lee, Anita S; Kitchin, John R; Nulwala, Hunaid B; Luebke, David R; Damodaran, Krishnan

    2013-04-24

    Density Functional Theory is used to investigate a weakly coordinating room-temperature ionic liquid, 1-ethyl-3-methyl imidazolium tetracyanoborate ([Emim]{sup +}[TCB]{sup -}). Four locally stable conformers of the ion pair were located. Atoms-in-molecules (AIM) and electron density analysis indicated the existence of several hydrogen bonds. Further investigation through the Natural Bond Orbital (NBO) and Natural Energy Decomposition Analysis (NEDA) calculations provided insight into the origin of interactions in the [Emim]{sup +}[TCB]{sup -} ion pair. Strength of molecular interactions in the ionic liquid was correlated with frequency shifts of the characteristic vibrations of the ion pair. Harmonic vibrations of the ion pair were also compared with the experimental Raman and Infrared spectra. Vibrational frequencies were assigned by visualizing displacements of atoms around their equilibrium positions and through Potential Energy Distribution (PED) analysis.

  18. Delineation of Polypharmacology across the Human Structural Kinome Using a Functional Site Interaction Fingerprint Approach.

    Science.gov (United States)

    Zhao, Zheng; Xie, Li; Xie, Lei; Bourne, Philip E

    2016-05-12

    Targeted polypharmacology of kinases has emerged as a promising strategy to design efficient and safe therapeutics. Here, we perform a systematic study of kinase-ligand binding modes for the human structural kinome at scale (208 kinases, 1777 unique ligands, and their complexes) by integrating chemical genomics and structural genomics data and by introducing a functional site interaction fingerprint (Fs-IFP) method. New insights into kinase-ligand binding modes were obtained. We establish relationships between the features of binding modes, the ligands, and the binding pockets, respectively. We also drive the intrinsic binding specificity and which correlation with amino acid conservation. Third, we explore the landscape of the binding modes and highlight the regions of "selectivity pocket" and "selectivity entrance". Finally, we demonstrate that Fs-IFP similarity is directly correlated to the experimentally determined profile. These improve our understanding of kinase-ligand interactions and contribute to the design of novel polypharmacological therapies targeting kinases.

  19. Connecting functional and statistical definitions of genotype by genotype interactions in coevolutionary studies

    Directory of Open Access Journals (Sweden)

    Katy Denise Heath

    2014-04-01

    Full Text Available Predicting how species interactions evolve requires that we understand the mechanistic basis of coevolution, and thus the functional genotype-by-genotype interactions (G × G that drive reciprocal natural selection. Theory on host-parasite coevolution provides testable hypotheses for empiricists, but depends upon models of functional G × G that remain loosely tethered to the molecular details of any particular system. In practice, reciprocal cross-infection studies are often used to partition the variation in infection or fitness in a population that is attributable to G × G (statistical G × G. Here we use simulations to demonstrate that within-population statistical G × G likely tells us little about the existence of coevolution, its strength, or the genetic basis of functional G × G. Combined with studies of multiple populations or points in time, mapping and molecular techniques can bridge the gap between natural variation and mechanistic models of coevolution, while model-based statistics can formally confront coevolutionary models with cross-infection data. Together these approaches provide a robust framework for inferring the infection genetics underlying statistical G × G, helping unravel the genetic basis of coevolution.

  20. Functional plant types drive plant interactions in a Mediterranean mountain range

    Directory of Open Access Journals (Sweden)

    Petr eMacek

    2016-05-01

    Full Text Available Shrubs have both positive (facilitation and negative (competition effects on understory plants, the net interaction effect being modulated by abiotic conditions. Overall shrubs influence to great extent the structure of plant communities where they have significant presence. Interactions in a plant community are quite diverse but little is known about their variability and effects at community level. Here we checked the effects of co-occurring shrub species from different functional groups on a focal understory species, determining mechanisms driving interaction outcome, and tested whether effects measured on the focal species were a proxy for effects measured at the community level. Growth, physiological, and reproductive traits of Euphorbia nicaeensis, our focal species, were recorded on individuals growing in association with four dominant shrub species and in adjacent open areas. We also recorded community composition and environmental conditions in each microhabitat.Shrubs provided environmental conditions for plant growth, which contrasted with open areas, including moister soil, greater N content, higher air temperatures, and lower radiation. Shrub-associated individuals showed lower reproductive effort and greater allocation to growth, while most physiological traits remained unaffected. Euphorbia individuals were bigger and had more leaf N under N-fixing than under non-fixing species. Soil moisture was also higher under N-fixing shrubs; therefore soil conditions in the understory may counter reduced light conditions.There was a significant effect of species identity and functional types in the outcome of plant interactions with consistent effects at individual and community levels. The contrasting allocation strategies to reproduction and growth in Euphorbia plants, either associated or not with shrubs, showed high phenotypic plasticity and evidence its ability to cope with contrasting environmental conditions.

  1. Functional Plant Types Drive Plant Interactions in a Mediterranean Mountain Range.

    Science.gov (United States)

    Macek, Petr; Prieto, Iván; Macková, Jana; Pistón, Nuria; Pugnaire, Francisco I

    2016-01-01

    Shrubs have positive (facilitation) and negative (competition) effects on understory plants, the net interaction effect being modulated by abiotic conditions. Overall shrubs influence to great extent the structure of plant communities where they have significant presence. Interactions in a plant community are quite diverse but little is known about their variability and effects at community level. Here we checked the effects of co-occurring shrub species from different functional types on a focal understory species, determining mechanisms driving interaction outcome, and tested whether effects measured on the focal species were a proxy for effects measured at the community level. Growth, physiological, and reproductive traits of Euphorbia nicaeensis, our focal species, were recorded on individuals growing in association with four dominant shrub species and in adjacent open areas. We also recorded community composition and environmental conditions in each microhabitat. Shrubs provided environmental conditions for plant growth, which contrasted with open areas, including moister soil, greater N content, higher air temperatures, and lower radiation. Shrub-associated individuals showed lower reproductive effort and greater allocation to growth, while most physiological traits remained unaffected. Euphorbia individuals were bigger and had more leaf N under N-fixing than under non-fixing species. Soil moisture was also higher under N-fixing shrubs; therefore soil conditions in the understory may counter reduced light conditions. There was a significant effect of species identity and functional types in the outcome of plant interactions with consistent effects at individual and community levels. The contrasting allocation strategies to reproduction and growth in Euphorbia plants, either associated or not with shrubs, showed high phenotypic plasticity and evidence its ability to cope with contrasting environmental conditions.

  2. Great interactions: How binding incorrect partners can teach us about protein recognition and function.

    Science.gov (United States)

    Vamparys, Lydie; Laurent, Benoist; Carbone, Alessandra; Sacquin-Mora, Sophie

    2016-10-01

    Protein-protein interactions play a key part in most biological processes and understanding their mechanism is a fundamental problem leading to numerous practical applications. The prediction of protein binding sites in particular is of paramount importance since proteins now represent a major class of therapeutic targets. Amongst others methods, docking simulations between two proteins known to interact can be a useful tool for the prediction of likely binding patches on a protein surface. From the analysis of the protein interfaces generated by a massive cross-docking experiment using the 168 proteins of the Docking Benchmark 2.0, where all possible protein pairs, and not only experimental ones, have been docked together, we show that it is also possible to predict a protein's binding residues without having any prior knowledge regarding its potential interaction partners. Evaluating the performance of cross-docking predictions using the area under the specificity-sensitivity ROC curve (AUC) leads to an AUC value of 0.77 for the complete benchmark (compared to the 0.5 AUC value obtained for random predictions). Furthermore, a new clustering analysis performed on the binding patches that are scattered on the protein surface show that their distribution and growth will depend on the protein's functional group. Finally, in several cases, the binding-site predictions resulting from the cross-docking simulations will lead to the identification of an alternate interface, which corresponds to the interaction with a biomolecular partner that is not included in the original benchmark. Proteins 2016; 84:1408-1421. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

  3. Interaction of boron with graphite: A van der Waals density functional study

    Science.gov (United States)

    Liu, Juan; Wang, Chen; Liang, Tongxiang; Lai, Wensheng

    2016-08-01

    Boron doping has been widely investigated to improve oxidation resistance of graphite. In this work the interaction of boron with graphite is investigated by a van der Waals density-functional approach (vdW-DF). The traditional density-functional theory (DFT) is well accounted for the binding in boron-substituted graphite. However, to investigate the boron atom on graphite surface and the interstitial impurities require use of a description of graphite interlayer binding. Traditional DFT cannot describe the vdW physics, for instance, GGA calculations show no relevant binding between graphite sheets. LDA shows some binding, but they fail to provide an accurate account of vdW forces. In this paper, we compare the calculation results of graphite lattice constant and cohesive energy by several functionals, it shows that vdW-DF such as two optimized functionals optB88-vdW and optB86b-vdW give much improved results than traditional DFT. The vdW-DF approach is then applied to study the interaction of boron with graphite. Boron adsorption, substitution, and intercalation are discussed in terms of structural parameters and electronic structures. When adsorbing on graphite surface, boron behaves as π electron acceptor. The π electron approaches boron atom because of more electropositive of boron than carbon. For substitution situation, the hole introduced by boron mainly concentrates on boron and the nearest three carbon atoms. The B-doped graphite system with the hole has less ability to offer electrons to oxygen, ultimately resulted in the inhibition of carbon oxidation. For interstitial doping, vdW-DFs show more accurate formation energy than LDA. PBE functional cannot describe the interstitial boron in graphite reasonably because of the ignoring binding of graphite sheets. The investigation of electron structures of boron doped graphite will play an important role in understanding the oxidation mechanism in further study.

  4. Mentalizing and motivation neural function during social interactions in autism spectrum disorders.

    Science.gov (United States)

    Assaf, Michal; Hyatt, Christopher J; Wong, Christina G; Johnson, Matthew R; Schultz, Robert T; Hendler, Talma; Pearlson, Godfrey D

    2013-01-01

    Autism Spectrum Disorders (ASDs) are characterized by core deficits in social functions. Two theories have been suggested to explain these deficits: mind-blindness theory posits impaired mentalizing processes (i.e. decreased ability for establishing a representation of others' state of mind), while social motivation theory proposes that diminished reward value for social information leads to reduced social attention, social interactions, and social learning. Mentalizing and motivation are integral to typical social interactions, and neuroimaging evidence points to independent brain networks that support these processes in healthy individuals. However, the simultaneous function of these networks has not been explored in individuals with ASDs. We used a social, interactive fMRI task, the Domino game, to explore mentalizing- and motivation-related brain activation during a well-defined interval where participants respond to rewards or punishments (i.e. motivation) and concurrently process information about their opponent's potential next actions (i.e. mentalizing). Thirteen individuals with high-functioning ASDs, ages 12-24, and 14 healthy controls played fMRI Domino games against a computer-opponent and separately, what they were led to believe was a human-opponent. Results showed that while individuals with ASDs understood the game rules and played similarly to controls, they showed diminished neural activity during the human-opponent runs only (i.e. in a social context) in bilateral middle temporal gyrus (MTG) during mentalizing and right Nucleus Accumbens (NAcc) during reward-related motivation (Pcluster motivation networks, respectively, activate normally in a non-social context, they fail to respond in an otherwise identical social context in ASD compared to controls. We discuss implications to both the mind-blindness and social motivation theories of ASD and the importance of social context in research and treatment protocols.

  5. Characterization of the TRBP domain required for Dicer interaction and function in RNA interference

    Directory of Open Access Journals (Sweden)

    El Far Mohamed

    2009-05-01

    Full Text Available Abstract Background Dicer, Ago2 and TRBP are the minimum components of the human RNA-induced silencing complex (RISC. While Dicer and Ago2 are RNases, TRBP is the double-stranded RNA binding protein (dsRBP that loads small interfering RNA into the RISC. TRBP binds directly to Dicer through its C-terminal domain. Results We show that the TRBP binding site in Dicer is a 165 amino acid (aa region located between the ATPase and the helicase domains. The binding site in TRBP is a 69 aa domain, called C4, located at the C-terminal end of TRBP. The TRBP1 and TRBP2 isoforms, but not TRBPs lacking the C4 site (TRBPsΔC4, co-immunoprecipitated with Dicer. The C4 domain is therefore necessary to bind Dicer, irrespective of the presence of RNA. Immunofluorescence shows that while full-length TRBPs colocalize with Dicer, TRBPsΔC4 do not. tarbp2-/- cells, which do not express TRBP, do not support RNA interference (RNAi mediated by short hairpin or micro RNAs against EGFP. Both TRBPs, but not TRBPsΔC4, were able to rescue RNAi function. In human cells with low RNAi activity, addition of TRBP1 or 2, but not TRBPsΔC4, rescued RNAi function. Conclusion The mapping of the interaction sites between TRBP and Dicer show unique domains that are required for their binding. Since TRBPsΔC4 do not interact or colocalize with Dicer, we suggest that TRBP and Dicer, both dsRBPs, do not interact through bound dsRNA. TRBPs, but not TRBPsΔC4, rescue RNAi activity in RNAi-compromised cells, indicating that the binding of Dicer to TRBP is critical for RNAi function.

  6. Na+/K+-ATPase E960 and phospholemman F28 are critical for their functional interaction

    Science.gov (United States)

    Khafaga, Mounir; Bossuyt, Julie; Mamikonian, Luiza; Li, Joseph C.; Lee, Linda L.; Yarov-Yarovoy, Vladimir; Despa, Sanda; Bers, Donald M.

    2012-01-01

    Na+-K+-ATPase (NKA) establishes the transmembrane [Na+] gradient in cells. In heart, phospholemman (PLM) inhibits NKA activity by reducing its apparent Na+ affinity, an effect that is relieved by PLM phosphorylation. The NKA crystal structure suggests regions of PLM–NKA interaction, but the sites important for functional effects in live cells are not known. We tested wild type (WT) and CFP–NKA-α1 point mutants (alanine substitution at F956, E960, L964, and F967) for fluorescence resonance energy transfer (FRET) with WT–PLM–YFP in HEK293 cells. NKA–PLM FRET was unaltered with F956A or F967A, reduced with L964A, and nearly abolished with E960A. Mutating the PLM site (F28A) identified by structural analysis to interact with E960-NKA also nearly abolished NKA–PLM FRET. In contrast, NKA–PLM coimmunoprecipitation was only slightly reduced by E960A–NKA or F28A–PLM mutants, consistent with an additional interaction site. FRET titrations indicate that the additional site has higher affinity than that between E960–NKA and F28–PLM. To test whether the FRET-preventing mutations also prevent PLM functional effects, we measured NKA-mediated Na+-transport in intact cells. For WT–NKA, PLM reduced apparent Na+-affinity of NKA and PLM phosphorylation reversed the effect. In contrast, for E960A–NKA the apparent Na+-affinity was unaltered by either PLM or forskolin-induced PLM phosphorylation. We conclude that E960 on NKA and F28 on PLM are critical for PLM effects on both NKA function and NKA–PLM FRET, but also there is at least one additional site that is critical for tethering PLM to NKA. PMID:23185013

  7. Large-scale identification of human protein function using topological features of interaction network

    Science.gov (United States)

    Li, Zhanchao; Liu, Zhiqing; Zhong, Wenqian; Huang, Menghua; Wu, Na; Xie, Yun; Dai, Zong; Zou, Xiaoyong

    2016-11-01

    The annotation of protein function is a vital step to elucidate the essence of life at a molecular level, and it is also meritorious in biomedical and pharmaceutical industry. Developments of sequencing technology result in constant expansion of the gap between the number of the known sequences and their functions. Therefore, it is indispensable to develop a computational method for the annotation of protein function. Herein, a novel method is proposed to identify protein function based on the weighted human protein-protein interaction network and graph theory. The network topology features with local and global information are presented to characterise proteins. The minimum redundancy maximum relevance algorithm is used to select 227 optimized feature subsets and support vector machine technique is utilized to build the prediction models. The performance of current method is assessed through 10-fold cross-validation test, and the range of accuracies is from 67.63% to 100%. Comparing with other annotation methods, the proposed way possesses a 50% improvement in the predictive accuracy. Generally, such network topology features provide insights into the relationship between protein functions and network architectures. The source code of Matlab is freely available on request from the authors.

  8. An Infrastructural IP for Interactive MPEG-4 SoC Functional Verification

    Directory of Open Access Journals (Sweden)

    Trio Adiono

    2013-09-01

    Full Text Available This paper introduces a specific architecture including an infrastructural IP for functional verification and diagnostics, which is suitable for functional core-based testing of an MPEG4 SoC. Our advanced MPEG4 SoC results in a high complexity SoC with limited physical access to many different functional cores. The proposed test method provides direct monitoring and control for each core, which enables core verification at actual speed. It significantly decreases the verification time due to the large number of required test vectors in typical MPEG4 verification. Furthermore, it also makes the system scalable for functional core expansion due to upgrading of standards. The proposed infrastructural IP is also linked to PC-based interactive tools to simplify the verification of individual and integrated cores. It also provides detailed diagnostic data that enables simple system debugging. The debugging tools also feature test-pattern generation and simulation of expected values. Actual system implementation has shown full functionality of our proposed method.

  9. An Infrastructural IP for Interactive MPEG-4 SoC Functional Verification

    Directory of Open Access Journals (Sweden)

    Trio Adiono

    2009-05-01

    Full Text Available This paper introduces a specific architecture including an infrastructural IP for functional verification and diagnostics, which is suitable for functional core-based testing of an MPEG4 SoC. Our advanced MPEG4 SoC results in a high complexity SoC with limited physical access to many different functional cores. The proposed test method provides direct monitoring and control for each core, which enables core verification at actual speed. It significantly decreases the verification time due to the large number of required test vectors in typical MPEG4 verification. Furthermore, it also makes the system scalable for functional core expansion due to upgrading of standards. The proposed infrastructural IP is also linked to PC-based interactive tools to simplify the verification of individual and integrated cores. It also provides detailed diagnostic data that enables simple system debugging. The debugging tools also feature test-pattern generation and simulation of expected values. Actual system implementation has shown full functionality of our proposed method.

  10. A functional interaction approach to the definition of meso regions: The case of the Czech Republic

    Directory of Open Access Journals (Sweden)

    Erlebach Martin

    2016-06-01

    Full Text Available The definition of functional meso regions for the territory of the Czech Republic is articulated in this article. Functional regions reflect horizontal interactions in space and are presented as a useful tool for various types of geographical analyses, and also for spatial planning, economic policy designs, etc. This paper attempts to add to the discussion on the need to delineate areal units at different hierarchical levels, and to understand the functional flows and spatial behaviours of the population in a given space. Three agglomerative methods are applied in the paper (the CURDS regionalisation algorithm, Intramax, and cluster analysis, and they have not been used previously in Czech geography for the delineation of functional meso regions. Existing functional regions at the micro-level, based on daily travel-to-work flows from the 2001 census, have served as the building blocks. The analyses have produced five regional systems at the meso level, based on daily labour commuting movements of the population. Basic statistics and a characterisation of these systems are provided in this paper.

  11. Age Differences in Interhemispheric Interactions: Callosal Structure, Physiological Function, and Behavior

    Directory of Open Access Journals (Sweden)

    Brett W Fling

    2011-03-01

    Full Text Available There is a fundamental gap in understanding how brain structural and functional network connectivity are interrelated, how they change with age, and how such changes contribute to older adults’ sensorimotor deficits. Recent neuroimaging approaches including resting state functional connectivity MRI (fcMRI and diffusion tensor imaging (DTI have been used to assess brain functional (fcMRI and structural (DTI network connectivity, allowing for more integrative assessments of distributed neural systems than in the past. Declines in corpus callosum size and microstructure with advancing age have been well documented, but their contributions to age deficits in unimanual and bimanual function are not well defined. Our recent work implicates age-related declines in callosal size and integrity as a key contributor to unimanual and bimanual control deficits. Moreover, our data provide evidence for a fundamental shift in the balance of excitatory and inhibitory interhemispheric processes that occurs with age, resulting in age differences in the relationship between functional and structural network connectivity. Training studies suggest that the balance of interhemispheric interactions can be shifted with experience, making this a viable target for future interventions.

  12. Functional Interaction between Class II Histone Deacetylases and ICP0 of Herpes Simplex Virus Type 1

    Science.gov (United States)

    Lomonte, Patrick; Thomas, Joëlle; Texier, Pascale; Caron, Cécile; Khochbin, Saadi; Epstein, Alberto L.

    2004-01-01

    This study describes the physical and functional interactions between ICP0 of herpes simplex virus type 1 and class II histone deacetylases (HDACs) 4, 5, and 7. Class II HDACs are mainly known for their participation in the control of cell differentiation through the regulation of the activity of the transcription factor MEF2 (myocyte enhancer factor 2), implicated in muscle development and neuronal survival. Immunofluorescence experiments performed on transfected cells showed that ICP0 colocalizes with and reorganizes the nuclear distribution of ectopically expressed class I and II HDACs. In addition, endogenous HDAC4 and at least one of its binding partners, the corepressor protein SMRT (for silencing mediator of retinoid and thyroid receptor), undergo changes in their nuclear distribution in ICP0-transfected cells. As a result, during infection endogenous HDAC4 colocalizes with ICP0. Coimmunoprecipitation and glutathione S-transferase pull-down assays confirmed that class II but not class I HDACs specifically interacted with ICP0 through their amino-terminal regions. This region, which is not conserved in class I HDACs but homologous to the MITR (MEF2-interacting transcription repressor) protein, is responsible for the repression, in a deacetylase-independent manner, of MEF2 by sequestering it under an inactive form in the nucleus. Consequently, we show that ICP0 is able to overcome the HDAC5 amino-terminal- and MITR-induced MEF2A repression in gene reporter assays. This is the first report of a viral protein interacting with and controlling the repressor activity of class II HDACs. We discuss the putative consequences of such an interaction for the biology of the virus both during lytic infection and reactivation from latency. PMID:15194749

  13. Identification of functionally important TonB-ExbD periplasmic domain interactions in vivo.

    Science.gov (United States)

    Ollis, Anne A; Postle, Kathleen

    2012-06-01

    In gram-negative bacteria, the cytoplasmic membrane proton-motive force energizes the active transport of TonB-dependent ligands through outer membrane TonB-gated transporters. In Escherichia coli, cytoplasmic membrane proteins ExbB and ExbD couple the proton-motive force to conformational changes in TonB, which are hypothesized to form the basis of energy transduction through direct contact with the transporters. While the role of ExbB is not well understood, contact between periplasmic domains of TonB and ExbD is required, with the conformational response of TonB to presence or absence of proton motive force being modulated through ExbD. A region (residues 92 to 121) within the ExbD periplasmic domain was previously identified as being important for TonB interaction. Here, the specific sites of periplasmic domain interactions between that region and the TonB carboxy terminus were identified by examining 270 combinations of 45 TonB and 6 ExbD individual cysteine substitutions for disulfide-linked heterodimer formation. ExbD residues A92C, K97C, and T109C interacted with multiple TonB substitutions in four regions of the TonB carboxy terminus. Two regions were on each side of the TonB residues known to interact with the TonB box of TonB-gated transporters, suggesting that ExbD positions TonB for correct interaction at that site. A third region contained a functionally important glycine residue, and the fourth region involved a highly conserved predicted amphipathic helix. Three ExbD substitutions, F103C, L115C, and T121C, were nonreactive with any TonB cysteine substitutions. ExbD D25, a candidate to be on a proton translocation pathway, was important to support efficient TonB-ExbD heterodimerization at these specific regions.

  14. Functional characterization of the HuR:CD83 mRNA interaction.

    Directory of Open Access Journals (Sweden)

    Dorothea Pieper

    Full Text Available Maturation of dendritic cells (DC is characterized by expression of CD83, a surface protein that appears to be necessary for the effective activation of naïve T-cells and T-helper cells by DC. Lately it was shown that CD83 expression is regulated on the posttranscriptional level by interaction of the shuttle protein HuR with a novel posttranscriptional regulatory RNA element (PRE, which is located in the coding region of the CD83 transcript. Interestingly, this interaction commits the CD83 mRNA to efficient nuclear export via the CRM1 pathway. To date, however, the structural basis of this interaction, which potentially involves three distinct RNA recognition motifs (RRM1-3 in HuR and a complex three-pronged RNA stem-loop element in CD83 mRNA, has not been investigated in detail. In the present work we analyzed this interaction in vitro and in vivo using various HuR- and CD83 mRNA mutants. We are able to demonstrate that both, RRM1 and RRM2 are crucial for binding, whereas RRM3 as well as the HuR hinge region contributed only marginally to this protein:RNA interaction. Furthermore, mutation of uridine rich patches within the PRE did not disturb HuR:CD83 mRNA complex formation while, in contrast, the deletion of specific PRE subfragments from the CD83 mRNA prevented HuR binding in vitro and in vivo. Interestingly, the observed inhibition of HuR binding to CD83 mRNA does not lead to a nuclear trapping of the transcript but rather redirected this transcript from the CRM1- towards the NXF1/TAP-specific nuclear export pathway. Thus, the presence of a functional PRE permits nucleocytoplasmic trafficking of the CD83 transcript via the CRM1 pathway.

  15. Functional Characterization of PknI-Rv2159c Interaction in Redox Homeostasis of Mycobacterium tuberculosis

    Directory of Open Access Journals (Sweden)

    Arunkumar Venkatesan

    2016-10-01

    Full Text Available Mycobacterium tuberculosis adapts to stress conditions by responding to the signals from its external environment. M. tuberculosis genome encodes 11 eukaryotic like serine/threonine protein kinases (STPK and their importance in regulating the physiology and virulence of the bacteria are being explored. Previous study from our lab identified the M. tuberculosis STPK, PknI interacts with two peroxidase proteins such as Rv2159c and Rv0148. In this study, we have characterized the biological function behind the PknI-Rv2159c interaction in M. tuberculosis. Point mutation of Ala-Gly-Trp motif identified that only Ala49 and Gly50 amino acids of Rv2159c are responsible for interaction and there is no phosphorylation involved in the PknI-Rv2159c interaction. Rv2159c is a member from the carboxymuconolactone decarboxylase family with peroxidase activity. Enzymatic assays with catalytic site point mutants showed that Cys84 of Rv2159c was responsible for its alkylhydroperoxidase activity. Interestingly, interaction with PknI increased its peroxidase activity by several folds. Gene knockdown of Rv2159c in M. tuberculosis showed increased sensitivity to peroxides such as cumene hydroperoxide and hydrogen peroxide. Proteomic analysis of differentially expressing Rv2159c strains by 2D gel electrophoresis and mass spectrometry revealed the differential abundance of 21 proteins. The total absence of oxidoreductase, GuaB1 suggests the essential role of Rv2159c in redox maintenance. Our findings provide new insights on signaling mechanisms of PknI in maintaining the redox homeostasis during oxidative stresses.

  16. Functional roles of a tetraloop/receptor interacting module in a cyclic di-GMP riboswitch.

    Science.gov (United States)

    Fujita, Yuki; Tanaka, Takahiro; Furuta, Hiroyuki; Ikawa, Yoshiya

    2012-02-01

    Riboswitches are a class of structural RNAs that regulate transcription and translation through specific recognition of small molecules. Riboswitches are attractive not only as drug targets for novel antibiotics but also as modular tools for controlling gene expression. Sequence comparison of a class of riboswitches that sense cyclic di-GMP (type-I c-di-GMP riboswitches) revealed that this type of riboswitch frequently shows a GAAA loop/receptor interaction between P1 and P3 elements. In the crystal structures of a type-I c-di-GMP riboswitch from Vibrio cholerae (the Vc2 riboswitch), the GNRA loop/receptor interaction assembled P2 and P3 stems to organize a ligand-binding pocket. In this study, the functional importance of the GAAA loop-receptor interaction in the Vc2 riboswitch was examined. A series of variant Vc2 riboswitches with mutations in the GAAA loop/receptor interaction were assayed for their switching abilities. In mutants with mutations in the P2 GAAA loop, expression of the reporter gene was reduced to approximately 40% - 60% of that in the wild-type. However, mutants in which the P3 receptor motif was substituted with base pairs were as active as the wild-type. These results suggested that the GAAA loop/receptor interaction does not simply establish the RNA 3D structure but docking of P2 GAAA loop reduces the flexibility of the GAAA receptor motif in the P3 element. This mechanism was supported by a variant riboswitch bearing a theophylline aptamer module in P3 the structural rigidity of which could be modulated by the small molecule theophylline.

  17. Discovery of novel interacting partners of PSMD9, a proteasomal chaperone: Role of an Atypical and versatile PDZ-domain motif interaction and identification of putative functional modules

    Science.gov (United States)

    Sangith, Nikhil; Srinivasaraghavan, Kannan; Sahu, Indrajit; Desai, Ankita; Medipally, Spandana; Somavarappu, Arun Kumar; Verma, Chandra; Venkatraman, Prasanna

    2014-01-01

    PSMD9 (Proteasome Macropain non-ATPase subunit 9), a proteasomal assembly chaperone, harbors an uncharacterized PDZ-like domain. Here we report the identification of five novel interacting partners of PSMD9 and provide the first glimpse at the structure of the PDZ-domain, including the molecular details of the interaction. We based our strategy on two propositions: (a) proteins with conserved C-termini may share common functions and (b) PDZ domains interact with C-terminal residues of proteins. Screening of C-terminal peptides followed by interactions using full-length recombinant proteins, we discovered hnRNPA1 (an RNA binding protein), S14 (a ribosomal protein), CSH1 (a growth hormone), E12 (a transcription factor) and IL6 receptor as novel PSMD9-interacting partners. Through multiple techniques and structural insights, we clearly demonstrate for the first time that human PDZ domain interacts with the predicted Short Linear Sequence Motif (SLIM) at the C-termini of the client proteins. These interactions are also recapitulated in mammalian cells. Together, these results are suggestive of the role of PSMD9 in transcriptional regulation, mRNA processing and editing, hormone and receptor activity and protein translation. Our proof-of-principle experiments endorse a novel and quick method for the identification of putative interacting partners of similar PDZ-domain proteins from the proteome and for discovering novel functions. PMID:25009770

  18. Discovery of novel interacting partners of PSMD9, a proteasomal chaperone: Role of an Atypical and versatile PDZ-domain motif interaction and identification of putative functional modules

    Directory of Open Access Journals (Sweden)

    Nikhil Sangith

    2014-01-01

    Full Text Available PSMD9 (Proteasome Macropain non-ATPase subunit 9, a proteasomal assembly chaperone, harbors an uncharacterized PDZ-like domain. Here we report the identification of five novel interacting partners of PSMD9 and provide the first glimpse at the structure of the PDZ-domain, including the molecular details of the interaction. We based our strategy on two propositions: (a proteins with conserved C-termini may share common functions and (b PDZ domains interact with C-terminal residues of proteins. Screening of C-terminal peptides followed by interactions using full-length recombinant proteins, we discovered hnRNPA1 (an RNA binding protein, S14 (a ribosomal protein, CSH1 (a growth hormone, E12 (a transcription factor and IL6 receptor as novel PSMD9-interacting partners. Through multiple techniques and structural insights, we clearly demonstrate for the first time that human PDZ domain interacts with the predicted Short Linear Sequence Motif (SLIM at the C-termini of the client proteins. These interactions are also recapitulated in mammalian cells. Together, these results are suggestive of the role of PSMD9 in transcriptional regulation, mRNA processing and editing, hormone and receptor activity and protein translation. Our proof-of-principle experiments endorse a novel and quick method for the identification of putative interacting partners of similar PDZ-domain proteins from the proteome and for discovering novel functions.

  19. Regulatory T Cells in Tumor-Associated Tertiary Lymphoid Structures Suppress Anti-tumor T Cell Responses.

    Science.gov (United States)

    Joshi, Nikhil S; Akama-Garren, Elliot H; Lu, Yisi; Lee, Da-Yae; Chang, Gregory P; Li, Amy; DuPage, Michel; Tammela, Tuomas; Kerper, Natanya R; Farago, Anna F; Robbins, Rebecca; Crowley, Denise M; Bronson, Roderick T; Jacks, Tyler

    2015-09-15

    Infiltration of regulatory T (Treg) cells into many tumor types correlates with poor patient prognoses. However, mechanisms of intratumoral Treg cell function remain to be elucidated. We investigated Treg cell function in a genetically engineered mouse model of lung adenocarcinoma and found that Treg cells suppressed anti-tumor responses in tumor-associated tertiary lymphoid structures (TA-TLSs). TA-TLSs have been described in human lung cancers, but their function remains to be determined. TLSs in this model were spatially associated with >90% of tumors and facilitated interactions between T cells and tumor-antigen-presenting dendritic cells (DCs). Costimulatory ligand expression by DCs and T cell proliferation rates increased in TA-TLSs upon Treg cell depletion, leading to tumor destruction. Thus, we propose that Treg cells in TA-TLSs can inhibit endogenous immune responses against tumors, and targeting these cells might provide therapeutic benefit for cancer patients.

  20. Keeping the heart in balance: the functional interactions of myoglobin with nitrogen oxides

    DEFF Research Database (Denmark)

    Flögel, Ulrich; Fago, Angela; Rassaf, Tienush

    2010-01-01

    in the heart. By a dynamic cycle, in which a decrease in tissue O2 tension drives the conversion of Mb from being a NO scavenger under normoxia to a NO producer during hypoxia, mitochondrial respiration is reversibly adapted to the intracellular O2 tension. Therefore, Mb may act as an important O2 sensor...... through which NO can regulate muscle energetics and function. As Mb is widespread throughout the fauna, the diverse oxygen-dependent interactions between Mb and nitrogen oxides may not only be of relevance for mammals but also for other vertebrates as evidenced by comparable phenotypes of ‘artificial...

  1. Na+/K+-ATPase E960 and phospholemman F28 are critical for their functional interaction

    OpenAIRE

    Khafaga, Mounir; Bossuyt, Julie; Mamikonian, Luiza; Li, Joseph C.; Lee, Linda L.; Yarov-Yarovoy, Vladimir; Despa, Sanda; Bers, Donald M.

    2012-01-01

    Na+-K+-ATPase (NKA) establishes the transmembrane [Na+] gradient in cells. In heart, phospholemman (PLM) inhibits NKA activity by reducing its apparent Na+ affinity, an effect that is relieved by PLM phosphorylation. The NKA crystal structure suggests regions of PLM–NKA interaction, but the sites important for functional effects in live cells are not known. We tested wild type (WT) and CFP–NKA-α1 point mutants (alanine substitution at F956, E960, L964, and F967) for fluorescence resonance ene...

  2. CD28–B7 Interaction Modulates Short- and Long-Lived Plasma Cell Function

    OpenAIRE

    2012-01-01

    The interaction of CD28, which is constitutively expressed on T cells, with B7.1/B7.2 expressed on APCs is critical for T cell activation. CD28 is also expressed on murine and human plasma cells but its function on these cells remains unclear. There are two types of plasma cells: short-lived ones that appear in the secondary lymphoid tissue shortly after Ag exposure, and long-lived plasma cells that mainly reside in the bone marrow. We demonstrate that CD28-deficient murine short- and long-li...

  3. Interaction of atomic hydrogen with anthracene and polyacene from density functional theory

    Science.gov (United States)

    Ferullo, Ricardo M.; Castellani, Norberto J.; Belelli, Patricia G.

    2016-03-01

    The interaction of atomic hydrogen with two linear polycyclic aromatic hydrocarbons (PAHs), anthracene and polyacene (the polymer of benzene), was studied within the density functional theory (DFT). Using a proper dispersion-corrected method (DFT-D) the preferential physisorption sites were explored. The activation barrier for the bond formation between a peripheral C and the incoming H was calculated to be 58.5 and 34.1 meV with pure DFT on anthracene and polyacene at its antiferromagnetic ground state, respectively. DFT-D, although improves the description of the physisorbed state, tends to underestimate the chemisorption barriers due an artifact arising from the dispersion correction.

  4. A correlated basis-function description of 16O with realistic interactions

    Science.gov (United States)

    Boscá, M. C.

    1994-01-01

    The correlated basis-function theory is applied at the lowest order to analyze the ground state and low-energy spectrum of the 16O nucleus. Results are quoted for both the Urbana and the Argonne υ 14 nucleon-nucleon interactions. The work includes state-dependent correlations and their radial components are determined by solving a set of Euler-Lagrange equations. The matrix elements are computed by using a cluster expansion and the sequential condition is imposed in order to insure convergence. The results clearly disagree with the experimental values.

  5. TreeQ-VISTA: An Interactive Tree Visualization Tool withFunctional Annotation Query Capabilities

    Energy Technology Data Exchange (ETDEWEB)

    Gu, Shengyin; Anderson, Iain; Kunin, Victor; Cipriano, Michael; Minovitsky, Simon; Weber, Gunther; Amenta, Nina; Hamann, Bernd; Dubchak,Inna

    2007-05-07

    Summary: We describe a general multiplatform exploratorytool called TreeQ-Vista, designed for presenting functional annotationsin a phylogenetic context. Traits, such as phenotypic and genomicproperties, are interactively queried from a relational database with auser-friendly interface which provides a set of tools for users with orwithout SQL knowledge. The query results are projected onto aphylogenetic tree and can be displayed in multiple color groups. A richset of browsing, grouping and query tools are provided to facilitatetrait exploration, comparison and analysis.Availability: The program,detailed tutorial and examples are available online athttp://genome-test.lbl.gov/vista/TreeQVista.

  6. Interactive edgewise mechanisms: form and function comparison with conventional edgewise brackets.

    Science.gov (United States)

    Voudouris, J C

    1997-02-01

    As the frequency of use of the interactive twin (I-twin) edgewise mechanisms and techniques become increasingly prevalent, it is important to consider how they compare with conventional twin (c-twin) edgewise bracket systems. Optimum intrabracket and interbracket forces in I-twins balance with capillary blood pressures. An unbiased, experimental in vitro, scanning electromicroscopy and in vivo clinical investigation of 83 patients was conducted to compare the frictional resistance of three different I-twin bracket systems, type A (Sigma, American Orthodontics), type B (Interactwin, Ormco Corp.), and type C (Damon, A-company) with three c-twins counterparts respectively types D, E, and F. The three interactive twin brackets were each self-seating by an integrated arm component and made significant incremental improvements to the conventional twins in three different ways. First, the I-twin types reduced frictional resistance by using arm engagement with a lower coefficient of friction and a reduced seating force against the arch wire. The reduced seating force friction produced initially small interbracket arch wire deflections for biocompatible tooth movement and, combined with a wide twin bracket, produced accurate rotation corrections. Reduced friction within the I-twin bracket consequently permitted the effective use of light forces for flowing biomechanics that maximized anchorage. In evaluating friction, two distinctly different interaction forces acting to seat the arch wire were also identified. Type A demonstrated active interaction with round arch wires that resulted in a low functional seating force responsible for early and complete tooth control in comparison to the high seating force of c-twins. Types B and C both showed passive interaction with seating force friction approximately equal to zero that required large rectangular dimension arch wires for full bracket expression. Second, a significant reduction in the time taken to change arch wires was

  7. Functional renormalization group approach for inhomogeneous one-dimensional Fermi systems with finite-ranged interactions

    Science.gov (United States)

    Weidinger, Lukas; Bauer, Florian; von Delft, Jan

    2017-01-01

    We introduce an equilibrium formulation of the functional renormalization group (fRG) for inhomogeneous systems capable of dealing with spatially finite-ranged interactions. In the general third-order truncated form of fRG, the dependence of the two-particle vertex is described by O (N4) independent variables, where N is the dimension of the single-particle system. In a previous paper [Bauer et al., Phys. Rev. B 89, 045128 (2014), 10.1103/PhysRevB.89.045128], the so-called coupled-ladder approximation (CLA) was introduced and shown to admit a consistent treatment for models with a purely onsite interaction, reducing the vertex to O (N2) independent variables. In this work, we introduce an extended version of this scheme, called the extended coupled ladder approximation (eCLA), which includes a spatially extended feedback between the individual channels, measured by a feedback length L , using O (N2L2) independent variables for the vertex. We apply the eCLA in a static approximation and at zero temperature to three types of one-dimensional model systems, focusing on obtaining the linear response conductance. First, we study a model of a quantum point contact (QPC) with a parabolic barrier top and on-site interactions. In our setup, where the characteristic length lx of the QPC ranges between approximately 4-10 sites, eCLA achieves convergence once L becomes comparable to lx. It also turns out that the additional feedback stabilizes the fRG flow. This enables us, second, to study the geometric crossover between a QPC and a quantum dot, again for a one-dimensional model with on-site interactions. Third, the enlarged feedback also enables the treatment of a finite-ranged interaction extending over up to L sites. Using a simple estimate for the form of such a finite-ranged interaction in a QPC with a parabolic barrier top, we study its effects on the conductance and the density. We find that for low densities and sufficiently large interaction ranges the conductance

  8. Quadrupole Collective Dynamics from Energy Density Functionals: Collective Hamiltonian and the Interacting Boson Model

    CERN Document Server

    Nomura, K; Otsuka, T; Shimizu, N; Vretenar, D

    2011-01-01

    Microscopic energy density functionals (EDF) have become a standard tool for nuclear structure calculations, providing an accurate global description of nuclear ground states and collective excitations. For spectroscopic applications this framework has to be extended to account for collective correlations related to restoration of symmetries broken by the static mean field, and for fluctuations of collective variables. In this work we compare two approaches to five-dimensional quadrupole dynamics: the collective Hamiltonian for quadrupole vibrations and rotations, and the Interacting Boson Model. The two models are compared in a study of the evolution of non-axial shapes in Pt isotopes. Starting from the binding energy surfaces of $^{192,194,196}$Pt, calculated with a microscopic energy density functional, we analyze the resulting low-energy collective spectra obtained from the collective Hamiltonian, and the corresponding IBM-2 Hamiltonian. The calculated excitation spectra and transition probabilities for t...

  9. Exact out-of-time-ordered correlation functions for an interacting lattice fermion model

    CERN Document Server

    Tsuji, Naoto; Ueda, Masahito

    2016-01-01

    An exact solution for local equilibrium and nonequilibrium out-of-time-ordered correlation (OTOC) functions is obtained for a lattice fermion model with on-site interactions, namely the Falicov-Kimball (FK) model, in the large dimensional and thermodynamic limit. Our approach is based on the nonequilibrium dynamical mean-field theory generalized to an extended Kadanoff-Baym contour. We find that the OTOC is enhanced at intermediate coupling around the metal-insulator phase transition, implying that the system is most scrambled in that regime. In the high-temperature limit, the OTOC remains nontrivially finite, even though dynamical charge correlations probed by an ordinary response function are suppressed. We propose an experiment to measure OTOCs of fermionic lattice systems including the FK and Hubbard models in ultracold atomic systems.

  10. Density-functional theory cannot be constrained to completely overcome self-interaction error

    CERN Document Server

    Moynihan, Glenn; O'Regan, David D

    2016-01-01

    In approximate density functional theory (DFT), the self-interaction error is a pervasive electron delocalization associated with underestimated insulating gaps. It exhibits a predominantly quadratic energy-density curve that is amenable to correction using computationally efficient, constraint-resembling methods such as DFT + Hubbard U (DFT+U). Constrained DFT (cDFT) exactly enforces conditions on DFT by means of self-consistently optimized Lagrange multipliers, and its use to automate DFT+U type corrections is a compelling possibility. We show that constraints beyond linear order are incompatible with cDFT. For DFT+U, we overcome this by separating its Hubbard U parameters into linear and quadratic terms. For a one-electron system, the resulting generalized DFT+U method can recover the exact subspace occupancy and free-energy, but neither the exact total-energy nor the exact ionization potential, for reasonable parameters. Approximate functionals thus cannot be systematically corrected by constraining their...

  11. Generalized thermoelastic interaction in functional graded material with fractional order three-phase lag heat transfer

    Institute of Scientific and Technical Information of China (English)

    Ibrahim A. Abbas

    2015-01-01

    The present work is concerned with the solution of a problem on thermoelastic interactions in a functional graded material due to thermal shock in the context of the fractional order three-phase lag model. The governing equations of fractional order generalized thermoelasticity with three-phase lag model for functionally graded materials (FGM) (i.e., material with spatially varying material properties) are established. The analytical solution in the transform domain is obtained by using the eigenvalue approach. The inversion of Laplace transform is done numerically. The graphical results indicate that the fractional parameter has significant effects on all the physical quantities. Thus, we can consider the theory of fractional order generalized thermoelasticity an improvement on studying elastic materials.

  12. Quantum Monte Carlo with reoptimized perturbatively selected configuration-interaction wave functions

    CERN Document Server

    Giner, Emmanuel; Toulouse, Julien

    2016-01-01

    We explore the use in quantum Monte Carlo (QMC) of trial wave functions consisting of a Jastrow factor multiplied by a truncated configuration-interaction (CI) expansion in Slater determinants obtained from a CI perturbatively selected iteratively (CIPSI) calculation. In the CIPSI algorithm, the CI expansion is iteratively enlarged by selecting the best determinants using perturbation theory, which provides an optimal and automatic way of constructing truncated CI expansions approaching the full CI limit. We perform a systematic study of variational Monte Carlo (VMC) and fixed-node diffusion Monte Carlo (DMC) total energies of first-row atoms from B to Ne with different levels of optimization of the parameters (Jastrow parameters, coefficients of the determinants, and orbital parameters) in these trial wave functions. The results show that the reoptimization of the coefficients of the determinants in VMC (together with the Jastrow factor) leads to an important lowering of both VMC and DMC total energies, and ...

  13. Twenty weeks of home-based interactive training of children with cerebral palsy improves functional abilities

    DEFF Research Database (Denmark)

    Lorentzen, Jakob; Greve, Line Z; Kliim-Due, Mette;

    2015-01-01

    BACKGROUND: Home-based training is becoming ever more important with increasing demands on the public health systems. We investigated whether individualized and supervised interactive home-based training delivered through the internet improves functional abilities in children with cerebral palsy...... (CP). METHODS: Thirty four children with CP (aged 9-16; mean age 10.9 ± 2.4 years) (GMFCS I-II; MACS I-II) were included in this non-randomized controlled clinical training study. 12 children (aged 7-16; mean age: 11.3+/-0.9 years) were allocated to a control group in which measurements were performed...... home training of children with CP is an efficient way to deliver training, which can enable functional motor improvements and increased activity to perform daily activities. TRIAL REGISTRATION: ISRCTN13188513 . Date of registration: 04/12/2014....

  14. Block renormalization group in a formalism with lattice wavelets: Correlation function formulas for interacting fermions

    Energy Technology Data Exchange (ETDEWEB)

    Pereira, E. [Departamento Fisica-ICEx, UFMG, CP 702, Belo Horizonte MG 30.161-970 (Brazil); Procacci, A. [Departamento Matematica-ICEx, UFMG, CP 702, Belo Horizonte MG 30.161-970 (Brazil)

    1997-03-01

    Searching for a general and technically simple multiscale formalism to treat interacting fermions, we develop a (Wilson{endash}Kadanoff) block renormalization group mechanism, which, due to the property of {open_quotes}orthogonality between scales,{close_quotes} establishes a trivial link between the correlation functions and the effective potential flow, leading to simple expressions for the generating and correlation functions. Everything is based on the existence of {open_quotes}special configurations{close_quotes} (lattice wavelets) for multiscale problems: using a simple linear change of variables relating the initial fields to these configurations, we establish the formalism. The algebraic formulas show a perfect parallel with those obtained for bosonic problems, considered in previous works. {copyright} 1997 Academic Press, Inc.

  15. Expression, regulation and function of epithelial-stromal interaction 1 (breast), EPSTI1

    DEFF Research Database (Denmark)

    Villadsen, René; Lind Nielsen, Helga; Rank, Fritz;

    2008-01-01

    in epithelial cells in close contact with stromal cells. Furthermore, preliminary data indicate that the expression was highest in estrogen receptor negative tumors. By comparison, in normal breast EPSTI1 was expressed primarily in the acini. To address a possible function of the protein we used a human breast...... epithelial cancer cell line, MCF-7, transfected with pRev-Tet-Off and pRevTRE with a FLAG-EPSTI1 insert. When cultured in 3-dimensional assays, the EPSTI1 expressing cells gave rise to more compact structures than the non-expressing cells, which resulted in loosely arranged/hollow structures......The transcript of epithelial-stromal interaction 1 (breast), EPSTI1, was originally found to be upregulated in invasive breast carcinomas as compared to normal breast tissue (Genomics 79:703, 2002). In the present study we investigated the expression, regulation and possible function of the protein...

  16. Communication: Excited states, dynamic correlation functions and spectral properties from full configuration interaction quantum Monte Carlo.

    Science.gov (United States)

    Booth, George H; Chan, Garnet Kin-Lic

    2012-11-21

    In this communication, we propose a method for obtaining isolated excited states within the full configuration interaction quantum Monte Carlo framework. This method allows for stable sampling with respect to collapse to lower energy states and requires no uncontrolled approximations. In contrast with most previous methods to extract excited state information from quantum Monte Carlo methods, this results from a modification to the underlying propagator, and does not require explicit orthogonalization, analytic continuation, transient estimators, or restriction of the Hilbert space via a trial wavefunction. Furthermore, we show that the propagator can directly yield frequency-domain correlation functions and spectral functions such as the density of states which are difficult to obtain within a traditional quantum Monte Carlo framework. We demonstrate this approach with pilot applications to the neon atom and beryllium dimer.

  17. Functional interaction between TRP4 and CFTR in mouse aorta endothelial cells

    Directory of Open Access Journals (Sweden)

    Droogmans Guy

    2001-05-01

    Full Text Available Abstract Background This study describes the functional interaction between the putative Ca2+ channel TRP4 and the cystic fibrosis transmembrane conductance regulator, CFTR, in mouse aorta endothelium (MAEC. Results MAEC cells express CFTR transcripts as shown by RT-PCR analysis. Application of a phosphorylating cocktail activated a Cl- current with characteristics similar to those of CFTR mediated currents in other cells types (slow activation by cAMP, absence of rectification, block by glibenclamide. The current is present in trp4 +/+ MAEC, but not in trp4 -/- cells, although the expression of CFTR seems unchanged in the trp4 deficient cells as judged from RT-PCR analysis. Conclusions It is concluded that TRP4 is necessary for CFTR activation in endothelium, possibly by providing a scaffold for the formation of functional CFTR channels.

  18. INTERACT

    DEFF Research Database (Denmark)

    Jochum, Elizabeth; Borggreen, Gunhild; Murphey, TD

    This paper considers the impact of visual art and performance on robotics and human-computer interaction and outlines a research project that combines puppetry and live performance with robotics. Kinesics—communication through movement—is the foundation of many theatre and performance traditions...... interaction between a human operator and an artificial actor or agent. We can apply insights from puppetry to develop culturally-aware robots. Here we describe the development of a robotic marionette theatre wherein robotic controllers assume the role of human puppeteers. The system has been built, tested...

  19. Hydrogen-bonding interactions between a nitrile-based functional ionic liquid and DMSO

    Science.gov (United States)

    Zheng, Yan-Zhen; Zhou, Yu; Deng, Geng; Yu, Zhi-Wu

    2016-11-01

    Task-specific ionic liquids (TSILs) have been introduced by incorporating additional functional groups in the cation or anion to impart specific properties or reactivates. In this work, the hydrogen-bonding interactions between a nitrile-functional TSIL 1-propylnitrile-3-methylimidazolium tetrafluoroborate ([PCNMIM][BF4]) and dimethyl sulphoxide (DMSO) were investigated in detail by attenuated total reflection infrared spectroscopy (ATR-IR), combined with hydrogen nuclear magnetic resonance (1H NMR) and density functional theory calculations (DFT). It was found that, first, introducing a nitrile group into the alkyl chain does not change the main interaction site in the cation. It is still the C2 hydrogen. So the v(C2-H) is more sensitive to the environmental change and can be used as an indicator of the environments change of IL. Second, the wavenumber shift changes of v(C2-H) have two turning points (xDMSO ≈ 0.6 and 0.9), dividing the dilution process into three stages. Combined with the calculation results, the dilution process is identified as: From larger ion clusters to smaller ion clusters (xDMSO 0.9). Introducing a nitrile group into the alkyl chain does not influence the dilution process of IL dissolving in DMSO. Third, the Ctbnd N in [PCNMIM][BF4] can work as an electron donor in forming hydrogen-bonds with the methyl group of [PCNMIM]+ and DMSO, but its strength is weaker than that formed by the imidazolium ring C-Hs. The dual roles of the cation to work as both electron acceptor and donor expand the wide applications of this nitrile-functional ionic liquid.

  20. Macrofauna assemblage composition and soil moisture interact to affect soil ecosystem functions

    Science.gov (United States)

    Collison, E. J.; Riutta, T.; Slade, E. M.

    2013-02-01

    Changing climatic conditions and habitat fragmentation are predicted to alter the soil moisture conditions of temperate forests. It is not well understood how the soil macrofauna community will respond to changes in soil moisture, and how changes to species diversity and community composition may affect ecosystem functions, such as litter decomposition and soil fluxes. Moreover, few studies have considered the interactions between the abiotic and biotic factors that regulate soil processes. Here we attempt to disentangle the interactive effects of two of the main factors that regulate soil processes at small scales - moisture and macrofauna assemblage composition. The response of assemblages of three common temperate soil invertebrates (Glomeris marginata Villers, Porcellio scaber Latreille and Philoscia muscorum Scopoli) to two contrasting soil moisture levels was examined in a series of laboratory mesocosm experiments. The contribution of the invertebrates to the leaf litter mass loss of two common temperate tree species of contrasting litter quality (easily decomposing Fraxinus excelsior L. and recalcitrant Quercus robur L.) and to soil CO2 fluxes were measured. Both moisture conditions and litter type influenced the functioning of the invertebrate assemblages, which was greater in high moisture conditions compared with low moisture conditions and on good quality vs. recalcitrant litter. In high moisture conditions, all macrofauna assemblages functioned at equal rates, whereas in low moisture conditions there were pronounced differences in litter mass loss among the assemblages. This indicates that species identity and assemblage composition are more important when moisture is limited. We suggest that complementarity between macrofauna species may mitigate the reduced functioning of some species, highlighting the importance of maintaining macrofauna species richness.

  1. RNase L Interacts with Filamin A To Regulate Actin Dynamics and Barrier Function for Viral Entry

    Science.gov (United States)

    Siddiqui, Mohammad Adnan; Dayal, Shubham; Naji, Merna; Ezelle, Heather J.; Zeng, Chun; Zhou, Aimin; Hassel, Bret A.

    2014-01-01

    ABSTRACT The actin cytoskeleton and its network of associated proteins constitute a physical barrier that viruses must circumvent to gain entry into cells for productive infection. The mechanisms by which the physical signals of infection are sensed by the host to activate an innate immune response are not well understood. The antiviral endoribonuclease RNase L is ubiquitously expressed in a latent form and activated upon binding 2-5A, a unique oligoadenylate produced during viral infections. We provide evidence that RNase L in its inactive form interacts with the actin-binding protein Filamin A to modulate the actin cytoskeleton and inhibit virus entry. Cells lacking either RNase L or Filamin A displayed increased virus entry which was exacerbated in cells lacking both proteins. RNase L deletion mutants that reduced Filamin A interaction displayed a compromised ability to restrict virus entry, supporting the idea of an important role for the RNase L-Filamin A complex in barrier function. Remarkably, both the wild type and a catalytically inactive RNase L mutant were competent to reduce virus entry when transfected into RNase L-deficient cells, indicating that this novel function of RNase L is independent of its enzymatic activity. Virus infection and RNase L activation disrupt its association with Filamin A and release RNase L to mediate its canonical nuclease-dependent antiviral activities. The dual functions of RNase L as a constitutive component of the actin cytoskeleton and as an induced mediator of antiviral signaling and effector functions provide insights into its mechanisms of antiviral activity and opportunities for the development of novel antiviral agents. PMID:25352621

  2. Salt Contribution to RNA Tertiary Structure Folding Stability

    Science.gov (United States)

    Tan, Zhi-Jie; Chen, Shi-Jie

    2011-01-01

    Accurate quantification of the ionic contribution to RNA folding stability could greatly enhance our ability to understand and predict RNA functions. Recently, motivated by the potential importance of ion correlation and fluctuation in RNA folding, we developed the tightly bound ion (TBI) model. Extensive experimental tests showed that the TBI model can lead to better treatment of multivalent ions than the Poisson-Boltzmann equation. In this study, we use the model to quantify the contribution of salt (Na+ and Mg2+) to the RNA tertiary structure folding free energy. Folding of the RNA tertiary structure often involves intermediates. We focus on the folding transition from an intermediate state to the native state, and compute the electrostatic folding free energy of the RNA. Based on systematic calculations for a variety of RNA molecules, we derive a set of formulas for the electrostatic free energy for tertiary structural folding as a function of the sequence length and compactness of the RNA and the Na+ and Mg2+ concentrations. Extensive comparisons with experimental data suggest that our model and the extracted empirical formulas are quite reliable. PMID:21723828

  3. Interactions and effects of BSA-functionalized single-walled carbon nanotubes on different cell lines

    Science.gov (United States)

    Muzi, Laura; Tardani, Franco; La Mesa, Camillo; Bonincontro, Adalberto; Bianco, Alberto; Risuleo, Gianfranco

    2016-04-01

    Functionalized carbon nanotubes (CNTs) have shown great promise in several biomedical contexts, spanning from drug delivery to tissue regeneration. Thanks to their unique size-related properties, single-walled CNTs (SWCNTs) are particularly interesting in these fields. However, their use in nanomedicine requires a clear demonstration of their safety in terms of tissue damage, toxicity and pro-inflammatory response. Thus, a better understanding of the cytotoxicity mechanisms, the cellular interactions and the effects that these materials have on cell survival and on biological membranes is an important first step for an appropriate assessment of their biocompatibility. In this study we show how bovine serum albumin (BSA) is able to generate homogeneous and stable dispersions of SWCNTs (BSA-CNTs), suggesting their possible use in the biomedical field. On the other hand, this study wishes to shed more light on the impact and the interactions of protein-stabilized SWCNTs with two different cell types exploiting multidisciplinary techniques. We show that BSA-CNTs are efficiently taken up by cells. We also attempt to describe the effect that the interaction with cells has on the dielectric characteristics of the plasma membrane and ion flux using electrorotation. We then focus on the BSA-CNTs’ acute toxicity using different cellular models. The novel aspect of this work is the evaluation of the membrane alterations that have been poorly investigated to date.

  4. Functional renormalization group analysis of Dzyaloshinsky-Moriya and Heisenberg spin interactions on the kagome lattice

    Science.gov (United States)

    Hering, Max; Reuther, Johannes

    2017-02-01

    We investigate the effects of Dzyaloshinsky-Moriya (DM) interactions on the frustrated J1-J2 kagome-Heisenberg model using the pseudofermion functional renormalization group (PFFRG) technique. In order to treat the off-diagonal nature of DM interactions, we develop an extended PFFRG scheme. We benchmark this approach in parameter regimes that have previously been studied with other methods and find good agreement of the magnetic phase diagram. Particularly, finite DM interactions are found to stabilize all types of noncollinear magnetic orders of the J1-J2 Heisenberg model (q =0 , √{3 }×√{3 } , and cuboc orders) and shrink the extents of magnetically disordered phases. We discuss our results in the light of the mineral herbertsmithite which has been experimentally predicted to host a quantum spin liquid at low temperatures. Our PFFRG data indicate that this material lies in close proximity to a quantum critical point. In parts of the experimentally relevant parameter regime for herbertsmithite, the spin-correlation profile is found to be in good qualitative agreement with recent inelastic-neutron-scattering data.

  5. Structure and function of the interacting domains of Spire and Fmn-family formins

    Energy Technology Data Exchange (ETDEWEB)

    Vizcarra, Christina L.; Kreutz, Barry; Rodal, Avital A.; Toms, Angela V.; Lu, Jun; Zheng, Wei; Quinlan, Margot E.; Eck, Michael J. (UCLA); (Brandeis); (DFCI)

    2012-07-11

    Evidence for cooperation between actin nucleators is growing. The WH2-containing nucleator Spire and the formin Cappuccino interact directly, and both are essential for assembly of an actin mesh during Drosophila oogenesis. Their interaction requires the kinase noncatalytic C-lobe domain (KIND) domain of Spire and the C-terminal tail of the formin. Here we describe the crystal structure of the KIND domain of human Spir1 alone and in complex with the tail of Fmn2, a mammalian ortholog of Cappuccino. The KIND domain is structurally similar to the C-lobe of protein kinases. The Fmn2 tail is coordinated in an acidic cleft at the base of the domain that appears to have evolved via deletion of a helix from the canonical kinase fold. Our functional analysis of Cappuccino reveals an unexpected requirement for its tail in actin assembly. In addition, we find that the KIND/tail interaction blocks nucleation by Cappuccino and promotes its displacement from filament barbed ends providing insight into possible modes of cooperation between Spire and Cappuccino.

  6. Density functional theory studies of interactions of ruthenium-arene complexes with base pair steps.

    Science.gov (United States)

    Mutter, Shaun T; Platts, James A

    2011-10-20

    Density functional theory (DFT) calculations have been performed to determine the strength and geometry of intermolecular interactions of "piano-stool" ruthenium arene complexes, which show potential as anticancer treatments. Model complexes with methane and benzene indicate that the coordinated arene has C-H···π acceptor ability similar to that of free benzene, whereas this arene acts as a much stronger C-H donor or partner in π-stacking than free benzene. The source of these enhanced interactions is identified as a combination of electrostatic and dispersion effects. Complexes of Ru-arene complexes with base-pair step fragments of DNA, in which the arene has the potential to act as an intercalator, have also been investigated. Binding energies are found to be sensitive to the size and nature of the arene, with larger and more flexible arenes having stronger binding. π-stacking and C-H···π interactions between arene and DNA bases and hydrogen bonds from coordinated N-H to DNA oxygen atoms, as well as covalent Ru-N bonding, contribute to the overall binding. The effect of complexation on DNA structure is also examined, with larger rise and more negative slide values than canonical B-DNA observed in all cases.

  7. Metal ion and inter-domain interactions as functional networks in E. coli topoisomerase I.

    Science.gov (United States)

    Sissi, Claudia; Cheng, Bokun; Lombardo, Valentina; Tse-Dinh, Yuk-Ching; Palumbo, Manlio

    2013-07-25

    Escherichia coli topoisomerase I (EcTopoI) is a type IA bacterial topoisomerase which is receiving large attention due to its potential application as novel target for antibacterial therapeutics. Nevertheless, a detailed knowledge of its mechanism of action at molecular level is to some extent lacking. This is partly due to the requirement of several factors (metal ions, nucleic acid) to the proper progress of the enzyme catalytic cycle. Additionally, each of them can differently affect the protein structure. Here we assess the role of the different components (DNA, metal ions, protein domains) in a dynamic environment as in solution by monitoring the catalytic as well as the structural properties of EcTopoI. Our results clearly indicated the interaction among these components as functionally relevant and underlined their mutual involvement. Some similarities with other enzymes of the same family emerged (for example DNA prevents divalent metal ions coordination at non selective binding sites). Interestingly, same interactions (C- and N-terminal domain interaction) appear to be peculiar of this bacterial topoisomerase which suggest they could be favorably exploited to the design of selective inhibitors for this class of enzyme.

  8. Role of APP Interactions with Heterotrimeric G Proteins: Physiological Functions and Pathological Consequences.

    Science.gov (United States)

    Copenhaver, Philip F; Kögel, Donat

    2017-01-01

    Following the discovery that the amyloid precursor protein (APP) is the source of β-amyloid peptides (Aβ) that accumulate in Alzheimer's disease (AD), structural analyses suggested that the holoprotein resembles a transmembrane receptor. Initial studies using reconstituted membranes demonstrated that APP can directly interact with the heterotrimeric G protein Gαo (but not other G proteins) via an evolutionarily G protein-binding motif in its cytoplasmic domain. Subsequent investigations in cell culture showed that antibodies against the extracellular domain of APP could stimulate Gαo activity, presumably mimicking endogenous APP ligands. In addition, chronically activating wild type APP or overexpressing mutant APP isoforms linked with familial AD could provoke Go-dependent neurotoxic responses, while biochemical assays using human brain samples suggested that the endogenous APP-Go interactions are perturbed in AD patients. More recently, several G protein-dependent pathways have been implicated in the physiological roles of APP, coupled with evidence that APP interacts both physically and functionally with Gαo in a variety of contexts. Work in insect models has demonstrated that the APP ortholog APPL directly interacts with Gαo in motile neurons, whereby APPL-Gαo signaling regulates the response of migratory neurons to ligands encountered in the developing nervous system. Concurrent studies using cultured mammalian neurons and organotypic hippocampal slice preparations have shown that APP signaling transduces the neuroprotective effects of soluble sAPPα fragments via modulation of the PI3K/Akt pathway, providing a mechanism for integrating the stress and survival responses regulated by APP. Notably, this effect was also inhibited by pertussis toxin, indicating an essential role for Gαo/i proteins. Unexpectedly, C-terminal fragments (CTFs) derived from APP have also been found to interact with Gαs, whereby CTF-Gαs signaling can promote neurite outgrowth

  9. Mechanisms driving change: altered species interactions and ecosystem function through global warming.

    Science.gov (United States)

    Traill, Lochran W; Lim, Matthew L M; Sodhi, Navjot S; Bradshaw, Corey J A

    2010-09-01

    1. We review the mechanisms behind ecosystem functions, the processes that facilitate energy transfer along food webs, and the major processes that allow the cycling of carbon, oxygen and nitrogen, and use case studies to show how these have already been, and will continue to be, altered by global warming. 2. Increased temperatures will affect the interactions between heterotrophs and autotrophs (e.g. pollination and seed dispersal), and between heterotrophs (e.g. predators-prey, parasites/pathogens-hosts), with generally negative ramifications for important ecosystem services (functions that provide direct benefit to human society such as pollination) and potential for heightened species co-extinction rates. 3. Mitigation of likely impacts of warming will require, in particular, the maintenance of species diversity as insurance for the provision of basic ecosystem services. Key to this will be long-term monitoring and focused research that seek to maintain ecosystem resilience in the face of global warming. 4. We provide guidelines for pursuing research that quantifies the nexus between ecosystem function and global warming. These include documentation of key functional species groups within systems, and understanding the principal outcomes arising from direct and indirect effects of a rapidly warming environment. Localized and targeted research and monitoring, complemented with laboratory work, will determine outcomes for resilience and guide adaptive conservation responses and long-term planning.

  10. Jmjd6, a JmjC Dioxygenase with Many Interaction Partners and Pleiotropic Functions

    Science.gov (United States)

    Kwok, Janice; O’Shea, Marie; Hume, David A.; Lengeling, Andreas

    2017-01-01

    Lysyl hydroxylation and arginyl demethylation are post-translational events that are important for many cellular processes. The jumonji domain containing protein 6 (JMJD6) has been reported to catalyze both lysyl hydroxylation and arginyl demethylation on diverse protein substrates. It also interacts directly with RNA. This review summarizes knowledge of JMJD6 functions that have emerged in the last 15 years and considers how a single Jumonji C (JmjC) domain-containing enzyme can target so many different substrates. New links and synergies between the three main proposed functions of Jmjd6 in histone demethylation, promoter proximal pause release of polymerase II and RNA splicing are discussed. The physiological context of the described molecular functions is considered and recently described novel roles for JMJD6 in cancer and immune biology are reviewed. The increased knowledge of JMJD6 functions has wider implications for our general understanding of the JmjC protein family of which JMJD6 is a member. PMID:28360925

  11. Determination of the exchange interaction energy from the polarization expansion of the wave function

    Science.gov (United States)

    Gniewek, Piotr; Jeziorski, Bogumił

    2016-10-01

    The exchange contribution to the energy of the hydrogen atom interacting with a proton is calculated from the polarization expansion of the wave function using the conventional surface-integral formula and two formulas involving volume integrals: the formula of the symmetry-adapted perturbation theory (SAPT) and the variational formula recommended by us. At large internuclear distances R , all three formulas yield the correct expression -(2 /e ) R e-R , but they approximate it with very different convergence rates. In the case of the SAPT formula, the convergence is geometric with the error falling as 3-K, where K is the order of the applied polarization expansion. The error of the surface-integral formula decreases exponentially as aK/(K +1 ) , where a =ln2 - 1/2. The variational formula performs best, its error decays as K1 /2[aK/(K+1 ) ] 2 . These convergence rates are much faster than those resulting from approximating the wave function through the multipole expansion. This shows the efficiency of the partial resummation of the multipole series effected by the polarization expansion. Our results demonstrate also the benefits of incorporating the variational principle into the perturbation theory of molecular interactions.

  12. Interaction between effects of genes coding for dopamine and glutamate transmission on striatal and parahippocampal function.

    Science.gov (United States)

    Pauli, Andreina; Prata, Diana P; Mechelli, Andrea; Picchioni, Marco; Fu, Cynthia H Y; Chaddock, Christopher A; Kane, Fergus; Kalidindi, Sridevi; McDonald, Colm; Kravariti, Eugenia; Toulopoulou, Timothea; Bramon, Elvira; Walshe, Muriel; Ehlert, Natascha; Georgiades, Anna; Murray, Robin; Collier, David A; McGuire, Philip

    2013-09-01

    The genes for the dopamine transporter (DAT) and the D-Amino acid oxidase activator (DAOA or G72) have been independently implicated in the risk for schizophrenia and in bipolar disorder and/or their related intermediate phenotypes. DAT and G72 respectively modulate central dopamine and glutamate transmission, the two systems most robustly implicated in these disorders. Contemporary studies have demonstrated that elevated dopamine function is associated with glutamatergic dysfunction in psychotic disorders. Using functional magnetic resonance imaging we examined whether there was an interaction between the effects of genes that influence dopamine and glutamate transmission (DAT and G72) on regional brain activation during verbal fluency, which is known to be abnormal in psychosis, in 80 healthy volunteers. Significant interactions between the effects of G72 and DAT polymorphisms on activation were evident in the striatum, parahippocampal gyrus, and supramarginal/angular gyri bilaterally, the right insula, in the right pre-/postcentral and the left posterior cingulate/retrosplenial gyri (P dopamine and the glutamate system, thought to be altered in psychosis, have an impact in executive processing which can be modulated by common genetic variation. Copyright © 2012 Wiley Periodicals, Inc., a Wiley company.

  13. Argumentation functions in solving conflicting situations of social interaction in students of different age

    Directory of Open Access Journals (Sweden)

    T.V. Morozova

    2013-10-01

    Full Text Available The paper describes the results of a study of functions of argumentation in solving conflicting situations of social interaction, with the participation of younger students (III and IV grade, middle school students (V and VII grade and high school students (X classes, 211 students overall. The starting point of the research was the idea that distress occurring in a contradictory situation, does not relieve externally, but requires a structural analysis of the situation and a decision from the subject. The hypothesis of the study was the assumption that the argument used by the subject in a situation, can have opposite functions: a real change in the situation or a formal removal of contradictions in order to reduce stress. The author notes that overcoming the contradictions is linked inevitably to the need to clarify the rules of interaction between the parties, and this in turn puts the subject under certain psychological risk (the risk of criticism, disapproval or punishment, the risk of loss of secondary benefits of ambiguous situation, etc. that impede productive action in a contradictory situation.

  14. Interaction between nanoparticles and cytokine proteins: impact on protein and particle functionality

    Science.gov (United States)

    Brown, David M.; Dickson, Claire; Duncan, Paul; Al-Attili, Furat; Stone, Vicki

    2010-05-01

    There is increased use of nanomaterials in many applications due to their unique properties, such as their high surface area and surface reactivity. However, the potential health effects to workers, consumers and the environment exposed to nanoparticles (NPs) is unknown. The aim of this study was to investigate whether NPs which may enter the body could adsorb proteins and whether this interaction affects both the particle and the protein function. The cytokines IL-8 and TNF-α were adsorbed significantly more by 14 nm carbon black (CB) compared with a similar dose of 260 nm CB. Uncoated 14 nm CB particles produced a significant increase in intracellular calcium [Ca2 + ]i which was greater than a similar mass dose of 260 nm CB. The 260 nm CB produced an increase in ICAM-1 expression in A549 epithelial cells at a comparable dose of 14 nm CB, and after coating with TNF-α 260 nm CB produced significantly more ICAM-1 expression compared with control cells. TNF-α bound to 14 nm CB induced a level of ICAM-1 expression that was no greater than the control level, suggesting that the TNF-α activity may be inhibited. These results suggest that NP-protein interaction results both in a decrease in protein function and particle activity in the cellular assays tested and this is currently being investigated.

  15. PTPN14 interacts with and negatively regulates the oncogenic function of YAP.

    Science.gov (United States)

    Liu, X; Yang, N; Figel, S A; Wilson, K E; Morrison, C D; Gelman, I H; Zhang, J

    2013-03-07

    The Hippo signaling pathway regulates cellular proliferation and survival, thus exerting profound effects on normal cell fate and tumorigenesis. The pivotal effector of this pathway is YAP, a transcriptional co-activator amplified in mouse and human cancers where it promotes epithelial-to-mesenchymal transition and malignant transformation. Here, we report a novel regulatory mechanism for the YAP oncogenic function via direct interaction with non-receptor tyrosine phosphatase 14 (PTPN14) through the WW domain of YAP and the PPxY domain of PTPN14. We also found that YAP is a direct substrate of PTPN14. In addition, luciferase reporter assay showed that the inhibition of the YAP transcriptional co-activator function by PTPN14 is mediated through their protein interactions and may result from an increase in the inactive cytoplasmic form of YAP. Last, knockdown of PTPN14 induces the nuclear retention of YAP and increases the YAP-dependent cell migration. In summary, our results indicate a potential regulatory role of PTPN14 on YAP and demonstrate a novel mechanism in YAP regulation.

  16. Method of Moments of Coupled-Cluster Equations: Externally Corrected Approaches Employing Configuration Interaction Wave Functions

    Directory of Open Access Journals (Sweden)

    Ian S.O. Pimienta

    2002-05-01

    Full Text Available Abstract: A new approach to the many-electron correlation problem, termed the method of moments of coupled-cluster equations (MMCC, is further developed and tested. The main idea of the MMCC theory is that of the noniterative energy corrections which, when added to the energies obtained in the standard coupled-cluster calculations, recover the exact (full configuration interaction energy. The MMCC approximations require that a guess is provided for the electronic wave function of interest. The idea of using simple estimates of the wave function, provided by the inexpensive configuration interaction (CI methods employing small sets of active orbitals to define higher–than–double excitations, is tested in this work. The CI-corrected MMCC methods are used to study the single bond breaking in HF and the simultaneous breaking of both O–H bonds in H2O.

  17. Structure of krypton isotopes within the interacting boson model derived from the Gogny energy density functional

    Science.gov (United States)

    Nomura, K.; Rodríguez-Guzmán, R.; Humadi, Y. M.; Robledo, L. M.; Abusara, H.

    2017-09-01

    The evolution and coexistence of the nuclear shapes as well as the corresponding low-lying collective states and electromagnetic transition rates are investigated along the krypton isotopic chain within the framework of the interacting boson model (IBM). The IBM Hamiltonian is determined through mean-field calculations based on the several parametrizations of the Gogny energy density functional and the relativistic mean-field Lagrangian. The mean-field energy surfaces, as functions of the axial β and triaxial γ quadrupole deformations, are mapped onto the expectation value of the interacting-boson Hamiltonian that explicitly includes the particle-hole excitations. The resulting boson Hamiltonian is then used to compute low-energy excitation spectra as well as E 2 and E 0 transition probabilities for Kr-10070. Our results point to a number of examples of prolate-oblate shape transitions and coexistence both on the neutron-deficient and neutron-rich sides. A reasonable agreement with the available experimental data is obtained for the considered nuclear properties.

  18. Disrupting functional interactions between platelet chemokines inhibits atherosclerosis in hyperlipidemic mice.

    Science.gov (United States)

    Koenen, Rory R; von Hundelshausen, Philipp; Nesmelova, Irina V; Zernecke, Alma; Liehn, Elisa A; Sarabi, Alisina; Kramp, Birgit K; Piccinini, Anna M; Paludan, Søren R; Kowalska, M Anna; Kungl, Andreas J; Hackeng, Tilman M; Mayo, Kevin H; Weber, Christian

    2009-01-01

    Atherosclerosis is characterized by chronic inflammation of the arterial wall due to chemokine-driven mononuclear cell recruitment. Activated platelets can synergize with chemokines to exacerbate atherogenesis; for example, by deposition of the chemokines platelet factor-4 (PF4, also known as CXCL4) and RANTES (CCL5), triggering monocyte arrest on inflamed endothelium. Homo-oligomerization is required for the recruitment functions of CCL5, and chemokine heteromerization has more recently emerged as an additional regulatory mechanism, as evidenced by a mutual modulation of CXCL8 and CXCL4 activities and by enhanced monocyte arrest resulting from CCL5-CXCL4 interactions. The CCL5 antagonist Met-RANTES reduces diet-induced atherosclerosis; however, CCL5 antagonism may not be therapeutically feasible, as suggested by studies using Ccl5-deficient mice which imply that direct CCL5 blockade would severely compromise systemic immune responses, delay macrophage-mediated viral clearance and impair normal T cell functions. Here we determined structural features of CCL5-CXCL4 heteromers and designed stable peptide inhibitors that specifically disrupt proinflammatory CCL5-CXCL4 interactions, thereby attenuating monocyte recruitment and reducing atherosclerosis without the aforementioned side effects. These results establish the in vivo relevance of chemokine heteromers and show the potential of targeting heteromer formation to achieve therapeutic effects.

  19. Interaction between nanoparticles and cytokine proteins: impact on protein and particle functionality

    Energy Technology Data Exchange (ETDEWEB)

    Brown, David M; Dickson, Claire; Duncan, Paul; Al-Attili, Furat; Stone, Vicki [School of Life Sciences, Edinburgh Napier University, 10 Colinton Road, Edinburgh, EH10 5DT (United Kingdom)

    2010-05-28

    There is increased use of nanomaterials in many applications due to their unique properties, such as their high surface area and surface reactivity. However, the potential health effects to workers, consumers and the environment exposed to nanoparticles (NPs) is unknown. The aim of this study was to investigate whether NPs which may enter the body could adsorb proteins and whether this interaction affects both the particle and the protein function. The cytokines IL-8 and TNF-{alpha} were adsorbed significantly more by 14 nm carbon black (CB) compared with a similar dose of 260 nm CB. Uncoated 14 nm CB particles produced a significant increase in intracellular calcium [Ca{sup 2+}]{sub i} which was greater than a similar mass dose of 260 nm CB. The 260 nm CB produced an increase in ICAM-1 expression in A549 epithelial cells at a comparable dose of 14 nm CB, and after coating with TNF-{alpha} 260 nm CB produced significantly more ICAM-1 expression compared with control cells. TNF-{alpha} bound to 14 nm CB induced a level of ICAM-1 expression that was no greater than the control level, suggesting that the TNF-{alpha} activity may be inhibited. These results suggest that NP-protein interaction results both in a decrease in protein function and particle activity in the cellular assays tested and this is currently being investigated.

  20. New parametrization of Skyrme's interaction for regularized multireference energy density functional calculations

    Science.gov (United States)

    Washiyama, K.; Bennaceur, K.; Avez, B.; Bender, M.; Heenen, P.-H.; Hellemans, V.

    2012-11-01

    Background: Symmetry restoration and configuration mixing in the spirit of the generator coordinate method based on energy density functionals have become widely used techniques in low-energy nuclear structure physics. Recently, it has been pointed out that these techniques are ill defined for standard Skyrme functionals, and a regularization procedure has been proposed to remove the resulting spuriosities from such calculations. This procedure imposes an integer power of the density for the density-dependent terms of the functional. At present, only dated parametrizations of the Skyrme interaction fulfill this condition.Purpose: To construct a set of parametrizations of the Skyrme energy density functional for multireference energy density functional calculations with regularization using the state-of-the-art fitting protocols.Method: The parametrizations were adjusted to reproduce ground-state properties of a selected set of doubly magic nuclei and properties of nuclear matter. Subsequently, these parameter sets were validated against properties of spherical and deformed nuclei.Results: Our parameter sets successfully reproduce the experimental binding energies and charge radii for a wide range of singly magic nuclei. Compared to the widely used SLy5 and to the SIII parametrization that has integer powers of the density, a significant improvement of the reproduction of the data is observed. Similarly, a good description of the deformation properties at A˜80 was obtained.Conclusions: We have constructed new Skyrme parametrizations with integer powers of the density and validated them against a broad set of experimental data for spherical and deformed nuclei. These parametrizations are tailor-made for regularized multireference energy density functional calculations and can be used to study correlations beyond the mean field in atomic nuclei.

  1. Hox gene function and interaction in the milkweed bug Oncopeltus fasciatus (Hemiptera).

    Science.gov (United States)

    Angelini, David R; Liu, Paul Z; Hughes, Cynthia L; Kaufman, Thomas C

    2005-11-15

    Studies in genetic model organisms such as Drosophila have demonstrated that the homeotic complex (Hox) genes impart segmental identity during embryogenesis. Comparative studies in a wide range of other insect taxa have shown that the Hox genes are expressed in largely conserved domains along the anterior-posterior body axis, but whether they are performing the same functions in different insects is an open question. Most of the Hox genes have been studied functionally in only a few holometabolous insects that undergo metamorphosis. Thus, it is unclear how the Hox genes are functioning in the majority of direct-developing insects and other arthropods. To address this question, we used a combination of RNAi and in situ hybridization to reveal the expression, functions, and regulatory interactions of the Hox genes in the milkweed bug Oncopeltus fasciatus. Our results reveal many similarities and some interesting differences compared to Drosophila. We find that the gene Antennapedia is required for the identity of all three thoracic segments, while Ultrabithorax, abdominal-A and Abdominal-B cooperate to pattern the abdomen. The three abdominal genes exhibit posterior prevalence like in Drosophila, but apparently via some post-transcriptional mechanism. The functions of the head genes proboscipedia, Deformed, and Sex combs reduced were shown previously, and here we find that the complex temporal expression of pb in the labium is like that of other insects, but its regulatory relationship with Scr is unique. Overall, our data reveal that the evolution of insect Hox genes has included many small changes within general conservation of expression and function, and that the milkweed bug provides a useful model for understanding the roles of Hox genes in a direct-developing insect.

  2. Physical Interactions and Functional Relationships of Neuroligin 2 and Midbrain Serotonin Transporters

    Directory of Open Access Journals (Sweden)

    Ran eYe

    2016-01-01

    Full Text Available The neurotransmitter serotonin (5-hydroxytryptamine, 5-HT modulates many key brain functions including those subserving sensation, emotion, reward and cognition. Efficient clearance of 5-HT after release is achieved by the antidepressant-sensitive 5-HT transporter (SERT, SLC6A4. To identify novel SERT regulators, we pursued a proteomic analysis of mouse midbrain SERT complexes, evaluating findings in the context of prior studies that established a SERT-linked transcriptome. Remarkably, both efforts converged on a relationship of SERT with the synaptic adhesion protein neuroligin 2 (NLGN2, a postsynaptic partner for presynaptic neurexins, and a protein well known to organize inhibitory GABAergic synapses. Western blots of midbrain reciprocal immunoprecipitations confirmed SERT/NLGN2 associations, and also extended to other NLGN2 associated proteins (e.g. -neurexin (NRXN, gephyrin. Midbrain SERT/NLGN2 interactions were found to be Ca2+-independent, supporting cis versus trans-synaptic interactions, and were absent in hippocampal preparations, consistent with interactions arising in somatodendritic compartments. Dual color in situ hybridization confirmed co-expression of Tph2 and Nlgn2 mRNA in the dorsal raphe, with immunocytochemical studies confirming SERT:NLGN2 co-localization in raphe cell bodies but not axons. Consistent with correlative mRNA expression studies, loss of NLGN2 expression in Nlgn2 null mice produced significant reductions in midbrain and hippocampal SERT expression and function. Additionally, dorsal raphe 5-HT neurons from Nlgn2 null mice exhibit reduced excitability, a loss of GABAA receptor-mediated IPSCs, and increased 5-HT1A autoreceptor sensitivity. Finally, Nlgn2 null mice display significant changes in behaviors known to be responsive to SERT and/or 5-HT receptor manipulations. We discuss our findings in relation to the possible coordination of intrinsic and extrinsic regulation afforded by somatodendritic SERT:NLGN2

  3. Physical Interactions and Functional Relationships of Neuroligin 2 and Midbrain Serotonin Transporters.

    Science.gov (United States)

    Ye, Ran; Quinlan, Meagan A; Iwamoto, Hideki; Wu, Hsiao-Huei; Green, Noah H; Jetter, Christopher S; McMahon, Douglas G; Veestra-VanderWeele, Jeremy; Levitt, Pat; Blakely, Randy D

    2015-01-01

    The neurotransmitter serotonin [5-hydroxytryptamine (5-HT)] modulates many key brain functions including those subserving sensation, emotion, reward, and cognition. Efficient clearance of 5-HT after release is achieved by the antidepressant-sensitive 5-HT transporter (SERT, SLC6A4). To identify novel SERT regulators, we pursued a proteomic analysis of mouse midbrain SERT complexes, evaluating findings in the context of prior studies that established a SERT-linked transcriptome. Remarkably, both efforts converged on a relationship of SERT with the synaptic adhesion protein neuroligin 2 (NLGN2), a post-synaptic partner for presynaptic neurexins, and a protein well-known to organize inhibitory GABAergic synapses. Western blots of midbrain reciprocal immunoprecipitations confirmed SERT/NLGN2 associations, and also extended to other NLGN2 associated proteins [e.g., α-neurexin (NRXN), gephyrin]. Midbrain SERT/NLGN2 interactions were found to be Ca(2+)-independent, supporting cis vs. trans-synaptic interactions, and were absent in hippocampal preparations, consistent with interactions arising in somatodendritic compartments. Dual color in situ hybridization confirmed co-expression of Tph2 and Nlgn2 mRNA in the dorsal raphe, with immunocytochemical studies confirming SERT:NLGN2 co-localization in raphe cell bodies but not axons. Consistent with correlative mRNA expression studies, loss of NLGN2 expression in Nlgn2 null mice produced significant reductions in midbrain and hippocampal SERT expression and function. Additionally, dorsal raphe 5-HT neurons from Nlgn2 null mice exhibit reduced excitability, a loss of GABAA receptor-mediated IPSCs, and increased 5-HT1A autoreceptor sensitivity. Finally, Nlgn2 null mice display significant changes in behaviors known to be responsive to SERT and/or 5-HT receptor manipulations. We discuss our findings in relation to the possible coordination of intrinsic and extrinsic regulation afforded by somatodendritic SERT:NLGN2 complexes.

  4. Central-peripheral neural network interactions evoked by vagus nerve stimulation: functional consequences on control of cardiac function.

    Science.gov (United States)

    Ardell, Jeffrey L; Rajendran, Pradeep S; Nier, Heath A; KenKnight, Bruce H; Armour, J Andrew

    2015-11-15

    Using vagus nerve stimulation (VNS), we sought to determine the contribution of vagal afferents to efferent control of cardiac function. In anesthetized dogs, the right and left cervical vagosympathetic trunks were stimulated in the intact state, following ipsilateral or contralateral vagus nerve transection (VNTx), and then following bilateral VNTx. Stimulations were performed at currents from 0.25 to 4.0 mA, frequencies from 2 to 30 Hz, and a 500-μs pulse width. Right or left VNS evoked significantly greater current- and frequency-dependent suppression of chronotropic, inotropic, and lusitropic function subsequent to sequential VNTx. Bradycardia threshold was defined as the current first required for a 5% decrease in heart rate. The threshold for the right vs. left vagus-induced bradycardia in the intact state (2.91 ± 0.18 and 3.47 ± 0.20 mA, respectively) decreased significantly with right VNTx (1.69 ± 0.17 mA for right and 3.04 ± 0.27 mA for left) and decreased further following bilateral VNTx (1.29 ± 0.16 mA for right and 1.74 ± 0.19 mA for left). Similar effects were observed following left VNTx. The thresholds for afferent-mediated effects on cardiac parameters were 0.62 ± 0.04 and 0.65 ± 0.06 mA with right and left VNS, respectively, and were reflected primarily as augmentation. Afferent-mediated tachycardias were maintained following β-blockade but were eliminated by VNTx. The increased effectiveness and decrease in bradycardia threshold with sequential VNTx suggest that 1) vagal afferents inhibit centrally mediated parasympathetic efferent outflow and 2) the ipsilateral and contralateral vagi exert a substantial buffering capacity. The intact threshold reflects the interaction between multiple levels of the cardiac neural hierarchy.

  5. Design strategies and functionality of the Visual Interface for Virtual Interaction Development (VIVID) tool

    Science.gov (United States)

    Nguyen, Lac; Kenney, Patrick J.

    1993-01-01

    Development of interactive virtual environments (VE) has typically consisted of three primary activities: model (object) development, model relationship tree development, and environment behavior definition and coding. The model and relationship tree development activities are accomplished with a variety of well-established graphic library (GL) based programs - most utilizing graphical user interfaces (GUI) with point-and-click interactions. Because of this GUI format, little programming expertise on the part of the developer is necessary to create the 3D graphical models or to establish interrelationships between the models. However, the third VE development activity, environment behavior definition and coding, has generally required the greatest amount of time and programmer expertise. Behaviors, characteristics, and interactions between objects and the user within a VE must be defined via command line C coding prior to rendering the environment scenes. In an effort to simplify this environment behavior definition phase for non-programmers, and to provide easy access to model and tree tools, a graphical interface and development tool has been created. The principal thrust of this research is to effect rapid development and prototyping of virtual environments. This presentation will discuss the 'Visual Interface for Virtual Interaction Development' (VIVID) tool; an X-Windows based system employing drop-down menus for user selection of program access, models, and trees, behavior editing, and code generation. Examples of these selection will be highlighted in this presentation, as will the currently available program interfaces. The functionality of this tool allows non-programming users access to all facets of VE development while providing experienced programmers with a collection of pre-coded behaviors. In conjunction with its existing, interfaces and predefined suite of behaviors, future development plans for VIVID will be described. These include incorporation

  6. Conformational Changes in the Capsid of a Calicivirus upon Interaction with Its Functional Receptor

    Energy Technology Data Exchange (ETDEWEB)

    Ossiboff, Robert J.; Zhou, Yi; Lightfoot, Patrick J.; Prasad, B.V. Venkataram; Parker, John S.L. (Baylor); (Cornell)

    2010-07-19

    Nonenveloped viral capsids are metastable structures that undergo conformational changes during virus entry that lead to interactions of the capsid or capsid fragments with the cell membrane. For members of the Caliciviridae, neither the nature of these structural changes in the capsid nor the factor(s) responsible for inducing these changes is known. Feline functional adhesion molecule A (fJAM-A) mediates the attachment and infectious viral entry of feline calicivirus (FCV). Here, we show that the infectivity of some FCV isolates is neutralized following incubation with the soluble receptor at 37 C. We used this property to select mutants resistant to preincubation with the soluble receptor. We isolated and sequenced 24 soluble receptor-resistant (srr) mutants and characterized the growth properties and receptor-binding activities of eight mutants. The location of the mutations within the capsid structure of FCV was mapped using a new 3.6-{angstrom} structure of native FCV. The srr mutations mapped to the surface of the P2 domain were buried at the protruding domain dimer interface or were present in inaccessible regions of the capsid protein. Coupled with data showing that both the parental FCV and the srr mutants underwent increases in hydrophobicity upon incubation with the soluble receptor at 37 C, these findings indicate that FCV likely undergoes conformational change upon interaction with its receptor. Changes in FCV capsid conformation following its interaction with fJAM-A may be important for subsequent interactions of the capsid with cellular membranes, membrane penetration, and genome delivery.

  7. Regulatory and functional interactions of plant growth regulators and plant glutathione S-transferases (GSTs).

    Science.gov (United States)

    Moons, Ann

    2005-01-01

    Plant glutathioneS-transferases (GSTs) are a heterogeneous superfamily of multifunctional proteins, grouped into six classes. The tau (GSTU) and phi (GSTF) class GSTs are the most represented ones and are plant-specific, whereas the smaller theta (GSTT) and zeta (GSTZ) classes are also found in animals. The lambda GSTs (GSTL) and the dehydroascorbate reductases (DHARs) are more distantly related. Plant GSTs perform a variety of pivotal catalytic and non-enzymatic functions in normal plant development and plant stress responses, roles that are only emerging. Catalytic functions include glutathione (GSH)-conjugation in the metabolic detoxification of herbicides and natural products. GSTs can also catalyze GSH-dependent peroxidase reactions that scavenge toxic organic hydroperoxides and protect from oxidative damage. GSTs can furthermore catalyze GSH-dependent isomerizations in endogenous metabolism, exhibit GSH-dependent thioltransferase safeguarding protein function from oxidative damage and DHAR activity functioning in redox homeostasis. Plant GSTs can also function as ligandins or binding proteins for phytohormones (i.e., auxins and cytokinins) or anthocyanins, thereby facilitating their distribution and transport. Finally, GSTs are also indirectly involved in the regulation of apoptosis and possibly also in stress signaling. Plant GST genes exhibit a diversity of expression patterns during biotic and abiotic stresses. Stress-induced plant growth regulators (i.e., jasmonic acid [JA], salicylic acid [SA], ethylene [ETH], and nitric oxide [NO] differentially activate GST gene expression. It is becoming increasingly evident that unique combinations of multiple, often interactive signaling pathways from various phytohormones and reactive oxygen species or antioxidants render the distinct transcriptional activation patterns of individual GSTs during stress. Underestimated post-transcriptional regulations of individual GSTs are becoming increasingly evident and roles

  8. Redox levels in aqueous solution: Effect of van der Waals interactions and hybrid functionals

    Science.gov (United States)

    Ambrosio, Francesco; Miceli, Giacomo; Pasquarello, Alfredo

    2015-12-01

    We investigate redox levels in aqueous solution using a combination of ab initio molecular dynamics (MD) simulations and thermodynamic integration methods. The molecular dynamics are performed with both the semilocal Perdew-Burke-Ernzerhof functional and a nonlocal functional (rVV10) accounting for van der Waals (vdW) interactions. The band edges are determined through three different schemes, namely, from the energy of the highest occupied and of the lowest unoccupied Kohn-Sham states, from total-energy differences, and from a linear extrapolation of the density of states. It is shown that the latter does not depend on the system size while the former two are subject to significant finite-size effects. For the redox levels, we provide a formulation in analogy to the definition of charge transition levels for defects in crystalline materials. We consider the H+/H2 level defining the standard hydrogen electrode, the OH-/OH∗ level corresponding to the oxidation of the hydroxyl ion, and the H2O/OH∗ level for the dehydrogenation of water. In spite of the large structural modifications induced in liquid water, vdW interactions do not lead to any significant structural effect on the calculated band gap and band edges. The effect on the redox levels is also small since the solvation properties of ionic species are little affected by vdW interactions. Since the electronic properties are not significantly affected by the underlying structural properties, it is justified to perform hybrid functional calculations on the configurations of our MD simulations. The redox levels calculated as a function of the fraction α of Fock exchange are found to remain constant, reproducing a general behavior previously observed for charge transition levels of defects. Comparison with experimental values shows very good agreement. At variance, the band edges and the band gap evolve linearly with α. For α ≃ 0.40, we achieve a band gap, band-edge positions, and redox levels in overall

  9. Redox levels in aqueous solution: Effect of van der Waals interactions and hybrid functionals

    Energy Technology Data Exchange (ETDEWEB)

    Ambrosio, Francesco, E-mail: Francesco.Ambrosio@epfl.ch; Miceli, Giacomo; Pasquarello, Alfredo [Chaire de Simulation à l’Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne (Switzerland)

    2015-12-28

    We investigate redox levels in aqueous solution using a combination of ab initio molecular dynamics (MD) simulations and thermodynamic integration methods. The molecular dynamics are performed with both the semilocal Perdew-Burke-Ernzerhof functional and a nonlocal functional (rVV10) accounting for van der Waals (vdW) interactions. The band edges are determined through three different schemes, namely, from the energy of the highest occupied and of the lowest unoccupied Kohn-Sham states, from total-energy differences, and from a linear extrapolation of the density of states. It is shown that the latter does not depend on the system size while the former two are subject to significant finite-size effects. For the redox levels, we provide a formulation in analogy to the definition of charge transition levels for defects in crystalline materials. We consider the H{sup +}/H{sub 2} level defining the standard hydrogen electrode, the OH{sup −}/OH{sup ∗} level corresponding to the oxidation of the hydroxyl ion, and the H{sub 2}O/OH{sup ∗} level for the dehydrogenation of water. In spite of the large structural modifications induced in liquid water, vdW interactions do not lead to any significant structural effect on the calculated band gap and band edges. The effect on the redox levels is also small since the solvation properties of ionic species are little affected by vdW interactions. Since the electronic properties are not significantly affected by the underlying structural properties, it is justified to perform hybrid functional calculations on the configurations of our MD simulations. The redox levels calculated as a function of the fraction α of Fock exchange are found to remain constant, reproducing a general behavior previously observed for charge transition levels of defects. Comparison with experimental values shows very good agreement. At variance, the band edges and the band gap evolve linearly with α. For α ≃ 0.40, we achieve a band gap, band

  10. Evidence for Heterodimerization and Functional Interaction of the Angiotensin Type 2 Receptor and the Receptor MAS.

    Science.gov (United States)

    Leonhardt, Julia; Villela, Daniel C; Teichmann, Anke; Münter, Lisa-Marie; Mayer, Magnus C; Mardahl, Maibritt; Kirsch, Sebastian; Namsolleck, Pawel; Lucht, Kristin; Benz, Verena; Alenina, Natalia; Daniell, Nicholas; Horiuchi, Masatsugu; Iwai, Masaru; Multhaup, Gerhard; Schülein, Ralf; Bader, Michael; Santos, Robson A; Unger, Thomas; Steckelings, Ulrike Muscha

    2017-06-01

    The angiotensin type 2 receptor (AT2R) and the receptor MAS are receptors of the protective arm of the renin-angiotensin system. They mediate strikingly similar actions. Moreover, in various studies, AT2R antagonists blocked the effects of MAS agonists and vice versa. Such cross-inhibition may indicate heterodimerization of these receptors. Therefore, this study investigated the molecular and functional interplay between MAS and the AT2R. Molecular interactions were assessed by fluorescence resonance energy transfer and by cross correlation spectroscopy in human embryonic kidney-293 cells transfected with vectors encoding fluorophore-tagged MAS or AT2R. Functional interaction of AT2R and MAS was studied in astrocytes with CX3C chemokine receptor-1 messenger RNA expression as readout. Coexpression of fluorophore-tagged AT2R and MAS resulted in a fluorescence resonance energy transfer efficiency of 10.8 ± 0.8%, indicating that AT2R and MAS are capable to form heterodimers. Heterodimerization was verified by competition experiments using untagged AT2R and MAS. Specificity of dimerization of AT2R and MAS was supported by lack of dimerization with the transient receptor potential cation channel, subfamily C-member 6. Dimerization of the AT2R was abolished when it was mutated at cysteine residue 35. AT2R and MAS stimulation with the respective agonists, Compound 21 or angiotensin-(1-7), significantly induced CX3C chemokine receptor-1 messenger RNA expression. Effects of each agonist were blocked by an AT2R antagonist (PD123319) and also by a MAS antagonist (A-779). Knockout of a single of these receptors made astrocytes unresponsive for both agonists. Our results suggest that MAS and the AT2R form heterodimers and that-at least in astrocytes-both receptors functionally depend on each other. © 2017 American Heart Association, Inc.

  11. Biochemical and functional interactions of a selective kappa opioid agonist with calcium

    Energy Technology Data Exchange (ETDEWEB)

    VonVoigtlander, P.F.; Ochoa, M.C.; Lewis, R.A.

    1987-01-01

    The discovery of the selective kappa opioid receptor agonist, U-50488H, has provided a tool for the study of the mechanisms and function of the kappa receptor-effector. We have investigated the interactions of this compound with calcium in several biochemical and functional studies to assess the involvement of calcium mechanisms in the kappa receptor-linked effector. In rat brain synaptosomes, U-50488H attenuated the uptake of /sup 45/Ca++ induced by K+ (40 mM) depolarization. This effect was concentration-related (U-50488H 10(-5) to 10(-7) M), was apparent in short (8-second) but not longer (1-minute) term incubations, and did not occur in the presence of a non-polarizing concentration (5.6 mM) of K+. Naloxone (10(-7) M) did not block this effect of U-50488H (10(-6) M), and higher concentrations (10(-5) M) alone blocked calcium uptake. We have found that the binding of the depolarizing amino acid analog, kainic acid, is enhanced by CaCl2. U-50488H (10(-4) to 10(-6) M) blocks this enhancement of /sup 3/H-kainic acid binding in vitro and also blocks the in vivo effects of kainic acid. In mice, intravenous injection of kainic acid causes scratching, convulsions, and death, depending on the dose administered. U-50488H blocks all of these effects (ED50 = 4.5 mg/kg for antagonism of convulsions induced by 27.5 mg/kg kainic acid). The convulsions induced by intracerebroventricularly administered kainic acid are also blocked by U-50488H as are those induced by similarly administered Bay K 8644, a calcium channel activator. All of these anticonvulsant effects of U-50488H were antagonized by naltrexone. Together these data indicate that the kappa agonist U-50488H has functionally relevant interactions with depolarization-related Ca++ mechanisms in the central nervous system.

  12. Microtubule-Actin Cross-Linking Factor 1: Domains, Interaction Partners, and Tissue-Specific Functions.

    Science.gov (United States)

    Goryunov, Dmitry; Liem, Ronald K H

    2016-01-01

    The cytoskeleton of most eukaryotic cells is composed of three principal filamentous components: actin filaments, microtubules (MTs), and intermediate filaments. It is a highly dynamic system that plays crucial roles in a wide range of cellular processes, including migration, adhesion, cytokinesis, morphogenesis, intracellular traffic and signaling, and structural flexibility. Among the large number of cytoskeleton-associated proteins characterized to date, microtubule-actin cross-linking factor 1 (MACF1) is arguably the most versatile integrator and modulator of cytoskeleton-related processes. MACF1 belongs to the plakin family of proteins, and within it, to the spectraplakin subfamily. These proteins are characterized by the ability to bridge MT and actin cytoskeletal networks in a dynamic fashion, which underlies their involvement in the regulation of cell migration, axonal extension, and vesicular traffic. Studying MACF1 functions has provided insights not only into the regulation of the cytoskeleton but also into molecular mechanisms of both normal cellular physiology and cellular pathology. Multiple MACF1 isoforms exist, composed of a large variety of alternatively spliced domains. Each of these domains mediates a specific set of interactions and functions. These functions are manifested in tissue and cell-specific phenotypes observed in conditional MACF1 knockout mice. The conditional models described to date reveal critical roles of MACF1 in mammalian skin, nervous system, heart muscle, and intestinal epithelia. Complete elimination of MACF1 is early embryonic lethal, indicating an essential role for MACF1 in early development. Further studies of MACF1 domains and their interactions will likely reveal multiple new roles of this protein in various tissues.

  13. Biomaterial design for specific cellular interactions: Role of surface functionalization and geometric features

    Science.gov (United States)

    Kolhar, Poornima

    The areas of drug delivery and tissue engineering have experienced extraordinary growth in recent years with the application of engineering principles and their potential to support and improve the field of medicine. The tremendous progress in nanotechnology and biotechnology has lead to this explosion of research and development in biomedical applications. Biomaterials can now be engineered at a nanoscale and their specific interactions with the biological tissues can be modulated. Various design parameters are being established and researched for design of drug-delivery carriers and scaffolds to be implanted into humans. Nanoparticles made from versatile biomaterial can deliver both small-molecule drugs and various classes of bio-macromolecules, such as proteins and oligonucleotides. Similarly in the field of tissue engineering, current approaches emphasize nanoscale control of cell behavior by mimicking the natural extracellular matrix (ECM) unlike, traditional scaffolds. Drug delivery and tissue engineering are closely connected fields and both of these applications require materials with exceptional physical, chemical, biological, and biomechanical properties to provide superior therapy. In the current study the surface functionalization and the geometric features of the biomaterials has been explored. In particular, a synthetic surface for culture of human embryonic stem cells has been developed, demonstrating the importance of surface functionalization in maintaining the pluripotency of hESCs. In the second study, the geometric features of the drug delivery carriers are investigated and the polymeric nanoneedles mediated cellular permeabilization and direct cytoplasmic delivery is reported. In the third study, the combined effect of surface functionalization and geometric modification of carriers for vascular targeting is enunciated. These studies illustrate how the biomaterials can be designed to achieve various cellular behaviors and control the

  14. Alcohol consumption in tertiary education students

    National Research Council Canada - National Science Library

    Reavley, Nicola J; Jorm, Anthony F; McCann, Terence V; Lubman, Dan I

    2011-01-01

    .... The aim of the current study was to survey students and staff within a tertiary education institution to investigate patterns of alcohol use, alcohol-related problems, knowledge of current National...

  15. Interaction potential for water dimer from symmetry-adapted perturbation theory based on density functional description of monomers

    NARCIS (Netherlands)

    Bukowski, R.; Szalewicz, K.; Groenenboom, G.C.; Avoird, A. van der

    2006-01-01

    A new six-dimensional interaction potential for the water dimer has been obtained by fitting interaction energies computed at 2510 geometries using a variant of symmetry-adapted perturbation theory (SAPT) based on density functional theory (DFT) description of monomers, referred to as SAPT(DFT). The

  16. Human Dopamine Receptors Interaction Network (DRIN): a systems biology perspective on topology, stability and functionality of the network.

    Science.gov (United States)

    Podder, Avijit; Jatana, Nidhi; Latha, N

    2014-09-21

    Dopamine receptors (DR) are one of the major neurotransmitter receptors present in human brain. Malfunctioning of these receptors is well established to trigger many neurological and psychiatric disorders. Taking into consideration that proteins function collectively in a network for most of the biological processes, the present study is aimed to depict the interactions between all dopamine receptors following a systems biology approach. To capture comprehensive interactions of candidate proteins associated with human dopamine receptors, we performed a protein-protein interaction network (PPIN) analysis of all five receptors and their protein partners by mapping them into human interactome and constructed a human Dopamine Receptors Interaction Network (DRIN). We explored the topology of dopamine receptors as molecular network, revealing their characteristics and the role of central network elements. More to the point, a sub-network analysis was done to determine major functional clusters in human DRIN that govern key neurological pathways. Besides, interacting proteins in a pathway were characterized and prioritized based on their affinity for utmost drug molecules. The vulnerability of different networks to the dysfunction of diverse combination of components was estimated under random and direct attack scenarios. To the best of our knowledge, the current study is unique to put all five dopamine receptors together in a common interaction network and to understand the functionality of interacting proteins collectively. Our study pinpointed distinctive topological and functional properties of human dopamine receptors that have helped in identifying potential therapeutic drug targets in the dopamine interaction network.

  17. Observations of Adolescent Peer Group Interactions as a Function of Within- and Between-Group Centrality Status

    Science.gov (United States)

    Ellis, Wendy E.; Dumas, Tara M.; Mahdy, Jasmine C.; Wolfe, David A.

    2012-01-01

    Observations of adolescent (n = 258; M age = 15.45) peer group triads (n = 86) were analyzed to identify conversation and interaction styles as a function of within-group and between-group centrality status. Group members' discussions about hypothetical dilemmas were coded for agreements, disagreements, commands, and opinions. Interactions during…

  18. Mobilization of interactions between functional diversity of plant and soil organisms on nitrogen availability and use

    Science.gov (United States)

    Drut, Baptiste; Cassagne, Nathalie; Cannavacciuolo, Mario; Brauman, Alain; Le Floch, Gaëtan; Cobo, Jose; Fustec, Joëlle

    2017-04-01

    Keywords: legumes, earthworms, microorganisms, nitrogen, interactions Both aboveground and belowground biodiversity and their interactions can play an important role in crop productivity. Plant functional diversity, such as legume based intercrops have been shown to improve yields through plant complementarity for nitrogen use (Corre-Hellou et al., 2006). Moreover, plant species or plant genotype may influence the structure of soil microorganism communities through the composition of rhizodeposits in the rhizosphere (Dennis et al., 2010). Belowground diversity can also positively influence plant performance especially related to functional dissimilarity between soil organisms (Eisenhauer, 2012). Earthworms through their burrowing activity influence soil microbial decomposers and nutrient availability and have thus been reported to increase plant growth (Brown, 1995; Brown et al., 2004). We hypothesize that i) plant functional (genetic and/or specific) diversity associated to functional earthworms diversity are key drivers of interactions balance to improve crop performances and ii) the improvement of plant performances can be related to change in the structure of soil microorganism communities due to the diversity of rhizodeposits and the burrowing activity of earthworms. In a first mesocosm experiment, we investigated the effect of a gradient of plant diversity - one cultivar of wheat (Triticum aestivum L.), 3 different wheat cultivars, and 3 different cultivars intercropped with clover (Trifolium hybridum L.) - and the presence of one (endogeic) or two (endogeic and anecic) categories of earthworms on biomass and nitrogen accumulation of wheat. In a second mesocosm experiment, we investigated the influence of three species with different rhizodeposition - wheat, rapeseed (Brassica napus L. ) and faba bean (Vicia faba L.) in pure stand or intercropped - and the presence of endogeic earthworms on microbial activity and nitrogen availability. In the first experiment

  19. An examination of student attitudes and understanding of exponential functions using interactive instructional multimedia

    Science.gov (United States)

    Singleton, Cynthia M.

    The purpose of this study was to examine students' attitudes and understanding of exponential functions using InterAct Math, a mathematics tutorial software. The researcher used a convenience sampling of a total of 78 students from two intact pre-calculus classes; the students in the experimental group totaled 41 and the control group totaled 37. The two groups were exposed to the same curriculum content taught by the same instructor, the researcher. The experimental group used the mathematics tutorial software as an integral part of the instructional delivery. The control group used traditional instruction without integration of the educational technology. Data were collected during a two week span using a mixed-methodology to address the major research questions: (1) Is there a statistically significant difference in the mean achievement test scores between the experimental and the control groups? (2) Is there a statistically significant difference in students' attitudes toward learning mathematics between the experimental group and the control group? The researcher utilized paired t-tests and independent t-tests as statistical methods to evaluate the effectiveness of the intervention and to establish whether there was a significant difference between the experimental and control groups. Based on the analyses of the quantitative data, it was established that the students who received the InterAct Math tutorial (experimental group) did not perform better than the control group on exponential functions, graphs and applications. However, the quantitative part of the study (Aiken-Dreger Mathematics Attitude Scale) revealed that, while students in the experimental and control groups started with similar attitudes about mathematics and the integration of technology, their attitudes were significantly different at the conclusion of the study. The fear of mathematics was reduced for the experimental group at the end of the study, and their enjoyment of the subject matter

  20. Interaction between carboxyl-functionalized carbon black nanoparticles and porous media

    Science.gov (United States)

    Kim, Song-Bae; Kang, Jin-Kyu; Yi, In-Geol

    2015-04-01

    Carbon nanomaterials, such as carbon nanotubes, fullerene, and graphene, have received considerable attention due to their unique physical and chemical characteristics, leading to mass production and widespread application in industrial, commercial, and environmental fields. During their life cycle from production to disposal, however, carbon nanomaterials are inevitably released into water and soil environments, which have resulted in concern about their health and environmental impacts. Carbon black is a nano-sized amorphous carbon powder that typically contains 90-99% elemental carbon. It can be produced from incomplete combustion of hydrocarbons in petroleum and coal. Carbon black is widely used in chemical and industrial products or applications such as ink pigments, coating plastics, the rubber industry, and composite reinforcements. Even though carbon black is strongly hydrophobic and tends to aggregate in water, it can be dispersed in aqueous media through surface functionalization or surfactant use. The aim of this study was therefore to investigate the transport behavior of carboxyl-functionalized carbon black nanoparticles (CBNPs) in porous media. Column experiments were performed for potassium chloride (KCl), a conservative tracer, and CBNPs under saturated flow conditions. Column experiments was conducted in duplicate using quartz sand, iron oxide-coated sand (IOCS), and aluminum oxide-coated sand (AOCS) to examine the effect of metal (Fe, Al) oxide presence on the transport of CBNPs. Breakthrough curves (BTCs) of CBNPs and chloride were obtained by monitoring effluent, and then mass recovery was quantified from these curves. Additionally, interaction energy profiles for CBNP-porous media were calculated using DLVO theory for sphere-plate geometry. The BTCs of chloride had relative peak concentrations ranging from 0.895 to 0.990. Transport parameters (pore-water velocity v, hydrodynamic dispersion coefficient D) obtained by the model fit from the

  1. Alcohol consumption in tertiary education students

    OpenAIRE

    Reavley Nicola J; Jorm Anthony F; McCann Terence V; Lubman Dan I

    2011-01-01

    Abstract Background Heavy alcohol consumption among adolescents and young adults is an issue of significant public concern. With approximately 50% of young people aged 18-24 attending tertiary education, there is an opportunity within these settings to implement programs that target risky drinking. The aim of the current study was to survey students and staff within a tertiary education institution to investigate patterns of alcohol use, alcohol-related problems, knowledge of current National...

  2. FUNCTIONAL INTERACTION OF LEXICAL AND GRAMMATICAL FACTORS IN THE ENGLISH VERB SYSTEM

    Directory of Open Access Journals (Sweden)

    Nina Sergeevna Kotova

    2017-03-01

    Full Text Available Purpose. The purpose of the research conducted is revealing the peculiarities of lexical paradigmatics influence upon the usage of aspect and temporal verb forms and the opposite impact as well, i.e. the influence of aspect and temporal verb forms upon the lexical meaning of this verb groups under specific conditions of functioning. The lexical paradigmatics is considered as the system of mutually contrasted semantic features of particular verb groups. In this case, we analyze the paradigmatics in the middle language hierarchy for each language level separately. Methodology. The research is conducted synchronically on the material of the contemporary English verb system. Interaction of lexical and grammatical factors in the English verb system is examined in a functional aspect. Such consideration gives a possibility to differentiate the intrasystem phenomena and phenomena of pragmatic character and expose the system-structural mutual relations of lexical and grammatical factors. The research material is the verb as massive word group. From the point of view of interaction of lexical and grammatical factors in the functional and semantic field representing aspectuality, we get interested in the meaning which realizes in the opposition ofatelicity – telicity(telicity correlates the action with the limit, and atelicity demotes the action irrespectively to its limit. The technique applied to the analysis of lexical and grammatical factors in the English verb system is complex combining descriptive and comparative and functional methods. Results. Interrelations and interdependency of lexical and grammatical paradigmatics create particular sustainability in using the lexical unit of this paradigm with aspect and temporal verb forms. In this case, the tendencies of the language sign developing and changing are expressed in the process of the mutual substitution and interpenetration of grammatical forms primarily under the influence of paradigmatic

  3. Loop Entropy Assists Tertiary Order: Loopy Stabilization of Stacking Motifs

    Directory of Open Access Journals (Sweden)

    Daniel P. Aalberts

    2011-11-01

    Full Text Available The free energy of an RNA fold is a combination of favorable base pairing and stacking interactions competing with entropic costs of forming loops. Here we show how loop entropy, surprisingly, can promote tertiary order. A general formula for the free energy of forming multibranch and other RNA loops is derived with a polymer-physics based theory. We also derive a formula for the free energy of coaxial stacking in the context of a loop. Simulations support the analytic formulas. The effects of stacking of unpaired bases are also studied with simulations.

  4. Artificial Intelligence Mechanisms on Interactive Modified Simplex Method with Desirability Function for Optimising Surface Lapping Process

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    Pongchanun Luangpaiboon

    2014-01-01

    Full Text Available A study has been made to optimise the influential parameters of surface lapping process. Lapping time, lapping speed, downward pressure, and charging pressure were chosen from the preliminary studies as parameters to determine process performances in terms of material removal, lap width, and clamp force. The desirability functions of the-nominal-the-best were used to compromise multiple responses into the overall desirability function level or D response. The conventional modified simplex or Nelder-Mead simplex method and the interactive desirability function are performed to optimise online the parameter levels in order to maximise the D response. In order to determine the lapping process parameters effectively, this research then applies two powerful artificial intelligence optimisation mechanisms from harmony search and firefly algorithms. The recommended condition of (lapping time, lapping speed, downward pressure, and charging pressure at (33, 35, 6.0, and 5.0 has been verified by performing confirmation experiments. It showed that the D response level increased to 0.96. When compared with the current operating condition, there is a decrease of the material removal and lap width with the improved process performance indices of 2.01 and 1.14, respectively. Similarly, there is an increase of the clamp force with the improved process performance index of 1.58.

  5. Coordinated modular functionality and prognostic potential of a heart failure biomarker-driven interaction network

    Directory of Open Access Journals (Sweden)

    Wagner Daniel R

    2010-05-01

    Full Text Available Abstract Background The identification of potentially relevant biomarkers and a deeper understanding of molecular mechanisms related to heart failure (HF development can be enhanced by the implementation of biological network-based analyses. To support these efforts, here we report a global network of protein-protein interactions (PPIs relevant to HF, which was characterized through integrative bioinformatic analyses of multiple sources of "omic" information. Results We found that the structural and functional architecture of this PPI network is highly modular. These network modules can be assigned to specialized processes, specific cellular regions and their functional roles tend to partially overlap. Our results suggest that HF biomarkers may be defined as key coordinators of intra- and inter-module communication. Putative biomarkers can, in general, be distinguished as "information traffic" mediators within this network. The top high traffic proteins are encoded by genes that are not highly differentially expressed across HF and non-HF patients. Nevertheless, we present evidence that the integration of expression patterns from high traffic genes may support accurate prediction of HF. We quantitatively demonstrate that intra- and inter-module functional activity may be controlled by a family of transcription factors known to be associated with the prevention of hypertrophy. Conclusion The systems-driven analysis reported here provides the basis for the identification of potentially novel biomarkers and understanding HF-related mechanisms in a more comprehensive and integrated way.

  6. Exact Partition Functions of Interacting Self-Avoiding Walks on Lattices

    Directory of Open Access Journals (Sweden)

    Hsieh Yu-Hsin

    2016-01-01

    Full Text Available Ideas and methods of statistical physics have been shown to be useful for understanding some interesting problems in physical systems, e.g. universality and scaling in critical systems. The interacting self-avoiding walk (ISAW on a lattice is the simplest model for homopolymers and serves as the framework of simple models for biopolymers, such as DNA, RNA, and protein, which are important components in complex systems in biology. In this paper, we briefly review our recent work on exact partition functions of ISAW. Based on zeros of these exact partition functions, we have developed a novel method in which both loci of zeros and thermodynamic functions associated with them are considered. With this method, the first zeros can be identified clearly without ambiguity. The critical point of a small system can then be defined as the peak position of the heat capacity component associated with the first zeros. For the system with two phase transitions, two pairs of first zeros corresponding to two phase transitions can be identified and overlapping Cυ can be well separated. ISAW on the simple cubic lattice is such a system where in addition to a standard collapse transition, there is another freezing transition occurring at a lower temperature. Our approach can give a clear scenario for the collapse and the freezing transitions.

  7. Integrating protein-protein interactions and text mining for protein function prediction

    Directory of Open Access Journals (Sweden)

    Leser Ulf

    2008-07-01

    Full Text Available Abstract Background Functional annotation of proteins remains a challenging task. Currently the scientific literature serves as the main source for yet uncurated functional annotations, but curation work is slow and expensive. Automatic techniques that support this work are still lacking reliability. We developed a method to identify conserved protein interaction graphs and to predict missing protein functions from orthologs in these graphs. To enhance the precision of the results, we furthermore implemented a procedure that validates all predictions based on findings reported in the literature. Results Using this procedure, more than 80% of the GO annotations for proteins with highly conserved orthologs that are available in UniProtKb/Swiss-Prot could be verified automatically. For a subset of proteins we predicted new GO annotations that were not available in UniProtKb/Swiss-Prot. All predictions were correct (100% precision according to the verifications from a trained curator. Conclusion Our method of integrating CCSs and literature mining is thus a highly reliable approach to predict GO annotations for weakly characterized proteins with orthologs.

  8. Stereodynamic tetrahydrobiisoindole “NU-BIPHEP(O”s: functionalization, rotational barriers and non-covalent interactions

    Directory of Open Access Journals (Sweden)

    Golo Storch

    2016-07-01

    Full Text Available Stereodynamic ligands offer intriguing possibilities in enantioselective catalysis. “NU-BIPHEPs” are a class of stereodynamic diphosphine ligands which are easily accessible via rhodium-catalyzed double [2 + 2 + 2] cycloadditions. This study explores the preparation of differently functionalized “NU-BIPHEP(O” compounds, the characterization of non-covalent adduct formation and the quantification of enantiomerization barriers. In order to explore the possibilities of functionalization, we studied modifications of the ligand backbone, e.g., with 3,5-dichlorobenzoyl chloride. Diastereomeric adducts with Okamoto-type cellulose derivatives and on-column deracemization were realized on the basis of non-covalent interactions. Enantioselective dynamic HPLC (DHPLC allowed for the determination of rotational barriers of ΔG‡298K = 92.2 ± 0.3 kJ mol−1 and 99.5 ± 0.1 kJ mol−1 underlining the stereodynamic properties of “NU-BIPHEPs” and “NU-BIPHEP(Os”, respectively. These results make the preparation of tailor-made functionalized stereodynamic ligands possible and give an outline for possible applications in enantioselective catalysis.

  9. Energy decomposition analysis of intermolecular interactions using a block-localized wave function approach

    Science.gov (United States)

    Mo, Yirong; Gao, Jiali; Peyerimhoff, Sigrid D.

    2000-04-01

    An energy decomposition scheme based on the block-localized wave function (BLW) method is proposed. The key of this scheme is the definition and the full optimization of the diabatic state wave function, where the charge transfer among interacting molecules is deactivated. The present energy decomposition (ED), BLW-ED, method is similar to the Morokuma decomposition scheme in definition of the energy terms, but differs in implementation and the computational algorithm. In addition, in the BLW-ED approach, the basis set superposition error is fully taken into account. The application of this scheme to the water dimer and the lithium cation-water clusters reveals that there is minimal charge transfer effect in hydrogen-bonded complexes. At the HF/aug-cc-PVTZ level, the electrostatic, polarization, and charge-transfer effects contribute 65%, 24%, and 11%, respectively, to the total bonding energy (-3.84 kcal/mol) in the water dimer. On the other hand, charge transfer effects are shown to be significant in Lewis acid-base complexes such as H3NSO3 and H3NBH3. In this work, the effect of basis sets used on the energy decomposition analysis is addressed and the results manifest that the present energy decomposition scheme is stable with a modest size of basis functions.

  10. Physiological Interactions of Nanoparticles in Energy Metabolism, Immune Function and Their Biosafety: A Review.

    Science.gov (United States)

    Gomes, Antony; Sengupta, Jayeeta; Datta, Poulami; Ghosh, Sourav; Gomes, Aparna

    2016-01-01

    Nanoparticles owing to their unique physico-chemical properties have found its application in various biological processes, including metabolic pathways taking place within the body. This review tried to focus the involvement of nanoparticles in metabolic pathways and its influence in the energy metabolism, a fundamental criteria for the survival and physiological activity of living beings. The human body utilizes energy derived from food resources through a series of biochemical reactions involving several enzymes, co-factors (metals, non-metals, vitamins etc.) through the metabolic pathways (glycolysis, tri carboxylic acid cycle, oxidative phosphorylation, electron transport chain, etc.) in cellular system. Energy metabolism is also involved in the immune networking of the body for self defence and against pathophysiology. The immune system comprises of different cells and tissues, bioactive molecules for self defence and to fight against diseases. In the recent times, it has been reported through in vivo and in vitro studies that nanoparticles have direct influence on body's immune functions, and can modulate immunity by either suppressing or enhancing it. A comprehensive overview of nanoparticles and its involvement in immune function of the body in normal and pathophysiological conditions has been discussed. Considering these perspectives on nanoparticle interaction another important area which has been highlighted is the biosafety issues which are necessary before therapeutic applications. It is expected that development of physiologically compatible nanoparticles controlling energy metabolic processes, immune functions may show new dimension in the pathophysiology linked with energy and immunity.

  11. Efficient basis sets for non-covalent interactions in XDM-corrected density-functional theory.

    Science.gov (United States)

    Johnson, Erin R; Otero-de-la-Roza, Alberto; Dale, Stephen G; DiLabio, Gino A

    2013-12-07

    In the development and application of dispersion-corrected density-functional theory, the effects of basis set incompleteness have been largely mitigated through the use of very large, nearly-complete basis sets. However, the use of such large basis sets makes application of these methods inefficient for large systems. In this work, we examine a series of basis sets, including Pople-style, correlation-consistent, and polarization-consistent bases, for their ability to efficiently and accurately predict non-covalent interactions when used in conjunction with the exchange-hole dipole moment (XDM) dispersion model. We find that the polarization-consistent 2 (pc-2) basis sets, and two modifications thereof with some diffuse functions removed, give performance of comparable quality to that obtained with aug-cc-pVTZ basis sets, while being roughly 12 to 23 times faster computationally. The behavior is explained, in part, by the role of diffuse functions in recovering small density changes in the intermolecular region. The general performance of the modified basis sets is tested by application of XDM to standard intermolecular benchmark sets at, and away from, equilibrium.

  12. Electronic Zero-Point Oscillations in the Strong-Interaction Limit of Density Functional Theory.

    Science.gov (United States)

    Gori-Giorgi, Paola; Vignale, Giovanni; Seidl, Michael

    2009-04-14

    The exchange-correlation energy in Kohn-Sham density functional theory can be expressed exactly in terms of the change in the expectation of the electron-electron repulsion operator when, in the many-electron Hamiltonian, this same operator is multiplied by a real parameter λ varying between 0 (Kohn-Sham system) and 1 (physical system). In this process, usually called adiabatic connection, the one-electron density is kept fixed by a suitable local one-body potential. The strong-interaction limit of density functional theory, defined as the limit λ→∞, turns out to be like the opposite noninteracting Kohn-Sham limit (λ→0) mathematically simpler than the physical (λ = 1) case and can be used to build an approximate interpolation formula between λ→0 and λ→∞ for the exchange-correlation energy. Here we extend the systematic treatment of the λ→∞ limit [Phys. Rev. A 2007, 75, 042511] to the next leading term, describing zero-point oscillations of strictly correlated electrons, with numerical examples for small spherical atoms. We also propose an improved approximate functional for the zero-point term and a revised interpolation formula for the exchange-correlation energy satisfying more exact constraints.

  13. Interactions

    DEFF Research Database (Denmark)

    The main theme of this anthology is the unique interaction between mathematics, physics and philosophy during the beginning of the 20th century. Seminal theories of modern physics and new fundamental mathematical structures were discovered or formed in this period. Significant physicists...... such as Lorentz and Einstein as well as mathematicians such as Poincare, Minkowski, Hilbert and Weyl contributed to this development. They created the new physical theories and the mathematical disciplines that play such paramount roles in their mathematical formulations. These physicists and mathematicians were...

  14. Non-coding RNA interact to regulate neuronal development and function

    Directory of Open Access Journals (Sweden)

    Bharat Ravi Iyengar

    2014-02-01

    Full Text Available The human brain is one of the most complex biological systems, and the cognitive abilities have greatly expanded compared to invertebrates without much expansion in the number of protein coding genes. This suggests that gene regulation plays a very important role in the development and function of nervous system, by acting at multiple levels such as transcription and translation. In this article we discuss the regulatory roles of three classes of ncRNAs – miRNAs, piRNAs and lncRNA, in the process of neurogenesis and nervous function including control of synaptic plasticity and potential roles in neurodegenerative diseases. miRNAs are involved in diverse processes including neurogenesis where they channelize the cellular physiology towards neuronal differentiation. miRNAs can also indirectly influence neurogenesis by regulating the proliferation and self renewal of neural stem cells and are dysregulated in several neurodegenerative diseases. miRNAs are also known to regulate synaptic plasticity and are usually found to be co-expressed with their targets. The dynamics of gene regulation is thus dependent on the local architecture of the gene regulatory network around the miRNA and its targets. piRNAs had been classically known to regulate transposons in the germ cells. However, piRNAs have been, recently, found to be expressed in the brain and possibly function by imparting epigenetic changes by DNA methylation. piRNAs are known to be maternally inherited and we assume that they may play a role in early development. We also explore the possible function of piRNAs in regulating the expasnsion of transposons in the brain. Brain is known to express several lncRNA but functional roles in brain development are attributed to a few lncRNA while functions of most of the them remain unknown. We review the roles of some known lncRNA and explore the other possible functions of lncRNAs including their interaction with miRNAs.

  15. Tertiary Logistics in the Focus of All Logistics

    OpenAIRE

    Ratko Zelenika; Mirjana Grèiæ; Helga Pavliæ Skender

    2008-01-01

    Trade logistics, traffic logistics, transport logistics and warehouse logistics are just some of the tertiary logistics which enables production processes of all economic sector products and services. Tertiary logistics representing the tertiary economic sector is the most sofisticated and the most important logistics due to the characteristics of the tertiary sector as a service sector that promotes business conditions in all economic sectors. Accordingly, tertiary logistics has a crucial ro...

  16. Circadian Clocks and the Interaction between Stress Axis and Adipose Function

    Directory of Open Access Journals (Sweden)

    Isa Kolbe

    2015-01-01

    Full Text Available Many physiological processes and most endocrine functions show fluctuations over the course of the day. These so-called circadian rhythms are governed by an endogenous network of cellular clocks and serve as an adaptation to daily and, thus, predictable changes in the organism’s environment. Circadian clocks have been described in several tissues of the stress axis and in adipose cells where they regulate the rhythmic and stimulated release of stress hormones, such as glucocorticoids, and various adipokine factors. Recent work suggests that both adipose and stress axis clock systems reciprocally influence each other and adrenal-adipose rhythms may be key players in the development and therapy of metabolic disorders. In this review, we summarize our current understanding of adrenal and adipose tissue rhythms and clocks and how they might interact to regulate energy homoeostasis and stress responses under physiological conditions. Potential chronotherapeutic strategies for the treatment of metabolic and stress disorders are discussed.

  17. Interpreting the functional role of a novel interaction motif in prokaryotic sodium channels.

    Science.gov (United States)

    Sula, Altin; Wallace, B A

    2017-06-05

    Voltage-gated sodium channels enable the translocation of sodium ions across cell membranes and play crucial roles in electrical signaling by initiating the action potential. In humans, mutations in sodium channels give rise to several neurological and cardiovascular diseases, and hence they are targets for pharmaceutical drug developments. Prokaryotic sodium channel crystal structures have provided detailed views of sodium channels, which by homology have suggested potentially important functionally related structural features in human sodium channels. A new crystal structure of a full-length prokaryotic channel, NavMs, in a conformation we proposed to represent the open, activated state, has revealed a novel interaction motif associated with channel opening. This motif is associated with disease when mutated in human sodium channels and plays an important and dynamic role in our new model for channel activation. © 2017 Sula and Wallace.

  18. INTERACTING WITH INTERIORS: FUNCTIONALITY, COMFORT AND DECORATION IN LISBON AT THE TRANSITION OF XXTH CENTURY

    Directory of Open Access Journals (Sweden)

    Maria Margarida Rendeiro

    2013-07-01

    Full Text Available This paper pursues to establish that space becomes place whenever the individual uses it and interacts with the environment and with others. It is also shows that the interiors are more than functional units and are key signifiers in the determination of the identity of the dweller. This paper shows the research oriented towards the period of transition from XIX to XX centuries and uses architecture and literature as key research sources. A semiotic approach complements and provides an insight into the potential meaning of decoration and room allocation, in particular, as far as the determination of the public and private spheres are concerned. The Parisian model offered interesting recreations of the French trend adapted into a Portuguese environment, historically defined and ideologically planned.

  19. Multirate Simulations of String Vibrations Including Nonlinear Fret-String Interactions Using the Functional Transformation Method

    Science.gov (United States)

    Trautmann, L.; Rabenstein, R.

    2004-12-01

    The functional transformation method (FTM) is a well-established mathematical method for accurate simulations of multidimensional physical systems from various fields of science, including optics, heat and mass transfer, electrical engineering, and acoustics. This paper applies the FTM to real-time simulations of transversal vibrating strings. First, a physical model of a transversal vibrating lossy and dispersive string is derived. Afterwards, this model is solved with the FTM for two cases: the ideally linearly vibrating string and the string interacting nonlinearly with the frets. It is shown that accurate and stable simulations can be achieved with the discretization of the continuous solution at audio rate. Both simulations can also be performed with a multirate approach with only minor degradations of the simulation accuracy but with preservation of stability. This saves almost 80% of the computational cost for the simulation of a six-string guitar and therefore it is in the range of the computational cost for digital waveguide simulations.

  20. Multiple functions of capsid proteins in (+) stranded RNA viruses during plant-virus interactions.

    Science.gov (United States)

    Weber, Philipp H; Bujarski, Jozef J

    2015-01-22

    In addition to providing a protective shell for genomic RNA(s), the coat (capsid) proteins (CPs) of plus-stranded RNA viruses play a variety of other functions that condition the plant-virus relationship. In this review we outline the extensive research progress that has been made within the last decade on those CP characteristics that relate to virus infectivity, pathogenicity, symptom expression, interactions with host factors, virus movement, vector transmission, host range, as well as those used to study virus evolution. By discussing the examples among a variety of plant RNA viruses we show that in addition to general features and pathways, the involvement of CPs may assume very distinct tasks that depend on the particular virus life style. Research perspectives and potential applications are discussed at the end.

  1. Antibiosis functions during interactions of Trichoderma afroharzianum and Trichoderma gamsii with plant pathogenic Rhizoctonia and Pythium.

    Science.gov (United States)

    Zhang, Xinjian; Harvey, Paul R; Stummer, Belinda E; Warren, Rosemary A; Zhang, Guangzhi; Guo, Kai; Li, Jishun; Yang, Hetong

    2015-09-01

    Trichoderma afroharzianum is one of the best characterized Trichoderma species, and strains have been utilized as plant disease suppressive inoculants. In contrast, Trichoderma gamsii has only recently been described, and there is limited knowledge of its disease suppressive efficacies. Comparative studies of changes in gene expression during interactions of these species with their target plant pathogens will provide fundamental information on pathogen antibiosis functions. In the present study, we used complementary DNA amplified fragment length polymorphism (cDNA-AFLP) analysis to investigate changes in transcript profiling of T. afroharzianum strain LTR-2 and T. gamsii strain Tk7a during in vitro interactions with plant pathogenic Rhizoctonia solani and Pythium irregulare. Considerable differences were resolved in the overall expression profiles of strains LTR-2 and Tk7a when challenged with either plant pathogen. In strain LTR-2, previously reported mycoparasitism-related genes such as chitinase, polyketide synthase, and non-ribosomal peptide synthetase were found to be differentially expressed. This was not so for strain Tk7a, with the only previously reported antibiosis-associated genes being small secreted cysteine-rich proteins. Although only one differentially expressed gene was common to both strains LTR-2 and Tk7a, numerous genes reportedly associated with pathogen antibiosis processes were differentially expressed in both strains, including degradative enzymes and membrane transport proteins. A number of novel potential antibiosis-related transcripts were found from strains LTR-2 and Tk7a and remain to be identified. The expression kinetics of 20 Trichoderma (10 from strain LTR-2, 10 from strain Tk7a) transcript-derived fragments (TDFs) were quantified by quantitative reverse transcription PCR (RT-qPCR) at pre- and post-mycelia contact stages of Trichoderma-prey interactions, thereby confirming differential gene expression. Collectively, this research

  2. Electron-phonon interaction using Wannier functions: from single-layer graphene to cuprate superconductors

    Science.gov (United States)

    Giustino, Feliciano

    2008-03-01

    The interaction between electrons and phonons is central to many phenomena, including electrical and thermal transport and superconductivity. Recently the electron-phonon (e-ph) interaction has been the focus of intense research efforts in the physics of high-temperature superconductivity and nanoscale transport. Despite the continued interest in the e-ph problem, first-principles calculations remain challenging due to the large computational effort required to describe e-ph scattering processes in the proximity of the Fermi surface. In this talk I will present a method based on Wannier functions which greatly reduces the computational cost of e-ph calculations [1,2]. The underlying idea is to exploit the spatial localization of electrons and phonons in the maximally localized Wannier representation. After describing the method I will review recent applications to materials of current interest. I will discuss how the e-ph interaction affects the dynamics of Dirac fermions in graphene [3], the origin of superconductivity in boron-doped diamond [1], and the relation between Fermi surface topology and superconductivity in super-hard carbides. I will conclude this presentation by discussing the role of phonons in the angle-resolved photoemission spectra of cuprates [4]. [1] F. Giustino, J.R. Yates, I. Souza, M.L. Cohen, and S.G. Louie, Phys. Rev. Lett. 98, 047005 (2007). [2] F. Giustino, M.L. Cohen, and S.G. Louie, Phys. Rev. B 76, 165108 (2007). [3] C.-H. Park, F. Giustino, M.L. Cohen, and S.G. Louie, Phys. Rev. Lett. 99, 086804 (2007). [4] F. Giustino, M.L. Cohen, and S.G. Louie, http://arXiv:0710.2146.

  3. Effect of the Interaction between Recanalization and Collateral Circulation on Functional Outcome in Acute Ischaemic Stroke.

    Science.gov (United States)

    Mangiafico, Salvatore; Saia, Valentina; Nencini, Patrizia; Romani, Ilaria; Palumbo, Vanessa; Pracucci, Giovanni; Consoli, Arturo; Rosi, Andrea; Renieri, Leonardo; Nappini, Sergio; Limbucci, Nicola; Inzitari, Domenico; Gensini, Gian Franco

    2014-12-01

    Identification of patients with acute ischaemic stroke who could most benefit from arterial recanalization after endovascular treatment remains an unsettled issue. Although several classifications of collateral circulation have been proposed, the clinical role of collaterals is still debated. We evaluated the effect of the collateral circulation in relation to recanalization as a predictor of clinical outcome. Data were prospectively collected from 103 patients consecutively treated for proximal middle cerebral or internal carotid artery occlusion. The collateral circulation was evaluated with a novel semiquantitative-qualitative score, the Careggi collateral score (CCS), in six grades. Both CCS and recanalization grades (TICI) were analysed in relation to clinical outcome. A statistical analysis was performed to evaluate the effect of interaction between recanalization and collateral circulation on clinical outcome. Out of the 103 patients, 37 (36.3%) had poor collaterals, and 65 (63.7%) had good collaterals. Patients with good collaterals had lower basal National Institute of Health Stroke Scale (NIHSS), more distal occlusion, smaller lesions at 24h CT scan and better functional outcome. After multivariate analysis, the interaction between recanalization and collateral grades was significantly stronger as a predictor of good outcome (OR 6.87, 95% CI 2.11-22.31) or death (OR 4.66, 95%CI 1.48-14.73) compared to the effect of the single variables. Collaterals showed an effect of interaction with the recanalization grade in determining a favourable clinical outcome. Assessment of the collateral circulation might help predict clinical results after recanalization in patients undergoing endovascular treatment for acute ischaemic stroke.

  4. AB Initio Protein Tertiary Structure Prediction: Comparative-Genetic Algorithm with Graph Theoretical Methods

    Energy Technology Data Exchange (ETDEWEB)

    Gregurick, S. K.

    2001-04-20

    During the period from September 1, 1998 until September 1, 2000 I was awarded a Sloan/DOE postdoctoral fellowship to work in collaboration with Professor John Moult at the Center for Advanced Research in Biotechnology (CARB). Our research project, ''Ab Initio Protein Tertiary Structure Prediction and a Comparative Genetic algorithm'', yielded promising initial results. In short, the project is designed to predict the native fold, or native tertiary structure, of a given protein by inputting only the primary sequence of the protein (one or three letter code). The algorithm is based on a general learning, or evolutionary algorithm and is called Genetic Algorithm (GAS). In our particular application of GAS, we search for native folds, or lowest energy structures, using two different descriptions for the interactions of the atoms and residues in a given protein sequence. One potential energy function is based on a free energy description, while the other function is a threading potential derived by Moult and Samudrala. This modified genetic algorithm was loosely termed a Comparative Genetic Algorithm and was designed to search for native folded structures on both potential energy surfaces, simultaneously. We tested the algorithm on a series of peptides ranging from 11 to 15 residues in length, which are thought to be independent folding units and thereby will fold to native structures independent of the larger protein environment. Our initial results indicated a modest increase in accuracy, as compared to a standard Genetic Algorithm. We are now in the process of improving the algorithm to increase the sensitivity to other inputs, such as secondary structure requirements. The project did not involve additional students and as of yet, the work has not been published.

  5. Density functional studies of endosulphan and its interaction with glycine and GABA

    Indian Academy of Sciences (India)

    C N Ramachandran; Brijesh Kumar Mishra; Ashwani Kumar Tiwari

    2012-01-01

    Density functional theoretic (DFT) methods are employed to study the interactions between endosulphan and two amino acids, namely glycine and -aminobutyric acid (GABA). Two conformers of each isomer - and -endosulphan are considered in the study. The DFT methods B3LYP, M05, M05-2X, M06 and M06-2X in conjunction with the basis set 6-31++G∗∗ are used. The complexes of - and -endosulphan with amino acids are stabilized by a strong hydrogen bond. In addition, there are several weak C-H…O interactions present between the two moieties. Among the DFT methods used, M06-2X method shows the highest stabilization energy for all the complexes. The M06-2X/6-31++G∗∗ method predicts that among the four conformers of endosulphan, the conformer in which the S=O points up, forms the most stable complex with both glycine and GABA, with stabilization energies −15.24 kcal/mol and −14.39 kcal/mol, respectively. The conformer in which the S=O points down, forms the least stable complex with both amino acids with stabilization energies −7.14 and −7.85 kcal/mol, respectively.

  6. Structural and functional interaction between the human DNA repair proteins DNA ligase IV and XRCC4.

    Science.gov (United States)

    Wu, Peï-Yu; Frit, Philippe; Meesala, SriLakshmi; Dauvillier, Stéphanie; Modesti, Mauro; Andres, Sara N; Huang, Ying; Sekiguchi, JoAnn; Calsou, Patrick; Salles, Bernard; Junop, Murray S

    2009-06-01

    Nonhomologous end-joining represents the major pathway used by human cells to repair DNA double-strand breaks. It relies on the XRCC4/DNA ligase IV complex to reseal DNA strands. Here we report the high-resolution crystal structure of human XRCC4 bound to the carboxy-terminal tandem BRCT repeat of DNA ligase IV. The structure differs from the homologous Saccharomyces cerevisiae complex and reveals an extensive DNA ligase IV binding interface formed by a helix-loop-helix structure within the inter-BRCT linker region, as well as significant interactions involving the second BRCT domain, which induces a kink in the tail region of XRCC4. We further demonstrate that interaction with the second BRCT domain of DNA ligase IV is necessary for stable binding to XRCC4 in cells, as well as to achieve efficient dominant-negative effects resulting in radiosensitization after ectopic overexpression of DNA ligase IV fragments in human fibroblasts. Together our findings provide unanticipated insight for understanding the physical and functional architecture of the nonhomologous end-joining ligation complex.

  7. Structural and Functional Interaction Between the Human DNA Repair Proteins DNA ligase IV and XRCC4

    Energy Technology Data Exchange (ETDEWEB)

    Wu, P.; Meesala, S; Dauvillier, S; Modesti, M; Andres, S; Huang, Y; Sekiguchi, J; Calsou, P; Salles, B; Junop, M

    2009-01-01

    Nonhomologous end-joining represents the major pathway used by human cells to repair DNA double-strand breaks. It relies on the XRCC4/DNA ligase IV complex to reseal DNA strands. Here we report the high-resolution crystal structure of human XRCC4 bound to the carboxy-terminal tandem BRCT repeat of DNA ligase IV. The structure differs from the homologous Saccharomyces cerevisiae complex and reveals an extensive DNA ligase IV binding interface formed by a helix-loop-helix structure within the inter-BRCT linker region, as well as significant interactions involving the second BRCT domain, which induces a kink in the tail region of XRCC4. We further demonstrate that interaction with the second BRCT domain of DNA ligase IV is necessary for stable binding to XRCC4 in cells, as well as to achieve efficient dominant-negative effects resulting in radiosensitization after ectopic overexpression of DNA ligase IV fragments in human fibroblasts. Together our findings provide unanticipated insight for understanding the physical and functional architecture of the nonhomologous end-joining ligation complex.

  8. DNA homologous recombination factor SFR1 physically and functionally interacts with estrogen receptor alpha.

    Directory of Open Access Journals (Sweden)

    Yuxin Feng

    Full Text Available Estrogen receptor alpha (ERα, a ligand-dependent transcription factor, mediates the expression of its target genes by interacting with corepressors and coactivators. Since the first cloning of SRC1, more than 280 nuclear receptor cofactors have been identified, which orchestrate target gene transcription. Aberrant activity of ER or its accessory proteins results in a number of diseases including breast cancer. Here we identified SFR1, a protein involved in DNA homologous recombination, as a novel binding partner of ERα. Initially isolated in a yeast two-hybrid screen, the interaction of SFR1 and ERα was confirmed in vivo by immunoprecipitation and mammalian one-hybrid assays. SFR1 co-localized with ERα in the nucleus, potentiated ER's ligand-dependent and ligand-independent transcriptional activity, and occupied the ER binding sites of its target gene promoters. Knockdown of SFR1 diminished ER's transcriptional activity. Manipulating SFR1 expression by knockdown and overexpression revealed a role for SFR1 in ER-dependent and -independent cancer cell proliferation. SFR1 differs from SRC1 by the lack of an intrinsic activation function. Taken together, we propose that SFR1 is a novel transcriptional modulator for ERα and a potential target in breast cancer therapy.

  9. Functionalized polystyrene nanoparticles as a platform for studying bio–nano interactions

    Science.gov (United States)

    Loos, Cornelia; Syrovets, Tatiana; Musyanovych, Anna; Mailänder, Volker; Landfester, Katharina; Nienhaus, G Ulrich

    2014-01-01

    Summary Nanoparticles of various shapes, sizes, and materials carrying different surface modifications have numerous technological and biomedical applications. Yet, the mechanisms by which nanoparticles interact with biological structures as well as their biological impact and hazards remain poorly investigated. Due to their large surface to volume ratio, nanoparticles usually exhibit properties that differ from those of bulk materials. Particularly, the surface chemistry of the nanoparticles is crucial for their durability and solubility in biological media as well as for their biocompatibility and biodistribution. Polystyrene does not degrade in the cellular environment and exhibits no short-term cytotoxicity. Because polystyrene nanoparticles can be easily synthesized in a wide range of sizes with distinct surface functionalizations, they are perfectly suited as model particles to study the effects of the particle surface characteristics on various biological parameters. Therefore, we have exploited polystyrene nanoparticles as a convenient platform to study bio–nano interactions. This review summarizes studies on positively and negatively charged polystyrene nanoparticles and compares them with clinically used superparamagnetic iron oxide nanoparticles. PMID:25671136

  10. Impact of flame-wall interaction on premixed flame dynamics and transfer function characteristics

    KAUST Repository

    Kedia, K.S.

    2011-01-01

    In this paper, we numerically investigate the response of a perforated-plate stabilized laminar methane-air premixed flame to imposed inlet velocity perturbations. A flame model using detailed chemical kinetics mechanism is applied and heat exchange between the burner plate and the gas mixture is incorporated. Linear transfer functions, for low mean inlet velocity oscillations, are analyzed for different equivalence ratio, mean inlet velocity, plate thermal conductivity and distance between adjacent holes. The oscillations of the heat exchange rate at the top of the burner surface plays a critical role in driving the growth of the perturbations over a wide range of conditions, including resonance. The flame response to the perturbations at its base takes the form of consumption speed oscillations in this region. Flame stand-off distance increases/decreases when the flame-wall interaction strengthens/weakens, impacting the overall dynamics of the heat release. The convective lag between the perturbations and the flame base response govern the phase of heat release rate oscillations. There is an additional convective lag between the perturbations at the flame base and the flame tip which has a weaker impact on the heat release rate oscillations. At higher frequencies, the flame-wall interaction is weaker and the heat release oscillations are driven by the flame area oscillations. The response of the flame to higher amplitude oscillations are used to gain further insight into the mechanisms. © 2010 Published by Elsevier Inc. on behalf of The Combustion Institute. All rights reserved.

  11. Functional interaction of caveolin-1 with Bruton's tyrosine kinase and Bmx.

    Science.gov (United States)

    Vargas, Leonardo; Nore, Beston F; Berglof, Anna; Heinonen, Juhana E; Mattsson, Pekka T; Smith, C I Edvard; Mohamed, Abdalla J

    2002-03-15

    Bruton's tyrosine kinase (Btk), a member of the Tec family of protein-tyrosine kinases, has been shown to be crucial for B cell development, differentiation, and signaling. Mutations in the Btk gene lead to X-linked agammaglobulinemia in humans and X-linked immunodeficiency in mice. Using a co-transfection approach, we present evidence here that Btk interacts physically with caveolin-1, a 22-kDa integral membrane protein, which is the principal structural and regulatory component of caveolae membranes. In addition, we found that native Bmx, another member of the Tec family kinases, is associated with endogenous caveolin-1 in primary human umbilical vein endothelial cells. Second, in transient transfection assays, expression of caveolin-1 leads to a substantial reduction in the in vivo tyrosine phosphorylation of both Btk and its constitutively active form, E41K. Furthermore, a caveolin-1 scaffolding peptide (amino acids 82--101) functionally suppressed the autokinase activity of purified recombinant Btk protein. Third, we demonstrate that mouse splenic B-lymphocytes express substantial amounts of caveolin-1. Interestingly, caveolin-1 was found to be constitutively phosphorylated on tyrosine 14 in these cells. The expression of caveolin-1 in B-lymphocytes and its interaction with Btk may have implications not only for B cell activation and signaling, but also for antigen presentation.

  12. Toward a cumulative science of functional integration: A meta-analysis of psychophysiological interactions.

    Science.gov (United States)

    Smith, David V; Gseir, Mouad; Speer, Megan E; Delgado, Mauricio R

    2016-08-01

    Much of the work in cognitive neuroscience is shifting from a focus on single brain regions to a focus on the connectivity between multiple brain regions. These inter-regional connectivity patterns contribute to a wide range of behaviors and are studied with models of functional integration. The rapid expansion of the literature on functional integration offers an opportunity to scrutinize the consistency and specificity of one of the most popular approaches for quantifying connectivity: psychophysiological interaction (PPI) analysis. We performed coordinate-based meta-analyses on 284 PPI studies, which allowed us to test (a) whether those studies consistently converge on similar target regions and (b) whether the identified target regions are specific to the chosen seed region and psychological context. Our analyses revealed two key results. First, we found that different types of PPI studies-e.g., those using seeds such as amygdala and dorsolateral prefrontal cortex (DLPFC) and contexts such as emotion and cognitive control, respectively-each consistently converge on similar target regions, thus supporting the reliability of PPI as a tool for studying functional integration. Second, we also found target regions that were specific to the chosen seed region and psychological context, indicating distinct patterns of brain connectivity. For example, the DLPFC seed reliably contributed to a posterior cingulate cortex target during cognitive control but contributed to an amygdala target in other contexts. Our results point to the robustness of PPI while highlighting common and distinct patterns of functional integration, potentially advancing models of brain connectivity. Hum Brain Mapp 37:2904-2917, 2016. © 2016 Wiley Periodicals, Inc.

  13. Planar Cell Polarity Effector Fritz Interacts with Dishevelled and Has Multiple Functions in Regulating PCP.

    Science.gov (United States)

    Wang, Ying; Naturale, Victor F; Adler, Paul N

    2017-04-03

    The Planar cell Polarity Effector (PPE) genes inturned, fuzzy, and fritz are downstream components in the frizzled/starry night signaling pathway, and their function is instructed by upstream Planar Cell Polarity (PCP) core genes such as frizzled and dishevelled PPE proteins accumulate asymmetrically in wing cells and function in a protein complex mediated by direct interactions between In and Frtz and In and Fy. How the PCP proteins instruct the accumulation of PPE protein is unknown. We found a likely direct interaction between Dishevelled and Fritz and Dishevelled and Fuzzy that could play a role in this. We previously found that mild overexpression of frtz rescued a weak in allele. To determine if this was due to extra Frtz stabilizing mutant In or due to Frtz being able to bypass the need for In we generate a precise deletion of the inturned gene (in(PD) ). We found that mild overexpression of Fritz partially rescued in(PD) , indicating that fritz has In independent activity in PCP. Previous studies of PPE proteins used fixed tissues, and did not provide any insights into the dynamic properties of PPE proteins. We used CRISPR/Cas9 genome editing technology to edit the fritz gene to add a green fluorescent protein tag. fritz(m)(NeonGreen) provides complete rescue activity and works well for in vivo imaging. Our data showed that Fritz is very dynamic in epidermal cells and preferentially distributed to discrete membrane subdomains ("puncta"). Surprisingly, we found it in stripes in developing bristles. Copyright © 2017 Wang et al.

  14. Planar Cell Polarity Effector Fritz Interacts with Dishevelled and Has Multiple Functions in Regulating PCP

    Science.gov (United States)

    Wang, Ying; Naturale, Victor F.; Adler, Paul N.

    2017-01-01

    The Planar cell Polarity Effector (PPE) genes inturned, fuzzy, and fritz are downstream components in the frizzled/starry night signaling pathway, and their function is instructed by upstream Planar Cell Polarity (PCP) core genes such as frizzled and dishevelled. PPE proteins accumulate asymmetrically in wing cells and function in a protein complex mediated by direct interactions between In and Frtz and In and Fy. How the PCP proteins instruct the accumulation of PPE protein is unknown. We found a likely direct interaction between Dishevelled and Fritz and Dishevelled and Fuzzy that could play a role in this. We previously found that mild overexpression of frtz rescued a weak in allele. To determine if this was due to extra Frtz stabilizing mutant In or due to Frtz being able to bypass the need for In we generate a precise deletion of the inturned gene (inPD). We found that mild overexpression of Fritz partially rescued inPD, indicating that fritz has In independent activity in PCP. Previous studies of PPE proteins used fixed tissues, and did not provide any insights into the dynamic properties of PPE proteins. We used CRISPR/Cas9 genome editing technology to edit the fritz gene to add a green fluorescent protein tag. fritzmNeonGreen provides complete rescue activity and works well for in vivo imaging. Our data showed that Fritz is very dynamic in epidermal cells and preferentially distributed to discrete membrane subdomains (“puncta”). Surprisingly, we found it in stripes in developing bristles. PMID:28258110

  15. Per capita interactions and stress tolerance drive stress-induced changes in biodiversity effects on ecosystem functions.

    Science.gov (United States)

    Baert, Jan M; Janssen, Colin R; Sabbe, Koen; De Laender, Frederik

    2016-08-18

    Environmental stress changes the relationship between biodiversity and ecosystem functions, but the underlying mechanisms are poorly understood. Because species interactions shape biodiversity-ecosystem functioning relationships, changes in per capita interactions under stress (as predicted by the stress gradient hypothesis) can be an important driver of stress-induced changes in these relationships. To test this hypothesis, we measure productivity in microalgae communities along a diversity and herbicide gradient. On the basis of additive partitioning and a mechanistic community model, we demonstrate that changes in per capita interactions do not explain effects of herbicide stress on the biodiversity-productivity relationship. Instead, assuming that the per capita interactions remain unaffected by stress, causing species densities to only change through differences in stress tolerance, suffices to predict the stress-induced changes in the biodiversity-productivity relationship and community composition. We discuss how our findings set the stage for developing theory on how environmental stress changes biodiversity effects on ecosystem functions.

  16. Adolescent Maturation of Dopamine D1 and D2 Receptor Function and Interactions in Rodents

    Science.gov (United States)

    Dwyer, Jennifer B.; Leslie, Frances M.

    2016-01-01

    Adolescence is a developmental period characterized by heightened vulnerability to illicit drug use and the onset of neuropsychiatric disorders. These clinical phenomena likely share common neurobiological substrates, as mesocorticolimbic dopamine systems actively mature during this period. Whereas prior studies have examined age-dependent changes in dopamine receptor binding, there have been fewer functional analyses. The aim of the present study was therefore to determine whether the functional consequences of D1 and D2-like activation are age-dependent. Adolescent and adult rats were given direct D1 and D2 agonists, alone and in combination. Locomotor and stereotypic behaviors were measured, and brains were collected for analysis of mRNA expression for the immediate early genes (IEGs), cfos and arc. Adolescents showed enhanced D2-like receptor control of locomotor and repetitive behaviors, which transitioned to dominant D1-like mechanisms in adulthood. When low doses of agonists were co-administered, adults showed supra-additive behavioral responses to D1/D2 combinations, whereas adolescents did not, which may suggest age differences in D1/D2 synergy. D1/D2-stimulated IEG expression was particularly prominent in the bed nucleus of the stria terminalis (BNST). Given the BNST’s function as an integrator of corticostriatal, hippocampal, and stress-related circuitry, and the importance of neural network dynamics in producing behavior, an exploratory functional network analysis of regional IEG expression was performed. This data-driven analysis demonstrated similar developmental trajectories as those described in humans and suggested that dopaminergic drugs alter forebrain coordinated gene expression age dependently. D1/D2 recruitment of stress nuclei into functional networks was associated with low behavioral output in adolescents. Network analysis presents a novel tool to assess pharmacological action, and highlights critical developmental changes in functional

  17. A Comparative Study of the Spontaneous Social Interactions of Children with High-Functioning Autism and Children with Asperger's Disorder

    Science.gov (United States)

    Macintosh, Kathleen; Dissanayake, Cheryl

    2006-01-01

    A comparative observational study was undertaken of the spontaneous social interactions of children with high-functioning autism and Asperger's disorder. The sample comprised 20 children with high-functioning autism, 19 children with Asperger's disorder and 17 typically developing children matched on chronological age and overall mental age. A…

  18. Consistent structures and interactions by density functional theory with small atomic orbital basis sets

    Science.gov (United States)

    Grimme, Stefan; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas

    2015-08-01

    A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of "low-cost" electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods

  19. Consistent structures and interactions by density functional theory with small atomic orbital basis sets.

    Science.gov (United States)

    Grimme, Stefan; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas

    2015-08-07

    A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of "low-cost" electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods

  20. Physical and functional interactions between USF and Sp1 proteins regulate human deoxycytidine kinase promoter activity.

    Science.gov (United States)

    Ge, Yubin; Jensen, Tanya L; Matherly, Larry H; Taub, Jeffrey W

    2003-12-12

    Deoxycytidine kinase (EC 2.7.1.74, dCK) is central to drug activity of anticancer and antiviral agents such as cytosine arabinoside (araC) and gemcitabine. HepG2 hepatocellular carcinoma cells were used to study the transcriptional regulation of dCK. 5'-Deletion and site-directed mutagenesis of the dCK upstream region (positions -464 to -27) confirmed the importance of two GC-boxes (positions -317 to -309 and -213 to -206) and two E-boxes (positions -302 to -297 and -278 to -273). In vitro electromobility shift assays with HepG2 nuclear extracts and in vivo chromatin immunoprecipitation assays with HepG2 chromatin extracts confirmed the presence of bound Sp1/Sp3 and USF1/2. Co-transfections in HepG2 cells showed that USF1 and USF2a stimulated and Sp1 repressed promoter activity from a dCK-luciferase reporter gene construct. In Sp- and USF-null Drosophila Mel-2 cells, both Sp1 and USF1 stimulated dCK promoter activity in a dose-dependent manner, however, both Sp3 and USF2a were effectively inert. Combined Sp1 and USF1 showed additive transactivation at lower concentrations of Sp1. Sp1 was inhibitory at higher levels. Stimulation by combined USF1/USF2a with Sp1 was similar to that for USF1 alone with Sp1, whereas transactivation by Sp1 and USF2a without USF1 was synergistic. Physical interactions between USF and Sp proteins were confirmed by immunoprecipitations with Sp- and USF-specific antibodies. Domain mapping of USF1 and USF2a localized the functional interactions between USF and Sp proteins to the DNA binding domain of USF. Identifying the physical and functional interactions between Sp and USF proteins may lead to a better understanding of the basis for differential expression of the dCK gene in tumor cells and may foster strategies for up-regulating dCK gene expression and improving chemotherapy with araC and gemcitabine.

  1. Consistent structures and interactions by density functional theory with small atomic orbital basis sets

    Energy Technology Data Exchange (ETDEWEB)

    Grimme, Stefan, E-mail: grimme@thch.uni-bonn.de; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas [Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn (Germany)

    2015-08-07

    A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of “low-cost” electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT

  2. A multi-functional imaging approach to high-content protein interaction screening.

    Directory of Open Access Journals (Sweden)

    Daniel R Matthews

    Full Text Available Functional imaging can provide a level of quantification that is not possible in what might be termed traditional high-content screening. This is due to the fact that the current state-of-the-art high-content screening systems take the approach of scaling-up single cell assays, and are therefore based on essentially pictorial measures as assay indicators. Such phenotypic analyses have become extremely sophisticated, advancing screening enormously, but this approach can still be somewhat subjective. We describe the development, and validation, of a prototype high-content screening platform that combines steady-state fluorescence anisotropy imaging with fluorescence lifetime imaging (FLIM. This functional approach allows objective, quantitative screening of small molecule libraries in protein-protein interaction assays. We discuss the development of the instrumentation, the process by which information on fluorescence resonance energy transfer (FRET can be extracted from wide-field, acceptor fluorescence anisotropy imaging and cross-checking of this modality using lifetime imaging by time-correlated single-photon counting. Imaging of cells expressing protein constructs where eGFP and mRFP1 are linked with amino-acid chains of various lengths (7, 19 and 32 amino acids shows the two methodologies to be highly correlated. We validate our approach using a small-scale inhibitor screen of a Cdc42 FRET biosensor probe expressed in epidermoid cancer cells (A431 in a 96 microwell-plate format. We also show that acceptor fluorescence anisotropy can be used to measure variations in hetero-FRET in protein-protein interactions. We demonstrate this using a screen of inhibitors of internalization of the transmembrane receptor, CXCR4. These assays enable us to demonstrate all the capabilities of the instrument, image processing and analytical techniques that have been developed. Direct correlation between acceptor anisotropy and donor FLIM is observed for FRET

  3. Soil invertebrate/micro-invertebrate interactions: disproportionate effects of species on food web structure and function.

    Science.gov (United States)

    Moore, J C; DeRuiter, P C; Hunt, H W

    1993-06-01

    The preservation of biodiversity requires an appreciation of food web structure and an understanding of how disturbance alters their structure and function. Theoretical and empirical studies of food webs demonstrate that food webs possess a regular structure. Food chain length appears limited to three to four transfers, and, complexity and diversity are constrained. When ecosystem energetics are considered, species within food webs are seen to form interactive assemblages that process matter at different rates and respond to disturbance differently. Disturbance may affect the diversity of a system, or, may influence the relative importance of one species assemblage over another. Moreover, predicting the impact of disturbance on a system is difficult as species that comprise and process a small fraction of the system's biomass may control a disproportionate fraction of the system's biomass and diversity. Seven food webs at four sites were used in a modeling exercise to demonstrate this point. Field studies involving the role of mycorrhizal fungi yielded results consistent with the modeling studies as the types of plant species present, the level of production and the diversity of production were related to the levels of mycorrhizal fungi in the soils following disturbance. The results indicate that all species are important to ecosystem structure and function and that the monitoring of ecosystems and conservation efforts should expand their emphasis to the preservation of ecosystem integrity as well as that of individual species.

  4. Dynamical density functional theory for arbitrary-shape colloidal fluids including inertia and hydrodynamic interactions

    Science.gov (United States)

    Duran-Olivencia, Miguel A.; Goddard, Ben; Kalliadasis, Serafim

    2015-11-01

    Over the last few decades the classical density-functional theory (DFT) and its dynamic extensions (DDFTs) have become a remarkably powerful tool in the study of colloidal fluids. Recently there has been extensive research to generalise all previous DDFTs finally yielding a general DDFT equation (for spherical particles) which takes into account both inertia and hydrodynamic interactions (HI) which strongly influence non-equilibrium properties. The present work will be devoted to a further generalisation of such a framework to systems of anisotropic particles. To this end, the kinetic equation for the Brownian particle distribution function is derived starting from the Liouville equation and making use of Zwanzig's projection-operator techniques. By averaging over all but one particle, a DDFT equation is finally obtained with some similarities to that for spherical colloids. However, there is now an inevitable translational-rotational coupling which affects the diffusivity of asymmetric particles. Lastly, in the overdamped (high friction) limit the theory is notably simplified leading to a DDFT equation which agrees with previous derivations. We acknowledge financial support from European Research Council via Advanced Grant No. 247031.

  5. [Functional interactions between promoters of neighboring yellow and CG3777 genes in Drosophila melanogaster].

    Science.gov (United States)

    Leman, D V; Parshikov, A F; Georgiev, P G; Maksimenko, O G

    2012-12-01

    It was shown by us previously that the transcription of the yellow gene can be affected by the promoter of the neighboring gene CG3777, which has a similar expression profile. In the present work, we continued studying the functional interactions between the promoters of the yellow and CG3777 genes in transgenic Drosophila strains. In this work, we used the failure of the yeast activator GAL4 to stimulate transcription from the promoter of the yellow gene for the case when GAL4-binding sites are localized at the 3'-end of the gene. It has been found that, if the 983-bp CG3777 gene promoter is inserted in transgenic strains in the same orientation with the yellow gene promoter, downstream from the sites of the GAL4 activator, the CG3777 promoter provides a strong stimulation of the yellow gene by the GAL4 activator. When the promoters of the yellow and CG3777 genes are inserted in opposite orientations relative to one another, no stimulation of the yellow gene by GAL4 is observed. Additional results obtained in the work demonstrate that the functional interacton between the CG3777 and yellow promoters depends on their mutual orientation and position relative to the GAL4-binding sites.

  6. Interaction of cholesterol with carbon nanotubes: A density functional theory study

    Science.gov (United States)

    Ciani, Anthony J.; Gupta, Bikash C.; Batra, Inder P.

    2008-07-01

    Carbon nanotubes (CNT) are being presented as medical devices at an increasing rate. To date, they have been suggested as targets for the thermal ablation of cancers, as delivery systems for pharmaceuticals, and as bio-sensors. A common thread amongst these applications is that CNTs are used as a delivery vector for some pharmaceutical into the body. We consider here the possibility that CNTs might be used as a device to trap and remove chemicals, particularly cholesterol, from a living organism. We have performed ab-initio calculations to determine how cholesterol might interact with CNTs placed inside the body. We have found that cholesterol exhibits no particular affinity for or effect on a bare CNT; however, its binding energy can be increased by functionalizing the CNT with a Ca adatom. We found that a Ca adatom on the wall of a CNT increases the binding energy of cholesterol to a CNT by around 1.5 eV, regardless of the nanotube's diameter. The presence of the cholesterol does not affect the band structure of the CNT, but the Ca atom does have an effect near the Fermi level. This indicates that a CNT based detector could function by detecting the alteration to the electronic structure caused by the induced adsorption of an adatom in the trinary system of CNT + cholesterol + adatom.

  7. Determination of the exchange interaction energy from the polarization expansion of the wave function

    CERN Document Server

    Gniewek, Piotr

    2016-01-01

    The exchange contribution to the energy of the hydrogen atom interacting with a proton is calculated from the polarization expansion of the wave function using the conventional surface-integral formula and two formulas involving volume integrals: the formula of the symmetry-adapted perturbation theory (SAPT) and the variational formula recommended by us. At large internuclear distances $R$, all three formulas yield the correct expression $-(2/e)Re^{-R}$, but approximate it with very different convergence rates. In the case of the SAPT formula, the convergence is geometric with the error falling as $3^{-K}$, where $K$ is the order of the applied polarization expansion. The error of the surface-integral formula decreases exponentially as $a^K/(K+1)!$, where $a=\\ln2 -\\tfrac{1}{2}$. The variational formula performs best, its error decays as $K^{1/2} [a^{ K}/(K+1)!]^2$. These convergence rates are much faster than those resulting from approximating the wave function through the multipole expansion. This shows the ...

  8. The independent and interacting effects of hedonic hunger and executive function on binge eating.

    Science.gov (United States)

    Manasse, Stephanie M; Espel, Hallie M; Forman, Evan M; Ruocco, Anthony C; Juarascio, Adrienne S; Butryn, Meghan L; Zhang, Fengqing; Lowe, Michael R

    2015-06-01

    Poor executive function (EF; pre-frontal cognitive control processes governing goal-directed behavior) and elevated hedonic hunger (i.e., preoccupation with palatable foods in the absence of physiological hunger) are theoretical risk and maintenance factors for binge eating (BE) distinct from general obesity. Recent theoretical models posit that dysregulated behavior such as BE may result from a combination of elevated appetitive drive (e.g., hedonic hunger) and decreased EF (e.g., inhibitory control and delayed discounting). The present study sought to test this model in distinguishing BE from general obesity by examining the independent and interactive associations of EF and hedonic hunger with BE group status (i.e., odds of categorization in BE group versus non-BE group). Treatment-seeking overweight and obese women with BE (n = 31) and without BE (OW group; n = 43) were assessed on measures of hedonic hunger and EF (inhibitory control and delay discounting). Elevated hedonic hunger increased the likelihood of categorization in the BE group, regardless of EF. When hedonic hunger was low, poor EF increased the likelihood of categorization in the BE group. Results indicate that the interplay of increased appetitive drives and decreased cognitive function may distinguish BE from overweight/obesity. Future longitudinal investigations of the combinatory effect of hedonic hunger and EF in increasing risk for developing BE are warranted, and may inform future treatment development to target these factors.

  9. Functional interaction of CP2 with GATA-1 in the regulation of erythroid promoters.

    Science.gov (United States)

    Bosè, Francesca; Fugazza, Cristina; Casalgrandi, Maura; Capelli, Alessia; Cunningham, John M; Zhao, Quan; Jane, Stephen M; Ottolenghi, Sergio; Ronchi, Antonella

    2006-05-01

    We observed that binding sites for the ubiquitously expressed transcription factor CP2 were present in regulatory regions of multiple erythroid genes. In these regions, the CP2 binding site was adjacent to a site for the erythroid factor GATA-1. Using three such regulatory regions (from genes encoding the transcription factors GATA-1, EKLF, and p45 NF-E2), we demonstrated the functional importance of the adjacent CP2/GATA-1 sites. In particular, CP2 binds to the GATA-1 HS2 enhancer, generating a ternary complex with GATA-1 and DNA. Mutations in the CP2 consensus greatly impaired HS2 activity in transient transfection assays with K562 cells. Similar results were obtained by transfection of EKLF and p45 NF-E2 mutant constructs. Chromatin immunoprecipitation with K562 cells showed that CP2 binds in vivo to all three regulatory elements and that both GATA-1 and CP2 were present on the same GATA-1 and EKLF regulatory elements. Adjacent CP2/GATA-1 sites may represent a novel module for erythroid expression of a number of genes. Additionally, coimmunoprecipitation and glutathione S-transferase pull-down experiments demonstrated a physical interaction between GATA-1 and CP2. This may contribute to the functional cooperation between these factors and provide an explanation for the important role of ubiquitous CP2 in the regulation of erythroid genes.

  10. Epistatic interactions influence terrestrial-marine functional shifts in cetacean rhodopsin.

    Science.gov (United States)

    Dungan, Sarah Z; Chang, Belinda S W

    2017-03-15

    Like many aquatic vertebrates, whales have blue-shifting spectral tuning substitutions in the dim-light visual pigment, rhodopsin, that are thought to increase photosensitivity in underwater environments. We have discovered that known spectral tuning substitutions also have surprising epistatic effects on another function of rhodopsin, the kinetic rates associated with light-activated intermediates. By using absorbance spectroscopy and fluorescence-based retinal release assays on heterologously expressed rhodopsin, we assessed both spectral and kinetic differences between cetaceans (killer whale) and terrestrial outgroups (hippo, bovine). Mutation experiments revealed that killer whale rhodopsin is unusually resilient to pleiotropic effects on retinal release from key blue-shifting substitutions (D83N and A292S), largely due to a surprisingly specific epistatic interaction between D83N and the background residue, S299. Ancestral sequence reconstruction indicated that S299 is an ancestral residue that predates the evolution of blue-shifting substitutions at the origins of Cetacea. Based on these results, we hypothesize that intramolecular epistasis helped to conserve rhodopsin's kinetic properties while enabling blue-shifting spectral tuning substitutions as cetaceans adapted to aquatic environments. Trade-offs between different aspects of molecular function are rarely considered in protein evolution, but in cetacean and other vertebrate rhodopsins, may underlie multiple evolutionary scenarios for the selection of specific amino acid substitutions.

  11. Synchronous neural interactions assessed by magnetoencephalography: a functional biomarker for brain disorders

    Science.gov (United States)

    Georgopoulos, Apostolos P.; Karageorgiou, Elissaios; Leuthold, Arthur C.; Lewis, Scott M.; Lynch, Joshua K.; Alonso, Aurelio A.; Aslam, Zaheer; Carpenter, Adam F.; Georgopoulos, Angeliki; Hemmy, Laura S.; Koutlas, Ioannis G.; Langheim, Frederick J. P.; Riley McCarten, J.; McPherson, Susan E.; Pardo, José V.; Pardo, Patricia J.; Parry, Gareth J.; Rottunda, Susan J.; Segal, Barbara M.; Sponheim, Scott R.; Stanwyck, John J.; Stephane, Massoud; Westermeyer, Joseph J.

    2007-12-01

    We report on a test to assess the dynamic brain function at high temporal resolution using magnetoencephalography (MEG). The essence of the test is the measurement of the dynamic synchronous neural interactions, an essential aspect of the brain function. MEG signals were recorded from 248 axial gradiometers while 142 human subjects fixated a spot of light for 45-60 s. After fitting an autoregressive integrative moving average (ARIMA) model and taking the stationary residuals, all pairwise, zero-lag, partial cross-correlations (PCCij0) and their z-transforms (zij0) between i and j sensors were calculated, providing estimates of the strength and sign (positive, negative) of direct synchronous coupling at 1 ms temporal resolution. We found that subsets of zij0 successfully classified individual subjects to their respective groups (multiple sclerosis, Alzheimer's disease, schizophrenia, Sjögren's syndrome, chronic alcoholism, facial pain, healthy controls) and gave excellent external cross-validation results. Contribution by the authors: Designed research (APG); acquired data (AAA, IGK, FJPL, ACL, SML, JJS); analyzed data (APG, EK, ACL, JKL); wrote the paper (APG, EK, ACL, SML); contributed subjects (AAA, ZA, AFC, AG, LSH, IGK, FJPL, SML, JRM, SEM, JVP, PJP, GJP, SJR, BMS, SRS, MS, JJS, JJW); discussed results (All); contributed equally (ZA, AFC, AG, LSH, FJPL, JRM, SEM, JVP, PJP, GJP, SJR, BMS, SRS, MS, JJS, JJW).

  12. On the evaluation of the non-interacting kinetic energy in density functional theory.

    Science.gov (United States)

    Peach, Michael J G; Griffiths, David G J; Tozer, David J

    2012-04-14

    The utility of both an orbital-free and a single-orbital expression for computing the non-interacting kinetic energy in density functional theory is investigated for simple atomic systems. The accuracy of both expressions is governed by the extent to which the Kohn-Sham equation is solved for the given exchange-correlation functional and so special attention is paid to the influence of finite Gaussian basis sets. The orbital-free expression is a statement of the virial theorem and its accuracy is quantified. The accuracy of the single-orbital expression is sensitive to the choice of Kohn-Sham orbital. The use of particularly compact orbitals is problematic because the failure to solve the Kohn-Sham equation exactly in regions where the orbital has decayed to near-zero leads to unphysical behaviour in regions that contribute to the kinetic energy, rendering it inaccurate. This problem is particularly severe for core orbitals, which would otherwise appear attractive due to their formally nodeless nature. The most accurate results from the single-orbital expression are obtained using the relatively diffuse, highest occupied orbitals, although special care is required at orbital nodes.

  13. Structure-Function Relations of Strigolactone Analogs: Activity as Plant Hormones and Plant Interactions

    Institute of Scientific and Technical Information of China (English)

    Maja Cohen; Cristina Prandi; Ernesto G. Occhiato; Silvia Tabasso; Smadar Wininger; Nathalie Resnick; Yosef Steinberger

    2013-01-01

    Strigolactones (SLs) have several functions as signaling molecules in their interactions with symbiotic arbuscular mycorrhizal (AM) fungi and the parasitic weeds Orobanche and Striga.SLs are also a new class of plant hormone regulating plant development.In all three organisms,a specific and sensitive receptor-mediated perception system is suggested.By comparing the activity of synthetic SL analogs on Arabidopsis root-hair elongation,Orobanche aegyptiaca seed germination,and hyphal branching of the AM fungus Glomus intraradices,we found that each of the tested organisms differs in its response to the various examined synthetic SL analogs.Structure-function relations of the SL analogs suggest substitutions on the A-ring as the cause of this variation.Moreover,the description of competitive antagonistic analogs suggests that the A-ring of SL can affect not only affinity to the receptor,but also the molecule's ability to activate it.The results support the conclusion that Arabidopsis,Orobanche,and AM fungi possess variations in receptor sensitivity to SL analogs,probably due to variation in SL receptors among the different species.

  14. Cytoskeleton and Golgi-apparatus interactions: a two-way road of function and structure

    Directory of Open Access Journals (Sweden)

    Egea G

    2015-01-01

    Full Text Available Gustavo Egea,1 Carla Serra-Peinado,1 María P Gavilan,2 Rosa M Rios21Departament de Biologia Cel·lular, Immulogia i Neurociències, Facultat de Medicina and Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS, Universitat de Barcelona, Barcelona, Spain; 2Departamento de Señalización Celular, CSIC-Centro Andaluz de Biomedicina y Medicina Regenerativa (CABIMER, Seville, SpainAbstract: The Golgi apparatus is the result of a complex and dynamic interaction between a large variety of molecules that determine its architecture, protein and lipid transports, and those that integrate signals from outside and inside the cell. The cytoskeleton facilitates the functional integration of all these processes. Association and coordination between microtubules and actin filaments, as well as their respective binding and regulatory proteins, are clearly necessary for Golgi structure and function. Protein sorting, membrane fission and fusion, and the motion of Golgi-derived transport carriers are all affected by both cytoskeleton elements.Keywords: cytoskeleton, Golgi apparatus, membrane trafficking, secretory pathway, actin, microtubules

  15. Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions

    Science.gov (United States)

    Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.; Mundy, Chistopher J.

    2017-10-01

    Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for models of electrolyte solution. Here, we provide definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation and isolate the effects of charge and cavitation, comparing to the Born (linear response) model. We show that using uncorrected Ewald summation leads to unphysical values for the single ion solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. This suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation.

  16. Analytic, group-theoretic wave functions for confined, correlated N-body systems with general two-body interactions

    Science.gov (United States)

    Dunn, M.; Watson, D. K.; Loeser, J. G.

    2006-08-01

    In this paper, we develop an analytic N-body wave function for identical particles under quantum confinement with a general two-body interaction. A systematic approach to correlation is developed by combining three theoretical methods: dimensional perturbation theory, the FG method of Wilson et. al., and the group theory of the symmetric group. Analytic results are achieved for a completely general interaction potential. Unlike conventional perturbation methods which are applicable only for weakly interacting systems, this analytic approach is applicable to both weakly and strongly interacting systems. This method directly accounts for each two-body interaction, rather than an average interaction so even lowest-order results include beyond-mean-field effects. One major advantage is that N appears as a parameter in the analytical expressions for the energy so results for different N are easy to obtain.

  17. Desmin: molecular interactions and putative functions of the muscle intermediate filament protein

    Directory of Open Access Journals (Sweden)

    M.L. Costa

    2004-12-01

    Full Text Available Desmin is the intermediate filament (IF protein occurring exclusively in muscle and endothelial cells. There are other IF proteins in muscle such as nestin, peripherin, and vimentin, besides the ubiquitous lamins, but they are not unique to muscle. Desmin was purified in 1977, the desmin gene was characterized in 1989, and knock-out animals were generated in 1996. Several isoforms have been described. Desmin IFs are present throughout smooth, cardiac and skeletal muscle cells, but can be more concentrated in some particular structures, such as dense bodies, around the nuclei, around the Z-line or in costameres. Desmin is up-regulated in muscle-derived cellular adaptations, including conductive fibers in the heart, electric organs, some myopathies, and experimental treatments with drugs that induce muscle degeneration, like phorbol esters. Many molecules have been reported to associate with desmin, such as other IF proteins (including members of the membrane dystroglycan complex, nebulin, the actin and tubulin binding protein plectin, the molecular motor dynein, the gene regulatory protein MyoD, DNA, the chaperone alphaB-crystallin, and proteases such as calpain and caspase. Desmin has an important medical role, since it is used as a marker of tumors' origin. More recently, several myopathies have been described, with accumulation of desmin deposits. Yet, after almost 30 years since its identification, the function of desmin is still unclear. Suggested functions include myofibrillogenesis, mechanical support for the muscle, mitochondrial localization, gene expression regulation, and intracellular signaling. This review focuses on the biochemical interactions of desmin, with a discussion of its putative functions.

  18. Interaction between anesthesia, gender, and functional outcome task following diffuse traumatic brain injury in rats.

    Science.gov (United States)

    O'Connor, Christine A; Cernak, Ibolja; Vink, Robert

    2003-06-01

    A number of experimental and clinical studies have demonstrated that functional outcome following traumatic brain injury differs between males and females. Some studies report that females have a better outcome than males following trauma while others report the opposite. In experimental studies, some of the contradictory results may be due to the different experimental conditions, including type of anesthesia and the outcome measures employed. In the present study we have used three different anesthetic protocols and four different outcome measures to determine how these parameters interact and affect functional outcome following traumatic brain injury in male and female rats. Diffuse traumatic brain injury was induced in adult male and female animals using the impact-acceleration brain injury model. Mortality in female animals was no different than males when using halothane anesthesia, slightly better than males when using isoflurane anesthesia, but significantly worse than males under pentobarbital anesthesia. Female animals always performed better than males on rotarod tests of motor outcome, with this effect being unrelated to anesthetic effects. Conversely, in cognitive tests using the Barnes Maze, only isoflurane-anesthetized females performed better than their male counterparts. Similarly, in an open field activity task, females always performed better than males after trauma, with isoflurane-anesthetized females also performing significantly better than the halothane-anesthetized female group after injury. Our results suggest that female animals do better than males after diffuse traumatic brain injury, although this observation is dependent upon the type of anesthesia and the functional task employed. Isoflurane is particularly protective in females, pentobarbital is deleterious to female outcome, while halothane anesthesia has the least influence on gender-related outcome.

  19. Earthworm-Mycorrhiza Interactions Can Affect the Diversity, Structure and Functioning of Establishing Model Grassland Communities

    Science.gov (United States)

    Zaller, Johann G.; Heigl, Florian; Grabmaier, Andrea; Lichtenegger, Claudia; Piller, Katja; Allabashi, Roza; Frank, Thomas; Drapela, Thomas

    2011-01-01

    Both earthworms and arbuscular mycorrhizal fungi (AMF) are important ecosystem engineers co-occurring in temperate grasslands. However, their combined impacts during grassland establishment are poorly understood and have never been studied. We used large mesocosms to study the effects of different functional groups of earthworms (i.e., vertically burrowing anecics vs. horizontally burrowing endogeics) and a mix of four AMF taxa on the establishment, diversity and productivity of plant communities after a simulated seed rain of 18 grassland species comprising grasses, non-leguminous forbs and legumes. Moreover, effects of earthworms and/or AMF on water infiltration and leaching of ammonium, nitrate and phosphate were determined after a simulated extreme rainfall event (40 l m−2). AMF colonisation of all three plant functional groups was altered by earthworms. Seedling emergence and diversity was reduced by anecic earthworms, however only when AMF were present. Plant density was decreased in AMF-free mesocosms when both anecic and endogeic earthworms were active; with AMF also anecics reduced plant density. Plant shoot and root biomass was only affected by earthworms in AMF-free mesocosms: shoot biomass increased due to the activity of either anecics or endogeics; root biomass increased only when anecics were active. Water infiltration increased when earthworms were present in the mesocosms but remained unaffected by AMF. Ammonium leaching was increased only when anecics or a mixed earthworm community was active but was unaffected by AMF; nitrate and phosphate leaching was neither affected by earthworms nor AMF. Ammonium leaching decreased with increasing plant density, nitrate leaching decreased with increasing plant diversity and density. In order to understand the underlying processes of these interactions further investigations possibly under field conditions using more diverse belowground communities are required. Nevertheless, this study demonstrates that

  20. Earthworm-mycorrhiza interactions can affect the diversity, structure and functioning of establishing model grassland communities.

    Directory of Open Access Journals (Sweden)

    Johann G Zaller

    Full Text Available Both earthworms and arbuscular mycorrhizal fungi (AMF are important ecosystem engineers co-occurring in temperate grasslands. However, their combined impacts during grassland establishment are poorly understood and have never been studied. We used large mesocosms to study the effects of different functional groups of earthworms (i.e., vertically burrowing anecics vs. horizontally burrowing endogeics and a mix of four AMF taxa on the establishment, diversity and productivity of plant communities after a simulated seed rain of 18 grassland species comprising grasses, non-leguminous forbs and legumes. Moreover, effects of earthworms and/or AMF on water infiltration and leaching of ammonium, nitrate and phosphate were determined after a simulated extreme rainfall event (40 l m(-2. AMF colonisation of all three plant functional groups was altered by earthworms. Seedling emergence and diversity was reduced by anecic earthworms, however only when AMF were present. Plant density was decreased in AMF-free mesocosms when both anecic and endogeic earthworms were active; with AMF also anecics reduced plant density. Plant shoot and root biomass was only affected by earthworms in AMF-free mesocosms: shoot biomass increased due to the activity of either anecics or endogeics; root biomass increased only when anecics were active. Water infiltration increased when earthworms were present in the mesocosms but remained unaffected by AMF. Ammonium leaching was increased only when anecics or a mixed earthworm community was active but was unaffected by AMF; nitrate and phosphate leaching was neither affected by earthworms nor AMF. Ammonium leaching decreased with increasing plant density, nitrate leaching decreased with increasing plant diversity and density. In order to understand the underlying processes of these interactions further investigations possibly under field conditions using more diverse belowground communities are required. Nevertheless, this study

  1. Higher order structural effects stabilizing the reverse Watson-Crick Guanine-Cytosine base pair in functional RNAs

    National Research Council Canada - National Science Library

    Chawla, Mohit; Abdel-Azeim, Safwat; Oliva, Romina; Cavallo, Luigi

    2014-01-01

    The G:C reverse Watson-Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains...

  2. Resting State fMRI in Mice Reveals Anesthesia Specific Signatures of Brain Functional Networks and Their Interactions

    Science.gov (United States)

    Bukhari, Qasim; Schroeter, Aileen; Cole, David M.; Rudin, Markus

    2017-01-01

    fMRI studies in mice typically require the use of anesthetics. Yet, it is known that anesthesia alters responses to stimuli or functional networks at rest. In this work, we have used Dual Regression analysis Network Modeling to investigate the effects of two commonly used anesthetics, isoflurane and medetomidine, on rs-fMRI derived functional networks, and in particular to what extent anesthesia affected the interaction within and between these networks. Experimental data have been used from a previous study (Grandjean et al., 2014). We applied multivariate ICA analysis and Dual Regression to infer the differences in functional connectivity between isoflurane- and medetomidine-anesthetized mice. Further network analysis was performed to investigate within- and between-network connectivity differences between these anesthetic regimens. The results revealed five major networks in the mouse brain: lateral cortical, associative cortical, default mode, subcortical, and thalamic network. The anesthesia regime had a profound effect both on within- and between-network interactions. Under isoflurane anesthesia predominantly intra- and inter-cortical interactions have been observed, with only minor interactions involving subcortical structures and in particular attenuated cortico-thalamic connectivity. In contrast, medetomidine-anesthetized mice displayed subcortical functional connectivity including interactions between cortical and thalamic ICA components. Combining the two anesthetics at low dose resulted in network interaction that constituted the superposition of the interaction observed for each anesthetic alone. The study demonstrated that network modeling is a promising tool for analyzing the brain functional architecture in mice and comparing alterations therein caused by different physiological or pathological states. Understanding the differential effects of anesthetics on brain networks and their interaction is essential when interpreting fMRI data recorded under

  3. Resting State fMRI in Mice Reveals Anesthesia Specific Signatures of Brain Functional Networks and Their Interactions.

    Science.gov (United States)

    Bukhari, Qasim; Schroeter, Aileen; Cole, David M; Rudin, Markus

    2017-01-01

    fMRI studies in mice typically require the use of anesthetics. Yet, it is known that anesthesia alters responses to stimuli or functional networks at rest. In this work, we have used Dual Regression analysis Network Modeling to investigate the effects of two commonly used anesthetics, isoflurane and medetomidine, on rs-fMRI derived functional networks, and in particular to what extent anesthesia affected the interaction within and between these networks. Experimental data have been used from a previous study (Grandjean et al., 2014). We applied multivariate ICA analysis and Dual Regression to infer the differences in functional connectivity between isoflurane- and medetomidine-anesthetized mice. Further network analysis was performed to investigate within- and between-network connectivity differences between these anesthetic regimens. The results revealed five major networks in the mouse brain: lateral cortical, associative cortical, default mode, subcortical, and thalamic network. The anesthesia regime had a profound effect both on within- and between-network interactions. Under isoflurane anesthesia predominantly intra- and inter-cortical interactions have been observed, with only minor interactions involving subcortical structures and in particular attenuated cortico-thalamic connectivity. In contrast, medetomidine-anesthetized mice displayed subcortical functional connectivity including interactions between cortical and thalamic ICA components. Combining the two anesthetics at low dose resulted in network interaction that constituted the superposition of the interaction observed for each anesthetic alone. The study demonstrated that network modeling is a promising tool for analyzing the brain functional architecture in mice and comparing alterations therein caused by different physiological or pathological states. Understanding the differential effects of anesthetics on brain networks and their interaction is essential when interpreting fMRI data recorded under

  4. Spectrofluorometric and thermal gravimetric study on binding interaction of thiabendazole with hemoglobin on epoxy-functionalized magnetic nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Maltas, Esra, E-mail: maltasesra@gmail.com; Ozmen, Mustafa

    2015-09-01

    The interaction of thiabendazole (Tbz) with hemoglobin (Hb) on epoxy-functionalized iron oxide nanoparticles was presented in this study. The binding capacity of Tbz was determined by measuring at an excitation wavelength of 299 nm using fluorescence spectroscopy. The thermodynamic parameters of the Hb–Tbz interaction were calculated from Stern–Volmer and van't Hoff equations. The values of enthalpy change, ∆H, and entropy change, ∆S, were found to be 0.20 kJ mol{sup −1} and 0.70 J mol{sup −1} K{sup −1}, respectively, which indicates that the hydrophilic interaction plays a main role in the binding process. The interaction ability was confirmed by Fourier transform infrared spectroscopy (FT-IR) and scanning electron microscopy (SEM). Also, the thermal behavior of the Hb–Tbz interaction on functionalized iron oxide nanoparticles was studied by using the thermogravimetric analysis (TGA) technique in the temperature range of 25–950 °C, and then the kinetic parameters for the thermal decomposition were determined using the Horowitz–Metzger method. - Highlights: • Hb was immobilized by covalent attachment on GPTS–SPIONs. • Interaction of Tbz with Hb–GPTS–SPIONs was studied. • Thermodynamic parameters for interaction were calculated. • Hydrophilic interaction plays a main role in the binding process.

  5. Ghost-interaction correction in ensemble density-functional theory for excited states with and without range separation

    Science.gov (United States)

    Alam, Md. Mehboob; Knecht, Stefan; Fromager, Emmanuel

    2016-07-01

    Ensemble density-functional theory (eDFT) suffers from the so-called "ghost-interaction" error when approximate exchange-correlation functionals are used. In this work, we present a rigorous ghost-interaction correction (GIC) scheme in the context of range-separated eDFT. The method relies on an exact decomposition of the ensemble short-range exchange-correlation energy into a multideterminantal exact exchange term, which involves the long-range interacting ensemble density matrix, instead of the Kohn-Sham (KS) one, and a complementary density-functional correlation energy. A generalized adiabatic connection formula is derived for the latter. In order to perform practical calculations, the complementary correlation functional is simply modeled by its ground-state local density approximation (LDA), while long-range interacting ground- and excited-state wave functions are obtained self-consistently by combining a long-range configuration-interaction calculation with a short-range LDA potential. We show that the GIC reduces the curvature of approximate range-separated ensemble energies drastically while providing considerably more accurate excitation energies, even for charge-transfer and double excitations. Interestingly, the method performs well also in the context of standard KS-eDFT, which is recovered when the range-separation parameter is set to 0.

  6. Structural and functional aspects of trypsin–gold nanoparticle interactions: An experimental investigation

    Energy Technology Data Exchange (ETDEWEB)

    Nidhin, Marimuthu [Department of Chemistry, Amity School of Applied Sciences, Center for Nanoscience and Technology, Amity University Haryana Amity Education Valley, Gurgaon, Haryana 122413 (India); Ghosh, Debasree [Department of Nanotechnology, Amity School of Applied Sciences, Center for Nanoscience and Technology, Amity University Haryana Amity Education Valley, Gurgaon, Haryana 122413 (India); Yadav, Himanshu; Yadav, Nitu [Department of Chemistry, Amity School of Applied Sciences, Center for Nanoscience and Technology, Amity University Haryana Amity Education Valley, Gurgaon, Haryana 122413 (India); Majumder, Sudip, E-mail: sudip22m@gmail.com [Department of Chemistry, Amity School of Applied Sciences, Center for Nanoscience and Technology, Amity University Haryana Amity Education Valley, Gurgaon, Haryana 122413 (India)

    2015-12-15

    Highlights: • Trypsin undergoes activation on incubation with gold nanoparticles. • Enhanced activity depends on the stoichiometry of the mixture. • Higher concentration of nanoparticles damage stability and conformation of trypsin. • Gold nanoparticles undergo morphological change on incubation with trypsin. - Abstract: Trypsin (Trp) is arguably the most important member of the serine proteases. Constructs made up of gold nanoparticles (GNP) with trypsin have been known to exhibit increased efficiency and stability in various experiments. Here we report simple Trp–GNP constructs mixed in different trypsin-to-GNP ratios which exhibit higher efficiencies in biochemical assay, varying resistance to autolysis and higher ability in cell trypsinization. Trp–GNP constructs in different trypsin-to-GNP ratios exhibit prolonged and sustained activity compared to native trypsin in N-α-p-benzoyl-p-nitroanilide (BAPNA) assay as monitored by UV-Visible spectroscopy. The activity was monitored as a function of decreasing rate of linear release of p-nitro aniline (resulting from the cleavage of BAPNA by trypsin) with time during the assay, whose absorbance was measured at 410 nm (λ{sub max} p-nitro aniline). We have done extensive studies to understand structural basis of this trypsin GNP interaction by using atomic force microscopy (AFM), transmission electron microscopy (TEM) and circular dichroism (CD) techniques. Our findings suggest that on interaction, the gold nanoparticles probably form an adherent layer on trypsin that effectively changes the morphology and dimensions of the nanoconstructs. However, trypsin-to-GNP ratio is extremely important, as higher concentration of GNP might damage the conformation of protein. Stability studies related to denaturation show that 1:1 Trp–GNP constructs exhibit maximum stability and high efficiency in all assays performed.

  7. Environmental conditions and biotic interactions influence ecosystem structure and function in a drying stream

    Science.gov (United States)

    Ludlam, J.P.; Magoulick, D.D.

    2010-01-01

    Benthic consumers influence stream ecosystem structure and function, but these interactions depend on environmental context. We experimentally quantified the effects of central stoneroller minnows (Campostoma anomalum (Rafinesque) and Meek's crayfish (Orconectes meeki meeki (Faxon)) on benthic communities using electric exclusion quadrats in Little Mulberry Creek before (June) and during (August) seasonal stream drying. Unglazed ceramic tiles were deployed in June and August to measure periphyton and invertebrate abundance, and leafpack decomposition and primary production were also measured in August. Relationships between stoneroller and crayfish density and the size of consumer effects were evaluated with multiple linear regression models. Average chlorophyll a abundance was greater on exposed than exclusion tiles in August, but not in June. Sediment dry mass, periphyton ash-free dry mass (AFDM), and chironomid densities on tiles did not differ among treatments in either period. Leaf packs decayed faster in exposed than exclusion treatments (kexposed = 0.038 ?? 0.013, kexclusion = 0.007 ?? 0.002), but consumer effects were stronger in some pools than others. Leafpack invertebrate biomass and abundance and tile primary productivity did not differ among treatments. Consumer effects on chlorophyll a were related to crayfish and stoneroller density, and effects on chironomid density were related to stoneroller density. These results contrast with a previous exclusion experiment in Little Mulberry Creek that demonstrated strong consumer effects. The influence of stream drying on consumer effects appears to have been reduced by strong spates, underscoring the importance of conducting multi-year studies to determine the magnitude of variability in ecological interactions. ?? US Government: USGS 2010.

  8. The CCR4-NOT complex physically and functionally interacts with TRAMP and the nuclear exosome.

    Directory of Open Access Journals (Sweden)

    Nowel Azzouz

    Full Text Available BACKGROUND: Ccr4-Not is a highly conserved multi-protein complex consisting in yeast of 9 subunits, including Not5 and the major yeast deadenylase Ccr4. It has been connected functionally in the nucleus to transcription by RNA polymerase II and in the cytoplasm to mRNA degradation. However, there has been no evidence so far that this complex is important for RNA degradation in the nucleus. METHODOLOGY/PRINCIPAL FINDINGS: In this work we point to a new role for the Ccr4-Not complex in nuclear RNA metabolism. We determine the importance of the Ccr4-Not complex for the levels of non-coding nuclear RNAs, such as mis-processed and polyadenylated snoRNAs, whose turnover depends upon the nuclear exosome and TRAMP. Consistently, mutation of both the Ccr4-Not complex and the nuclear exosome results in synthetic slow growth phenotypes. We demonstrate physical interactions between the Ccr4-Not complex and the exosome. First, Not5 co-purifies with the exosome. Second, several exosome subunits co-purify with the Ccr4-Not complex. Third, the Ccr4-Not complex is important for the integrity of large exosome-containing complexes. Finally, we reveal a connection between the Ccr4-Not complex and TRAMP through the association of the Mtr4 helicase with the Ccr4-Not complex and the importance of specific subunits of Ccr4-Not for the association of Mtr4 with the nuclear exosome subunit Rrp6. CONCLUSIONS/SIGNIFICANCE: We propose a model in which the Ccr4-Not complex may provide a platform contributing to dynamic interactions between the nuclear exosome and its co-factor TRAMP. Our findings connect for the first time the different players involved in nuclear and cytoplasmic RNA degradation.

  9. Density functional theory study of nitrogen atoms and molecules interacting with Fe(1 1 1) surfaces

    Science.gov (United States)

    Nosir, M. A.; Martin-Gondre, L.; Bocan, G. A.; Díez Muiño, R.

    2016-09-01

    We present Density functional theory (DFT) calculations for the investigation of the structural relaxation of Fe(1 1 1), as well as for the study of the interaction of nitrogen atoms and molecules with this surface. We perform spin polarized DFT calculations using VASP (Vienna Ab-initio Simulation Package) code. We use the supercell approach and up to 19 slab layers for the relaxation of the Fe(1 1 1) surface. We find a contraction of the first two interlayer distances with a relative value of Δ12 = - 7.8 % and Δ23 = - 21.7 % with respect to the bulk reference. The third interlayer distance is however expanded with a relative change of Δ34 = 9.7 % . Early experimental studies of the surface relaxation using Low Energy Electron Diffraction (LEED) and Medium Energy Ion Scattering (MEIS) showed contradictory results, even on the relaxation general trend. Our current theoretical results support the LEED conclusions and are consistent qualitatively with other recent theoretical calculations. In addition, we study the interaction energy of nitrogen atoms and molecules on the Fe(1 1 1) surface. The nitrogen atoms are adsorbed in the hollow site of the unit cell, with an adsorption energy consistent with the one found in previous studies. In addition, we find the three molecularly adsorbed states that are observed experimentally. Two of them correspond to the adsorbed molecule oriented normal to the surface and a third one corresponds to the molecule adsorbed parallel to the surface. We conclude that our results are accurate enough to be used to build a full six-dimensional potential energy surface for the N2 system.

  10. Interaction of hepatitis B virus with tumor suppressor gene p53: its significance and biological function

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The mechanism of the interaction of hepatitis B virus (HBV) with tumor suppressor p53 and its role in the hepatocarcinogenesis have been studied by PCR-directed sequencing, gel shift assays and in situ ultraviolet cross-linking assay. The biological function of the interaction of HBV with p53 gene was investigated by co-transfection of chloramphenicol acetyltransferase (CAT) reporter gene, p53 and HBV DNA, and quantitative PCR. Among the 16 primary hepatocellular carcinoma (PHC) samples, 13 were HBV-DNA positive,10 HBxAg positive and 9 p53 protein positive. The p53 gene point mutation was found in 5 samples, one of which had a G to T substitution located at codon 249. After analyzing the HBV genome by a computer program, a p53 response element binding sequence was found in HBV genome at upstream of enhancer I, from 1047 to 1059 nucleotides. This sequence could specifically bind to p53 protein, increase p53 protein accumulation in the PHC cells and stimulate the transactivating activity of p53 and HBV replication .The results also revealed that HBxAg could combine with p53 protein to form a complex in the cells and enhance CAT expression. Immunocytochemical staining showed that p53 protein complex was located in the cytoplasm and the process of p53 entry to nuclei was, in part, blocked. From our results, we conclude that the mutation of p53 gene at codon 249 is infrequent in HBV-associated PHC, the DNA-protein binding between HBV and p53, and the protein-protein binding between HBxAg and p53 might lead to the reduction or inactivation of p53 protein, which in turn resulting in HBV-associated hepatocarcinogenesis.

  11. Preparation of Functional Fluorescent Microspheres Used for HTS and Their Interaction with Biomolecules

    Institute of Scientific and Technical Information of China (English)

    LIU Bai-ling; LI Song-Jun

    2004-01-01

    There is considerable interest in protein adsorption onto microspheres because of its importance in a wide range of biomedical applications, such as artificial tissues and organs, drug delivery systems, biosensors, solid-phase immunoassays, immunomagnetic cell separation and immobilized enzymes or catalyst. It has been well known that the interaction between proteins and microspheres plays important roles in this process. Major interaction involved in the adsorption can be classified as electrostatic, hydrophobic and hydrogen-bonding. Indeed, adsorption of proteins onto microspheres is a complex process and often can involve many dynamic steps, from the initial attachment of the protein on the surface of microspheres to the equilibrium. Also the conformation of proteins probably occurs to a certain degree of deformation or structural change due to the large area of contact. Recently, much interest has been shown in sulfonated microspheres, since sulfonate-group itself is one of components in bio-bodies, as well as is sensitive to the change of pH or ionic strength. Indeed, so far, scanty investigations have been performed in the full range. Also few researches have involved the data on adsorption rate and the maximum amount of protein adsorbed, or the reversibility of the process and conformational change of protein adsorbed as well.In present study, BSA (bovine serum albumin) was chosen as the model protein and sulfonated PMMA [poly(methyl methacrylate)] microspheres as the matrix to investigate the adsorption process.The purpose is to show some information especially the intrinsic information involved by the adsorption process Adsorption of BSA onto sulfonated microspheres (MS) has been investigated as a function of time, protein concentration and pH. The adsorption appears to be a reversible process and the presence of sulfonate groups can play important roles in the adsorption process, so as to increase the amount of protein adsorbed and influences the

  12. Human epithelial cells exposed to functionalized multiwalled carbon nanotubes: interactions and cell surface modifications.

    Science.gov (United States)

    Fanizza, C; Casciardi, S; Incoronato, F; Cavallo, D; Ursini, C L; Ciervo, A; Maiello, R; Fresegna, A M; Marcelloni, A M; Lega, D; Alvino, A; Baiguera, S

    2015-09-01

    With the expansion of the production and applications of multiwalled carbon nanotubes (MWCNTs) in several industrial and science branches, the potential adverse effects on human health have attracted attention. Numerous studies have been conducted to evaluate how chemical functionalization may affect MWCNT effects; however, controversial data have been reported, showing either increased or reduced toxicity. In particular, the impact of carboxylation on MWCNT cytotoxicity is far from being completely understood. The aim of this work was the evaluation of the modifications induced by carboxylated-MWCNTs (MWCNTs-COOH) on cell surface and the study of cell-MWCNT-COOH interactions by means of field emission scanning electron microscope (FESEM). Human pulmonary epithelial cells (A549) were incubated with MWCNTs-COOH for different exposure times and concentrations (10 μg/mL for 1, 2, 4 h; 5, 10, 20 μg/mL for 24 h). At short incubation time, MWCNTs-COOH were easily observed associated with plasma membrane and in contact with microvilli. After 24 h exposure, FESEM analysis revealed that MWCNTs-COOH induced evident changes in the cellular surface in comparison to control cells: treated cells showed blebs, holes and a depletion of the microvilli density in association with structure modifications, such as widening and/or lengthening. In particular, an increase of cells showing holes and microvilli structure alterations was observed at 20 μg/mL concentration. FESEM analysis showed nanotube agglomerates, of different sizes, entering into the cell with two different mechanisms: inward bending of the membrane followed by nanotube sinking, and nanotube internalization directly through holes. The observed morphological microvilli modifications, induced by MWCNTs-COOH, could affect epithelial functions, such as the control of surfactant production and secretion, leading to pathological conditions, such as alveolar proteinosis. More detailed studies will be, however, necessary to

  13. Functional trait composition of aquatic plants can serve to disentangle multiple interacting stressors in lowland streams

    Energy Technology Data Exchange (ETDEWEB)

    Baattrup-Pedersen, Annette, E-mail: abp@bios.au.dk [Department of Bioscience, Aarhus University, Vejlsøvej 25, P.O. Box 314, DK-8600 Silkeborg (Denmark); Göthe, Emma [Department of Bioscience, Aarhus University, Vejlsøvej 25, P.O. Box 314, DK-8600 Silkeborg (Denmark); Riis, Tenna [Department of Bioscience, Aarhus University, Ole Worms Allé 1, Building 1135, Room 217, DK-8000 Aarhus C (Denmark); O' Hare, Matthew T. [Centre for Ecology and Hydrology, Bush Estate, Penicuik EH26 0QB (United Kingdom)

    2016-02-01

    stress. The ability to disentangle several stressors is particularly important in lowland stream environments where several stressors act in concert since the impact of the most important stressor can be targeted first, which is essential to improve the ecological status. - Highlights: • Functional trait composition of aquatic plants can distinguish hydromorphological degradation from eutrophication in streams • A conceptual framework on how eutrophication and hydromorphological degradation interact on functional trait composition • Weed cutting can set aside light as a factor controlling trait-abundance pattern in eutrophic lowland streams.

  14. PyramidalExplorer: A New Interactive Tool to Explore Morpho-Functional Relations of Human Pyramidal Neurons.

    Science.gov (United States)

    Toharia, Pablo; Robles, Oscar D; Fernaud-Espinosa, Isabel; Makarova, Julia; Galindo, Sergio E; Rodriguez, Angel; Pastor, Luis; Herreras, Oscar; DeFelipe, Javier; Benavides-Piccione, Ruth

    2015-01-01

    This work presents PyramidalExplorer, a new tool to interactively explore and reveal the detailed organization of the microanatomy of pyramidal neurons with functionally related models. It consists of a set of functionalities that allow possible regional differences in the pyramidal cell architecture to be interactively discovered by combining quantitative morphological information about the structure of the cell with implemented functional models. The key contribution of this tool is the morpho-functional oriented design that allows the user to navigate within the 3D dataset, filter and perform Content-Based Retrieval operations. As a case study, we present a human pyramidal neuron with over 9000 dendritic spines in its apical and basal dendritic trees. Using PyramidalExplorer, we were able to find unexpected differential morphological attributes of dendritic spines in particular compartm