Learning Analytics for Networked Learning Models

ERIC Educational Resources Information Center

Joksimovic, Srecko; Hatala, Marek; Gaševic, Dragan

2014-01-01

Teaching and learning in networked settings has attracted significant attention recently. The central topic of networked learning research is human-human and human-information interactions occurring within a networked learning environment. The nature of these interactions is highly complex and usually requires a multi-dimensional approach to…

Collaborative Research Methodology for Investigating Teaching and Learning: The Use of Interactive Whiteboard Technology

ERIC Educational Resources Information Center

Armstrong, Victoria; Barnes, Sally; Sutherland, Rosamund; Curran, Sarah; Mills, Simon; Thompson, Ian

2005-01-01

This paper discusses the results of a research project which aimed to capture, analyse and communicate the complex interactions between students, teachers and technology that occur in the classroom. Teachers and researchers used an innovative research design developed through the InterActive Education Project (Sutherland et al., 2003). Video case…

Understanding Structure and Bonding of Multilayered Metal–Organic Nanostructures

PubMed Central

2013-01-01

For organic and hybrid electronic devices, the physicochemical properties of the contained interfaces play a dominant role. To disentangle the various interactions occurring at such heterointerfaces, we here model a complex, yet prototypical, three-component system consisting of a Cu–phthalocyanine (CuPc) film on a 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) monolayer adsorbed on Ag(111). The two encountered interfaces are similar, as in both cases there would be no bonding without van der Waals interactions. Still, they are also distinctly different, as only at the Ag(111)–PTCDA interface do massive charge-rearrangements occur. Using recently developed theoretical tools, we show that it has become possible to provide atomistic insight into the physical and chemical processes in this comparatively complex nanostructure distinguishing between interactions involving local rearrangements of the charge density and long-range van der Waals attraction. PMID:23447750

Machine Learning for Detecting Gene-Gene Interactions

PubMed Central

McKinney, Brett A.; Reif, David M.; Ritchie, Marylyn D.; Moore, Jason H.

2011-01-01

Complex interactions among genes and environmental factors are known to play a role in common human disease aetiology. There is a growing body of evidence to suggest that complex interactions are ‘the norm’ and, rather than amounting to a small perturbation to classical Mendelian genetics, interactions may be the predominant effect. Traditional statistical methods are not well suited for detecting such interactions, especially when the data are high dimensional (many attributes or independent variables) or when interactions occur between more than two polymorphisms. In this review, we discuss machine-learning models and algorithms for identifying and characterising susceptibility genes in common, complex, multifactorial human diseases. We focus on the following machine-learning methods that have been used to detect gene-gene interactions: neural networks, cellular automata, random forests, and multifactor dimensionality reduction. We conclude with some ideas about how these methods and others can be integrated into a comprehensive and flexible framework for data mining and knowledge discovery in human genetics. PMID:16722772

Mud, Macrofauna and Microbes: An ode to benthic organism-abiotic interactions at varying scales

EPA Science Inventory

Benthic environments are dynamic habitats, subject to variable sources and rates of sediment delivery, reworking from the abiotic and biotic processes, and complex biogeochemistry. These activities do not occur in a vacuum, and interact synergistically to influence food webs, bi...

Cyclin A and the retinoblastoma gene product complex with a common transcription factor.

PubMed

Bandara, L R; Adamczewski, J P; Hunt, T; La Thangue, N B

1991-07-18

The retinoblastoma gene (Rb) product is a negative regulator of cellular proliferation, an effect that could be mediated in part at the transcriptional level through its ability to complex with the sequence-specific transcription factor DRTF1. This interaction is modulated by adenovirus E1a, which sequesters the Rb protein and several other cellular proteins, including cyclin A, a molecule that undergoes cyclical accumulation and destruction during each cell cycle and which is required for cell cycle progression. Cyclin A, which also complexes with DRTF1, facilitates the efficient assembly of the Rb protein into the complex. This suggests a role for cyclin A in regulating transcription and defines a transcription factor through which molecules that regulate the cell cycle in a negative fashion, such as Rb, and in a positive fashion, such as cyclin A, interact. Mutant loss-of-function Rb alleles, which occur in a variety of tumour cells, also fail to complex with E1a and large T antigen. Here we report on a naturally occurring loss-of-function Rb allele encoding a protein that fails to complex with DRTF1. This might explain how mutation in the Rb gene prevents negative growth control.

An Assembly Funnel Makes Biomolecular Complex Assembly Efficient

PubMed Central

Zenk, John; Schulman, Rebecca

2014-01-01

Like protein folding and crystallization, the self-assembly of complexes is a fundamental form of biomolecular organization. While the number of methods for creating synthetic complexes is growing rapidly, most require empirical tuning of assembly conditions and/or produce low yields. We use coarse-grained simulations of the assembly kinetics of complexes to identify generic limitations on yields that arise because of the many simultaneous interactions allowed between the components and intermediates of a complex. Efficient assembly occurs when nucleation is fast and growth pathways are few, i.e. when there is an assembly “funnel”. For typical complexes, an assembly funnel occurs in a narrow window of conditions whose location is highly complex specific. However, by redesigning the components this window can be drastically broadened, so that complexes can form quickly across many conditions. The generality of this approach suggests assembly funnel design as a foundational strategy for robust biomolecular complex synthesis. PMID:25360818

Characterization of the Androgen-sensitive MDA-kb2 Cell Line for Assessing Complex Environmental Mixtures, Presentation

EPA Science Inventory

Synthetic and natural steroidal androgens and estrogens and many other non-steroidal endocrine-active compounds commonly occur as complex mixtures in aquatic environments. It is important to understand the potential interactive effects of these mixtures to properly assess their r...

Skills for Children Entering Kindergarten

ERIC Educational Resources Information Center

Tindal, Gerald; Irvin, P. Shawn; Nese, Joseph F. T.; Slater, Steve

2015-01-01

Assessing kindergarten entry skills is complex, requiring attention to skill proficiency and interactive behaviors deemed critical for learning to occur. In our analysis of a state initiative, pilot data were collected on early literacy and numeracy and 2 aspects of important student interactions in the classroom (social and task behaviors) within…

Exploring whether and how ants affect reproductive fitness in Senna mexicana var. chapmanii

USDA-ARS?s Scientific Manuscript database

Extrafloral nectar (EFN) mediates food-for-protection mutualisms between plants and ants. Ant-plant mutualisms are keystone associations, occurring within a complex web of biotic interactions. As such, these interactions may affect plant fitness in a number of ways, both positive and negative. In S...

Instructional Context and Student Motivation, Learning, and Development: Commentary and Implications for School Psychologists

ERIC Educational Resources Information Center

Pendergast, Laura L.; Kaplan, Avi

2015-01-01

From an ecological perspective, learning and development in childhood and throughout the lifespan occur in the context of interactions within complex social networks. Collectively, the articles in this special issue illuminate three important themes related to teacher-student interactions within instructional contexts: relationships, competence,…

Testing spatial theories of plant coexistence: no consistent differences in intra- and interspecific interaction distances.

PubMed

Vogt, Deborah R; Murrell, David J; Stoll, Peter

2010-01-01

Plants stand still and interact with their immediate neighbors. Theory has shown that the distances over which these interactions occur may have important consequences for population and community dynamics. In particular, if intraspecific competition occurs over longer distances than interspecific competition (heteromyopia), coexistence can be promoted. We examined how intraspecific and interspecific competition scales with neighbor distance in a target-neighbor greenhouse competition experiment. Individuals from co-occurring forbs from calcareous grasslands were grown in isolation and with single conspecific or heterospecific neighbors at distances of 5, 10, or 15 cm (Plantago lanceolata vs. Plantago media and Hieracium pilosella vs. Prunella grandiflora). Neighbor effects were strong and declined with distance. Interaction distances varied greatly within and between species, but we found no evidence for heteromyopia. Instead, neighbor identity effects were mostly explained by relative size differences between target and neighbor. We found a complex interaction between final neighbor size and identity such that neighbor identity may become important only as the neighbor becomes very large compared with the target individual. Our results suggest that species-specific size differences between neighboring individuals determine both the strength of competitive interactions and the distance over which these interactions occur.

Exploring the unbinding of Leishmania (L.) amazonensis CPB derived-epitopes from H2 MHC class I proteins.

PubMed

Brandt, Artur M L; Batista, Paulo Ricardo; Souza-Silva, Franklin; Alves, Carlos Roberto; Caffarena, Ernesto Raul

2016-04-01

New strategies to control Leishmania disease demand an extensive knowledge about several aspects of infection including the understanding of its molecular events. In murine models, cysteine proteinase B from Leishmania amazonensis promotes regulation of immune response, and fragments from its C-terminus extension (cyspep) can play a decisive role in the host-parasite interaction. The interaction between cyspep-derived peptides and major histocompatibility complex (MHC) proteins is a crucial factor in Leishmania infections. Seven cyspep-derived peptides, previously identified as capable of interacting with H-2 (murine) MHC class I proteins, were studied in this work. We established a protocol to simulate the unbinding of these peptides from the cleft of H-2 receptors. From the simulations, we estimated the corresponding free energy of dissociation (ΔGd ) and described the molecular events that occur during the exit of peptides from the cleft. To test the reliability of this method, we first applied it to a calibration set of four crystallographic MHC/peptide complexes. Next, we explored the unbinding of the seven complexes mentioned above. Results were consistent with ΔGd values obtained from surface plasmon resonance (SPR) experiments. We also identified some of the primary interactions between peptides and H-2 receptors, and we detected three regions of influence for the interaction. This pattern was systematically observed for the peptides and helped determine a minimum distance for the real interaction between peptides and H-2 proteins occurring at ∼ 25 Å. © 2016 Wiley Periodicals, Inc.

Developing interprofessional education online: An ecological systems theory analysis.

PubMed

Bluteau, Patricia; Clouder, Lynn; Cureton, Debra

2017-07-01

This article relates the findings of a discourse analysis of an online asynchronous interprofessional learning initiative involving two UK universities. The impact of the initiative is traced over three intensive periods of online interaction, each of several-weeks duration occurring over a three-year period, through an analysis of a random sample of discussion forum threads. The corpus of rich data drawn from the forums is interpreted using ecological systems theory, which highlights the complexity of interaction of individual, social and cultural elements. Ecological systems theory adopts a life course approach to understand how development occurs through processes of progressively more complex reciprocal interaction between people and their environment. This lens provides a novel approach for analysis and interpretation of findings with respect to the impact of pre-registration interprofessional education and the interaction between the individual and their social and cultural contexts as they progress through 3/4 years of their programmes. Development is mapped over time (the chronosystem) to highlight the complexity of interaction across microsystems (individual), mesosystems (curriculum and institutional/care settings), exosystems (community/wider local context), and macrosystems (national context and culture). This article illustrates the intricacies of students' interprofessional development over time and the interactive effects of social ecological components in terms of professional knowledge and understanding, wider appreciation of health and social care culture and identity work. The implications for contemporary pre-registration interprofessional education and the usefulness and applicability of ecological systems theory for future research and development are considered.

High Selection Pressure Promotes Increase in Cumulative Adaptive Culture

PubMed Central

Vegvari, Carolin; Foley, Robert A.

2014-01-01

The evolution of cumulative adaptive culture has received widespread interest in recent years, especially the factors promoting its occurrence. Current evolutionary models suggest that an increase in population size may lead to an increase in cultural complexity via a higher rate of cultural transmission and innovation. However, relatively little attention has been paid to the role of natural selection in the evolution of cultural complexity. Here we use an agent-based simulation model to demonstrate that high selection pressure in the form of resource pressure promotes the accumulation of adaptive culture in spite of small population sizes and high innovation costs. We argue that the interaction of demography and selection is important, and that neither can be considered in isolation. We predict that an increase in cultural complexity is most likely to occur under conditions of population pressure relative to resource availability. Our model may help to explain why culture change can occur without major environmental change. We suggest that understanding the interaction between shifting selective pressures and demography is essential for explaining the evolution of cultural complexity. PMID:24489724

Chirality-selected phase behaviour in ionic polypeptide complexes

DOE PAGES

Perry, Sarah L.; Leon, Lorraine; Hoffmann, Kyle Q.; ...

2015-01-14

In this study, polyelectrolyte complexes present new opportunities for self-assembled soft matter. Factors determining whether the phase of the complex is solid or liquid remain unclear. Ionic polypeptides enable examination of the effects of stereochemistry on complex formation. Here we demonstrate that chirality determines the state of polyelectrolyte complexes, formed from mixing dilute solutions of oppositely charged polypeptides, via a combination of electrostatic and hydrogen-bonding interactions. Fluid complexes occur when at least one of the polypeptides in the mixture is racemic, which disrupts backbone hydrogen-bonding networks. Pairs of purely chiral polypeptides, of any sense, form compact, fibrillar solids with amore » β-sheet structure. Analogous behaviour occurs in micelles formed from polypeptide block copolymers with polyethylene oxide, where assembly into aggregates with either solid or fluid cores, and eventually into ordered phases at high concentrations, is possible. Chirality is an exploitable tool for manipulating material properties in polyelectrolyte complexation.« less

Mechanism of Aldolase Control of Sorting Nexin 9 Function in Endocytosis

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

Rangarajan, Erumbi S.; Park, HaJeung; Fortin, Emanuelle

Sorting nexin 9 (SNX9) functions in a complex with the GTPase dynamin-2 at clathrin-coated pits, where it provokes fission of vesicles to complete endocytosis. Here the SNX9-dynamin-2 complex binds to clathrin and adapter protein complex 2 (AP-2) that line these pits, and this occurs through interactions of the low complexity domain (LC4) of SNX9 with AP-2. Intriguingly, localization of the SNX9-dynamin-2 complex to clathrin-coated pits is blocked by interactions with the abundant glycolytic enzyme aldolase, which also binds to the LC4 domain of SNX9. The crystal structure of the LC4 motif of human SNX9 in complex with aldolase explains themore » biochemistry and biology of this interaction, where SNX9 binds near the active site of aldolase via residues 165-171 that are also required for the interactions of SNX9 with AP-2. Accordingly, SNX9 binding to aldolase is structurally precluded by the binding of substrate to the active site. Interactions of SNX9 with aldolase are far more extensive and differ from those of the actin-nucleating factor WASP with aldolase, indicating considerable plasticity in mechanisms that direct the functions of the aldolase as a scaffold protein.« less

Modeling disturbance and succession in forest landscapes using LANDIS: introduction

Treesearch

Brian R. Sturtevant; Eric J. Gustafson; Hong S. He

2004-01-01

Modeling forest landscape change is challenging because it involves the interaction of a variety of factors and processes, such as climate, succession, disturbance, and management. These processes occur at various spatial and temporal scales, and the interactions can be complex on heterogeneous landscapes. Because controlled field experiments designed to investigate...

Identification and characterization of protein interactions in the mammalian mRNA processing body using a novel two-hybrid assay

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

Bloch, Donald B., E-mail: bloch@helix.mgh.harvard.edu; Nobre, Rita A.; Bernstein, Gillian A.

2011-09-10

Components of the mRNA processing body (P-body) regulate critical steps in mRNA storage, transport, translation and degradation. At the core of the P-body is the decapping complex, which removes the 5' cap from de-adenylated mRNAs and mediates an irreversible step in mRNA degradation. The assembly of P-bodies in Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster has been previously described. Less is known about the assembly of mammalian P-bodies. To investigate the interactions that occur between components of mammalian P-bodies, we developed a fluorescence-based, two-hybrid assay system. The assay depends on the ability of one P-body component, fused to an exogenousmore » nuclear localization sequence (NLS), to recruit other P-body components to the nucleus. The assay was used to investigate interactions between P-body components Ge-1, DCP2, DCP1, EDC3, RAP55, and RCK. The results of this study show that the modified two-hybrid assay can be used to identify protein interactions that occur in a macromolecular complex. The assay can also be used to efficiently detect protein interaction domains. The results provide important insights into mammalian P-body assembly and demonstrate similarities, and critical differences, between P-body assembly in mammalian cells compared with that of other species. -- Research highlights: {yields} A two-hybrid assay was developed to study interactions in macromolecular complexes. {yields} The assay was applied to interactions between components of mRNA P-bodies. {yields} The assay effectively and efficiently identified protein interaction domains. {yields} P-body assembly in mammalian cells differs from that in other species.« less

Deciphering the Interdependence between Ecological and Evolutionary Networks.

PubMed

Melián, Carlos J; Matthews, Blake; de Andreazzi, Cecilia S; Rodríguez, Jorge P; Harmon, Luke J; Fortuna, Miguel A

2018-05-24

Biological systems consist of elements that interact within and across hierarchical levels. For example, interactions among genes determine traits of individuals, competitive and cooperative interactions among individuals influence population dynamics, and interactions among species affect the dynamics of communities and ecosystem processes. Such systems can be represented as hierarchical networks, but can have complex dynamics when interdependencies among levels of the hierarchy occur. We propose integrating ecological and evolutionary processes in hierarchical networks to explore interdependencies in biological systems. We connect gene networks underlying predator-prey trait distributions to food webs. Our approach addresses longstanding questions about how complex traits and intraspecific trait variation affect the interdependencies among biological levels and the stability of meta-ecosystems. Copyright © 2018 Elsevier Ltd. All rights reserved.

Study of interactions of an anticancer drug neratinib with bovine serum albumin: Spectroscopic and molecular docking approach

NASA Astrophysics Data System (ADS)

Wani, Tanveer A.; Bakheit, Ahmed H.; Abounassif, M. A.; Zargar, Seema

2018-03-01

Binding of therapeutic agents to plasma proteins, particularly to serum albumin, provides valuable information in the drug development. This study was designed to evaluate the binding interaction of neratinib with bovine serum albumin (BSA). Neratinib blocks HER2 signaling and is effective in trastuzumab-resistant breast cancer treatment. Spectrofluorometric, UV spectrophotometric, and fourier transform infrared (FT-IR) and molecular docking experiments were performed to study this interaction. The fluorescence of BSA is attributed to the presence of tryptophan (Trp) residues. The fluorescence of BSA in presence of neratinib was studied using the excitation wavelength of 280 nm and the emission was measured at 300-500 nm at three different temperatures. Neratinib quenched the BSA intrinsic fluorescence by static mechanism. A complex formation occurred due to the interaction leading to BSA absorption shift. The fluorescence, UV- absorption, three dimensional fluorescence and FT-IR data showed conformational changes occurred in BSA after interaction with neratinib. The binding constant values decreased as the temperature increased suggesting an instable complex formation at high temperature. Site I (sub-domain IIA) was observed as the principal binding site for neratinib. Hydrogen bonding and Van der Waals forces were suggested to be involved in the BSA-neratinib interaction due to the negative values of entropy and enthalpy changes.

Study of Interactions of an Anticancer Drug Neratinib With Bovine Serum Albumin: Spectroscopic and Molecular Docking Approach.

PubMed

Wani, Tanveer A; Bakheit, Ahmed H; Abounassif, M A; Zargar, Seema

2018-01-01

Binding of therapeutic agents to plasma proteins, particularly to serum albumin, provides valuable information in the drug development. This study was designed to evaluate the binding interaction of neratinib with bovine serum albumin (BSA). Neratinib blocks HER2 signaling and is effective in trastuzumab-resistant breast cancer treatment. Spectrofluorometric, UV spectrophotometric, and fourier transform infrared (FT-IR) and molecular docking experiments were performed to study this interaction. The fluorescence of BSA is attributed to the presence of tryptophan (Trp) residues. The fluorescence of BSA in presence of neratinib was studied using the excitation wavelength of 280 nm and the emission was measured at 300-500 nm at three different temperatures. Neratinib quenched the BSA intrinsic fluorescence by static mechanism. A complex formation occurred due to the interaction leading to BSA absorption shift. The fluorescence, UV- absorption, three dimensional fluorescence and FT-IR data showed conformational changes occurred in BSA after interaction with neratinib. The binding constant values decreased as the temperature increased suggesting an instable complex formation at high temperature. Site I (sub-domain IIA) was observed as the principal binding site for neratinib. Hydrogen bonding and Van der Waals forces were suggested to be involved in the BSA-neratinib interaction due to the negative values of entropy and enthalpy changes.

Study of Interactions of an Anticancer Drug Neratinib With Bovine Serum Albumin: Spectroscopic and Molecular Docking Approach

PubMed Central

Wani, Tanveer A.; Bakheit, Ahmed H.; Abounassif, M. A.; Zargar, Seema

2018-01-01

Binding of therapeutic agents to plasma proteins, particularly to serum albumin, provides valuable information in the drug development. This study was designed to evaluate the binding interaction of neratinib with bovine serum albumin (BSA). Neratinib blocks HER2 signaling and is effective in trastuzumab-resistant breast cancer treatment. Spectrofluorometric, UV spectrophotometric, and fourier transform infrared (FT-IR) and molecular docking experiments were performed to study this interaction. The fluorescence of BSA is attributed to the presence of tryptophan (Trp) residues. The fluorescence of BSA in presence of neratinib was studied using the excitation wavelength of 280 nm and the emission was measured at 300-500 nm at three different temperatures. Neratinib quenched the BSA intrinsic fluorescence by static mechanism. A complex formation occurred due to the interaction leading to BSA absorption shift. The fluorescence, UV- absorption, three dimensional fluorescence and FT-IR data showed conformational changes occurred in BSA after interaction with neratinib. The binding constant values decreased as the temperature increased suggesting an instable complex formation at high temperature. Site I (sub-domain IIA) was observed as the principal binding site for neratinib. Hydrogen bonding and Van der Waals forces were suggested to be involved in the BSA-neratinib interaction due to the negative values of entropy and enthalpy changes. PMID:29564326

Acute stress in adulthood impoverishes social choices and triggers aggressiveness in preclinical models.

PubMed

Nosjean, Anne; Cressant, Arnaud; de Chaumont, Fabrice; Olivo-Marin, Jean-Christophe; Chauveau, Frédéric; Granon, Sylvie

2014-01-01

Adult C57BL/6J mice are known to exhibit high level of social flexibility while mice lacking the β2 subunit of nicotinic receptors (β2(-/-) mice) present social rigidity. We asked ourselves what would be the consequences of a restraint acute stress (45 min) on social interactions in adult mice of both genotypes, hence the contribution of neuronal nicotinic receptors in this process. We therefore dissected social interaction complexity of stressed and not stressed dyads of mice in a social interaction task. We also measured plasma corticosterone levels in our experimental conditions. We showed that a single stress exposure occurring in adulthood reduced and disorganized social interaction complexity in both C57BL/6J and β2(-/-) mice. These stress-induced maladaptive social interactions involved alteration of distinct social categories and strategies in both genotypes, suggesting a dissociable impact of stress depending on the functioning of the cholinergic nicotinic system. In both genotypes, social behaviors under stress were coupled to aggressive reactions with no plasma corticosterone changes. Thus, aggressiveness appeared a general response independent of nicotinic function. We demonstrate here that a single stress exposure occurring in adulthood is sufficient to impoverish social interactions: stress impaired social flexibility in C57BL/6J mice whereas it reinforced β2(-/-) mice behavioral rigidity.

Bacillus subtilis glutamine synthetase regulates its own synthesis by acting as a chaperone to stabilize GlnR-DNA complexes.

PubMed

Fisher, Susan H; Wray, Lewis V

2008-01-22

The Bacillus subtilis GlnR repressor controls gene expression in response to nitrogen availability. Because all GlnR-regulated genes are expressed constitutively in mutants lacking glutamine synthetase (GS), GS is required for repression by GlnR. Feedback-inhibited GS (FBI-GS) was shown to activate GlnR DNA binding with an in vitro electophoretic mobility shift assay (EMSA). The activation of GlnR DNA binding by GS in these experiments depended on the feedback inhibitor glutamine and did not occur with mutant GS proteins defective in regulating GlnR activity in vivo. Although stable GS-GlnR-DNA ternary complexes were not observed in the EMSA experiments, cross-linking experiments showed that a protein-protein interaction occurs between GlnR and FBI-GS. This interaction was reduced in the absence of the feedback inhibitor glutamine and with mutant GS proteins. Because FBI-GS significantly reduced the dissociation rate of the GlnR-DNA complexes, the stability of these complexes is enhanced by FBI-GS. These results argue that FBI-GS acts as a chaperone that activates GlnR DNA binding through a transient protein-protein interaction that stabilizes GlnR-DNA complexes. GS was shown to control the activity of the B. subtilis nitrogen transcription factor TnrA by forming a stable complex between FBI-GS and TnrA that inhibits TnrA DNA binding. Thus, B. subtilis GS is an enzyme with dual catalytic and regulatory functions that uses distinct mechanisms to control the activity of two different transcription factors.

Nanoindentation methods for wood-adhesive bond lines

Treesearch

Joseph E. Jakes; Donald S. Stone; Charles R. Frihart

2008-01-01

As an adherend, wood is structurally, chemically, and mechanically more complex than metals or plastics, and the largest source of this complexity is wood’s chemical and mechanical inhomogeneities. Understanding and predicting the performance of adhesively bonded wood requires knowledge of the interactions occurring at length scales ranging from the macro down to the...

Self-Report Data on the Interactive Nature of Stress in Canadian Elementary School Principals.

ERIC Educational Resources Information Center

McMurray, J. G.

Stress has been defined as a stimulus event, a complex personal response to the interaction of various personal and environmental factors. When a demand, real or imagined, is perceived, a stress response will occur unless appropriate coping responses are present. The terms burnout or excessive distress refer to the experience of physical,…

Interaction and formation mechanism of binary complex between zein and propylene glycol alginate.

PubMed

Sun, Cuixia; Dai, Lei; Gao, Yanxiang

2017-02-10

The anti-solvent co-precipitation method was used to fabricate the zein-propylene glycol alginate (PGA) binary complex with different mass ratios of zein to PGA (20:1, 10:1, 5:1, 2:1 and 1:1) at pH 4.0. Results showed that attractive electrostatic interaction between zein and PGA occurred and negatively charged binary complex with large size and high turbidity was formed due to the charge neutralization. Hydrogen bonding and hydrophobic effects were involved in the interactions between zein and PGA, leading to the changed secondary structure and improved thermal stability of zein. Aggregates in the irregular shape with large size were obviously observed in the AFM images. PGA alone exhibited a fine filamentous network structure, while zein-PGA binary complex showed a rough branch-like pattern and the surface of "branch" was closely adsorbed by lots of spherical zein particles. Q in zein-PGA binary complex dispersions presented the improved photochemical and thermal stability. The potential mechanism of a two-step process was proposed to explain the formation of zein-PGA binary complexes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Imaging dynamic and selective low-complexity domain interactions that control gene transcription.

PubMed

Chong, Shasha; Dugast-Darzacq, Claire; Liu, Zhe; Dong, Peng; Dailey, Gina M; Cattoglio, Claudia; Heckert, Alec; Banala, Sambashiva; Lavis, Luke; Darzacq, Xavier; Tjian, Robert

2018-06-21

Many eukaryotic transcription factors (TFs) contain intrinsically disordered low-complexity domains (LCDs), but how they drive transactivation remains unclear. Here, live-cell single-molecule imaging reveals that TF-LCDs form local high-concentration interaction hubs at synthetic and endogenous genomic loci. TF-LCD hubs stabilize DNA binding, recruit RNA polymerase II (Pol II), and activate transcription. LCD-LCD interactions within hubs are highly dynamic, display selectivity with binding partners, and are differentially sensitive to disruption by hexanediols. Under physiological conditions, rapid and reversible LCD-LCD interactions occur between TFs and the Pol II machinery without detectable phase separation. Our findings reveal fundamental mechanisms underpinning transcriptional control and suggest a framework for developing single-molecule imaging screens for novel drugs targeting gene regulatory interactions implicated in disease. Copyright © 2018, American Association for the Advancement of Science.

Octa- and hexametallic iron(III)-potassium phosphonate cages.

PubMed

Gopal, Kandasamy; Tuna, Floriana; Winpenny, Richard E P

2011-12-07

Two new iron(III)-potassium phosphonate cage complexes with {K(2)Fe(6)} and {K(2)Fe(4)} cores are reported. Magnetic studies reveal antiferromagnetic interactions between the Fe(III) centres occur in these cages.

Fort Collins Science Center Ecosystem Dynamics Branch

USGS Publications Warehouse

Wilson, Jim; Melcher, C.; Bowen, Z.

2009-01-01

Complex natural resource issues require understanding a web of interactions among ecosystem components that are (1) interdisciplinary, encompassing physical, chemical, and biological processes; (2) spatially complex, involving movements of animals, water, and airborne materials across a range of landscapes and jurisdictions; and (3) temporally complex, occurring over days, weeks, or years, sometimes involving response lags to alteration or exhibiting large natural variation. Scientists in the Ecosystem Dynamics Branch of the U.S. Geological Survey, Fort Collins Science Center, investigate a diversity of these complex natural resource questions at the landscape and systems levels. This Fact Sheet describes the work of the Ecosystems Dynamics Branch, which is focused on energy and land use, climate change and long-term integrated assessments, herbivore-ecosystem interactions, fire and post-fire restoration, and environmental flows and river restoration.

Physical interactions between bacteriophage and Escherichia coli proteins required for initiation of lambda DNA replication.

PubMed

Liberek, K; Osipiuk, J; Zylicz, M; Ang, D; Skorko, J; Georgopoulos, C

1990-02-25

The process of initiation of lambda DNA replication requires the assembly of the proper nucleoprotein complex at the origin of replication, ori lambda. The complex is composed of both phage and host-coded proteins. The lambda O initiator protein binds specifically to ori lambda. The lambda P initiator protein binds to both lambda O and the host-coded dnaB helicase, giving rise to an ori lambda DNA.lambda O.lambda P.dnaB structure. The dnaK and dnaJ heat shock proteins have been shown capable of dissociating this complex. The thus freed dnaB helicase unwinds the duplex DNA template at the replication fork. In this report, through cross-linking, size chromatography, and protein affinity chromatography, we document some of the protein-protein interactions occurring at ori lambda. Our results show that the dnaK protein specifically interacts with both lambda O and lambda P, and that the dnaJ protein specifically interacts with the dnaB helicase.

FACTORS INFLUENCING LIGHT-INDUCED MORTALITY OF ENTEROCOCCI IN SEDIMENT SUSPENSIONS

EPA Science Inventory

Contamination of recreational waters by pathogenic microorganisms occurs through complex, poorly understood interactions involving variable microbial sources, hydrodynamic transport, arid microbial fate processes. Fecal indicator bacteria such as enterococci have been used to ass...

Emotional contagion and proto-organizing in human interaction dynamics

PubMed Central

Hazy, James K.; Boyatzis, Richard E.

2015-01-01

This paper combines the complexity notions of phase transitions and tipping points with recent advances in cognitive neuroscience to propose a general theory of human proto-organizing. It takes as a premise that a necessary prerequisite for organizing, or “proto-organizing,” occurs through emotional contagion in subpopulations of human interaction dynamics in complex ecosystems. Emotional contagion is posited to engender emotional understanding and identification with others, a social process that acts as a mechanism that enables (or precludes) cooperative responses to opportunities and risks. Propositions are offered and further research is suggested. PMID:26124736

Interaction of the univalent silver cation with [Gly6]-antamanide: Experimental and theoretical study

NASA Astrophysics Data System (ADS)

Makrlík, Emanuel; Böhm, Stanislav; Kvíčala, Jaroslav; Vaňura, Petr; Ruzza, Paolo

2018-03-01

On the basis of extraction experiments and γ-activity measurements, the extraction constant corresponding to the equilibrium Ag+(aq) + 1.Na+(nb) ⇄ 1.Ag+ (nb) + Na+(aq) occurring in the two-phase water - nitrobenzene system (1 = [Gly6]-antamanide; aq = aqueous phase, nb = nitrobenzene phase) was determined as log Kex (Ag+,1·Na+) = 1.5 ± 0.1. Further, the stability constant of the 1·Ag+ complex in nitrobenzene saturated with water was calculated for a temperature of 25 °C: log βnb (1·Ag+) = 4.5 ± 0.2. Finally, by using quantum chemical DFT calculations, the most probable structure of the cationic complex species 1·Ag+ was derived. In the resulting complex, the "central" cation Ag+ is coordinated by four noncovalent interactions to the corresponding four carbonyl oxygen atoms of the parent ligand 1. Besides, the whole 1·Ag+ complex structure is stabilized by two intramolecular hydrogen bonds. The interaction energy of the considered 1·Ag+ complex was found to be -465.5 kJ/mol, confirming also the formation of this cationic species.

Inhibition of the Membrane Attack Complex by Dengue Virus NS1 through Interaction with Vitronectin and Terminal Complement Proteins

PubMed Central

Conde, Jonas Nascimento; da Silva, Emiliana Mandarano; Allonso, Diego; Coelho, Diego Rodrigues; Andrade, Iamara da Silva; de Medeiros, Luciano Neves; Menezes, Joice Lima; Barbosa, Angela Silva

2016-01-01

ABSTRACT Dengue virus (DENV) infects millions of people worldwide and is a major public health problem. DENV nonstructural protein 1 (NS1) is a conserved glycoprotein that associates with membranes and is also secreted into the plasma in DENV-infected patients. The present study describes a novel mechanism by which NS1 inhibits the terminal complement pathway. We first identified the terminal complement regulator vitronectin (VN) as a novel DENV2 NS1 binding partner by using a yeast two-hybrid system. This interaction was further assessed by enzyme-linked immunosorbent assay (ELISA) and surface plasmon resonance (SPR) assay. The NS1-VN complex was also detected in plasmas from DENV-infected patients, suggesting that this interaction occurs during DENV infection. We also demonstrated that the DENV2 NS1 protein, either by itself or by interacting with VN, hinders the formation of the membrane attack complex (MAC) and C9 polymerization. Finally, we showed that DENV2, West Nile virus (WNV), and Zika virus (ZIKV) NS1 proteins produced in mammalian cells inhibited C9 polymerization. Taken together, our results points to a role for NS1 as a terminal pathway inhibitor of the complement system. IMPORTANCE Dengue is the most important arthropod-borne viral disease nowadays and is caused by dengue virus (DENV). The flavivirus NS1 glycoprotein has been characterized functionally as a complement evasion protein that can attenuate the activation of the classical, lectin, and alternative pathways. The present study describes a novel mechanism by which DENV NS1 inhibits the terminal complement pathway. We identified the terminal complement regulator vitronectin (VN) as a novel DENV NS1 binding partner, and the NS1-VN complex was detected in plasmas from DENV-infected patients, suggesting that this interaction occurs during DENV infection. We also demonstrated that the NS1-VN complex inhibited membrane attack complex (MAC) formation, thus interfering with the complement terminal pathway. Interestingly, NS1 itself also inhibited MAC activity, suggesting a direct role of this protein in the inhibition process. Our findings imply a role for NS1 as a terminal pathway inhibitor of the complement system. PMID:27512066

Acute stress in adulthood impoverishes social choices and triggers aggressiveness in preclinical models

PubMed Central

Nosjean, Anne; Cressant, Arnaud; de Chaumont, Fabrice; Olivo-Marin, Jean-Christophe; Chauveau, Frédéric; Granon, Sylvie

2015-01-01

Adult C57BL/6J mice are known to exhibit high level of social flexibility while mice lacking the β2 subunit of nicotinic receptors (β2−/− mice) present social rigidity. We asked ourselves what would be the consequences of a restraint acute stress (45 min) on social interactions in adult mice of both genotypes, hence the contribution of neuronal nicotinic receptors in this process. We therefore dissected social interaction complexity of stressed and not stressed dyads of mice in a social interaction task. We also measured plasma corticosterone levels in our experimental conditions. We showed that a single stress exposure occurring in adulthood reduced and disorganized social interaction complexity in both C57BL/6J and β2−/− mice. These stress-induced maladaptive social interactions involved alteration of distinct social categories and strategies in both genotypes, suggesting a dissociable impact of stress depending on the functioning of the cholinergic nicotinic system. In both genotypes, social behaviors under stress were coupled to aggressive reactions with no plasma corticosterone changes. Thus, aggressiveness appeared a general response independent of nicotinic function. We demonstrate here that a single stress exposure occurring in adulthood is sufficient to impoverish social interactions: stress impaired social flexibility in C57BL/6J mice whereas it reinforced β2−/− mice behavioral rigidity. PMID:25610381

On the role of electrostatics in protein-protein interactions

NASA Astrophysics Data System (ADS)

Zhang, Zhe; Witham, Shawn; Alexov, Emil

2011-06-01

The role of electrostatics in protein-protein interactions and binding is reviewed in this paper. A brief outline of the computational modeling, in the framework of continuum electrostatics, is presented and the basic electrostatic effects occurring upon the formation of the complex are discussed. The effect of the salt concentration and pH of the water phase on protein-protein binding free energy is demonstrated which indicates that the increase of the salt concentration tends to weaken the binding, an observation that is attributed to the optimization of the charge-charge interactions across the interface. It is pointed out that the pH-optimum (pH of optimal binding affinity) varies among the protein-protein complexes, and perhaps is a result of their adaptation to particular subcellular compartments. The similarities and differences between hetero- and homo-complexes are outlined and discussed with respect to the binding mode and charge complementarity.

On the role of electrostatics on protein-protein interactions

PubMed Central

Zhang, Zhe; Witham, Shawn; Alexov, Emil

2011-01-01

The role of electrostatics on protein-protein interactions and binding is reviewed in this article. A brief outline of the computational modeling, in the framework of continuum electrostatics, is presented and basic electrostatic effects occurring upon the formation of the complex are discussed. The role of the salt concentration and pH of the water phase on protein-protein binding free energy is demonstrated and indicates that the increase of the salt concentration tends to weaken the binding, an observation that is attributed to the optimization of the charge-charge interactions across the interface. It is pointed out that the pH-optimum (pH of optimal binding affinity) varies among the protein-protein complexes, and perhaps is a result of their adaptation to particular subcellular compartment. At the end, the similarities and differences between hetero- and homo-complexes are outlined and discussed with respect to the binding mode and charge complementarity. PMID:21572182

Global Mapping of the Yeast Genetic Interaction Network

NASA Astrophysics Data System (ADS)

Tong, Amy Hin Yan; Lesage, Guillaume; Bader, Gary D.; Ding, Huiming; Xu, Hong; Xin, Xiaofeng; Young, James; Berriz, Gabriel F.; Brost, Renee L.; Chang, Michael; Chen, YiQun; Cheng, Xin; Chua, Gordon; Friesen, Helena; Goldberg, Debra S.; Haynes, Jennifer; Humphries, Christine; He, Grace; Hussein, Shamiza; Ke, Lizhu; Krogan, Nevan; Li, Zhijian; Levinson, Joshua N.; Lu, Hong; Ménard, Patrice; Munyana, Christella; Parsons, Ainslie B.; Ryan, Owen; Tonikian, Raffi; Roberts, Tania; Sdicu, Anne-Marie; Shapiro, Jesse; Sheikh, Bilal; Suter, Bernhard; Wong, Sharyl L.; Zhang, Lan V.; Zhu, Hongwei; Burd, Christopher G.; Munro, Sean; Sander, Chris; Rine, Jasper; Greenblatt, Jack; Peter, Matthias; Bretscher, Anthony; Bell, Graham; Roth, Frederick P.; Brown, Grant W.; Andrews, Brenda; Bussey, Howard; Boone, Charles

2004-02-01

A genetic interaction network containing ~1000 genes and ~4000 interactions was mapped by crossing mutations in 132 different query genes into a set of ~4700 viable gene yeast deletion mutants and scoring the double mutant progeny for fitness defects. Network connectivity was predictive of function because interactions often occurred among functionally related genes, and similar patterns of interactions tended to identify components of the same pathway. The genetic network exhibited dense local neighborhoods; therefore, the position of a gene on a partially mapped network is predictive of other genetic interactions. Because digenic interactions are common in yeast, similar networks may underlie the complex genetics associated with inherited phenotypes in other organisms.

Analysis of trehalose-6-phosphate synthase (TPS) gene family suggests the formation of TPS complexes in rice.

PubMed

Zang, Baisheng; Li, Haowen; Li, Wenjun; Deng, Xing Wang; Wang, Xiping

2011-08-01

Trehalose-6-phosphate (T6P), an intermediate in the trehalose biosynthesis pathway, is emerging as an important regulator of plant metabolism and development. T6P levels are potentially modulated by a group of trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP) homologues. In this study, we have isolated 11 TPS genes encoding proteins with both TPS and TPP domains, from rice. Functional complement assays performed in yeast tps1 and tps2 mutants, revealed that only OsTPS1 encodes an active TPS enzyme and no OsTPS protein possesses TPP activity. By using a yeast two-hybrid analysis, a complicated interaction network occurred among OsTPS proteins, and the TPS domain might be essential for this interaction to occur. The interaction between OsTPS1 and OsTPS8 in vivo was confirmed by bimolecular fluorescence complementation and coimmunoprecipitation assays. Furthermore, our gel filtration assay showed that there may exist two forms of OsTPS1 (OsTPS1a and OsTPS1b) with different elution profiles in rice. OsTPS1b was particularly cofractionated with OsTPS5 and OsTPS8 in the 360 kDa complex, while OsTPS1a was predominantly incorporated into the complexes larger than 360 kDa. Collectively, these results suggest that OsTPS family members may form trehalose-6-phosphate synthase complexes and therefore potentially modify T6P levels to regulate plant development.

vEmbryo In Silico Models: Predicting Vascular Developmental Toxicity

EPA Science Inventory

The cardiovascular system is the first to function in the vertebrate embryo, reflecting the critical need for nutrient delivery and waste removal during organogenesis. Blood vessel development occurs by complex interacting signaling networks, including extra-cellular matrix remod...

Allylic amination reactivity of Ni, Pd, and Pt heterobimetallic and monometallic complexes.

PubMed

Carlsen, Ryan W; Ess, Daniel H

2016-06-14

Transition metal heterobimetallic complexes with dative metal-metal interactions have the potential for novel fast reactivity. There are few studies that both compare the reactivity of different metal centers in heterobimetallic complexes and compare bimetallic reactivity to monometallic reactivity. Here we report density-functional calculations that show the reactivity of [Cl2Ti(N(t)BuPPh2)2M(II)(η(3)-methallyl)] heterobimetallic complexes for allylic amination follows M = Ni > Pd > Pt. This reactivity trend was not anticipated since the amine addition transition state involves M(II) to M(0) reduction and this could disadvantage Ni. Comparison of heterobimetallic complexes to the corresponding monometallic (CH2)2(N(t)BuPPh2)2M(II)(η(3)-methallyl) complexes reveals that this reactivity trend is due to the bimetallic interaction and that the bimetallic interaction significantly lowers the barrier height for amine addition by >10 kcal mol(-1). The impact of the early transition metal center on the amination addition barrier height depends on the late transition metal center. The lowest barrier heights for this reaction occur when late and early transition metal centers are from the same periodic table row.

Eu(III)-Fulvic Acid Complexation: Evidence of Fulvic Acid Concentration Dependent Interactions by Time-Resolved Luminescence Spectroscopy.

PubMed

Kouhail, Yasmine Z; Benedetti, Marc F; Reiller, Pascal E

2016-04-05

Europium speciation is investigated by time-resolved luminescence spectroscopy (TRLS) in the presence of Suwannee River fulvic acid (SRFA). From complexation isotherms built at different total Eu(III) concentrations, pH values, ionic strength, and SRFA concentrations, it appears that two luminescence behaviors of Eu(III) are occurring. The first part, at the lowest CSRFA values, is showing the typical luminescence evolution of Eu(III) complexed by humic substances--that is, the increase of the asymmetry ratio between the (5)D0 → (7)F2 and (5)D0 → (7)F1 transitions up to a plateau--, and the occurrence of a biexponential decay--the first decay being faster than free Eu(3+). At higher CSRFA, a second luminescence mode is detected as the asymmetry ratio is increasing again after the previous plateau, and could correspond to the formation of another type of complex, and/or it can reflect a different spatial organization of complexed europium within the SRFA structure. The luminescence decay keeps on evolving but link to hydration number is not straightforward due to quenching mechanisms. The Eu(III) chemical environment evolution with CSRFA is also ionic strength dependent. These observations suggest that in addition to short-range interactions--intraparticulate complexation--, there might be interactions at longer range--interparticulate repulsion--between particles that are complexing Eu(III) at high CSRFA. These interactions are not yet accounted by the different complexation models.

Synergisms between microbial pathogens in plant disease complexes: a growing trend

PubMed Central

Lamichhane, Jay Ram; Venturi, Vittorio

2015-01-01

Plant diseases are often thought to be caused by one species or even by a specific strain. Microbes in nature, however, mostly occur as part of complex communities and this has been noted since the time of van Leeuwenhoek. Interestingly, most laboratory studies focus on single microbial strains grown in pure culture; we were therefore unaware of possible interspecies and/or inter-kingdom interactions of pathogenic microbes in the wild. In human and animal infections, it is now being recognized that many diseases are the result of multispecies synergistic interactions. This increases the complexity of the disease and has to be taken into consideration in the development of more effective control measures. On the other hand, there are only a few reports of synergistic pathogen–pathogen interactions in plant diseases and the mechanisms of interactions are currently unknown. Here we review some of these reports of synergism between different plant pathogens and their possible implications in crop health. Finally, we briefly highlight the recent technological advances in diagnostics as these are beginning to provide important insights into the microbial communities associated with complex plant diseases. These examples of synergistic interactions of plant pathogens that lead to disease complexes might prove to be more common than expected and understanding the underlying mechanisms might have important implications in plant disease epidemiology and management. PMID:26074945

Modal interactions due to friction in the nonlinear vibration response of the "Harmony" test structure: Experiments and simulations

NASA Astrophysics Data System (ADS)

Claeys, M.; Sinou, J.-J.; Lambelin, J.-P.; Todeschini, R.

2016-08-01

The nonlinear vibration response of an assembly with friction joints - named "Harmony" - is studied both experimentally and numerically. The experimental results exhibit a softening effect and an increase of dissipation with excitation level. Modal interactions due to friction are also evidenced. The numerical methodology proposed groups together well-known structural dynamic methods, including finite elements, substructuring, Harmonic Balance and continuation methods. On the one hand, the application of this methodology proves its capacity to treat a complex system where several friction movements occur at the same time. On the other hand, the main contribution of this paper is the experimental and numerical study of evidence of modal interactions due to friction. The simulation methodology succeeds in reproducing complex form of dynamic behavior such as these modal interactions.

Interacting agricultural pests and their effect on crop yield: application of a Bayesian decision theory approach to the joint management of Bromus tectorum and Cephus cinctus.

PubMed

Keren, Ilai N; Menalled, Fabian D; Weaver, David K; Robison-Cox, James F

2015-01-01

Worldwide, the landscape homogeneity of extensive monocultures that characterizes conventional agriculture has resulted in the development of specialized and interacting multitrophic pest complexes. While integrated pest management emphasizes the need to consider the ecological context where multiple species coexist, management recommendations are often based on single-species tactics. This approach may not provide satisfactory solutions when confronted with the complex interactions occurring between organisms at the same or different trophic levels. Replacement of the single-species management model with more sophisticated, multi-species programs requires an understanding of the direct and indirect interactions occurring between the crop and all categories of pests. We evaluated a modeling framework to make multi-pest management decisions taking into account direct and indirect interactions among species belonging to different trophic levels. We adopted a Bayesian decision theory approach in combination with path analysis to evaluate interactions between Bromus tectorum (downy brome, cheatgrass) and Cephus cinctus (wheat stem sawfly) in wheat (Triticum aestivum) systems. We assessed their joint responses to weed management tactics, seeding rates, and cultivar tolerance to insect stem boring or competition. Our results indicated that C. cinctus oviposition behavior varied as a function of B. tectorum pressure. Crop responses were more readily explained by the joint effects of management tactics on both categories of pests and their interactions than just by the direct impact of any particular management scheme on yield. In accordance, a C. cinctus tolerant variety should be planted at a low seeding rate under high insect pressure. However as B. tectorum levels increase, the C. cinctus tolerant variety should be replaced by a competitive and drought tolerant cultivar at high seeding rates despite C. cinctus infestation. This study exemplifies the necessity of accounting for direct and indirect biological interactions occurring within agroecosystems and propagating this information from the statistical analysis stage to the management stage.

Thermodynamic compatibility and interactions between Speckled Sugar bean protein and xanthan gum for production of multilayer O/W emulsion.

PubMed

Rahmati, Nazanin Fatemeh; Koocheki, Arash; Varidi, Mehdi; Kadkhodaee, Rassoul

2018-03-01

Thermodynamic compatibility and probable interactions between Speckled Sugar been protein (SSBP) and xanthan gum for production of multilayer O/W emulsion (30% oil) were investigated. Different interactions were observed between SSBP and xanthan at different pH (3-7) including electrostatic interactions and hydrogen bonding. These interactions were predominant at pH 3. When low xanthan gum concentration (0.1%) was used, phase separation and complex coacervation observed at this pH (negative effect of interactions). However, at pH 5, only 0.1% xanthan was enough to drastically reduce non-dissolved protein and its precipitation which normally occurs at this pH. In addition, incompatibility or segregative phase behavior which normally occurs when protein and polysaccharide have same charges was not observed (positive effects of interactions). Protein-gum interactions influenced emulsion properties (zeta potential, particle size, PDI, rheology, emulsion capacity, heat stability and creaming rate). Interactions had considerable influence on emulsion shelf life and produced completely stable emulsions at all pH values. Results confirmed that SSBP-xanthan gum mixture has a high potential for production of multilayer emulsions.

Dynamic assembly of Hda and the sliding clamp in the regulation of replication licensing.

PubMed

Kim, Jin S; Nanfara, Michael T; Chodavarapu, Sundari; Jin, Kyeong S; Babu, Vignesh M P; Ghazy, Mohamed A; Chung, Scisung; Kaguni, Jon M; Sutton, Mark D; Cho, Yunje

2017-04-20

Regulatory inactivation of DnaA (RIDA) is one of the major regulatory mechanisms of prokaryotic replication licensing. In RIDA, the Hda-sliding clamp complex loaded onto DNA directly interacts with adenosine triphosphate (ATP)-bound DnaA and stimulates the hydrolysis of ATP to inactivate DnaA. A prediction is that the activity of Hda is tightly controlled to ensure that replication initiation occurs only once per cell cycle. Here, we determined the crystal structure of the Hda-β clamp complex. This complex contains two pairs of Hda dimers sandwiched between two β clamp rings to form an octamer that is stabilized by three discrete interfaces. Two separate surfaces of Hda make contact with the β clamp, which is essential for Hda function in RIDA. The third interface between Hda monomers occludes the active site arginine finger, blocking its access to DnaA. Taken together, our structural and mutational analyses of the Hda-β clamp complex indicate that the interaction of the β clamp with Hda controls the ability of Hda to interact with DnaA. In the octameric Hda-β clamp complex, the inability of Hda to interact with DnaA is a novel mechanism that may regulate Hda function. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Dynamic assembly of Hda and the sliding clamp in the regulation of replication licensing

PubMed Central

Kim, Jin S.; Nanfara, Michael T.; Chodavarapu, Sundari; Jin, Kyeong S.; Babu, Vignesh M. P.; Ghazy, Mohamed A.; Chung, Scisung

2017-01-01

Abstract Regulatory inactivation of DnaA (RIDA) is one of the major regulatory mechanisms of prokaryotic replication licensing. In RIDA, the Hda–sliding clamp complex loaded onto DNA directly interacts with adenosine triphosphate (ATP)-bound DnaA and stimulates the hydrolysis of ATP to inactivate DnaA. A prediction is that the activity of Hda is tightly controlled to ensure that replication initiation occurs only once per cell cycle. Here, we determined the crystal structure of the Hda–β clamp complex. This complex contains two pairs of Hda dimers sandwiched between two β clamp rings to form an octamer that is stabilized by three discrete interfaces. Two separate surfaces of Hda make contact with the β clamp, which is essential for Hda function in RIDA. The third interface between Hda monomers occludes the active site arginine finger, blocking its access to DnaA. Taken together, our structural and mutational analyses of the Hda–β clamp complex indicate that the interaction of the β clamp with Hda controls the ability of Hda to interact with DnaA. In the octameric Hda–β clamp complex, the inability of Hda to interact with DnaA is a novel mechanism that may regulate Hda function. PMID:28168278

Structural and functional analysis of the human POT1-TPP1 telomeric complex

DOE PAGES

Rice, Cory; Shastrula, Prashanth Krishna; Kossenkov, Andrew V.; ...

2017-04-10

POT1 and TPP1 are part of the shelterin complex and are essential for telomere length regulation and maintenance. Naturally occurring mutations of the telomeric POT1–TPP1 complex are implicated in familial glioma, melanoma and chronic lymphocytic leukaemia. Here we report the atomic structure of the interacting portion of the human telomeric POT1–TPP1 complex and suggest how several of these mutations contribute to malignant cancer. The POT1 C-terminus (POT1C) forms a bilobal structure consisting of an OB-fold and a holiday junction resolvase domain. TPP1 consists of several loops and helices involved in extensive interactions with POT1C. Biochemical data shows that several ofmore » the cancer-associated mutations, partially disrupt the POT1–TPP1 complex, which affects its ability to bind telomeric DNA efficiently. A defective POT1–TPP1 complex leads to longer and fragile telomeres, which in turn promotes genomic instability and cancer.« less

Structural and functional analysis of the human POT1-TPP1 telomeric complex

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

Rice, Cory; Shastrula, Prashanth Krishna; Kossenkov, Andrew V.

POT1 and TPP1 are part of the shelterin complex and are essential for telomere length regulation and maintenance. Naturally occurring mutations of the telomeric POT1–TPP1 complex are implicated in familial glioma, melanoma and chronic lymphocytic leukaemia. Here we report the atomic structure of the interacting portion of the human telomeric POT1–TPP1 complex and suggest how several of these mutations contribute to malignant cancer. The POT1 C-terminus (POT1C) forms a bilobal structure consisting of an OB-fold and a holiday junction resolvase domain. TPP1 consists of several loops and helices involved in extensive interactions with POT1C. Biochemical data shows that several ofmore » the cancer-associated mutations, partially disrupt the POT1–TPP1 complex, which affects its ability to bind telomeric DNA efficiently. A defective POT1–TPP1 complex leads to longer and fragile telomeres, which in turn promotes genomic instability and cancer.« less

DNA Polymerase α Subunit Residues and Interactions Required for Efficient Initiation Complex Formation Identified by a Genetic Selection.

PubMed

Lindow, Janet C; Dohrmann, Paul R; McHenry, Charles S

2015-07-03

Biophysical and structural studies have defined many of the interactions that occur between individual components or subassemblies of the bacterial replicase, DNA polymerase III holoenzyme (Pol III HE). Here, we extended our knowledge of residues and interactions that are important for the first step of the replicase reaction: the ATP-dependent formation of an initiation complex between the Pol III HE and primed DNA. We exploited a genetic selection using a dominant negative variant of the polymerase catalytic subunit that can effectively compete with wild-type Pol III α and form initiation complexes, but cannot elongate. Suppression of the dominant negative phenotype was achieved by secondary mutations that were ineffective in initiation complex formation. The corresponding proteins were purified and characterized. One class of mutant mapped to the PHP domain of Pol III α, ablating interaction with the ϵ proofreading subunit and distorting the polymerase active site in the adjacent polymerase domain. Another class of mutation, found near the C terminus, interfered with τ binding. A third class mapped within the known β-binding domain, decreasing interaction with the β2 processivity factor. Surprisingly, mutations within the β binding domain also ablated interaction with τ, suggesting a larger τ binding site than previously recognized. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Analytical methods to determine the comparative DNA binding studies of curcumin-Cu(II) complexes

NASA Astrophysics Data System (ADS)

Rajesh, Jegathalaprathaban; Rajasekaran, Marichamy; Rajagopal, Gurusamy; Athappan, Periakaruppan

2012-11-01

DNA interaction studies of two mononuclear [1:1(1); 1:2(2)] copper(II) complexes of curcumin have been studied. The interaction of these complexes with CT-DNA has been explored by physical methods to propose modes of DNA binding of the complexes. Absorption spectral titrations of complex 1 with CT-DNA shows a red-shift of 3 nm with the DNA binding affinity of Kb, 5.21 × 104 M-1 that are higher than that obtained for 2 (red-shift, 2 nm; Kb, 1.73 × 104 M-1) reveal that the binding occurs in grooves as a result of the interaction is via exterior phosphates. The CD spectra of these Cu(II) complexes show a red shift of 3-10 nm in the positive band with increase in intensities. This spectral change of induced CD due to the hydrophobic interaction of copper complexes with DNA is the characteristic of B to A conformational change. The EB displacement assay also reveals the same trend as observed in UV-Vis spectral titration. The addition of complexes 1 and 2 to the DNA bound ethidium bromide (EB) solutions causes an obvious reduction in emission intensities indicating that these complexes competitively bind to DNA with EB. The positive shift of both the Epc and E0' accompanied by reduction of peak currents in differential pulse voltammogram (DPV), upon adding different concentrations of DNA to the metal complexes, are obviously in favor of strong binding to DNA. The super coiled plasmid pUC18 DNA cleavage ability of Cu(II) complexes in the presence of reducing agent reveals the single strand DNA cleavage (ssDNA) is observed. The hydroxyl radical (HOrad ) and the singlet oxygen are believed to be the reactive species responsible for the cleavage.

Study of interactions between anionic exopolysaccharides produced by newly isolated probiotic bacteria and sodium caseinate.

PubMed

Abid, Yousra; Joulak, Ichrak; Ben Amara, Chedia; Casillo, Angela; Attia, Hamadi; Gharsallaoui, Adem; Azabou, Samia

2018-07-01

The present study aims to evaluate the interactions between four exopolysaccharides (EPS) produced by probiotic bacteria and sodium caseinate (Cas) in order to simulate their behavior in dairy products. Complexation between the produced EPS samples and Cas was investigated as a function of polysaccharide to protein ratio. The highest turbidity and average size of complexes were formed at an EPS/Cas ratio of 3 (corresponding to 1 g/L of EPS and 0.33 g/L of Cas) as a result of the combination of individual complexes to form aggregates. Zeta potential measurements and Cas surface hydrophobicity results suggested that complex formation occurred essentially through electrostatic attractions with a possible contribution of hydrophobic interaction for EPS-GM which was produced by Bacillus tequilensis-GM. Afterwards, the effect of pH on the complexation between biopolymers was studied when EPS and Cas concentrations were maintained constant at 1 and 0.33 g/L, respectively. pH was adjusted to 3.0 and 3.5, respectively. Results showed that the highest amount and sizes of EPS/Cas complexes were formed at pH 3.5 and that EPS-GM enabled to obtain the biggest and highest amount of aggregates. Therefore, the obtained results support the fact that the simultaneous presence of EPS and Cas in dairy products results in complexes formation via electrostatic interactions depending on EPS/Cas ratio and pH of the medium. Copyright © 2018 Elsevier B.V. All rights reserved.

NMR and molecular modeling of wine tannins binding to saliva proteins: revisiting astringency from molecular and colloidal prospects.

PubMed

Cala, Olivier; Pinaud, Noël; Simon, Cécile; Fouquet, Eric; Laguerre, Michel; Dufourc, Erick J; Pianet, Isabelle

2010-11-01

In organoleptic science, the association of tannins to saliva proteins leads to the poorly understood phenomenon of astringency. To decipher this interaction at molecular and colloidal levels, the binding of 4 procyanidin dimers (B1-4) and 1 trimer (C2) to a human saliva proline-rich peptide, IB7(14), was studied. Interactions have been characterized by measuring dissociation constants, sizes of complexes, number, and nature of binding sites using NMR (chemical shift variations, diffusion-ordered spectroscopy, and saturation transfer diffusion). The binding sites were identified using molecular mechanics, and the hydrophilic/hydrophobic nature of the interactions was resolved by calculating the molecular lipophilicity potential within the complexes. The following comprehensive scheme can be proposed: 1) below the tannin critical micelle concentration (CMC), interaction is specific, and the procyanidin anchorage always occurs on the same three IB7(14) sites. The tannin 3-dimensional structure plays a key role in the binding force and in the tannin's ability to act as a bidentate ligand: tannins adopting an extended conformation exhibit higher affinity toward protein and initiate the formation of a network. 2) Above the CMC, after the first specific hydrophilic interaction has taken place, a random hydrophobic stacking occurs between tannins and proteins. The whole process is discussed in the general frame of wine tannins eliciting astringency.

Sawflies and ponderosa pine: hypothetical response surfaces for pine genotype, ontogenic stage, and stress level

Treesearch

Michael R. Wagner

1991-01-01

Patterns that occur in nature are the result of a complex set of current and historical factors that interact with one another and the adaptive plasticity of plants. Scientists are forced to assess such processes on the basis of series of "snapshots" over a relatively short time that represent only part of the grand pattern. In the case of insects interacting...

Quantum chemical study of the structure and properties of citrinin

USDA-ARS?s Scientific Manuscript database

Citrinin is a well known polyketide mycotoxin produced by fungal species that naturally occur in certain agricultural commodities, including red yeast rice. This toxin possesses complex intramolecular hydrogen bonding interactions which influence its mode of action and selective detection. Detailed ...

Using an agent-based model to analyze the dynamic communication network of the immune response

PubMed Central

2011-01-01

Background The immune system behaves like a complex, dynamic network with interacting elements including leukocytes, cytokines, and chemokines. While the immune system is broadly distributed, leukocytes must communicate effectively to respond to a pathological challenge. The Basic Immune Simulator 2010 contains agents representing leukocytes and tissue cells, signals representing cytokines, chemokines, and pathogens, and virtual spaces representing organ tissue, lymphoid tissue, and blood. Agents interact dynamically in the compartments in response to infection of the virtual tissue. Agent behavior is imposed by logical rules derived from the scientific literature. The model captured the agent-to-agent contact history, and from this the network topology and the interactions resulting in successful versus failed viral clearance were identified. This model served to integrate existing knowledge and allowed us to examine the immune response from a novel perspective directed at exploiting complex dynamics, ultimately for the design of therapeutic interventions. Results Analyzing the evolution of agent-agent interactions at incremental time points from identical initial conditions revealed novel features of immune communication associated with successful and failed outcomes. There were fewer contacts between agents for simulations ending in viral elimination (win) versus persistent infection (loss), due to the removal of infected agents. However, early cellular interactions preceded successful clearance of infection. Specifically, more Dendritic Agent interactions with TCell and BCell Agents, and more BCell Agent interactions with TCell Agents early in the simulation were associated with the immune win outcome. The Dendritic Agents greatly influenced the outcome, confirming them as hub agents of the immune network. In addition, unexpectedly high frequencies of Dendritic Agent-self interactions occurred in the lymphoid compartment late in the loss outcomes. Conclusions An agent-based model capturing several key aspects of complex system dynamics was used to study the emergent properties of the immune response to viral infection. Specific patterns of interactions between leukocyte agents occurring early in the response significantly improved outcome. More interactions at later stages correlated with persistent inflammation and infection. These simulation experiments highlight the importance of commonly overlooked aspects of the immune response and provide insight into these processes at a resolution level exceeding the capabilities of current laboratory technologies. PMID:21247471

Yeast silencing factor Sir4 and a subset of nucleoporins form a complex distinct from nuclear pore complexes

PubMed Central

Ptak, Christopher; Roesner, Ulyss K.

2017-01-01

Interactions occurring at the nuclear envelope (NE)–chromatin interface influence both NE structure and chromatin organization. Insights into the functions of NE–chromatin interactions have come from the study of yeast subtelomeric chromatin and its association with the NE, including the identification of various proteins necessary for tethering subtelomeric chromatin to the NE and the silencing of resident genes. Here we show that four of these proteins—the silencing factor Sir4, NE-associated Esc1, the SUMO E3 ligase Siz2, and the nuclear pore complex (NPC) protein Nup170—physically and functionally interact with one another and a subset of NPC components (nucleoporins or Nups). Importantly, this group of Nups is largely restricted to members of the inner and outer NPC rings, but it lacks numerous others including cytoplasmically and nucleoplasmically positioned Nups. We propose that this Sir4-associated Nup complex is distinct from holo-NPCs and that it plays a role in subtelomeric chromatin organization and NE tethering. PMID:28883038

Yeast silencing factor Sir4 and a subset of nucleoporins form a complex distinct from nuclear pore complexes.

PubMed

Lapetina, Diego L; Ptak, Christopher; Roesner, Ulyss K; Wozniak, Richard W

2017-10-02

Interactions occurring at the nuclear envelope (NE)-chromatin interface influence both NE structure and chromatin organization. Insights into the functions of NE-chromatin interactions have come from the study of yeast subtelomeric chromatin and its association with the NE, including the identification of various proteins necessary for tethering subtelomeric chromatin to the NE and the silencing of resident genes. Here we show that four of these proteins-the silencing factor Sir4, NE-associated Esc1, the SUMO E3 ligase Siz2, and the nuclear pore complex (NPC) protein Nup170-physically and functionally interact with one another and a subset of NPC components (nucleoporins or Nups). Importantly, this group of Nups is largely restricted to members of the inner and outer NPC rings, but it lacks numerous others including cytoplasmically and nucleoplasmically positioned Nups. We propose that this Sir4-associated Nup complex is distinct from holo-NPCs and that it plays a role in subtelomeric chromatin organization and NE tethering. © 2017 Lapetina et al.

Study of DNA-emodin interaction by FTIR and UV-vis spectroscopy.

PubMed

Saito, Samuel T; Silva, Givaldo; Pungartnik, Cristina; Brendel, Martin

2012-06-04

Emodin, a plant- and fungus-derived anthraquinone, exerts genotoxic and antioxidative effects and shows promise in antitumor and antibacterial therapies. The aim of this study was to examine the molecular interactions of emodin with DNA in aqueous solution at physiological pH using spectroscopic methods. Fourier Transform Infrared (FTIR) Spectroscopy and UV absorption spectra were used to determine the structural features, the binding mode and the association constants. Our UV-spectroscopic results indicate that emodin interacts with DNA by intercalation and by external binding. FTIR results suggest that emodin interaction occurs preferably via adenine and thymine base pairs and also weakly with the phosphate backbone of the DNA double helix. The binding constant for emodin-DNA complex formation is estimated to be K=5.59×10(3)M(-1). No significant changes of DNA conformation were observed upon emodin-DNA complexation. Copyright © 2012 Elsevier B.V. All rights reserved.

Effect of phosphorylation of myelin basic protein by MAPK on its interactions with actin and actin binding to a lipid membrane in vitro.

PubMed

Boggs, Joan M; Rangaraj, Godha; Gao, Wen; Heng, Yew-Meng

2006-01-17

Myelin basic protein (MBP) binds to negatively charged lipids on the cytosolic surface of oligodendrocyte membranes and is most likely responsible for adhesion of these surfaces in the multilayered myelin sheath. It can also polymerize actin, bundle F-actin filaments, and bind actin filaments to lipid bilayers through electrostatic interactions. MBP consists of a number of posttranslationally modified isomers of varying charge, some resulting from phosphorylation at several sites by different kinases, including mitogen-activated protein kinase (MAPK). Phosphorylation of MBP in oligodendrocytes occurs in response to various extracellular stimuli. Phosphorylation/dephosphorylation of MBP also occurs in the myelin sheath in response to electrical activity in the brain. Here we investigate the effect of phosphorylation of MBP on its interaction with actin in vitro by phosphorylating the most highly charged unmodified isomer, C1, at two sites with MAPK. Phosphorylation decreased the ability of MBP to polymerize actin and to bundle actin filaments but had no effect on the dissociation constant of the MBP-actin complex or on the ability of Ca2+-calmodulin to dissociate the complex. The most significant effect of phosphorylation on the MBP-actin complex was a dramatic reduction in its ability to bind to negatively charged lipid bilayers. The effect was much greater than that reported earlier for another charge isomer of MBP, C8, in which six arginines were deiminated to citrulline, resulting in a reduction of net positive charge of 6. These results indicate that although average electrostatic forces are the primary determinant of the interaction of MBP with actin, phosphorylation may have an additional effect due to a site-specific electrostatic effect or to a conformational change. Thus, phosphorylation of MBP, which occurs in response to various extracellular signals in both myelin and oligodendrocytes, attenuates the ability of MBP to polymerize and bundle actin and to bind it to a negatively charged membrane.

Computational structure analysis of biomacromolecule complexes by interface geometry.

PubMed

Mahdavi, Sedigheh; Salehzadeh-Yazdi, Ali; Mohades, Ali; Masoudi-Nejad, Ali

2013-12-01

The ability to analyze and compare protein-nucleic acid and protein-protein interaction interface has critical importance in understanding the biological function and essential processes occurring in the cells. Since high-resolution three-dimensional (3D) structures of biomacromolecule complexes are available, computational characterizing of the interface geometry become an important research topic in the field of molecular biology. In this study, the interfaces of a set of 180 protein-nucleic acid and protein-protein complexes are computed to understand the principles of their interactions. The weighted Voronoi diagram of the atoms and the Alpha complex has provided an accurate description of the interface atoms. Our method is implemented in the presence and absence of water molecules. A comparison among the three types of interaction interfaces show that RNA-protein complexes have the largest size of an interface. The results show a high correlation coefficient between our method and the PISA server in the presence and absence of water molecules in the Voronoi model and the traditional model based on solvent accessibility and the high validation parameters in comparison to the classical model. Copyright © 2013 Elsevier Ltd. All rights reserved.

MIMO: an efficient tool for molecular interaction maps overlap

PubMed Central

2013-01-01

Background Molecular pathways represent an ensemble of interactions occurring among molecules within the cell and between cells. The identification of similarities between molecular pathways across organisms and functions has a critical role in understanding complex biological processes. For the inference of such novel information, the comparison of molecular pathways requires to account for imperfect matches (flexibility) and to efficiently handle complex network topologies. To date, these characteristics are only partially available in tools designed to compare molecular interaction maps. Results Our approach MIMO (Molecular Interaction Maps Overlap) addresses the first problem by allowing the introduction of gaps and mismatches between query and template pathways and permits -when necessary- supervised queries incorporating a priori biological information. It then addresses the second issue by relying directly on the rich graph topology described in the Systems Biology Markup Language (SBML) standard, and uses multidigraphs to efficiently handle multiple queries on biological graph databases. The algorithm has been here successfully used to highlight the contact point between various human pathways in the Reactome database. Conclusions MIMO offers a flexible and efficient graph-matching tool for comparing complex biological pathways. PMID:23672344

Emotional valence and context of social influences on drug abuse-related behavior in animal models of social stress and prosocial interaction.

PubMed

Neisewander, J L; Peartree, N A; Pentkowski, N S

2012-11-01

Social factors are important determinants of drug dependence and relapse. We reviewed pre-clinical literature examining the role of social experiences from early life through the development of drug dependence and relapse, emphasizing two aspects of these experiences: (1) whether the social interaction is appetitive or aversive and (2) whether the social interaction occurs within or outside of the drug-taking context. The models reviewed include neonatal care, isolation, social defeat, chronic subordination, and prosocial interactions. We review results from these models in regard to effects on self-administration and conditioned place preference established with alcohol, psychostimulants, and opiates. We suggest that in general, when the interactions occur outside of the drug-taking context, prosocial interactions are protective against drug abuse-related behaviors, whereas social stressors facilitate these behaviors. By contrast, positive or negative social interactions occurring within the drug-taking context may interact with other risk factors to enhance or inhibit these behaviors. Despite differences in the nature and complexity of human social behavior compared to other species, the evolving animal literature provides useful models for understanding social influences on drug abuse-related behavior that will allow for research on the behavioral and biological mechanisms involved. The models have contributed to understanding social influences on initiation and maintenance of drug use, but more research is needed to understand social influences on drug relapse.

Interpolymer complexation: comparisons of bulk and interfacial structures.

PubMed

Cattoz, Beatrice; de Vos, Wiebe M; Cosgrove, Terence; Crossman, Martin; Espidel, Youssef; Prescott, Stuart W

2015-04-14

The interactions between the strong polyelectrolyte sodium poly(styrenesulfonate), NaPSS, and the neutral polymer poly(vinylpyrrolidone), PVP, were investigated in bulk and at the silica/solution interface using a combination of diffusion nuclear magnetic resonance spectroscopy (NMR), small-angle neutron scattering (SANS), solvent relaxation NMR, and ellipsometry. We show for the first time that complex formation occurs between NaPSS and PVP in solution; the complexes formed were shown not to be influenced by pH variation, whereas increasing the ionic strength increases the complexation of NaPSS but does not influence the PVP directly. The complexes formed contained a large proportion of NaPSS. Study of these interactions at the silica interface demonstrated that complexes also form at the nanoparticle interface where PVP is added in the system prior to NaPSS. For a constant PVP concentration and varying NaPSS concentration, the system remains stable until NaPSS is added in excess, which leads to depletion flocculation. Surface complex formation using the layer-by-layer technique was also reported at a planar silica interface.

Stacking and T-shape competition in aromatic-aromatic amino acid interactions.

PubMed

Chelli, Riccardo; Gervasio, Francesco Luigi; Procacci, Piero; Schettino, Vincenzo

2002-05-29

The potential of mean force of interacting aromatic amino acids is calculated using molecular dynamics simulations. The free energy surface is determined in order to study stacking and T-shape competition for phenylalanine-phenylalanine (Phe-Phe), phenylalanine-tyrosine (Phe-Tyr), and tyrosine-tyrosine (Tyr-Tyr) complexes in vacuo, water, carbon tetrachloride, and methanol. Stacked structures are favored in all solvents with the exception of the Tyr-Tyr complex in carbon tetrachloride, where T-shaped structures are also important. The effect of anchoring the two alpha-carbons (C(alpha)) at selected distances is investigated. We find that short and large C(alpha)-C(alpha) distances favor stacked and T-shaped structures, respectively. We analyze a set of 2396 protein structures resolved experimentally. Comparison of theoretical free energies for the complexes to the experimental analogue shows that Tyr-Tyr interaction occurs mainly at the protein surface, while Phe-Tyr and Phe-Phe interactions are more frequent in the hydrophobic protein core. This is confirmed by the Voronoi polyhedron analysis on the database protein structures. As found from the free energy calculation, analysis of the protein database has shown that proximal and distal interacting aromatic residues are predominantly stacked and T-shaped, respectively.

Biomechanics of plant-insect interactions.

PubMed

Whitney, Heather M; Federle, Walter

2013-02-01

Plant-insect interactions are determined by both chemical and physical mechanisms. Biomechanical factors play an important role across many ecological situations, including pollination, herbivory and plant carnivory, and have led to complex adaptations in both plants and insects. However, while mechanical factors involved in some highly specific interactions have been elucidated, more generalised effects may be widespread but are more difficult to isolate, due to the multifunctional properties of the plant surfaces and tissues where interactions occur. Novel methodologies are being developed to investigate the mechanisms of biomechanical interactions and discover to what extent adaptive structures could be exploited via biomimetics. Copyright © 2012 Elsevier Ltd. All rights reserved.

Interactive visualization of public health indicators to support policymaking: An exploratory study

PubMed Central

Zakkar, Moutasem; Sedig, Kamran

2017-01-01

Purpose The purpose of this study is to examine the use of interactive visualizations to represent data/information related to social determinants of health and public health indicators, and to investigate the benefits of such visualizations for health policymaking. Methods: The study developed a prototype for an online interactive visualization tool that represents the social determinants of health. The study participants explored and used the tool. The tool was evaluated using the informal user experience evaluation method. This method involves the prospective users of a tool to use and play with it and their feedback to be collected through interviews. Results: Using visualizations to represent and interact with health indicators has advantages over traditional representation techniques that do not allow users to interact with the information. Communicating healthcare indicators to policymakers is a complex task because of the complexity of the indicators, diversity of audiences, and different audience needs. This complexity can lead to information misinterpretation, which occurs when users of the health data ignore or do not know why, where, and how the data has been produced, or where and how it can be used. Conclusions: Public health policymaking is a complex process, and data is only one element among others needed in this complex process. Researchers and healthcare organizations should conduct a strategic evaluation to assess the usability of interactive visualizations and decision support tools before investing in these tools. Such evaluation should take into consideration the cost, ease of use, learnability, and efficiency of those tools, and the factors that influence policymaking. PMID:29026455

Dynamic interactions between cells and their extracellular matrix mediate embryonic development.

PubMed

Goody, Michelle F; Henry, Clarissa A

2010-06-01

Cells and their surrounding extracellular matrix microenvironment interact throughout all stages of life. Understanding the continuously changing scope of cell-matrix interactions in vivo is crucial to garner insights into both congenital birth defects and disease progression. A current challenge in the field of developmental biology is to adapt in vitro tools and rapidly evolving imaging technology to study cell-matrix interactions in a complex 4-D environment. In this review, we highlight the dynamic modulation of cell-matrix interactions during development. We propose that individual cell-matrix adhesion proteins are best considered as complex proteins that can play multiple, often seemingly contradictory roles, depending upon the context of the microenvironment. In addition, cell-matrix proteins can also exert different short versus long term effects. It is thus important to consider cell behavior in light of the microenvironment because of the constant and dynamic reciprocal interactions occurring between them. Finally, we suggest that analysis of cell-matrix interactions at multiple levels (molecules, cells, tissues) in vivo is critical for an integrated understanding because different information can be acquired from all size scales. Copyright 2010 Wiley-Liss, Inc.

Mechanistic Indicators of Childhood Asthma (MICA): piloting an integrative design for evaluating environmental health

EPA Science Inventory

Background: Modem methods in molecular biology and advanced computational tools show promise in elucidating complex interactions that occur between genes and environmental factors in diseases such as asthma; however appropriately designed studies are critical for these methods to...

The ubiquitin conjugating enzyme UbcH10 competes with UbcH3 for binding to the SCF complex, a ubiquitin ligase involved in cell cycle progression

USDA-ARS?s Scientific Manuscript database

Ubiquitylation, which regulates most biological pathways, occurs through an enzymatic cascade involving a ubiquitin (ub) activating enzyme (E1), a ub conjugating enzyme (E2) and a ub ligase (E3). UbcH3 is the E2 that interacts with SCF (Skp1/Cul1/F-box protein) complex and ubiquitylates many protein...

Inhibition of the Membrane Attack Complex by Dengue Virus NS1 through Interaction with Vitronectin and Terminal Complement Proteins.

PubMed

Conde, Jonas Nascimento; da Silva, Emiliana Mandarano; Allonso, Diego; Coelho, Diego Rodrigues; Andrade, Iamara da Silva; de Medeiros, Luciano Neves; Menezes, Joice Lima; Barbosa, Angela Silva; Mohana-Borges, Ronaldo

2016-11-01

Dengue virus (DENV) infects millions of people worldwide and is a major public health problem. DENV nonstructural protein 1 (NS1) is a conserved glycoprotein that associates with membranes and is also secreted into the plasma in DENV-infected patients. The present study describes a novel mechanism by which NS1 inhibits the terminal complement pathway. We first identified the terminal complement regulator vitronectin (VN) as a novel DENV2 NS1 binding partner by using a yeast two-hybrid system. This interaction was further assessed by enzyme-linked immunosorbent assay (ELISA) and surface plasmon resonance (SPR) assay. The NS1-VN complex was also detected in plasmas from DENV-infected patients, suggesting that this interaction occurs during DENV infection. We also demonstrated that the DENV2 NS1 protein, either by itself or by interacting with VN, hinders the formation of the membrane attack complex (MAC) and C9 polymerization. Finally, we showed that DENV2, West Nile virus (WNV), and Zika virus (ZIKV) NS1 proteins produced in mammalian cells inhibited C9 polymerization. Taken together, our results points to a role for NS1 as a terminal pathway inhibitor of the complement system. Dengue is the most important arthropod-borne viral disease nowadays and is caused by dengue virus (DENV). The flavivirus NS1 glycoprotein has been characterized functionally as a complement evasion protein that can attenuate the activation of the classical, lectin, and alternative pathways. The present study describes a novel mechanism by which DENV NS1 inhibits the terminal complement pathway. We identified the terminal complement regulator vitronectin (VN) as a novel DENV NS1 binding partner, and the NS1-VN complex was detected in plasmas from DENV-infected patients, suggesting that this interaction occurs during DENV infection. We also demonstrated that the NS1-VN complex inhibited membrane attack complex (MAC) formation, thus interfering with the complement terminal pathway. Interestingly, NS1 itself also inhibited MAC activity, suggesting a direct role of this protein in the inhibition process. Our findings imply a role for NS1 as a terminal pathway inhibitor of the complement system. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

A Three-Dimensional Eulerian Code for Simulation of High-Speed Multimaterial Interactions

DTIC Science & Technology

2011-08-01

PDE -based extension. The extension process is done on only the host cells on a particular processor. After extension the parallel communication is...condensation shocks, explosive debris transport, detonation in heterogeneous media and so on. In these flows complex interactions occur between the...A.22] and ijΩ is the spin tensor. The Jaumann derivative is used to ensure objectivity of the stress tensor with respect to rotation

Broadband Microwave Spectroscopy as a Tool to Study Intermolecular Interactions in the Diphenyl Ether - Water System

NASA Astrophysics Data System (ADS)

Fatima, Mariyam; Perez, Cristobal; Schnell, Melanie

2017-06-01

Many biological processes, such as chemical recognition and protein folding, are mainly controlled by the interplay of hydrogen bonds and dispersive forces. This interplay also occurs between organic molecules and solvent water molecules. Broadband rotational spectroscopy studies of weakly bound complexes are able to accurately reveal the structures and internal dynamics of molecular clusters isolated in the gas phase. Amongst them, water clusters with organic molecules are of particular interest. In this work, we investigate the interplay between different types of weak intermolecular interactions and how it controls the preferred interaction sites of aromatic ethers, where dispersive interactions may play a significant role. We present our results on diphenyl ether (C_{12}H_{10}O, 1,1'-Oxydibenzene) complexed with up to three molecules of water. Diphenyl ether is a flexible molecule, and it offers two competing binding sites for water: the ether oxygen and the aromatic π system. In order to determine the structure of the diphenyl ether-water complexes, we targeted transitions in the 2-8 GHz range using broadband rotational spectroscopy. We identify two isomers with one water, one with two water, and one with three water molecules. Further analysis from isotopic substitution measurements provided accurate structural information. The preferred interactions, as well as the observed structural changes induced upon complexation, will be presented and discussed.

Mapping a Noncovalent Protein-Peptide Interface by Top-Down FTICR Mass Spectrometry Using Electron Capture Dissociation

NASA Astrophysics Data System (ADS)

Clarke, David J.; Murray, Euan; Hupp, Ted; Mackay, C. Logan; Langridge-Smith, Pat R. R.

2011-08-01

Noncovalent protein-ligand and protein-protein complexes are readily detected using electrospray ionization mass spectrometry (ESI MS). Furthermore, recent reports have demonstrated that careful use of electron capture dissociation (ECD) fragmentation allows covalent backbone bonds of protein complexes to be dissociated without disruption of noncovalent protein-ligand interactions. In this way the site of protein-ligand interfaces can be identified. To date, protein-ligand complexes, which have proven tractable to this technique, have been mediated by ionic electrostatic interactions, i.e., ion pair interactions or salt bridging. Here we extend this methodology by applying ECD to study a protein-peptide complex that contains no electrostatics interactions. We analyzed the complex between the 21 kDa p53-inhibitor protein anterior gradient-2 and its hexapeptide binding ligand (PTTIYY). ECD fragmentation of the 1:1 complex occurs with retention of protein-peptide binding and analysis of the resulting fragments allows the binding interface to be localized to a C-terminal region between residues 109 and 175. These finding are supported by a solution-phase competition assay, which implicates the region between residues 108 and 122 within AGR2 as the PTTIYY binding interface. Our study expands previous findings by demonstrating that top-down ECD mass spectrometry can be used to determine directly the sites of peptide-protein interfaces. This highlights the growing potential of using ECD and related top-down fragmentation techniques for interrogation of protein-protein interfaces.

Structural model of the p14/SF3b155 · branch duplex complex.

PubMed

Schellenberg, Matthew J; Dul, Erin L; MacMillan, Andrew M

2011-01-01

Human p14 (SF3b14), a component of the spliceosomal U2 snRNP, interacts directly with the pre-mRNA branch adenosine within the context of the bulged duplex formed between the pre-mRNA branch region and U2 snRNA. This association occurs early in spliceosome assembly and persists within the fully assembled spliceosome. Analysis of the crystal structure of a complex containing p14 and a peptide derived from p14-associated SF3b155 combined with the results of cross-linking studies has suggested that the branch nucleotide interacts with a pocket on a non-canonical RNA binding surface formed by the complex. Here we report a structural model of the p14 · bulged duplex interaction based on a combination of X-ray crystallography of an adenine p14/SF3b155 peptide complex, biochemical comparison of a panel of disulfide cross-linked protein-RNA complexes, and small-angle X-ray scattering (SAXS). These studies reveal specific recognition of the branch adenosine within the p14 pocket and establish the orientation of the bulged duplex RNA bound on the protein surface. The intimate association of one surface of the bulged duplex with the p14/SF3b155 peptide complex described by this model buries the branch nucleotide at the interface and suggests that p14 · duplex interaction must be disrupted before the first step of splicing.

Structural model of the p14/SF3b155·branch duplex complex

PubMed Central

Schellenberg, Matthew J.; Dul, Erin L.; MacMillan, Andrew M.

2011-01-01

Human p14 (SF3b14), a component of the spliceosomal U2 snRNP, interacts directly with the pre-mRNA branch adenosine within the context of the bulged duplex formed between the pre-mRNA branch region and U2 snRNA. This association occurs early in spliceosome assembly and persists within the fully assembled spliceosome. Analysis of the crystal structure of a complex containing p14 and a peptide derived from p14-associated SF3b155 combined with the results of cross-linking studies has suggested that the branch nucleotide interacts with a pocket on a non-canonical RNA binding surface formed by the complex. Here we report a structural model of the p14•bulged duplex interaction based on a combination of X-ray crystallography of an adenine p14/SF3b155 peptide complex, biochemical comparison of a panel of disulfide cross-linked protein–RNA complexes, and small-angle X-ray scattering (SAXS). These studies reveal specific recognition of the branch adenosine within the p14 pocket and establish the orientation of the bulged duplex RNA bound on the protein surface. The intimate association of one surface of the bulged duplex with the p14/SF3b155 peptide complex described by this model buries the branch nucleotide at the interface and suggests that p14•duplex interaction must be disrupted before the first step of splicing. PMID:21062891

Synthesis, characterization, and binding assessment with human serum albumin of three bipyridine lanthanide(III) complexes.

PubMed

Aramesh-Boroujeni, Zahra; Bordbar, Abdol-Khalegh; Khorasani-Motlagh, Mozhgan; Sattarinezhad, Elham; Fani, Najme; Noroozifar, Meissam

2018-05-18

In this work, the terbium(III), dysprosium(III), and ytterbium(III) complexes containing 2, 2'-bipyridine (bpy) ligand have been synthesized and characterized using CHN elemental analysis, FT-IR, UV-Vis and 1 H-NMR techniques and their binding behavior with human serum albumin (HSA) was studied by UV-Vis, fluorescence and molecular docking examinations. The experimental data indicated that all three lanthanide complexes have high binding affinity to HSA with effective quenching of HSA fluorescence via static mechanism. The binding parameters, the type of interaction, the value of resonance energy transfer, and the binding distance between complexes and HSA were estimated from the analysis of fluorescence measurements and Förster theory. The thermodynamic parameters suggested that van der Waals interactions and hydrogen bonds play an important role in the binding mechanism. While, the energy transfer from HSA molecules to all these complexes occurs with high probability, the order of binding constants (BpyTb > BpyDy > BpyYb) represents the importance of radius of Ln 3+ ion in the complex-HSA interaction. The results of molecular docking calculation and competitive experiments assessed site 3 of HSA, located in subdomain IB, as the most probable binding site for these ligands and also indicated the microenvironment residues around the bound mentioned complexes. The computational results kept in good agreement with experimental data.

The Social Benefits of Intramural Sports

ERIC Educational Resources Information Center

Artinger, Lori; Clapham, Lisa; Hunt, Carla; Meigs, Matthew; Milord, Nadia; Sampson, Bryan; Forrester, Scott A.

2006-01-01

One of the distinguishing features of collegiate student recreational sports complexes is the sense of community that is intentionally introduced in the programs and services that occur within these facilities. Intramural sports programs provide a powerful medium for student interaction (Belch, Gebel, & Mass, 2001). This study was designed to…

Hydrogen Bonding Interaction between Atmospheric Gaseous Amides and Methanol.

PubMed

Zhao, Hailiang; Tang, Shanshan; Xu, Xiang; Du, Lin

2016-12-30

Amides are important atmospheric organic-nitrogen compounds. Hydrogen bonded complexes of methanol (MeOH) with amides (formamide, N -methylformamide, N , N -dimethylformamide, acetamide, N -methylacetamide and N , N -dimethylacetamide) have been investigated. The carbonyl oxygen of the amides behaves as a hydrogen bond acceptor and the NH group of the amides acts as a hydrogen bond donor. The dominant hydrogen bonding interaction occurs between the carbonyl oxygen and the OH group of methanol as well as the interaction between the NH group of amides and the oxygen of methanol. However, the hydrogen bonds between the CH group and the carbonyl oxygen or the oxygen of methanol are also important for the overall stability of the complexes. Comparable red shifts of the C=O, NH- and OH-stretching transitions were found in these MeOH-amide complexes with considerable intensity enhancement. Topological analysis shows that the electron density at the bond critical points of the complexes fall in the range of hydrogen bonding criteria, and the Laplacian of charge density of the O-H∙∙∙O hydrogen bond slightly exceeds the upper value of the Laplacian criteria. The energy decomposition analysis further suggests that the hydrogen bonding interaction energies can be mainly attributed to the electrostatic, exchange and dispersion components.

Hydrogen Bonding Interaction between Atmospheric Gaseous Amides and Methanol

PubMed Central

Zhao, Hailiang; Tang, Shanshan; Xu, Xiang; Du, Lin

2016-01-01

Amides are important atmospheric organic–nitrogen compounds. Hydrogen bonded complexes of methanol (MeOH) with amides (formamide, N-methylformamide, N,N-dimethylformamide, acetamide, N-methylacetamide and N,N-dimethylacetamide) have been investigated. The carbonyl oxygen of the amides behaves as a hydrogen bond acceptor and the NH group of the amides acts as a hydrogen bond donor. The dominant hydrogen bonding interaction occurs between the carbonyl oxygen and the OH group of methanol as well as the interaction between the NH group of amides and the oxygen of methanol. However, the hydrogen bonds between the CH group and the carbonyl oxygen or the oxygen of methanol are also important for the overall stability of the complexes. Comparable red shifts of the C=O, NH- and OH-stretching transitions were found in these MeOH–amide complexes with considerable intensity enhancement. Topological analysis shows that the electron density at the bond critical points of the complexes fall in the range of hydrogen bonding criteria, and the Laplacian of charge density of the O–H∙∙∙O hydrogen bond slightly exceeds the upper value of the Laplacian criteria. The energy decomposition analysis further suggests that the hydrogen bonding interaction energies can be mainly attributed to the electrostatic, exchange and dispersion components. PMID:28042825

Ab initio study of weakly bound halogen complexes: RX⋯PH3.

PubMed

Georg, Herbert C; Fileti, Eudes E; Malaspina, Thaciana

2013-01-01

Ab initio calculations were employed to study the role of ipso carbon hybridization in halogenated compounds RX (R=methyl, phenyl, acetyl, H and X=F, Cl, Br and I) and its interaction with a phosphorus atom, as occurs in the halogen bonded complex type RX⋯PH3. The analysis was performed using ab initio MP2, MP4 and CCSD(T) methods. Systematic energy analysis found that the interaction energies are in the range -4.14 to -11.92 kJ mol(-1) (at MP2 level without ZPE correction). Effects of electronic correlation levels were evaluated at MP4 and CCSD(T) levels and a reduction of up to 27% in interaction energy obtained in MP2 was observed. Analysis of the electrostatic maps confirms that the PhCl⋯PH3 and all MeX⋯PH3 complexes are unstable. NBO analysis suggested that the charge transfer between the moieties is bigger when using iodine than bromine and chlorine. The electrical properties of these complexes (dipole and polarizability) were determined and the most important observed aspect was the systematic increase at the dipole polarizability, given by the interaction polarizability. This increase is in the range of 0.7-6.7 u.a. (about 3-7%).

Effect of polymer molecular weight on chitosan-protein interaction.

PubMed

Bekale, L; Agudelo, D; Tajmir-Riahi, H A

2015-01-01

We present a comprehensive study of the interactions between chitosan nanoparticles (15, 100 and 200 kDa with the same degree of deacetylation 90%) and two model proteins, i.e., bovine (BSA) and human serum albumins (HSA), with the aim of correlating chitosan molecular weight (Mw) and the binding affinity of these naturally occurring polymers to protein. The effect of chitosan on the protein secondary structure and the influence of protein complexation on the shape of chitosan nanoparticles are discussed. A combination of multiple spectroscopic methods, transmission electron microscopy (TEM) and thermodynamic analysis were used to assess the polymer-protein complex formation. Results revealed that the three chitosan nanoparticles interact with BSA to form chitosan-BSA complexes, mainly through hydrophobic contacts with the affinity order: 200>100>15 kDa. However, HSA-chitosan complexation is mainly via electrostatic interactions with the stability order: 100>200>15 kDa. Furthermore, the association between polymer and protein causes a partial protein conformational change by a major reduction of α-helix from 63% (free BSA) to 57% (chitosan-BSA) and 57% (free HSA) to 51% (chitosan-HSA). Finally, TEM micrographs clearly revealed that the binding of serum albumins with chitosan nanoparticles induces a significant change in protein morphology and the shape of the polymer. Copyright © 2014 Elsevier B.V. All rights reserved.

Anks3 alters the sub-cellular localization of the Nek7 kinase

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

Ramachandran, Haribaskar; Engel, Christina; Müller, Barbara

2015-08-28

Nephronophthisis (NPH) is an autosomal recessive cystic kidney disease, and a frequent cause of end-stage renal failure in children. To date, 17 NPH-associated gene products (NPHPs) have been identified. Most NPHPs participate in large multi-protein complexes that localize to the cilium and/or basal body; however, the precise composition of these complexes and their biological function remain largely unknown. We recently observed that the ankyrin repeat protein Anks3 interacts with the NPH family member Anks6. Both Anks3 and Anks6 form complexes with multiple other NPHPs, suggesting that both proteins function in similar or overlapping signaling pathways. Here, we show that Anks3,more » but not Anks6 interacted with the NIMA-related kinase Nek7, and was heavily modified in the presence of Nek7, resulting in an approximately 20 kD increase in molecular weight. Although mass spectrometry revealed increased serine and threonine phosphorylation of Anks3 primarily within the N-terminal ankyrin repeats also required for Nek7 interaction, the molecular weight increase occurred even in the presence of a kinase-dead Nek7 mutant, indicating that this modification was not caused by Nek7-dependent Anks3 phosphorylation. Furthermore, the Anks3 modification was specific for Nek7, and did not occur in the presence of Nek8. Importantly, Anks3 retained Nek7 in the cytoplasm, suggesting that, Nek7 triggers the modification of Anks3, which in turn prevents the nuclear localization of Nek7. - Highlights: • Anks3 interacted with Nek7 kinase, and was heavily modified in the presence of Nek7. • Anks3 N-terminal ankyrin repeats, but not SAM domain required for Nek7 interaction. • Nek7 increased Ser/Thr phosphorylation of Anks3 primarily within ankyrin domain. • Interaction with Anks3 led to cytoplasmic retention and nuclear exclusion of Nek7.« less

Extracting physical chemistry from mechanics: a new approach to investigate DNA interactions with drugs and proteins in single molecule experiments.

PubMed

Rocha, M S

2015-09-01

In this review we focus on the idea of establishing connections between the mechanical properties of DNA-ligand complexes and the physical chemistry of DNA-ligand interactions. This type of connection is interesting because it opens the possibility of performing a robust characterization of such interactions by using only one experimental technique: single molecule stretching. Furthermore, it also opens new possibilities in comparing results obtained by very different approaches, in particular when comparing single molecule techniques to ensemble-averaging techniques. We start the manuscript reviewing important concepts of DNA mechanics, from the basic mechanical properties to the Worm-Like Chain model. Next we review the basic concepts of the physical chemistry of DNA-ligand interactions, revisiting the most important models used to analyze the binding data and discussing their binding isotherms. Then, we discuss the basic features of the single molecule techniques most used to stretch DNA-ligand complexes and to obtain "force × extension" data, from which the mechanical properties of the complexes can be determined. We also discuss the characteristics of the main types of interactions that can occur between DNA and ligands, from covalent binding to simple electrostatic driven interactions. Finally, we present a historical survey of the attempts to connect mechanics to physical chemistry for DNA-ligand systems, emphasizing a recently developed fitting approach useful to connect the persistence length of DNA-ligand complexes to the physicochemical properties of the interaction. Such an approach in principle can be used for any type of ligand, from drugs to proteins, even if multiple binding modes are present.

Structure of a SUMO-binding-motif mimic bound to Smt3p–Ubc9p: conservation of a noncovalent Ubiquitin-like protein–E2 complex as a platform for selective interactions within a SUMO pathway

PubMed Central

Duda, David M.; van Waardenburg, Robert C. A. M.; Borg, Laura A.; McGarity, Sierra; Nourse, Amanda; Waddell, M. Brett; Bjornsti, Mary-Ann; Schulman, Brenda A.

2007-01-01

Summary The SUMO ubiquitin-like proteins play regulatory roles in cell division, transcription, DNA repair, and protein subcellular localization. Paralleling other ubiquitin-like proteins, SUMO proteins are proteolytically processed to maturity, conjugated to targets by E1-E2-E3 cascades, and subsequently recognized by specific downstream effectors containing a SUMO-binding motif (SBM). SUMO and its E2 from the budding yeast S. cerevisiae, Smt3p and Ubc9p, are encoded by essential genes. Here we describe the 1.9 Å resolution crystal structure of a noncovalent Smt3p–Ubc9p complex. Unexpectedly, a heterologous portion of the crystallized complex derived from the expression construct mimics an SBM, and binds Smt3p in a manner resembling SBM binding to human SUMO family members. In the complex, Smt3p binds a surface distal from Ubc9's catalytic cysteine. The structure implies that a single molecule of Smt3p cannot bind concurrently to both the noncovalent binding site and the catalytic cysteine of a single Ubc9p molecule. However, formation of higher-order complexes can occur, where a single Smt3p covalently linked to one Ubc9p's catalytic cysteine also binds noncovalently to another molecule of Ubc9p. Comparison with other structures from the SUMO pathway suggests that formation of the noncovalent Smt3p–Ubc9p complex occurs mutually exclusively with many other Smt3p and Ubc9p interactions in the conjugation cascade. By contrast, high-resolution insights into how Smt3p–Ubc9p can also interact with downstream recognition machineries come from contacts with the SBM mimic. Interestingly, the overall architecture of the Smt3p–Ubc9p complex is strikingly similar to recent structures from the ubiquitin pathway. The results imply that noncovalent ubiquitin-like protein–E2 complexes are conserved platforms, which function as parts of larger assemblies involved many protein post-translational regulatory pathways. PMID:17475278

In vivo evidence for homo- and heterodimeric interactions of Arabidopsis thaliana dehydrins AtCOR47, AtERD10, and AtRAB18.

PubMed

Hernández-Sánchez, Itzell E; Maruri-López, Israel; Graether, Steffen P; Jiménez-Bremont, Juan F

2017-12-06

Dehydrins (DHNs) are intrinsically disordered proteins that play central roles in plant abiotic stress responses; however, how they work remains unclear. Herein, we report the in planta subcellular localization of Arabidopsis thaliana DHNs AtCOR47, AtERD10, and AtRAB18 through GFP translational fusions. To explore the dimerization ability of the Arabidopsis acidic DHNs AtCOR47 and AtERD10, we conducted an in planta DHN binding assay using the Bimolecular Fluorescence Complementation (BiFC) technique. Our analyses revealed homodimeric interactions for AtCOR47 and AtERD10; interestingly, heterodimeric associations also occurred with these DHNs, and these interactions were observed in the cytosol of tobacco cells. Furthermore, we evaluated whether Arabidopsis basic DHNs, such as AtRAB18, could also interact with itself and/or with AtCOR47 and AtERD10 in the BiFC system. Our data revealed homodimeric RAB18 complexes in the nucleus and cytosol, while heterodimeric associations between AtRAB18 and acidic DHNs occurred only in the cytosol. Finally, we demonstrated the presence of heterodimeric complexes among Arabidopsis AtCOR47, AtERD10, and AtRAB18 DHNs with their acidic ortholog the OpsDHN1 from Opuntia streptacantha; these heterodimeric interactions showed different subcellular distributions. Our results guide DHN research toward a new scenario where DHN/DHN oligomerization could be explored as a part of their molecular mechanism.

A supramolecular complex between proteinases and beta-cyclodextrin that preserves enzymatic activity: physicochemical characterization.

PubMed

Denadai, Angelo M L; Santoro, Marcelo M; Lopes, Miriam T P; Chenna, Angélica; de Sousa, Frederico B; Avelar, Gabriela M; Gomes, Marco R Túlio; Guzman, Fanny; Salas, Carlos E; Sinisterra, Rubén D

2006-01-01

Cyclodextrins are suitable drug delivery systems because of their ability to subtly modify the physical, chemical, and biological properties of guest molecules through labile interactions by formation of inclusion and/or association complexes. Plant cysteine proteinases from Caricaceae and Bromeliaceae are the subject of therapeutic interest, because of their anti-inflammatory, antitumoral, immunogenic, and wound-healing properties. In this study, we analyzed the association between beta-cyclodextrin (betaCD) and fraction P1G10 containing the bioactive proteinases from Carica candamarcensis, and described the physicochemical nature of the solid-state self-assembled complexes by Fourier transform infrared (FTIR) spectroscopy, thermogravimetry (TG), differential scanning calorimetry (DSC), X-ray powder diffraction (XRD), and nuclear magnetic resonance (NMR), as well as in solution by circular dichroism (CD), isothermal titration calorimetry (ITC), and amidase activity. The physicochemical analyses suggest the formation of a complex between P1G10 and betaCD. Higher secondary interactions, namely hydrophobic interactions, hydrogen bonding and van der Waals forces were observed at higher P1G10 : betaCD mass ratios. These results provide evidence of the occurrence of strong solid-state supramolecular non-covalent interactions between P1G10 and betaCD. Microcalorimetric analysis demonstrates that complexation results in a favorable enthalpic contribution, as has already been described during formation of similar betaCD inclusion compounds. The amidase activity of the complex shows that the enzyme activity is not readily available at 24 hours after dissolution of the complex in aqueous buffer; the proteinase becomes biologically active by the second day and remains stable until day 16, when a gradual decrease occurs, with basal activity attained by day 29. The reported results underscore the potential for betaCDs as candidates for complexing cysteine proteinases, resulting in supramolecular arrays with sustained proteolytic activity.

Insights into dynamic processes of cations in pyrochlores and other complex oxides

DOE PAGES

Uberuaga, Blas Pedro; Perriot, Romain

2015-08-26

Complex oxides are critical components of many key technologies, from solid oxide fuel cells and superionics to inert matrix fuels and nuclear waste forms. In many cases, understanding mass transport is important for predicting performance and, thus, extensive effort has been devoted to understanding mass transport in these materials. However, most work has focused on the behavior of oxygen while cation transport has received relatively little attention, even though cation diffusion is responsible for many phenomena, including sintering, radiation damage evolution, and deformation processes. Here, we use accelerated molecular dynamics simulations to examine the kinetics of cation defects in onemore » class of complex oxides, A₂B₂O₇ pyrochlore. In some pyrochlore chemistries, B cation defects are kinetically unstable, transforming to A cation defects and antisites at rates faster than they can diffuse. When this occurs, transport of B cations occurs through defect processes on the A sublattice. Further, these A cation defects, either interstitials or vacancies, can interact with antisite disorder, reordering the material locally, though this process is much more efficient for interstitials than vacancies. Whether this behavior occurs in a given pyrochlore depends on the A and B chemistry. Pyrochlores with a smaller ratio of cation radii exhibit this complex behavior, while those with larger ratios exhibit direct migration of B interstitials. Similar behavior has been reported in other complex oxides such as spinels and perovskites, suggesting that this coupling of transport between the A and B cation sublattices, while not universal, occurs in many complex oxide.« less

MECHANISTIC INDICATORS OF CHILDHOOD ASTHMA (MICA): A SYSTEMS BIOLOGY APPROACH FOR THE INTEGRATION OF MULTIFACTORIAL EXPOSURE AND ENVIRONMENTAL HEALTH DATA

EPA Science Inventory

Modem methods in molecular biology and advanced computational tools show promise in elucidating complex interactions that occur between genes and environmental factors in diseases such as asthma. However, appropriately designed studies are critical for these methods to reach the...

Desert grassland and shrubland ecosystems [chapter 5

Treesearch

Samuel R. Loftin; Richard Agllilar; Alice L. Chung-MacCoubrey; Wayne A. Robbie

1995-01-01

The productivity, stability, and health of the Middle Rio Grande Basin, arid and semiarid grassland and shrub land ecosystems depend upon complex interactions. These relationships occur between factors such as climate, domestic livestock, and wildlife use, and human activities such as urban development, agriculture, and recreation. These grassland/ shrub land...

Characterization of clinical and environmental Mycobacterium avium spp. isolates and their interaction with human macrophages

EPA Science Inventory

Members of the Mycobacterium avium complex (MAC) are naturally occurring bacteria in the environment. A link has been suggested between M. avium strains in drinking water and clinical isolates from infected individuals. There is a need to develop new screening methodologies tha...

Book Review: "The Rhizosphere: Biochemistry and Organic Substances at the Soil-Plant Interface, Second Edition"

USDA-ARS?s Scientific Manuscript database

The complexity of the biological, chemical, and physical interactions occurring in the volume of soil surrounding the root of a growing plant dictates that a multidisciplinary approach must be taken to improve our understanding of this rhizosphere. Hence, "The Rhizosphere: Biochemistry and Organic S...

Targeted Treatments in Autism and Fragile X Syndrome

ERIC Educational Resources Information Center

Gurkan, C. Kagan; Hagerman, Randi J.

2012-01-01

Autism is a neurodevelopmental disorder consisting of a constellation of symptoms that sometimes occur as part of a complex disorder characterized by impairments in social interaction, communication and behavioral domains. It is a highly disabling disorder and there is a need for treatment targeting the core symptoms. Although autism is accepted…

A Sociolinguistic Study of Differential Object Marking (DOM) in Two Varieties of Contemporary Spanish

ERIC Educational Resources Information Center

Balasch Rodriguez, Sonia

2011-01-01

This sociolinguistic-variationist investigation sheds light on two little-studied issues concerning Spanish DOM, or variable use of a before animate "direct objects" (DOs), in vernacular language: the complex interaction of co-occurring linguistic (type of verb; definiteness, specificity, grammatical number, topicality, type and…

Triangular Diagrams Teach Steady and Dynamic Behaviour of Catalytic Reactions.

ERIC Educational Resources Information Center

Klusacek, K.; And Others

1989-01-01

Illustrates how triangular diagrams can aid in presenting some of the rather complex transient interactions that occur among gas and surface species during heterogeneous catalytic reactions. The basic equations and numerical examples are described. Classroom use of the triangular diagram is discussed. Several diagrams and graphs are provided. (YP)

Analysis of Coiled-Coil Interactions between Core Proteins of the Spindle Pole Body

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

Zizlsperger, N.; Malashkevich, V; Pillay, S

2008-01-01

The spindle pole body (SPB) is a multiprotein complex that organizes microtubules in yeast. Due to its large size and association with the nuclear membrane, little is known about its detailed structure. In particular, although many SPB components and some of the interactions between them have been identified, the molecular details of how most of these interactions occur are not known. The prevalence of predicted coiled-coil regions in SPB proteins suggests that some interactions may occur via coiled coils. Here this hypothesis is supported by biochemical characterization of isolated coiled-coil peptides derived from SPB proteins. Formation of four strongly self-associatingmore » coiled-coil complexes from Spc29, Spc42, and Spc72 was demonstrated by circular dichroism (CD) spectroscopy and a fluorescence resonance energy transfer (FRET) assay. Many weaker self- and heteroassociations were also detected by CD, FRET, and/or cross-linking. The thermal stabilities of nine candidate homooligomers were assessed; six unfolded cooperatively with melting temperatures ranging from <11 to >50 C. Solution studies established that coiled-coil peptides derived from Spc42 and Spc72 form parallel dimers, and this was confirmed for Spc42 by a high-resolution crystal structure. These data contribute to a growing body of knowledge that will ultimately provide a detailed model of the SPB structure.« less

Binding of Signal Recognition Particle Gives Ribosome/Nascent Chain Complexes a Competitive Advantage in Endoplasmic Reticulum Membrane Interaction

PubMed Central

Neuhof, Andrea; Rolls, Melissa M.; Jungnickel, Berit; Kalies, Kai-Uwe; Rapoport, Tom A.

1998-01-01

Most secretory and membrane proteins are sorted by signal sequences to the endoplasmic reticulum (ER) membrane early during their synthesis. Targeting of the ribosome-nascent chain complex (RNC) involves the binding of the signal sequence to the signal recognition particle (SRP), followed by an interaction of ribosome-bound SRP with the SRP receptor. However, ribosomes can also independently bind to the ER translocation channel formed by the Sec61p complex. To explain the specificity of membrane targeting, it has therefore been proposed that nascent polypeptide-associated complex functions as a cytosolic inhibitor of signal sequence- and SRP-independent ribosome binding to the ER membrane. We report here that SRP-independent binding of RNCs to the ER membrane can occur in the presence of all cytosolic factors, including nascent polypeptide-associated complex. Nontranslating ribosomes competitively inhibit SRP-independent membrane binding of RNCs but have no effect when SRP is bound to the RNCs. The protective effect of SRP against ribosome competition depends on a functional signal sequence in the nascent chain and is also observed with reconstituted proteoliposomes containing only the Sec61p complex and the SRP receptor. We conclude that cytosolic factors do not prevent the membrane binding of ribosomes. Instead, specific ribosome targeting to the Sec61p complex is provided by the binding of SRP to RNCs, followed by an interaction with the SRP receptor, which gives RNC–SRP complexes a selective advantage in membrane targeting over nontranslating ribosomes. PMID:9436994

Emotional valence and context of social influences on drug abuse-related behavior in animal models of social stress and prosocial interaction

PubMed Central

Neisewander, J.L.; Peartree, N.A.; Pentkowski, N.S.

2014-01-01

Rationale Social factors are important determinants of drug dependence and relapse. Objectives We reviewed preclinical literature examining the role of social experiences from early life through the development of drug dependence and relapse, emphasizing two aspects of these experiences: 1) whether the social interaction is appetitive or aversive and 2) whether the social interaction occurs within or outside of the drug-taking context. Methods The models reviewed include neonatal care, isolation, social defeat, chronic subordination, and prosocial interactions. We review results from these models in regard to effects on self-administration and conditioned place preference established with alcohol, psychostimulants, and opiates. Results We suggest that in general, when the interactions occur outside of the drug-taking context, prosocial interactions are protective against drug abuse-related behaviors whereas social stressors facilitate these behaviors. By contrast, positive or negative social interactions occurring within the drug-taking context may interact with other risk factors to enhance or inhibit these behaviors. Conclusions Despite differences in the nature and complexity of human social behavior compared to other species, the evolving animal literature provides useful models for understanding social influences on drug abuse-related behavior that will allow for research on the behavioral and biological mechanisms involved. The models have contributed to understanding social influences on initiation and maintenance of drug use, but more research is needed to understand social influences on drug relapse. PMID:22955569

Cardiorespiratory interactions in neural circulatory control in humans.

PubMed

Shamsuzzaman, A S; Somers, V K

2001-06-01

The reflex mechanisms and interactions described in this overview provide some explanation for the range of neural circulatory responses evident during changes in breathing. The effects described represent the integrated responses to activation of several reflex mechanisms, including peripheral and central chemoreflexes, arterial baroreflexes, pulmonary stretch receptors, and ventricular mechanoreceptors. These interactions occur on a dynamic basis and the transfer characteristics of any single interaction are, in all likelihood, also highly dynamic. Nevertheless, it is only by attempting to understand individual reflexes and their modulating influences that a more thorough understanding of the responses to complex phenomena such as hyperventilation, apnea, and obstructive sleep apnea can be better understood.

Processes influencing the duration and decline of epizootics in Schistocephalus solidus.

PubMed

Heins, David C; Baker, John A; Green, Dillon M

2011-06-01

The interplay of intermediate host fish and plerocercoids of diphyllobothriidean cestodes results in epizootics that are deceptively simple, but conceal complex biotic and abiotic interactions shaping each event independently. Although general descriptions of epizootics and some details of biotic interactions between enemies are known, much remains to be discovered about the abiotic and biotic forces and their interactions driving epizootics. This study shows that the duration of an epizootic of Schistocephalus solidus was sustained by high prevalence, mean intensity, and PI (parasite index-parasite : host biomass ratio) levels among young-of-the-year and 1-yr-old threespine sticklebacks. Many infections and most parasite growth in young-of-the-year fish apparently occurred under the ice during the winter. Few new infections appear to have occurred among 1-yr-old fish, which may live 2 yr and sometimes 3 yr. The decline of the epizootic occurred as the recruitment of 1 to 2-yr-old hosts decreased significantly, followed by reduced infections of young-of-the-year fish. Thus, a major factor influencing parasite population dynamics was reduced transmission (probability of infection) as a result of overwinter host mortality among 1-yr-old fish. Mega-epizootics, named and described herein, appear to represent a "perfect storm" phenomenon dependent on a particular and rare combination of circumstances. Less extreme and more gradual epizootics may be more common and play out in myriad ways, because of complex abiotic and biotic factors influencing both parasite and host populations. The interplay of parasite and host resulting in reciprocal effects upon one another occurs during both the emergence and decline phases of an epizootic.

Sensemaking in a Value Based Context for Large Scale Complex Engineered Systems

NASA Astrophysics Data System (ADS)

Sikkandar Basha, Nazareen

The design and the development of Large-Scale Complex Engineered Systems (LSCES) requires the involvement of multiple teams and numerous levels of the organization and interactions with large numbers of people and interdisciplinary departments. Traditionally, requirements-driven Systems Engineering (SE) is used in the design and development of these LSCES. The requirements are used to capture the preferences of the stakeholder for the LSCES. Due to the complexity of the system, multiple levels of interactions are required to elicit the requirements of the system within the organization. Since LSCES involves people and interactions between the teams and interdisciplinary departments, it should be socio-technical in nature. The elicitation of the requirements of most large-scale system projects are subjected to creep in time and cost due to the uncertainty and ambiguity of requirements during the design and development. In an organization structure, the cost and time overrun can occur at any level and iterate back and forth thus increasing the cost and time. To avoid such creep past researches have shown that rigorous approaches such as value based designing can be used to control it. But before the rigorous approaches can be used, the decision maker should have a proper understanding of requirements creep and the state of the system when the creep occurs. Sensemaking is used to understand the state of system when the creep occurs and provide a guidance to decision maker. This research proposes the use of the Cynefin framework, sensemaking framework which can be used in the design and development of LSCES. It can aide in understanding the system and decision making to minimize the value gap due to requirements creep by eliminating ambiguity which occurs during design and development. A sample hierarchical organization is used to demonstrate the state of the system at the occurrence of requirements creep in terms of cost and time using the Cynefin framework. These trials are continued for different requirements and at different sub-system level. The results obtained show that the Cynefin framework can be used to improve the value of the system and can be used for predictive analysis. The decision makers can use these findings and use rigorous approaches and improve the design of Large Scale Complex Engineered Systems.

Enhanced photophysics of conjugated polymers

DOEpatents

Chen, Liaohai [Argonne, IL; Xu, Su [Santa Clara, CA; McBranch, Duncan [Santa Fe, NM; Whitten, David [Santa Fe, NM

2003-05-27

The addition of oppositely charged surfactant to fluorescent ionic conjugated polymer forms a polymer-surfactant complex that exhibits at least one improved photophysical property. The conjugated polymer is a fluorescent ionic polymer that typically has at least one ionic side chain or moiety that interacts with the specific surfactant selected. The photophysical property improvements may include increased fluorescence quantum efficiency, wavelength-independent emission and absorption spectra, and more stable fluorescence decay kinetics. The complexation typically occurs in a solution of a polar solvent in which the polymer and surfactant are soluble, but it may also occur in a mixture of solvents. The solution is commonly prepared with a surfactant molecule:monomer repeat unit of polymer ratio ranging from about 1:100 to about 1:1. A polymer-surfactant complex precipitate is formed as the ratio approaches 1:1. This precipitate is recoverable and usable in many forms.

Crystal structure and functional interpretation of the erythrocyte spectrin tetramerization domain complex

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

Ipsaro, Jonathan J.; Harper, Sandra L.; Messick, Troy E.

2010-09-07

As the principal component of the membrane skeleton, spectrin confers integrity and flexibility to red cell membranes. Although this network involves many interactions, the most common hemolytic anemia mutations that disrupt erythrocyte morphology affect the spectrin tetramerization domains. Although much is known clinically about the resulting conditions (hereditary elliptocytosis and pyropoikilocytosis), the detailed structural basis for spectrin tetramerization and its disruption by hereditary anemia mutations remains elusive. Thus, to provide further insights into spectrin assembly and tetramer site mutations, a crystal structure of the spectrin tetramerization domain complex has been determined. Architecturally, this complex shows striking resemblance to multirepeat spectrinmore » fragments, with the interacting tetramer site region forming a central, composite repeat. This structure identifies conformational changes in {alpha}-spectrin that occur upon binding to {beta}-spectrin, and it reports the first structure of the {beta}-spectrin tetramerization domain. Analysis of the interaction surfaces indicates an extensive interface dominated by hydrophobic contacts and supplemented by electrostatic complementarity. Analysis of evolutionarily conserved residues suggests additional surfaces that may form important interactions. Finally, mapping of hereditary anemia-related mutations onto the structure demonstrate that most, but not all, local hereditary anemia mutations map to the interacting domains. The potential molecular effects of these mutations are described.« less

Crystal Structure and Functional Interpretation of the Erythrocyte spectrin Tetramerization Domain Complex

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

J Ipsaro; S Harper; T Messick

2011-12-31

As the principal component of the membrane skeleton, spectrin confers integrity and flexibility to red cell membranes. Although this network involves many interactions, the most common hemolytic anemia mutations that disrupt erythrocyte morphology affect the spectrin tetramerization domains. Although much is known clinically about the resulting conditions (hereditary elliptocytosis and pyropoikilocytosis), the detailed structural basis for spectrin tetramerization and its disruption by hereditary anemia mutations remains elusive. Thus, to provide further insights into spectrin assembly and tetramer site mutations, a crystal structure of the spectrin tetramerization domain complex has been determined. Architecturally, this complex shows striking resemblance to multirepeat spectrinmore » fragments, with the interacting tetramer site region forming a central, composite repeat. This structure identifies conformational changes in {alpha}-spectrin that occur upon binding to {beta}-spectrin, and it reports the first structure of the {beta}-spectrin tetramerization domain. Analysis of the interaction surfaces indicates an extensive interface dominated by hydrophobic contacts and supplemented by electrostatic complementarity. Analysis of evolutionarily conserved residues suggests additional surfaces that may form important interactions. Finally, mapping of hereditary anemia-related mutations onto the structure demonstrate that most, but not all, local hereditary anemia mutations map to the interacting domains. The potential molecular effects of these mutations are described.« less

Whirlin and PDZ domain-containing 7 (PDZD7) proteins are both required to form the quaternary protein complex associated with Usher syndrome type 2.

PubMed

Chen, Qian; Zou, Junhuang; Shen, Zuolian; Zhang, Weiping; Yang, Jun

2014-12-26

Usher syndrome (USH) is the leading genetic cause of combined hearing and vision loss. Among the three USH clinical types, type 2 (USH2) occurs most commonly. USH2A, GPR98, and WHRN are three known causative genes of USH2, whereas PDZD7 is a modifier gene found in USH2 patients. The proteins encoded by these four USH genes have been proposed to form a multiprotein complex, the USH2 complex, due to interactions found among some of these proteins in vitro, their colocalization in vivo, and mutual dependence of some of these proteins for their normal in vivo localizations. However, evidence showing the formation of the USH2 complex is missing, and details on how this complex is formed remain elusive. Here, we systematically investigated interactions among the intracellular regions of the four USH proteins using colocalization, yeast two-hybrid, and pull-down assays. We show that multiple domains of the four USH proteins interact among one another. Importantly, both WHRN and PDZD7 are required for the complex formation with USH2A and GPR98. In this USH2 quaternary complex, WHRN prefers to bind to USH2A, whereas PDZD7 prefers to bind to GPR98. Interaction between WHRN and PDZD7 is the bridge between USH2A and GPR98. Additionally, the USH2 quaternary complex has a variable stoichiometry. These findings suggest that a non-obligate, short term, and dynamic USH2 quaternary protein complex may exist in vivo. Our work provides valuable insight into the physiological role of the USH2 complex in vivo and informs possible reconstruction of the USH2 complex for future therapy. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

A study of [Co2(alkyne)(binap)(CO)4] complexes (BINAP=(1,1'-binaphthalene)-2,2'-diylbis(diphenylphosphine)).

PubMed

Gibson, Susan E; Kaufmann, Karina A C; Loch, Jennifer A; Steed, Jonathan W; White, Andrew J P

2005-04-08

Understanding the interaction of chiral ligands, alkynes, and alkenes with cobaltcarbonyl sources is critical to learning more about the mechanism of the catalytic, asymmetric Pauson-Khand reaction. We have successfully characterized complexes of the type [Co2(alkyne)(binap)(CO)4] (BINAP=(1,1'-binaphthalene)-2,2'-diylbis(diphenylphosphine)) and shown that diastereomer interconversion occurs under Pauson-Khand reaction conditions when alkyne=HC[triple bond]CCO2Me. Attempts to isolate [Co2(alkyne)(binap)(CO)x] complexes with coordinated alkenes led to the formation of cobaltacyclopentadiene species.

Synthesis, spectroscopic characterization, biological screenings, DNA binding study and POM analyses of transition metal carboxylates.

PubMed

Uddin, Noor; Sirajuddin, Muhammad; Uddin, Nizam; Tariq, Muhammad; Ullah, Hameed; Ali, Saqib; Tirmizi, Syed Ahmed; Khan, Abdur Rehman

2015-04-05

This article contains the synthesis of a novel carboxylic acid derivative, its transition metal complexes and evaluation of biological applications. Six carboxylate complexes of transition metals, Zn(II) and Hg(II), have been successfully synthesized and characterized by FT-IR and NMR (1H, 13C). The ligand, HL, (4-[(2,6-Diethylphenyl)amino]-4-oxobutanoic acid) was also characterized by single crystal X-ray analysis. The complexation occurs via oxygen atoms of the carboxylate moiety. FT-IR date show the bidentate nature of the carboxylate moiety of the ligand as the Δν value in all complexes is less than that of the free ligand. The ligand and its complexes were screened for antifungal and antileishmanial activities. The results showed that the ligand and its complexes are active with few exceptions. UV-visible spectroscopy and viscometry results reveal that the ligand and its complexes interact with the DNA via intercalative mode of interaction. A new and efficient strategy to identify the pharmacophores and anti-pharmacophores sites in carboxylate derivatives for the antibacterial/antifungal activity using Petra, Osiris and Molinspiration (POM) analyses was also carried out. Copyright © 2014 Elsevier B.V. All rights reserved.

Synthesis, spectroscopic characterization, biological screenings, DNA binding study and POM analyses of transition metal carboxylates

NASA Astrophysics Data System (ADS)

Uddin, Noor; Sirajuddin, Muhammad; Uddin, Nizam; Tariq, Muhammad; Ullah, Hameed; Ali, Saqib; Tirmizi, Syed Ahmed; Khan, Abdur Rehman

2015-04-01

This article contains the synthesis of a novel carboxylic acid derivative, its transition metal complexes and evaluation of biological applications. Six carboxylate complexes of transition metals, Zn(II) and Hg(II), have been successfully synthesized and characterized by FT-IR and NMR (1H, 13C). The ligand, HL, (4-[(2,6-Diethylphenyl)amino]-4-oxobutanoic acid) was also characterized by single crystal X-ray analysis. The complexation occurs via oxygen atoms of the carboxylate moiety. FT-IR date show the bidentate nature of the carboxylate moiety of the ligand as the Δν value in all complexes is less than that of the free ligand. The ligand and its complexes were screened for antifungal and antileishmanial activities. The results showed that the ligand and its complexes are active with few exceptions. UV-visible spectroscopy and viscometry results reveal that the ligand and its complexes interact with the DNA via intercalative mode of interaction. A new and efficient strategy to identify the pharmacophores and anti-pharmacophores sites in carboxylate derivatives for the antibacterial/antifungal activity using Petra, Osiris and Molinspiration (POM) analyses was also carried out.

Enduring the shipboard stressor complex: a systems approach.

PubMed

Comperatore, Carlos A; Rivera, Pik Kwan; Kingsley, Leonard

2005-06-01

A high incidence of physiological and psychological stressors characterizes the maritime work environment in many segments of the commercial maritime industry and in the military. Traditionally, crewmembers work embedded in a complex of stressors. Stressors rarely act independently because most occur concurrently, simultaneously taxing physical and mental resources. Stressors such as extreme environmental temperatures, long work hours, heavy mental and physical workload, authoritative leadership, isolation from family and loved ones, lack of exercise, and unhealthy diets often combine to degrade crewmember health and performance, particularly on long voyages. This complex system of interacting stressors affects the ability of maritime crewmembers to maintain adequate levels of alertness and performance. An analytical systems approach methodology is described here as a viable method to identify workplace stressors and track their systemic interactions. A systems-based program for managing the stressor complex is then offered, together with the empirical research supporting its efficacy. Included is an example implementation of a stressor-control program aboard a U.S. Coast Guard cutter.

Tenascin-X promotes epithelial-to-mesenchymal transition by activating latent TGF-β

PubMed Central

Alcaraz, Lindsay B.; Exposito, Jean-Yves; Chuvin, Nicolas; Pommier, Roxane M.; Cluzel, Caroline; Martel, Sylvie; Sentis, Stéphanie; Bartholin, Laurent; Lethias, Claire

2014-01-01

Transforming growth factor β (TGF-β) isoforms are secreted as inactive complexes formed through noncovalent interactions between the bioactive TGF-β entity and its N-terminal latency-associated peptide prodomain. Extracellular activation of the latent TGF-β complex is a crucial step in the regulation of TGF-β function for tissue homeostasis. We show that the fibrinogen-like (FBG) domain of the matrix glycoprotein tenascin-X (TNX) interacts physically with the small latent TGF-β complex in vitro and in vivo, thus regulating the bioavailability of mature TGF-β to cells by activating the latent cytokine into an active molecule. Activation by the FBG domain most likely occurs through a conformational change in the latent complex and involves a novel cell adhesion–dependent mechanism. We identify α11β1 integrin as a cell surface receptor for TNX and show that this integrin is crucial to elicit FBG-mediated activation of latent TGF-β and subsequent epithelial-to-mesenchymal transition in mammary epithelial cells. PMID:24821840

Short-Range Temporal Interactions in Sleep; Hippocampal Spike Avalanches Support a Large Milieu of Sequential Activity Including Replay

PubMed Central

Mahoney, J. Matthew; Titiz, Ali S.; Hernan, Amanda E.; Scott, Rod C.

2016-01-01

Hippocampal neural systems consolidate multiple complex behaviors into memory. However, the temporal structure of neural firing supporting complex memory consolidation is unknown. Replay of hippocampal place cells during sleep supports the view that a simple repetitive behavior modifies sleep firing dynamics, but does not explain how multiple episodes could be integrated into associative networks for recollection during future cognition. Here we decode sequential firing structure within spike avalanches of all pyramidal cells recorded in sleeping rats after running in a circular track. We find that short sequences that combine into multiple long sequences capture the majority of the sequential structure during sleep, including replay of hippocampal place cells. The ensemble, however, is not optimized for maximally producing the behavior-enriched episode. Thus behavioral programming of sequential correlations occurs at the level of short-range interactions, not whole behavioral sequences and these short sequences are assembled into a large and complex milieu that could support complex memory consolidation. PMID:26866597

CH/π interactions in metal-porphyrin complexes with pyrrole and chelate rings as hydrogen acceptors.

PubMed

Medaković, Vesna B; Bogdanović, Goran A; Milčić, Miloš K; Janjić, Goran V; Zarić, Snežana D

2012-12-01

CH/π interactions in metal porphyrinato complexes were studied by analyzing data in crystal structures from the Cambridge Structural Database (CSD) and by quantum chemical calculations. The analysis of the data in the CSD shows that both five-membered pyrrole and six-membered chelate rings form CH/π interactions. The interactions occur more frequently with five-membered rings. The analysis of distances in crystal structures and calculated energies show stronger interactions with six-membered chelate rings, indicating that a larger number of interactions with five-membered rings are not the consequence of stronger interactions, but better accessibility of five-membered pyrrole rings. The calculated energies of the interactions with positions in six-membered rings are -2.09 to -2.83 kcal/mol, while the energies with five-membered rings are -2.05 to -2.26 kcal/mol. The results reveal that stronger interactions of six-membered rings are the consequence of stronger electrostatic interactions. Substituents on the porphyrin ring significantly strengthen the interactions. Substituents on the six-membered ring strengthen the interaction energy by about 20%. The results show that CH/π interactions play an important role in molecular recognition of metalloporphyrins. The significant influence of the substituents on interaction energies can be very important for the design of model systems in bioinorganic chemistry. Copyright © 2012 Elsevier Inc. All rights reserved.

What experimental approaches (eg, in vivo, in vitro, tissue retrieval) are effective in investigating the biologic effects of particles?

PubMed Central

Bostrom, Mathias; O'Keefe, Regis

2009-01-01

Understanding the complex cellular and tissue mechanisms and interactions resulting in periprosthetic osteolysis requires a number of experimental approaches, each of which has its own set of advantages and limitations. In vitro models allow for the isolation of individual cell populations and have furthered our understanding of particle-cell interactions; however, they are limited because they do not mimic the complex tissue environment in which multiple cell interactions occur. In vivo animal models investigate the tissue interactions associated with periprosthetic osteolysis, but the choice of species and whether the implant system is subjected to mechanical load or to unloaded conditions are critical in assessing whether these models can be extrapolated to the clinical condition. Rigid analysis of retrieved tissue from clinical cases of osteolysis offers a different approach to studying the biologic process of osteolysis, but it is limited in that the tissue analyzed represents the end-stage of this process and, thus, may not reflect this process adequately. PMID:18612016

What experimental approaches (eg, in vivo, in vitro, tissue retrieval) are effective in investigating the biologic effects of particles?

PubMed

Bostrom, Mathias; O'Keefe, Regis

2008-01-01

Understanding the complex cellular and tissue mechanisms and interactions resulting in periprosthetic osteolysis requires a number of experimental approaches, each of which has its own set of advantages and limitations. In vitro models allow for the isolation of individual cell populations and have furthered our understanding of particle-cell interactions; however, they are limited because they do not mimic the complex tissue environment in which multiple cell interactions occur. In vivo animal models investigate the tissue interactions associated with periprosthetic osteolysis, but the choice of species and whether the implant system is subjected to mechanical load or to unloaded conditions are critical in assessing whether these models can be extrapolated to the clinical condition. Rigid analysis of retrieved tissue from clinical cases of osteolysis offers a different approach to studying the biologic process of osteolysis, but it is limited in that the tissue analyzed represents the end-stage of this process and, thus, may not reflect this process adequately.

Cryptococcus interactions with macrophages: evasion and manipulation of the phagosome by a fungal pathogen.

PubMed

Johnston, Simon A; May, Robin C

2013-03-01

Cryptococcus is a potentially fatal fungal pathogen and a leading cause of death in immunocompromised patients. As an opportunistic and facultative intracellular pathogen of humans, Cryptococcus exhibits a complex set of interactions with the host immune system in general, and macrophages in particular. Cryptococcus is resistant to phagocytosis but is also able to survive and proliferate within the mature phagolysosome. It can cause the lysis of host cells, can be transferred between macrophages or exit non-lytically via vomocytosis. Efficient phagocytosis is reliant on opsonization and Cryptococcus has a number of anti-phagocytic strategies including formation of titan cells and a thick polysaccharide capsule. Following uptake, phagosome maturation appears to occur normally, but the internalized pathogen is able to survive and replicate. Here we review the interactions and host manipulation processes that occur within cryptococcal-infected macrophages and highlight areas for future research. © 2012 Blackwell Publishing Ltd.

Hexahistidine (6xHis) fusion-based assays for protein-protein interactions.

PubMed

Puckett, Mary C

2015-01-01

Fusion-protein tags provide a useful method to study protein-protein interactions. One widely used fusion tag is hexahistidine (6xHis). This tag has unique advantages over others due to its small size and the relatively low abundance of naturally occurring consecutive histidine repeats. 6xHis tags can interact with immobilized metal cations to provide for the capture of proteins and protein complexes of interest. In this chapter, a description of the benefits and uses of 6xHis-fusion proteins as well as a detailed method for performing a 6xHis-pulldown assay are described.

Molecular mechanism of transcription inhibition by phage T7 gp2 protein.

PubMed

Mekler, Vladimir; Minakhin, Leonid; Sheppard, Carol; Wigneshweraraj, Sivaramesh; Severinov, Konstantin

2011-11-11

Escherichia coli T7 bacteriophage gp2 protein is a potent inhibitor of host RNA polymerase (RNAP). gp2 inhibits formation of open promoter complex by binding to the β' jaw, an RNAP domain that interacts with downstream promoter DNA. Here, we used an engineered promoter with an optimized sequence to obtain and characterize a specific promoter complex containing RNAP and gp2. In this complex, localized melting of promoter DNA is initiated but does not propagate to include the point of the transcription start. As a result, the complex is transcriptionally inactive. Using a highly sensitive RNAP beacon assay, we performed quantitative real-time measurements of specific binding of the RNAP-gp2 complex to promoter DNA and various promoter fragments. In this way, the effect of gp2 on RNAP interaction with promoters was dissected. As expected, gp2 greatly decreased RNAP affinity to downstream promoter duplex. However, gp2 also inhibited RNAP binding to promoter fragments that lacked downstream promoter DNA that interacts with the β' jaw. The inhibition was caused by gp2-mediated decrease of the RNAP binding affinity to template and non-template strand segments of the transcription bubble downstream of the -10 promoter element. The inhibition of RNAP interactions with single-stranded segments of the transcription bubble by gp2 is a novel effect, which may occur via allosteric mechanism that is set in motion by the gp2 binding to the β' jaw. Copyright © 2011 Elsevier Ltd. All rights reserved.

Cold Flow Propulsion Test Complex Pulse Testing

NASA Technical Reports Server (NTRS)

McDougal, Kris

2016-01-01

When the propellants in a liquid rocket engine burn, the rocket not only launches and moves in space, it causes forces that interact with the vehicle itself. When these interactions occur under specific conditions, the vehicle's structures and components can become unstable. One instability of primary concern is termed pogo (named after the movement of a pogo stick), in which the oscillations (cycling movements) cause large loads, or pressure, against the vehicle, tanks, feedlines, and engine. Marshall Space Flight Center (MSFC) has developed a unique test technology to understand and quantify the complex fluid movements and forces in a liquid rocket engine that contribute strongly to both engine and integrated vehicle performance and stability. This new test technology was established in the MSFC Cold Flow Propulsion Test Complex to allow injection and measurement of scaled propellant flows and measurement of the resulting forces at multiple locations throughout the engine.

The role of the [CpM(CO)2](-) chromophore in the optical properties of the [Cp2ThMCp(CO)2](+) complexes, where M = Fe, Ru and Os. A theoretical view.

PubMed

Cantero-López, Plinio; Le Bras, Laura; Páez-Hernández, Dayán; Arratia-Pérez, Ramiro

2015-12-14

The chemical bond between actinide and the transition metal unsupported by bridging ligands is not well characterized. In this paper we study the electronic properties, bonding nature and optical spectra in a family of [Cp2ThMCp(CO)2](+) complexes where M = Fe, Ru, Os, based on the relativistic two component density functional theory calculations. The Morokuma-Ziegler energy decomposition analysis shows an important ionic contribution in the Th-M interaction with around 25% of covalent character. Clearly, charge transfer occurs on Th-M bond formation, however the orbital term most likely represents a strong charge rearrangement in the fragments due to the interaction. Finally the spin-orbit-ZORA calculation shows the possible NIR emission induced by the [FeCp(CO)2](-) chromophore accomplishing the antenna effect that justifies the sensitization of the actinide complexes.

Sulfur-induced structural motifs on copper and gold surfaces

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

Walen, Holly

The interaction of sulfur with copper and gold surfaces plays a fundamental role in important phenomena that include coarsening of surface nanostructures, and self-assembly of alkanethiols. Here, we identify and analyze unique sulfur-induced structural motifs observed on the low-index surfaces of these two metals. We seek out these structures in an effort to better understand the fundamental interactions between these metals and sulfur that lends to the stability and favorability of metal-sulfur complexes vs. chemisorbed atomic sulfur. The experimental observations presented here—made under identical conditions—together with extensive DFT analyses, allow comparisons and insights into factors that favor the existence ofmore » metal-sulfur complexes, vs. chemisorbed atomic sulfur, on metal terraces. We believe this data will be instrumental in better understanding the complex phenomena occurring between the surfaces of coinage metals and sulfur.« less

Logical Interactions in AN Expanded Space

NASA Astrophysics Data System (ADS)

Tadić, Bosiljka

Understanding the emergent behavior in many complex systems in the physical world and society requires a detailed study of dynamical phenomena occurring and mutually coupled at different scales. The brain processes underlying the social conduct of each, and the emergent social behavior of interacting individuals on a larger scale, represent striking examples of the multiscale complexity. Studies of the human brain, a paradigm of a complex functional system, are enabled by a wealth of brain imaging data that provide clues of how we comprehend space, time, languages, numbers, and differentiate normal from diseased individuals, for example. The social brain, a neural basis for social cognition, represents a dynamically organized part of the brain which is involved in the inference of thoughts, feelings, and intentions going on in the brains of others. Research in this currently unexplored area opens a new perspective on the genesis of the societal organization at different levels and the associated social values...

Characterization, stoichiometry, and stability of salivary protein-tannin complexes by ESI-MS and ESI-MS/MS.

PubMed

Canon, Francis; Paté, Franck; Meudec, Emmanuelle; Marlin, Thérèse; Cheynier, Véronique; Giuliani, Alexandre; Sarni-Manchado, Pascale

2009-12-01

Numerous protein-polyphenol interactions occur in biological and food domains particularly involving proline-rich proteins, which are representative of the intrinsically unstructured protein group (IUP). Noncovalent protein-ligand complexes are readily detected by electrospray ionization mass spectrometry (ESI-MS), which also gives access to ligand binding stoichiometry. Surprisingly, the study of interactions between polyphenolic molecules and proteins is still an area where ESI-MS has poorly benefited, whereas it has been extensively applied to the detection of noncovalent complexes. Electrospray ionization mass spectrometry has been applied to the detection and the characterization of the complexes formed between tannins and a human salivary proline-rich protein (PRP), namely IB5. The study of the complex stability was achieved by low-energy collision-induced dissociation (CID) measurements, which are commonly implemented using triple quadrupole, hybrid quadrupole time-of-flight, or ion trap instruments. Complexes composed of IB5 bound to a model polyphenol EgCG have been detected by ESI-MS and further analyzed by MS/MS. Mild ESI interface conditions allowed us to observe intact noncovalent PRP-tannin complexes with stoichiometries ranging from 1:1 to 1:5. Thus, ESI-MS shows its efficiency for (1) the study of PRP-tannin interactions, (2) the determination of stoichiometry, and (3) the study of complex stability. We were able to establish unambiguously both their stoichiometries and their overall subunit architecture via tandem mass spectrometry and solution disruption experiments. Our results prove that IB5.EgCG complexes are maintained intact in the gas phase.

Utterance complexity and stuttering on function words in preschool-age children who stutter.

PubMed

Richels, Corrin; Buhr, Anthony; Conture, Edward; Ntourou, Katerina

2010-09-01

The purpose of the present investigation was to examine the relation between utterance complexity and utterance position and the tendency to stutter on function words in preschool-age children who stutter (CWS). Two separate studies involving two different groups of participants (Study 1, n=30; Study 2, n=30) were conducted. Participants were preschool-age CWS between the age of 3, 0 and 5, 11 who engaged in 15-20min parent-child conversational interactions. From audio-video recordings of each interaction, every child utterance of each parent-child sample was transcribed. From these transcripts, for each participant, measures of language (e.g., length and complexity) and measures of stuttering (e.g., word type and utterance position) were obtained. Results of Study 1 indicated that children stuttered more frequently on function words, but that this tendency was not greater for complex than simple utterances. Results of Study 2, involving the assessment of utterance position and MLU quartile, indicated that that stuttering was more likely to occur with increasing sentence length, and that stuttering tended to occur at the utterance-initial position, the position where function words were also more likely to occur. Findings were taken to suggest that, although word-level influences cannot be discounted, utterance-level influences contribute to the loci of stuttering in preschool-age children, and may help account for developmental changes in the loci of stuttering. The reader will learn about and be able to: (a) describe the influence of word type (function versus content words), and grammatical complexity, on disfluent speech; (b) compare the effect of stuttering frequency based on the position of the word in the utterance; (c) discuss the contribution of utterance position on the frequency of stuttering on function words; and (d) explain possible reasons why preschoolers stutter more frequently on function words than content words.

Investigating noncovalent squarylium dye-protein interactions by capillary electrophoresis-frontal analysis.

PubMed

Yan, Weiying; Colyer, Christa L

2006-11-24

Noncovalent interactions between fluorescent probe molecules and protein analyte molecules, which typically occur with great speed and minimal sample handling, form the basis of many high sensitivity analytical techniques. Understanding the nature of these interactions and the composition of the resulting complexes represents an important area of study that can be facilitated by capillary electrophoresis (CE). Specifically, we will present how frontal analysis (FA) and Hummel-Dreyer (HD) methods can be implemented with CE to determine association constants and stoichiometries of noncovalent complexes of the red luminescent squarylium dye Red-1c with bovine serum albumin (BSA) and beta-lactoglobulin A. By adjusting solution conditions, such as pH or ionic strength, it is possible to selectively modify the binding process. As such, conditions for optimal selectivity for labeling reactions can be established by capillary electrophoresis-frontal analysis (CE-FA) investigations.

Demystifying the Complexities of Gravity Wave Dynamics in the Middle Atmosphere: a Roadmap to Improved Weather Forecasts through High-Fidelity Modeling

NASA Astrophysics Data System (ADS)

Mixa, T.; Fritts, D. C.; Bossert, K.; Laughman, B.; Wang, L.; Lund, T.; Kantha, L. H.

2017-12-01

Gravity waves play a profound role in the mixing of the atmosphere, transporting vast amounts of momentum and energy among different altitudes as they propagate vertically. Above 60km in the middle atmosphere, high wave amplitudes enable a series of complex, nonlinear interactions with the background environment that produce highly-localized wind and temperature variations which alter the layering structure of the atmosphere. These small-scale interactions account for a significant portion of energy transport in the middle atmosphere, but they are difficult to characterize, occurring at spatial scales that are both challenging to observe with ground instruments and prohibitively small to include in weather forecasting models. Using high fidelity numerical simulations, these nuanced wave interactions are analyzed to better our understanding of these dynamics and improve the accuracy of long-term weather forecasting.

Structure and Function of Iron-Loaded Synthetic Melanin

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

Li, Yiwen; Xie, Yijun; Wang, Zhao

We describe a synthetic method for increasing and controlling the iron loading of synthetic melanin nanoparticles and use the resulting materials to perform a systematic quantitative investigation on their structure- property relationship. A comprehensive analysis by magnetometry, electron paramagnetic resonance, and nuclear magnetic relaxation dispersion reveals the complexities of their magnetic behavior and how these intraparticle magnetic interactions manifest in useful material properties such as their performance as MRI contrast agents. This analysis allows predictions of the optimal iron loading through a quantitative modeling of antiferromagnetic coupling that arises from proximal iron ions. This study provides a detailed understanding ofmore » this complex class of synthetic biomaterials and gives insight into interactions and structures prevalent in naturally occurring melanins.« less

Versatile communication strategies among tandem WW domain repeats

PubMed Central

Dodson, Emma Joy; Fishbain-Yoskovitz, Vered; Rotem-Bamberger, Shahar

2015-01-01

Interactions mediated by short linear motifs in proteins play major roles in regulation of cellular homeostasis since their transient nature allows for easy modulation. We are still far from a full understanding and appreciation of the complex regulation patterns that can be, and are, achieved by this type of interaction. The fact that many linear-motif-binding domains occur in tandem repeats in proteins indicates that their mutual communication is used extensively to obtain complex integration of information toward regulatory decisions. This review is an attempt to overview, and classify, different ways by which two and more tandem repeats cooperate in binding to their targets, in the well-characterized family of WW domains and their corresponding polyproline ligands. PMID:25710931

A 1:2 crystalline complex of ApA:proflavine: a model for binding to single-stranded regions in RNA.

PubMed Central

Neidle, S; Taylor, G; Sanderson, M

1978-01-01

The structure of a 1"2 complex of adenylyl-(3',5')-adenosine phosphate and proflavine hemisulfate has been determined using the methods of x-ray crystallography. Since the ApA does not form a mini double helix, it may serve as a model for the interaction of planar molecules with single stranded nucleic acids. The dinucleotide adopts an extended conformation with the adenines in adjacent molecules forming base pairs. A most unusual feature of the molecule is that it does not obey the "rigid nucleotide" concept although none of the torsion angles occur in energetically unfavourable regions. This is most probably due to the strong interactions between the proflavine and the oligonucleotide. PMID:724521

Anaemia, iron deficiency and susceptibility to infection in children in sub-Saharan Africa, guideline dilemmas.

PubMed

Jonker, Femkje A M; Te Poel, Elodie; Bates, Imelda; Boele van Hensbroek, Michael

2017-06-01

Globally, anaemia, iron deficiency and infections are responsible for a majority of the morbidity and mortality that occurs among children. As iron is essential for erythropoiesis and the human immune system, as well as a crucial element for many pathogens, these three conditions often interact. This article considers the question - have the studies conducted so far unravelled the potential complex interaction between these factors sufficiently enough to be able to develop universally applicable guidelines about iron treatment in children? It is possible, however, that the area is too complex and diverse, with many sub-populations, and that not universal, but tailor-made guidelines are needed based on some agreed principles. © 2017 John Wiley & Sons Ltd.

Cross-kingdom interactions: Candida albicans and bacteria.

PubMed

Shirtliff, Mark E; Peters, Brian M; Jabra-Rizk, Mary Ann

2009-10-01

Bacteria and fungi are found together in a myriad of environments and particularly in a biofilm, where adherent species interact through diverse signaling mechanisms. Yet, despite billions of years of coexistence, the area of research exploring fungal-bacterial interactions, particularly within the context of polymicrobial infections, is still in its infancy. However, reports describing a multitude of wide-ranging interactions between the fungal pathogen Candida albicans and various bacterial pathogens are on the rise. An example of a mutually beneficial interaction is coaggregation, a phenomenon that takes place in oral biofilms where the adhesion of C. albicans to oral bacteria is considered crucial for its colonization of the oral cavity. In contrast, the interaction between C. albicans and Pseudomonas aeruginosa is described as being competitive and antagonistic in nature. Another intriguing interaction is that occurring between Staphylococcus aureus and C. albicans, which although not yet fully characterized, appears to be initially synergistic. These complex interactions between such diverse and important pathogens would have significant clinical implications if they occurred in an immunocompromised host. Therefore, understanding the mechanisms of adhesion and signaling involved in fungal-bacterial interactions may lead to the development of novel therapeutic strategies for impeding microbial colonization and development of polymicrobial disease. © 2009 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Staff perceptions of challenging parent-staff interactions and beneficial strategies in the Neonatal Intensive Care Unit.

PubMed

Friedman, Joshua; Friedman, Susan Hatters; Collin, Marc; Martin, Richard J

2018-01-01

To characterise neonatal intensive care unit (NICU) staff perceptions regarding factors which may lead to more challenging staff-parent interactions, and beneficial strategies for working with families with whom such interactions occur. A survey of 168 physician and nursing staff at two NICUs in American teaching hospitals inquired about their perceptions of challenging parent-staff interactions and situations in which such interactions were likely to occur. From a medical perspective, staff perceptions of challenging interactions were noted when infants had recent decompensation, high medical complexity, malformations or long duration of stay in the NICU. From a psychological/social perspective, a high likelihood of challenging interactions was noted with parents who were suspicious, interfere with equipment, or parents who hover in the NICU, express paranoid or delusional thoughts, repeat questions, perceive the staff as inaccessible, are managing addictions, or who require child protective services involvement. Frequent family meetings, grieving opportunities, education of parents, social work referrals, clearly defined rules, partnering in daily care and support groups were perceived as the most beneficial strategies for improving difficult interactions. This study delineates what staff perceive as challenging interactions and provides support for an educational and interventional role that incorporates mental health professionals. ©2017 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.

Association studies to transporting proteins of fac-ReI(CO)3(pterin)(H2O) complex.

PubMed

Ragone, Fabricio; Saavedra, Héctor H Martínez; García, Pablo F; Wolcan, Ezequiel; Argüello, Gerardo A; Ruiz, Gustavo T

2017-01-01

A new synthetic route to acquire the water soluble complex fac-Re I (CO) 3 (pterin)(H 2 O) was carried out in aqueous solution. The complex has been obtained with success via the fac-[Re I (CO) 3 (H 2 O) 3 ]Cl precursor complex. Re I (CO) 3 (pterin)(H 2 O) has been found to bind strongly with bovine and human serum albumins (BSA and HSA) with intrinsic-binding constants, K b , of 6.5 × 10 5 M -1 and 5.6 × 10 5 M -1 at 310 K, respectively. The interactions of serum albumins with Re I (CO) 3 (pterin)(H 2 O) were evaluated employing UV-vis fluorescence and absorption spectroscopy and circular dichroism. The results suggest that the serum albumins-Re I (CO) 3 (pterin)(H 2 O) interactions occurred in the domain IIA-binding pocket without loss of helical stability of the proteins. The comparison of the fluorescence quenching of BSA and HSA due to the binding to the Re(I) complex suggested that local interaction around the Trp 214 residue had taken place. The analysis of the thermodynamic parameters ΔG 0 , ΔH 0 , and ΔS 0 indicated that the hydrophobic interactions played a major role in both HSA-Re(I) and BSA-Re(I) association processes. All these experimental results suggest that these proteins can be considered as good carriers for transportation of Re I (CO) 3 (pterin)(H 2 O) complex. This is of significant importance in relation to the use of this Re(I) complex in several biomedical fields, such as photodynamic therapy and radiopharmacy.

Interactions between HIV-1 Reverse Transcriptase and the Downstream Template Strand in Stable Complexes with Primer-Template

PubMed Central

Rutvisuttinunt, Wiriya; Meyer, Peter R.; Scott, Walter A.

2008-01-01

Background Human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) forms stable ternary complexes in which RT is bound tightly at fixed positions on the primer-template (P/T). We have probed downstream interactions between RT and the template strand in the complex containing the incoming dNTP (+1 dNTP•RT•P/T complex) and in the complex containing the pyrophosphate analog, foscarnet (foscarnet•RT•P/T complex). Methods and Results UV-induced cross-linking between RT and the DNA template strand was most efficient when a bromodeoxyuridine residue was placed in the +2 position (the first template position downstream from the incoming dNTP). Furthermore, formation of the +1 dNTP•RT•P/T complex on a biotin-containing template inhibited binding of streptavidin when biotin was in the +2 position on the template but not when the biotin was in the +3 position. Streptavidin pre-bound to a biotin residue in the template caused RT to stall two to three nucleotides upstream from the biotin residue. The downstream border of the complex formed by the stalled RT was mapped by digestion with exonuclease RecJF. UV-induced cross-linking of the complex formed by the pyrophosphate analog, foscarnet, with RT and P/T occurred preferentially with bromodeoxyuridine in the +1 position on the template in keeping with the location of RT one base upstream in the foscarnet•RT•P/T complex (i.e., in the pre-translocation position). Conclusions For +1 dNTP•RT•P/T and foscarnet•RT•P/T stable complexes, tight interactions were observed between RT and the first unpaired template nucleotide following the bound dNTP or the primer terminus, respectively. PMID:18974785

Label-Free Biosensing with High Selectivity in Complex Media using Microtoroidal Optical Resonators

NASA Astrophysics Data System (ADS)

Ozgur, Erol; Toren, Pelin; Aktas, Ozan; Huseyinoglu, Ersin; Bayindir, Mehmet

2015-08-01

Although label-free biosensors comprised of optical microcavities inherently possess the capability of resolving molecular interactions at individual level, this extreme sensitivity restricts their convenience for large scale applications by inducing vulnerability towards non-specific interactions that readily occur within complex media. Therefore, the use of optical microresonators for biosensing is mostly limited within strictly defined laboratory conditions, instead of field applications as early detection of cancer markers in blood, or identification of contamination in food. Here, we propose a novel surface modification strategy suitable for but not limited to optical microresonator based biosensors, enabling highly selective biosensing with considerable sensitivity as well. Using a robust, silane-based surface coating which is simultaneously protein resistant and bioconjugable, we demonstrate that it becomes possible to perform biosensing within complex media, without compromising the sensitivity or reliability of the measurement. Functionalized microtoroids are successfully shown to resist nonspecific interactions, while simultaneously being used as sensitive biological sensors. This strategy could pave the way for important applications in terms of extending the use of state-of-the-art biosensors for solving problems similar to the aforementioned.

DNA–DNA kissing complexes as a new tool for the assembly of DNA nanostructures

PubMed Central

Barth, Anna; Kobbe, Daniela; Focke, Manfred

2016-01-01

Kissing-loop annealing of nucleic acids occurs in nature in several viruses and in prokaryotic replication, among other circumstances. Nucleobases of two nucleic acid strands (loops) interact with each other, although the two strands cannot wrap around each other completely because of the adjacent double-stranded regions (stems). In this study, we exploited DNA kissing-loop interaction for nanotechnological application. We functionalized the vertices of DNA tetrahedrons with DNA stem-loop sequences. The complementary loop sequence design allowed the hybridization of different tetrahedrons via kissing-loop interaction, which might be further exploited for nanotechnology applications like cargo transport and logical elements. Importantly, we were able to manipulate the stability of those kissing-loop complexes based on the choice and concentration of cations, the temperature and the number of complementary loops per tetrahedron either at the same or at different vertices. Moreover, variations in loop sequences allowed the characterization of necessary sequences within the loop as well as additional stability control of the kissing complexes. Therefore, the properties of the presented nanostructures make them an important tool for DNA nanotechnology. PMID:26773051

Protein-Protein Interactions in the Complex between the Enhancer Binding Protein NIFA and the Sensor NIFL from Azotobacter vinelandii

PubMed Central

Money, Tracy; Barrett, Jason; Dixon, Ray; Austin, Sara

2001-01-01

The enhancer binding protein NIFA and the sensor protein NIFL from Azotobacter vinelandii comprise an atypical two-component regulatory system in which signal transduction occurs via complex formation between the two proteins rather than by the phosphotransfer mechanism, which is characteristic of orthodox systems. The inhibitory activity of NIFL towards NIFA is stimulated by ADP binding to the C-terminal domain of NIFL, which bears significant homology to the histidine protein kinase transmitter domains. Adenosine nucleotides, particularly MgADP, also stimulate complex formation between NIFL and NIFA in vitro, allowing isolation of the complex by cochromatography. Using limited proteolysis of the purified proteins, we show here that changes in protease sensitivity of the Q linker regions of both NIFA and NIFL occurred when the complex was formed in the presence of MgADP. The N-terminal domain of NIFA adjacent to the Q linker was also protected by NIFL. Experiments with truncated versions of NIFA demonstrate that the central domain of NIFA is sufficient to cause protection of the Q linker of NIFL, although in this case, stable protein complexes are not detectable by cochromatography. PMID:11157949

Luminescence Studies of the Ligand Exchange Between Two Phenanthroline Complexes and Bovine Serum Albumin

NASA Astrophysics Data System (ADS)

Lin, H.-B.; Shen, Q.-H.

2017-03-01

The interactions between bovine serum albumin (BSA) and two Cu(II) phenanthroline complexes were studied by fluorescence and UV-visible absorption spectroscopy. The obtained results confirm that the phen ligand (phen = 1,10-phenanthroline) is dissociated from the two complexes and moves into the hydrophobic cavity of BSA and that the M-L complexes (M = Co2+, Cu2+; L = Hlact, imda; Hlact = lactic acid, H2imda = iminodiacetic acid) coordinate with the amino acids on the surface of the peptide in the solution. This mode of action significantly inhibits the denaturation of BSA. The calculated distance between the BSA and the two complexes suggests that the energy transfer from the excited state of BSA to a complex occurs with high efficiency.

Inside Out: Detecting Learners' Confusion to Improve Interactive Digital Learning Environments

ERIC Educational Resources Information Center

Arguel, Amaël; Lockyer, Lori; Lipp, Ottmar V.; Lodge, Jason M.; Kennedy, Gregor

2017-01-01

Confusion is an emotion that is likely to occur while learning complex information. This emotion can be beneficial to learners in that it can foster engagement, leading to deeper understanding. However, if learners fail to resolve confusion, its effect can be detrimental to learning. Such detrimental learning experiences are particularly…

CC-LR: Providing Interactive, Challenging and Attractive Collaborative Complex Learning Resources

ERIC Educational Resources Information Center

Caballé, S.; Mora, N.; Feidakis, M.; Gañán, D.; Conesa, J.; Daradoumis, T.; Prieto, J.

2014-01-01

Many researchers argue that students must be meaningfully engaged in the learning resources for effective learning to occur. However, current online learners still report a problematic lack of attractive and challenging learning resources that engage them in the learning process. This endemic problem is even more evident in online collaborative…

Strategies for Evaluating the Environment-Public Health Interaction of Long-Term Latency Disease: The Quandary of the Inconclusive Case-Control Study

EPA Science Inventory

Environmental links to disease are difficult to uncover because environmental exposures are variable in time and space, contaminants occur in complex mixtures, and many diseases have a long time delay between exposure and onset. Furthermore, individuals in a population have diff...

Heartbeat synchronized with ventilation

NASA Astrophysics Data System (ADS)

Schäfer, Carsten; Rosenblum, Michael G.; Kurths, Jürgen; Abel, Hans-Henning

1998-03-01

It is widely accepted that cardiac and respiratory rhythms in humans are unsynchronised. However, a newly developed data analysis technique allows any interaction that does occur in even weakly coupled complex systems to be observed. Using this technique, we found long periods of hidden cardiorespiratory synchronization, lasting up to 20 minutes, during spontaneous breathing at rest.

Towards a Theoretical Framework for Online Professional Discussions

ERIC Educational Resources Information Center

Adie, Lenore

2014-01-01

Sociocultural theories of learning and sociocultural theories of technology are explored as a way to view and to map the complex interactions that can occur in online professional discussions. The case of synchronous online moderation meetings are used as an example of the combination of variables that can impact on the development of shared…

Treatment Effectiveness in Preschool Autism: A Look at Affective Variables

ERIC Educational Resources Information Center

Tsakiris, Elizabeth A.

2009-01-01

Autism now occurs in 1 out of 150 births in the United States (Centers for Disease Control, 2008). Increasing numbers and complexity of the disorder make the need for identifying effective interventions critical. DSM-IVTR identifies core characteristics of autism as significant deficits in communication, social interaction, and symbolic play.…

­Understanding Information Flow Interaction along Separable Causal Paths in Environmental Signals

NASA Astrophysics Data System (ADS)

Jiang, P.; Kumar, P.

2017-12-01

Multivariate environmental signals reflect the outcome of complex inter-dependencies, such as those in ecohydrologic systems. Transfer entropy and information partitioning approaches have been used to characterize such dependencies. However, these approaches capture net information flow occurring through a multitude of pathways involved in the interaction and as a result mask our ability to discern the causal interaction within an interested subsystem through specific pathways. We build on recent developments of momentary information transfer along causal paths proposed by Runge [2015] to develop a framework for quantifying information decomposition along separable causal paths. Momentary information transfer along causal paths captures the amount of information flow between any two variables lagged at two specific points in time. Our approach expands this concept to characterize the causal interaction in terms of synergistic, unique and redundant information flow through separable causal paths. Multivariate analysis using this novel approach reveals precise understanding of causality and feedback. We illustrate our approach with synthetic and observed time series data. We believe the proposed framework helps better delineate the internal structure of complex systems in geoscience where huge amounts of observational datasets exist, and it will also help the modeling community by providing a new way to look at the complexity of real and modeled systems. Runge, Jakob. "Quantifying information transfer and mediation along causal pathways in complex systems." Physical Review E 92.6 (2015): 062829.

Ionic interactions in biological and physical systems: a variational treatment.

PubMed

Eisenberg, Bob

2013-01-01

Chemistry is about chemical reactions. Chemistry is about electrons changing their configurations as atoms and molecules react. Chemistry has for more than a century studied reactions as if they occurred in ideal conditions of infinitely dilute solutions. But most reactions occur in salt solutions that are not ideal. In those solutions everything (charged) interacts with everything else (charged) through the electric field, which is short and long range extending to the boundaries of the system. Mathematics has recently been developed to deal with interacting systems of this sort. The variational theory of complex fluids has spawned the theory of liquid crystals (or vice versa). In my view, ionic solutions should be viewed as complex fluids, particularly in the biological and engineering context. In both biology and electrochemistry ionic solutions are mixtures highly concentrated (to approximately 10 M) where they are most important, near electrodes, nucleic ids, proteins, active sites of enzymes, and ionic channels. Ca2+ is always involved in biological solutions because the concentration (really free energy per mole) of Ca2+ in a particular location is the signal that controls many biological functions. Such interacting systems are not simple fluids, and it is no wonder that analysis of interactions, such as the Hofmeister series, rooted in that tradition has not succeeded as one would hope. Here, we present a variational treatment of ard spheres in a frictional dielectric with the hope that such a treatment of an lectrolyte as a complex fluid will be productive. The theory automatically extends to spatially nonuniform boundary conditions and the nonequilibrium systems and flows they produce. The theory is unavoidably self-consistent since differential equations are derived (not assumed) from models of (Helmholtz free) nergy and dissipation of the electrolyte. The origin of the Hofmeister series is (in my view) an inverse problem that becomes well posed when enough data from disjoint experimental traditions are interpreted with a self-consistent theory.

Mutation of Hip’s Carboxy-Terminal Region Inhibits a Transitional Stage of Progesterone Receptor Assembly

PubMed Central

Prapapanich, Viravan; Chen, Shiying; Smith, David F.

1998-01-01

Steroid receptor complexes are assembled through an ordered, multistep pathway involving multiple components of the cytoplasmic chaperone machinery. Two of these components are Hsp70-binding proteins, Hip and Hop, that have some limited homology in their C-terminal regions, outside the sequences mapped for Hsp70 binding. Within this region of Hip is a DPEV sequence that occurs twice; in Hop, one DPEV sequence plus a partial second sequence occurs. In an effort to better understand Hip function as it relates to assembly of progesterone receptor complexes, the DPEV region of Hip was targeted for mutations. Each DPEV sequence was mutated to an APAV sequence, singly or in combination. The combined mutation, APAV2, was further combined with a deletion of Hip’s tetratricopeptide repeat region that is required for Hsp70 binding or with a deletion of Hip’s GGMP repeat. An additional mutant was prepared by truncation of Hip’s DPEV-containing C terminus. By comparing interactions of various Hip forms with Hsp70, it was determined that mutation of the DPEV sequences created a dominant inhibitory form of Hip. The mutant Hip-Hsp70 complex was not prevented from interacting with progesterone receptor, but the mutant caused a dose-dependent inhibition of receptor assembly with Hsp90. The behavior of the Hip mutant is consistent with a model in which Hip and Hop are required to facilitate the transition from an early receptor complex with Hsp70 into later complexes containing Hsp90. PMID:9447991

Determination of thermodynamic parameters for complexation of calcium and magnesium with chondroitin sulfate isomers using isothermal titration calorimetry: Implications for calcium kidney-stone research

NASA Astrophysics Data System (ADS)

Rodgers, Allen L.; Jackson, Graham E.

2017-04-01

Chondroitin sulfate (CS) occurs in human urine. It has several potential binding sites for calcium and as such may play an inhibitory role in calcium oxalate and calcium phosphate (kidney stone disease by reducing the supersaturation (SS) and crystallization of these salts. Urinary magnesium is also a role player in determining speciation in stone forming processes. This study was undertaken to determine the thermodynamic parameters for binding of the disaccharide unit of two different CS isomers with calcium and magnesium. These included the binding constant K. Experiments were performed using an isothermal titration calorimeter (ITC) at 3 different pH levels in the physiological range in human urine. Data showed that interactions between the CS isomers and calcium and magnesium occur via one binding site, thought to be sulfate, and that log K values are 1.17-1.93 and 1.77-1.80 for these two metals respectively. Binding was significantly stronger in Mg-CS than in Ca-CS complexes and was found to be dependent on pH in the latter but not in the former. Furthermore, binding in Ca-CS complexes was dependent on the location of the sulfate binding site. This was not the case in the Mg-CS complexes. Interactions were shown to be entropy driven and enthalpy unfavourable. These findings can be used in computational modeling studies to predict the effects of the calcium and magnesium CS complexes on the speciation of calcium and the SS of calcium salts in real urine samples.

Assembly of the stator in Escherichia coli ATP synthase. Complexation of alpha subunit with other F1 subunits is prerequisite for delta subunit binding to the N-terminal region of alpha

PubMed Central

Senior, Alan E.; Muharemagi, Alma; Wilke-Mounts, Susan

2008-01-01

Alpha subunit of Escherichia coli ATP synthase was expressed with a C-terminal 6-His tag and purified. Pure alpha was monomeric, competent in nucleotide binding, and had normal N-terminal sequence. In F1-subunit dissociation/reassociation experiments it supported full reconstitution of ATPase, and reassociated complexes were able to bind to F1-depleted membranes with restoration of ATP-driven proton pumping. Therefore interaction between the stator delta subunit and the N-terminal residue 1-22 region of alpha occurred normally when pure alpha was complexed with other F1 subunits. On the other hand, three different types of experiment showed that no interaction occurred between pure delta and isolated alpha subunit. Unlike in F1, the N-terminal region of isolated alpha was not susceptible to trypsin cleavage. Therefore, during assembly of ATP synthase, complexation of alpha subunit with other F1 subunits is prerequisite for delta subunit binding to the N-terminal region of alpha. We suggest that the N-terminal 1-22 residues of alpha are sequestered in isolated alpha until released by binding of beta to alpha subunit. This prevents 1/1 delta/alpha complexes from forming, and provides a satisfactory explanation of the stoichiometry of one delta per three alpha seen in the F1 sector of ATP synthase, assuming that steric hindrance prevents binding of more than one delta to the alpha3/beta3 hexagon. The cytoplasmic fragment of the b subunit (bsol) did not bind to isolated alpha. It might also be that complexation of alpha with beta subunits is prerequisite for direct binding of stator b subunit to the F1-sector. PMID:17176112

Tale of the Huanglongbing Disease Pyramid in the Context of the Citrus Microbiome.

PubMed

Wang, Nian; Stelinski, Lukasz L; Pelz-Stelinski, Kirsten S; Graham, James H; Zhang, Yunzeng

2017-04-01

The Huanglongbing (HLB) disease pyramid is composed of Liberibacters, psyllid vectors, citrus hosts, and the environment. The epidemiological outcomes for Liberibacter-associated plant diseases are collectively determined by the inherent relationships among plant-Liberibacters-psyllids, and how various environmental factors affect plant-Liberibacter-psyllid interactions. Citrus-Liberibacter-psyllid interactions occur in a complex microbiome system. In this review, we focus on the progress in understanding the HLB disease pyramid, and how the microbiome affects the HLB disease pyramid including the interaction between HLB and the citrus microbiome; the interaction between Liberibacters and psyllids; the interaction between Liberibacters and gut microbiota in psyllids; and the effect of HLB on selected above- and belowground citrus pathogens. Their implications for HLB management are also discussed.

Preparation and Characterization of Amylose Inclusion Complexes for Drug Delivery Applications.

PubMed

Carbinatto, Fernanda M; Ribeiro, Tatiana S; Colnago, Luiz Alberto; Evangelista, Raul Cesar; Cury, Beatriz S F

2016-01-01

Amylose complexes with nimesulide (NMS) and praziquantel (PZQ) were prepared by a simple and low cost method, so that high yield (>57%) and drug content (up to 68.16%) were achieved. The influence of drug:polymer ratio, temperature, and presence of palmitic acid on the complexes properties was evaluated. Differential scanning calorimetry, X-ray diffraction, and nuclear magnetic resonance data evidenced the drug-polymer interaction and the formation of inclusion complexes with semi-crystalline structures related to type II complexes. The drug release rates from complexes were lowered in acid media (pH 1.2) and phosphate buffer (pH 6.9). The presence of pancreatin promoted a significant acceleration of the release rates of both drugs, evidencing the enzymatic degradability of these complexes. The highest enzymatic resistance of PZQ1:30PA60°C complex makes the release time longer and the full release of PZQ in phosphate buffer with pancreatin occurred at 240 min, whereas the complexes with NMS and PZQ1:5PA90°C did it in 60 min. According to the Weibull model, the drug release process in media without enzyme occurred by complex mechanisms involving diffusion, swelling, and erosion. In media containing pancreatin, generally, the better correlation was with the first order, evidencing the acceleration of the release rates of drugs in the early stages of the test, due to enzymatic degradation.

Complexation of the calcium cation with antamanide: an experimental and theoretical study

NASA Astrophysics Data System (ADS)

Makrlík, Emanuel; Böhm, Stanislav; Vaňura, Petr; Ruzza, Paolo

2015-06-01

By using extraction experiments and γ-activity measurements, the extraction constant corresponding to the equilibrium Ca2+(aq) + 1 .Sr2+(nb) ? 1 .Ca2+(nb) + Sr2+(aq) occurring in the two-phase water-nitrobenzene system (1 = antamanide; aq = aqueous phase, nb = nitrobenzene phase) was determined as log Kex (Ca2+, 1 .Sr2+) = 1.6 ± 0.1. Further, the stability constant of the 1 .Ca2+ complex in nitrobenzene saturated with water was calculated for a temperature of 25 °C: log βnb (1 .Ca2+) = 10.9 ± 0.2. Finally, applying quantum mechanical density functional level of theory calculations, the most probable structure of the cationic complex species 1 .Ca2+ was derived. In the resulting complex, the 'central' cation Ca2+ is bound by six strong bonding interactions to the corresponding six carbonyl oxygen atoms of the parent ligand 1. Besides, the whole 1 .Ca2+ complex structure is stabilised by two intramolecular hydrogen bonds. The interaction energy of the considered 1 .Ca2+ complex, involving the Boys-Bernardi counterpoise corrections of the basis set superposition error, was found to be -1219.3 kJ/mol, confirming the formation of this cationic species.

Vibrational spectroscopic investigation of the gold complexation within the cascade structure of phosphorus-containing dendrimer.

PubMed

Furer, V L; Vandyukov, A E; Majoral, J P; Caminade, A M; Gottis, S; Laurent, R; Kovalenko, V I

2018-05-29

The interaction of the phosphoric dendrimer with gold was performed by means of vibrational spectroscopy and quantum chemistry. Stable complexes are formed with a PN-PS linkage, whereas with an isolated PS bond this does not occur. The change in geometric parameters and delocalization of electric charge under the influence of gold was discovered. The classification of bands in the experimental vibrational spectra of the dendrimer and its complex was carried out. HOMO of molecule of the dendrimer is localized on the SPNP linkage, whereas the LUMO is located on the terminal group. In the SPNP linkage there is a noticeable delocalization of the charge which leads to a change in the reactivity of this group. Interaction energy was estimated as the difference between the energies of the complex and the energies of the molecules of the dendrimer G' 0 and two molecules AuCl and is equal to 25.2 eV. The ionization energy IE and electron affinity EA for AuCl are higher than for dendrimer, therefore, when the complex is formed, these quantities increases. Chemical potential and the electrophilicity index in the complex also increases. Copyright © 2018 Elsevier B.V. All rights reserved.

Catching the role of anisotropic electronic distribution and charge transfer in halogen bonded complexes of noble gases

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

Bartocci, Alessio; Cappelletti, David; Pirani, Fernando

2015-05-14

The systems studied in this work are gas-phase weakly bound adducts of the noble-gas (Ng) atoms with CCl{sub 4} and CF{sub 4}. Their investigation was motivated by the widespread current interest for the intermolecular halogen bonding (XB), a structural motif recognized to play a role in fields ranging from elementary processes to biochemistry. The simulation of the static and dynamic behaviors of complex systems featuring XB requires the formulation of reliable and accurate model potentials, whose development relies on the detailed characterization of strength and nature of the interactions occurring in simple exemplary halogenated systems. We thus selected the prototypicalmore » Ng-CCl{sub 4} and Ng-CF{sub 4} and performed high-resolution molecular beam scattering experiments to measure the absolute scale of their intermolecular potentials, with high sensitivity. In general, we expected to probe typical van der Waals interactions, consisting of a combination of size (exchange) repulsion with dispersion/induction attraction. For the He/Ne-CF{sub 4}, the analysis of the glory quantum interference pattern, observable in the velocity dependence of the integral cross section, confirmed indeed this expectation. On the other hand, for the He/Ne/Ar-CCl{sub 4}, the scattering data unravelled much deeper potential wells, particularly for certain configurations of the interacting partners. The experimental data can be properly reproduced only including a shifting of the repulsive wall at shorter distances, accompanied by an increased role of the dispersion attraction, and an additional short-range stabilization component. To put these findings on a firmer ground, we performed, for selected geometries of the interacting complexes, accurate theoretical calculations aimed to evaluate the intermolecular interaction and the effects of the complex formation on the electron charge density of the constituting moieties. It was thus ascertained that the adjustments of the potential suggested by the analysis of the experiments actually reflect two chemically meaningful contributions, namely, a stabilizing interaction arising from the anisotropy of the charge distribution around the Cl atom in CCl{sub 4} and a stereospecific electron transfer that occurs at the intermolecular distances mainly probed by the experiments. Our model calculations suggest that the largest effect is for the vertex geometry of CCl{sub 4} while other geometries appear to play a minor to negligible role.« less

Decoding molecular interactions in microbial communities

PubMed Central

Abreu, Nicole A.; Taga, Michiko E.

2016-01-01

Microbial communities govern numerous fundamental processes on earth. Discovering and tracking molecular interactions among microbes is critical for understanding how single species and complex communities impact their associated host or natural environment. While recent technological developments in DNA sequencing and functional imaging have led to new and deeper levels of understanding, we are limited now by our inability to predict and interpret the intricate relationships and interspecies dependencies within these communities. In this review, we highlight the multifaceted approaches investigators have taken within their areas of research to decode interspecies molecular interactions that occur between microbes. Understanding these principles can give us greater insight into ecological interactions in natural environments and within synthetic consortia. PMID:27417261

Influence of Structure, Charge, and Concentration on the Pectin-Calcium-Surfactant Complexes.

PubMed

Joshi, Nidhi; Rawat, Kamla; Bohidar, H B

2016-05-12

Polymer-surfactant complex formation of pectin with different types of surfactants, cationic (cetyltrimethylammonium bromide, CTAB and dodecyl trimethylammonium bromide, DTAB), anionic (sodium dodecyl sulfate, SDS), and neutral (Triton X-100, TX-100), was investigated at room temperature in the presence and absence of cross-linker calcium chloride using light scattering, zeta potential, rheology, and UV-vis spectroscopic measurements where the surfactant concentration was maintained below their critical micellar concentration (CMC). Results indicated that the interaction of cationic surfactant with pectin in the presence and absence of calcium chloride was much stronger compared to anionic and neutral surfactants. The neutral surfactant showed identifiable interaction despite the absence of any charged headgroup, while anionic surfactant showed feeble or very weak interaction with the polymer. The pectin-CTAB or DTAB complex formation was attributed to associative electrostatic and hydrophobic interactions. On comparison between the cationic surfactants, it was found that CTAB interacts strongly with pectin because of its long hydrocarbon chain. The morphology of complexes formed exhibited random coil structures while at higher concentration of surfactant, rod-like or extended random coil structures were noticed. Thus, functional characteristics of the complex could be tuned by varying the type of surfactant (charge and structure) and its concentration. The differential network rigidity (pectin-CTAB versus pectin-DTAB gels) obtained from rheology measurements showed that addition of a very small amount of surfactant (concentration ≪ CMC) was required for enhancing network strength, while the presence of a large amount of surfactant resulted in the formation of fragile gels. No gel formation occurred when the surfactant concentration was close to their CMC values. Considering the importance of pectin in food and pharmaceutical industry, this study is relevant.

Humic acid protein complexation

NASA Astrophysics Data System (ADS)

Tan, W. F.; Koopal, L. K.; Weng, L. P.; van Riemsdijk, W. H.; Norde, W.

2008-04-01

Interactions of purified Aldrich humic acid (PAHA) with lysozyme (LSZ) are investigated. In solution LSZ is moderately positively and PAHA negatively charged at the investigated pH values. The proton binding of PAHA and of LSZ is determined by potentiometric proton titrations at various KCl concentrations. It is also measured for two mixtures of PAHA-LSZ and compared with theoretically calculated proton binding assuming no mutual interaction. The charge adaptation due to PAHA-LSZ interaction is relatively small and only significant at low and high pH. Next to the proton binding, the mass ratio PAHA/LSZ at the iso-electric point (IEP) of the complex at given solution conditions is measured together with the pH using the Mütek particle charge detector. From the pH changes the charge adaptation due to the interaction can be found. Also these measurements show that the net charge adaptation is weak for PAHA-LSZ complexes at their IEP. PAHA/LSZ mass ratios in the complexes at the IEP are measured at pH 5 and 7. At pH 5 and 50 mmol/L KCl the charge of the complex is compensated for 30-40% by K +; at pH 7, where LSZ has a rather low positive charge, this is 45-55%. At pH 5 and 5 mmol/L KCl the PAHA/LSZ mass ratio at the IEP of the complex depends on the order of addition. When LSZ is added to PAHA about 25% K + is included in the complex, but no K + is incorporated when PAHA is added to LSZ. The flocculation behavior of the complexes is also different. After LSZ addition to PAHA slow precipitation occurs (6-24 h) in the IEP, but after addition of PAHA to LSZ no precipitation can be seen after 12 h. Clearly, PAHA/LSZ complexation and the colloidal stability of PAHA-LSZ aggregates depend on the order of addition. Some implications of the observed behavior are discussed.

Polyamines: naturally occurring small molecule modulators of electrostatic protein-protein interactions.

PubMed

Berwanger, Anja; Eyrisch, Susanne; Schuster, Inge; Helms, Volkhard; Bernhardt, Rita

2010-02-01

Modulations of protein-protein interactions are a key step in regulating protein function, especially in networks. Modulators of these interactions are supposed to be candidates for the development of novel drugs. Here, we describe the role of the small, polycationic and highly abundant natural polyamines that could efficiently bind to charged spots at protein interfaces as modulators of such protein-protein interactions. Using the mitochondrial cytochrome P45011A1 (CYP11A1) electron transfer system as a model, we have analyzed the capability of putrescine, spermidine, and spermine at physiologically relevant concentrations to affect the protein-protein interactions between adrenodoxin reductase (AdR), adrenodoxin (Adx), and CYP11A1. The actions of polyamines on the individual components, on their association/dissociation, on electron transfer, and on substrate conversion were examined. These studies revealed modulating effects of polyamines on distinct interactions and on the entire system in a complex way. Modulation via changed protein-protein interactions appeared plausible from docking experiments that suggested favourable high-affinity binding sites of polyamines (spermine>spermidine>putrescine) at the AdR-Adx interface. Our findings imply for the first time that small endogenous compounds are capable of interfering with distinct components of transient protein complexes and might control protein functions by modulating electrostatic protein-protein interactions.

Nonlinear shallow ocean-wave soliton interactions on flat beaches.

PubMed

Ablowitz, Mark J; Baldwin, Douglas E

2012-09-01

Ocean waves are complex and often turbulent. While most ocean-wave interactions are essentially linear, sometimes two or more waves interact in a nonlinear way. For example, two or more waves can interact and yield waves that are much taller than the sum of the original wave heights. Most of these shallow-water nonlinear interactions look like an X or a Y or two connected Ys; at other times, several lines appear on each side of the interaction region. It was thought that such nonlinear interactions are rare events: they are not. Here we report that such nonlinear interactions occur every day, close to low tide, on two flat beaches that are about 2000 km apart. These interactions are closely related to the analytic, soliton solutions of a widely studied multidimensional nonlinear wave equation. On a much larger scale, tsunami waves can merge in similar ways.

Partners in crime: The role of tandem modules in gene transcription.

PubMed

Sharma, Rajal; Zhou, Ming-Ming

2015-09-01

Histones and their modifications play an important role in the regulation of gene transcription. Numerous modifications, such as acetylation, phosphorylation, methylation, ubiquitination, and SUMOylation, have been described. These modifications almost always co-occur and thereby increase the combinatorial complexity of post-translational modification detection. The domains that recognize these histone modifications often occur in tandem in the context of larger proteins and complexes. The presence of multiple modifications can positively or negatively regulate the binding of these tandem domains, influencing downstream cellular function. Alternatively, these tandem domains can have novel functions from their independent parts. Here we summarize structural and functional information known about major tandem domains and their histone binding properties. An understanding of these interactions is key for the development of epigenetic therapy. © 2015 The Protein Society.

3dRPC: a web server for 3D RNA-protein structure prediction.

PubMed

Huang, Yangyu; Li, Haotian; Xiao, Yi

2018-04-01

RNA-protein interactions occur in many biological processes. To understand the mechanism of these interactions one needs to know three-dimensional (3D) structures of RNA-protein complexes. 3dRPC is an algorithm for prediction of 3D RNA-protein complex structures and consists of a docking algorithm RPDOCK and a scoring function 3dRPC-Score. RPDOCK is used to sample possible complex conformations of an RNA and a protein by calculating the geometric and electrostatic complementarities and stacking interactions at the RNA-protein interface according to the features of atom packing of the interface. 3dRPC-Score is a knowledge-based potential that uses the conformations of nucleotide-amino-acid pairs as statistical variables and that is used to choose the near-native complex-conformations obtained from the docking method above. Recently, we built a web server for 3dRPC. The users can easily use 3dRPC without installing it locally. RNA and protein structures in PDB (Protein Data Bank) format are the only needed input files. It can also incorporate the information of interface residues or residue-pairs obtained from experiments or theoretical predictions to improve the prediction. The address of 3dRPC web server is http://biophy.hust.edu.cn/3dRPC. yxiao@hust.edu.cn.

The role of fuels for understanding fire behavior and fire effects

Treesearch

E. Louise Loudermilk; J. Kevin Hiers; Joseph J. O' Brien

2018-01-01

Fire ecology, which has emerged as a critical discipline, links the complex interactions that occur between fire regimes and ecosystems. The ecology of fuels, a first principle in fire ecology, identifies feedbacks between vegetation and fire behavior-a cyclic process that starts with fuels influencing fire behavior, which in turn governs patterns of postfire...

Development and Application of Learning Materials to Help Students Understand Ten Statements Describing the Nature of Scientific Observation

ERIC Educational Resources Information Center

Kim, Sangsoo; Park, Jongwon

2018-01-01

Observing scientific events or objects is a complex process that occurs through the interaction between the observer's knowledge or expectations, the surrounding context, physiological features of the human senses, scientific inquiry processes, and the use of observational instruments. Scientific observation has various features specific to this…

Unexpected redwood mortality from synergies between wildfire and an emerging infectious disease

Treesearch

Margaret R. Metz; J. Morgan Varner; Kerri M. Frangioso; Ross K. Meentemeyer; David M. Rizzo

2014-01-01

An under-examined component of global change is the alteration of disturbance regimes due to warming climates, continued species invasions, and accelerated land-use change. These drivers of global change are themselves novel ecosystem disturbances that may interact with historically occurring disturbances in complex ways. Here we use the natural experiment presented by...

RNA sequencing of contaminated seeds reveals the state of the seed permissive for pre-harvest aflatoxin contamination and points to a potential susceptibility factor

USDA-ARS?s Scientific Manuscript database

Pre-harvest aflatoxin contamination (PAC) is a major problem facing peanut production worldwide. Produced by the ubiquitous soil fungus, Aspergillus flavus, aflatoxin is the most potent naturally occurring known carcinogen. The interaction between fungus and host resulting in PAC is complex, and b...

Molecular Signature That Determines the Acute Tolerance of G Protein-Coupled Receptors

PubMed Central

Min, Chengchun; Zhang, Xiaohan; Zheng, Mei; Sun, Ningning; Acharya, Srijan; Zhang, Xiaowei; Kim, Kyeong-Man

2017-01-01

Desensitization and acute tolerance are terms used to describe the attenuation of receptor responsiveness by prolonged or intermittent exposure to an agonist. Unlike desensitization of G protein-coupled receptors (GPCRs), which is commonly explained by steric hindrance caused by the β-arrestins that are translocated to the activated receptors, molecular mechanisms involved in the acute tolerance of GPCRs remain unclear. Our studies with several GPCRs and related mutants showed that the acute tolerance of GPCRs could occur independently of agonist-induced β-arrestin translocation. A series of co-immunoprecipitation experiments revealed a correlation between receptor tolerance and interactions among receptors, β-arrestin2, and Gβγ. Gβγ displayed a stable interaction with receptors and β-arrestin2 in cells expressing GPCRs that were prone to undergo tolerance compared to the GPCRs that were resistant to acute tolerance. Strengthening the interaction between Gβγ and β-arrestin rendered the GPCRs to acquire the tendency of acute tolerance. Overall, stable interaction between the receptor and Gβγ complex is required for the formation of a complex with β-arrestin, and determines the potential of a particular GPCR to undergo acute tolerance. Rather than turning off the signal, β-arrestins seem to contribute on continuous signaling when they are in the context of complex with receptor and Gβγ. PMID:27956717

The N-terminal domain of the mammalian nucleoporin p62 interacts with other nucleoporins of the FXFG family during interphase

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

Stochaj, Ursula; Banski, Piotr; Kodiha, Mohamed

2006-08-01

Nuclear pore complexes (NPCs) provide the only sites for macromolecular transport between nucleus and cytoplasm. The nucleoporin p62, a component of higher eukaryotic NPCs, is located at the central gated channel and involved in nuclear trafficking of various cargos. p62 is organized into an N-terminal segment that contains FXFG repeats and binds the soluble transport factor NTF2, whereas the C-terminal portion associates with other nucleoporins and importin-{beta}1. We have now identified new components that interact specifically with the p62 N-terminal domain. Using the p62 N-terminal segment as bait, we affinity-purified nucleoporins Nup358, Nup214 and Nup153 from crude cell extracts. Inmore » ligand binding assays, the N-terminal p62 segment associated with Nup358 and p62, suggesting their direct binding to the p62 N-terminal portion. Furthermore, p62 was isolated in complex with Nup358, Nup214 and Nup153 from growing HeLa cells, indicating that the interactions Nup358/p62, Nup214/p62 and p62/Nup153 also occur in vivo. The formation of Nup358/p62 and p62/Nup153 complexes was restricted to interphase cells, whereas Nup214/p62 binding was detected in interphase as well as during mitosis. Our results support a model of complex interactions between FXFG containing nucleoporins, and we propose that some of these interactions may contribute to the movement of cargo across the NPC.« less

Cigarette smoke disrupts the integrity of airway adherens junctions through the aberrant interaction of p120-catenin with the cytoplasmic tail of MUC1

PubMed Central

Zhang, Lili; Gallup, Marianne; Zlock, Lorna; Basbaum, Carol; Finkbeiner, Walter E.; McNamara, Nancy A.

2014-01-01

Adherens junctions (AJs) containing epithelial cadherin (E-cad) bound to p120-catenin (p120ctn) and β-catenin (β-ctn) play a crucial role in regulating cell–cell adhesion. Cigarette smoke abrogates cell–cell adhesion between epithelial cells by disrupting E-cad, a hallmark of epithelial–mesenchymal transition (EMT), yet the underlying mechanism remains unknown. We used an organotypic culture of primary human bronchial epithelial (HBE) cells treated with smoke-concentrated medium (Smk) to establish an essential role for the interaction between p120ctn and the cytoplasmic tail of MUC1 (MUC1-CT) in regulating E-cad disruption. Within the first 4 h of smoke exposure, apical MUC1-CT repositioned to the basolateral membrane of pseudo-stratified HBE cells, where it interacted with p120ctn. A time-dependent increase in MUC1-CT/p120ctn complexes occurred in conjunction with a time-dependent dissociation of p120ctn/E-cad/β-ctn complexes, as well as the coordinated degradation of p120ctn and E-cad. Interestingly, Smk induced a similar interaction between MUC1-CT and β-ctn, but this occurred 44 h after MUC1-CT’s initial interaction with p120ctn, and well after the AJs were destroyed. Blocking MUC1-CT’s interaction with p120ctn using a MUC1-CT dominant-negative peptide, PMIP, successfully abolished Smk’s disruptive effects on AJs and recovered apical-basolateral polarity of HBE cells. The MUC1-CT/p120ctn interaction was highly dependent on EGFR/Src/Jnk-mediated tyrosine phosphorylation (TyrP) of MUC1-CT. Accordingly, EGFR, Src or Jnk inhibitors (AG1478, PP2, SP600125, respectively) abrogated Smk-induced MUC1-CT-TyrP, MUC1-CT/p120ctn interaction, AJ disruption, and loss of cellular polarity. Our work identified MUC1-CT and p120ctn as important regulators of epithelial polarity and cell-cell adhesion during a smoke-induced EMT-like process. Novel therapeutics designed to inhibit MUC1-CT/p120ctn complex formation may prevent EMT in the smoker’s airway. PMID:22833523

Theoretical study of interactions between cysteine and perfluoropropanoic acid in gas and aqueous phase

NASA Astrophysics Data System (ADS)

Holmes, Tiffani M.; Doskocz, Jacek; Wright, Terrance; Hill, Glake A.

The interaction of perfluoropropanoic acid (PFPA) with the amino acid cysteine was investigated using density functional theory. Previous studies suggest that the peroxisome proliferator chemical, perfluorooctanoic acid, is circulated throughout the body by way of sulfur-containing amino acids. We present conformational analysis of the interactions of PFPA, a small model of perfluorooctanoic acid, with the sulfur-containing amino acid which occur by the process of hydrogen bonding, in which the hydrogen of the sulfhydryl group interacts with the carboxyl oxygen, and the amino nitrogen forms a hydrogen bond with the hydrogen of the bond OH group of the fluorinated alkyl. We also show in our structures a recently characterized weak nonbonded interaction between divalent sulfur and a main chain carboxyl oxygen in proteins. B3LYP calculated free energies and interaction energies predict low-energy, high-interaction conformations for complex systems of perfluorinated fatty acid interactions with cysteine.

DEAD-box helicase DDX27 regulates 3′ end formation of ribosomal 47S RNA and stably associates with the PeBoW-complex

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

Kellner, Markus; Rohrmoser, Michaela; Forné, Ignasi

PeBoW, a trimeric complex consisting of pescadillo (Pes1), block of proliferation (Bop1), and the WD repeat protein 12 (WDR12), is essential for processing and maturation of mammalian 5.8S and 28S ribosomal RNAs. Applying a mass spectrometric analysis, we identified the DEAD-box helicase DDX27 as stably associated factor of the PeBoW-complex. DDX27 interacts with the PeBoW-complex via an evolutionary conserved F×F motif in the N-terminal domain and is recruited to the nucleolus via its basic C-terminal domain. This recruitment is RNA-dependent and occurs independently of the PeBoW-complex. Interestingly, knockdown of DDX27, but not of Pes1, induces the accumulation of an extendedmore » form of the primary 47S rRNA. We conclude that DDX27 can interact specifically with the Pes1 and Bop1 but fulfils critical function(s) for proper 3′ end formation of 47S rRNA independently of the PeBoW-complex. - Highlights: • DEAD-box helicase DDX27 is a new constituent of the PeBoW-complex. • The N-terminal F×F motif of DDX27 interacts with the PeBoW components Pes1 and Bop1. • Nucleolar anchoring of DDX27 via its basic C-terminal domain is RNA dependent. • Knockdown of DDX27 induces a specific defect in 3′ end formation of 47S rRNA.« less

The roles of USH1 proteins and PDZ domain-containing USH proteins in USH2 complex integrity in cochlear hair cells.

PubMed

Zou, Junhuang; Chen, Qian; Almishaal, Ali; Mathur, Pranav Dinesh; Zheng, Tihua; Tian, Cong; Zheng, Qing Y; Yang, Jun

2017-02-01

Usher syndrome (USH) is the most common cause of inherited deaf-blindness, manifested as USH1, USH2 and USH3 clinical types. The protein products of USH2 causative and modifier genes, USH2A, ADGRV1, WHRN and PDZD7, interact to assemble a multiprotein complex at the ankle link region of the mechanosensitive stereociliary bundle in hair cells. Defects in this complex cause stereociliary bundle disorganization and hearing loss. The four USH2 proteins also interact in vitro with USH1 proteins including myosin VIIa, USH1G (SANS), CIB2 and harmonin. However, it is unclear whether the interactions between USH1 and USH2 proteins occur in vivo and whether USH1 proteins play a role in USH2 complex assembly in hair cells. In this study, we identified a novel interaction between myosin VIIa and PDZD7 by FLAG pull-down assay. We further investigated the role of the above-mentioned four USH1 proteins in the cochlear USH2 complex assembly using USH1 mutant mice. We showed that only myosin VIIa is indispensable for USH2 complex assembly at ankle links, indicating the potential transport and/or anchoring role of myosin VIIa for USH2 proteins in hair cells. However, myosin VIIa is not required for USH2 complex assembly in photoreceptors. We further showed that, while PDZ protein harmonin is not involved, its paralogous USH2 proteins, PDZD7 and whirlin, function synergistically in USH2 complex assembly in cochlear hair cells. In summary, our studies provide novel insight into the functional relationship between USH1 and USH2 proteins in the cochlea and the retina as well as the disease mechanisms underlying USH1 and USH2. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

The Molecular Recognition Paradigm of Environmental Chemicals with Biomacromolecules.

PubMed

Zhang, Wenjing; Pan, Liumeng; Wang, Haifei; Lv, Xuan; Ding, Keke

2017-01-01

The interactions of ligands with biomacromolecules play a fundamental role in almost all bioprocesses occuring in living organisms. The binding of ligands can cause the conformational changes of biomacromolecules, possibly affecting their physiological functions. The interactions of ligands with biomacromolecules are thus becoming a research hotspot. However, till now, there still lacks a systematic compilation of review with the focus on the interactions between environmental chemicals and biomacromolecules. In this review, we focus on the molecular recognition paradigm of environmental chemicals with biomacromolecules and chemical basis for driving the complex formation. The state-of-the-art review on in vitro and in silico studies on interaction of organic chemicals with transport proteins, nuclear receptors and CYP450 enzymes was provided, and the enantioselective interactions of chiral environmental chemicals was also mentioned.

Quantitative functional characterization of conserved molecular interactions in the active site of mannitol 2-dehydrogenase

PubMed Central

Lucas, James E; Siegel, Justin B

2015-01-01

Enzyme active site residues are often highly conserved, indicating a significant role in function. In this study we quantitate the functional contribution for all conserved molecular interactions occurring within a Michaelis complex for mannitol 2-dehydrogenase derived from Pseudomonas fluorescens (pfMDH). Through systematic mutagenesis of active site residues, we reveal that the molecular interactions in pfMDH mediated by highly conserved residues not directly involved in reaction chemistry can be as important to catalysis as those directly involved in the reaction chemistry. This quantitative analysis of the molecular interactions within the pfMDH active site provides direct insight into the functional role of each molecular interaction, several of which were unexpected based on canonical sequence conservation and structural analyses. PMID:25752240

Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation.

PubMed

Glyde, Robert; Ye, Fuzhou; Darbari, Vidya Chandran; Zhang, Nan; Buck, Martin; Zhang, Xiaodong

2017-07-06

Gene transcription is carried out by RNA polymerases (RNAPs). For transcription to occur, the closed promoter complex (RPc), where DNA is double stranded, must isomerize into an open promoter complex (RPo), where the DNA is melted out into a transcription bubble and the single-stranded template DNA is delivered to the RNAP active site. Using a bacterial RNAP containing the alternative σ 54 factor and cryoelectron microscopy, we determined structures of RPc and the activator-bound intermediate complex en route to RPo at 3.8 and 5.8 Å. Our structures show how RNAP-σ 54 interacts with promoter DNA to initiate the DNA distortions required for transcription bubble formation, and how the activator interacts with RPc, leading to significant conformational changes in RNAP and σ 54 that promote RPo formation. We propose that DNA melting is an active process initiated in RPc and that the RNAP conformations of intermediates are significantly different from that of RPc and RPo. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Transcription initiation complex structures elucidate DNA opening.

PubMed

Plaschka, C; Hantsche, M; Dienemann, C; Burzinski, C; Plitzko, J; Cramer, P

2016-05-19

Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) structures of yeast initiation complexes containing closed and open DNA at resolutions of 8.8 Å and 3.6 Å, respectively. DNA is positioned and retained over the Pol II cleft by a network of interactions between the TATA-box-binding protein TBP and transcription factors TFIIA, TFIIB, TFIIE, and TFIIF. DNA opening occurs around the tip of the Pol II clamp and the TFIIE 'extended winged helix' domain, and can occur in the absence of TFIIH. Loading of the DNA template strand into the active centre may be facilitated by movements of obstructing protein elements triggered by allosteric binding of the TFIIE 'E-ribbon' domain. The results suggest a unified model for transcription initiation with a key event, the trapping of open promoter DNA by extended protein-protein and protein-DNA contacts.

Community structure of fish larvae in mangroves with different root types in Labuhan coastal area, Sepulu - Madura

NASA Astrophysics Data System (ADS)

Muzaki, Farid Kamal; Giffari, Aninditha; Saptarini, Dian

2017-06-01

Mangrove root complexity and shading are well known to give positive correlation for both juveniles and adult fishes. However, it is remain unclear whether that complexity would affect the community of fish larvae (ichthyoplankton). This study aimed to address the question, especially in mangrove area in coastal area of Sepulu, Madura which projected as a mangrove protection area. Sampling periods were from March to May, 2016. The samples of fish larvae were collected by plankton net (mesh-size 0.150 and 0.265 mm) from six different locations representing different root types (stilt root, pneumatophore, combination of stilt root-pneumatophore and unvegetated area). As the results, 6 families were identified, namely Gobiidae, Blennidae, Pomacentridae, Carangidae, Engraulidae and Ambassidae, respectively. Gobiidae seems to be the most abundant and widely dispersed in the area. Results of two-way AnovadanTukey HSD (both at p=0.05) indicate that there were significant difference in the larval abundance regarding locations, sampling periods and interaction of both factors. As for number of taxa, significant difference occurred only from factors of locations and sampling periods, but not for interaction of both factors. Highest larval abundance and number of taxa occurred in Rhizophoraspp (with stilt root), indicating that root complexity would affect the community of fish larvae. Ordination by canonical analysis shows that different taxa of the fish larvae are tend to be distributed on different locations.

Neutralization by Metal Ions of the Toxicity of Sodium Selenide

PubMed Central

Dauplais, Marc; Lazard, Myriam; Blanquet, Sylvain; Plateau, Pierre

2013-01-01

Inert metal-selenide colloids are found in animals. They are believed to afford cross-protection against the toxicities of both metals and selenocompounds. Here, the toxicities of metal salt and sodium selenide mixtures were systematically studied using the death rate of Saccharomyces cerevisiae cells as an indicator. In parallel, the abilities of these mixtures to produce colloids were assessed. Studied metal cations could be classified in three groups: (i) metal ions that protect cells against selenium toxicity and form insoluble colloids with selenide (Ag+, Cd2+, Cu2+, Hg2+, Pb2+ and Zn2+), (ii) metal ions which protect cells by producing insoluble metal-selenide complexes and by catalyzing hydrogen selenide oxidation in the presence of dioxygen (Co2+ and Ni2+) and, finally, (iii) metal ions which do not afford protection and do not interact (Ca2+, Mg2+, Mn2+) or weakly interact (Fe2+) with selenide under the assayed conditions. When occurring, the insoluble complexes formed from divalent metal ions and selenide contained equimolar amounts of metal and selenium atoms. With the monovalent silver ion, the complex contained two silver atoms per selenium atom. Next, because selenides are compounds prone to oxidation, the stabilities of the above colloids were evaluated under oxidizing conditions. 5,5'-dithiobis-(2-nitrobenzoic acid) (DTNB), the reduction of which can be optically followed, was used to promote selenide oxidation. Complexes with cadmium, copper, lead, mercury or silver resisted dissolution by DTNB treatment over several hours. With nickel and cobalt, partial oxidation by DTNB occurred. On the other hand, when starting from ZnSe or FeSe complexes, full decompositions were obtained within a few tens of minutes. The above properties possibly explain why ZnSe and FeSe nanoparticles were not detected in animals exposed to selenocompounds. PMID:23342137

Two-amino acids change in the nsp4 of SARS coronavirus abolishes viral replication.

PubMed

Sakai, Yusuke; Kawachi, Kengo; Terada, Yutaka; Omori, Hiroko; Matsuura, Yoshiharu; Kamitani, Wataru

2017-10-01

Infection with coronavirus rearranges the host cell membrane to assemble a replication/transcription complex in which replication of the viral genome and transcription of viral mRNA occur. Although coexistence of nsp3 and nsp4 is known to cause membrane rearrangement, the mechanisms underlying the interaction of these two proteins remain unclear. We demonstrated that binding of nsp4 with nsp3 is essential for membrane rearrangement and identified amino acid residues in nsp4 responsible for the interaction with nsp3. In addition, we revealed that the nsp3-nsp4 interaction is not sufficient to induce membrane rearrangement, suggesting the participation of other factors such as host proteins. Finally, we showed that loss of the nsp3-nsp4 interaction eliminated viral replication by using an infectious cDNA clone and replicon system of SARS-CoV. These findings provide clues to the mechanism of the replication/transcription complex assembly of SARS-CoV and could reveal an antiviral target for the treatment of betacoronavirus infection. Copyright © 2017 Elsevier Inc. All rights reserved.

Using Förster-Resonance Energy Transfer to Measure Protein Interactions Between Bcl-2 Family Proteins on Mitochondrial Membranes.

PubMed

Pogmore, Justin P; Pemberton, James M; Chi, Xiaoke; Andrews, David W

2016-01-01

The Bcl-2 family of proteins regulates the process of mitochondrial outer membrane permeabilization, causing the release of cytochrome c and committing a cell to apoptosis. The majority of the functional interactions between these proteins occur at, on, or within the mitochondrial outer membrane, complicating structural studies of the proteins and complexes. As a result most in vitro studies of these protein-protein interactions use truncated proteins and/or detergents which can cause artificial interactions. Herein, we describe a detergent-free, fluorescence-based, in vitro technique to study binding between full-length recombinant Bcl-2 family proteins, particularly cleaved BID (cBID) and BCL-XL, on the membranes of purified mitochondria.

Two-dimensional correlation spectroscopic analysis on the interaction between humic acids and aluminum coagulant.

PubMed

Jin, Pengkang; Song, Jina; Wang, Xiaochang C; Jin, Xin

2018-02-01

In this study, two-dimensional correlation spectroscopy integrated with synchronous fluorescence and infrared absorption spectroscopy was employed to investigate the interaction between humic acids and aluminum coagulant at slightly acidic and neutral pH. Higher fluorescence quenching was produced for fulvic-like and humic-like fractions at pH5. At pH5, the humic-like fractions originating from the carboxylic acid, carboxyl and polysaccharide compounds were bound to aluminum first, followed by the fulvic-like fractions originating from the carboxyl and polysaccharide compounds. This finding also demonstrated that the activated functional groups of HA were involved in forming the Al-HA complex, which was accompanied by the removal of other groups by co-precipitation. Meanwhile, at pH7, almost no fluorescence quenching occurred, and surface complexation was observed to occur, in which the activated functional groups were absorbed on the amorphous Al(OH) 3 . Two-dimensional FT-IR correlation spectroscopy indicated the sequence of HA structural change during coagulation with aluminum, with IR bands affected in the order of COOH>COO - >NH deformation of amide II>aliphatic hydroxyl COH at pH5, and COO - >aliphatic hydroxyl COH at pH7. This study provides a promising pathway for analysis and insight into the priority of functional groups in the interaction between organic matters and metal coagulants. Copyright © 2017. Published by Elsevier B.V.

A walk on the tundra: Host-parasite interactions in an extreme environment.

PubMed

Kutz, Susan J; Hoberg, Eric P; Molnár, Péter K; Dobson, Andy; Verocai, Guilherme G

2014-08-01

Climate change is occurring very rapidly in the Arctic, and the processes that have taken millions of years to evolve in this very extreme environment are now changing on timescales as short as decades. These changes are dramatic, subtle and non-linear. In this article, we discuss the evolving insights into host-parasite interactions for wild ungulate species, specifically, muskoxen and caribou, in the North American Arctic. These interactions occur in an environment that is characterized by extremes in temperature, high seasonality, and low host species abundance and diversity. We believe that lessons learned in this system can guide wildlife management and conservation throughout the Arctic, and can also be generalized to more broadly understand host-parasite interactions elsewhere. We specifically examine the impacts of climate change on host-parasite interactions and focus on: (I) the direct temperature effects on parasites; (II) the importance of considering the intricacies of host and parasite ecology for anticipating climate change impacts; and (III) the effect of shifting ecological barriers and corridors. Insights gained from studying the history and ecology of host-parasite systems in the Arctic will be central to understanding the role that climate change is playing in these more complex systems.

A walk on the tundra: Host–parasite interactions in an extreme environment

PubMed Central

Kutz, Susan J.; Hoberg, Eric P.; Molnár, Péter K.; Dobson, Andy; Verocai, Guilherme G.

2014-01-01

Climate change is occurring very rapidly in the Arctic, and the processes that have taken millions of years to evolve in this very extreme environment are now changing on timescales as short as decades. These changes are dramatic, subtle and non-linear. In this article, we discuss the evolving insights into host–parasite interactions for wild ungulate species, specifically, muskoxen and caribou, in the North American Arctic. These interactions occur in an environment that is characterized by extremes in temperature, high seasonality, and low host species abundance and diversity. We believe that lessons learned in this system can guide wildlife management and conservation throughout the Arctic, and can also be generalized to more broadly understand host–parasite interactions elsewhere. We specifically examine the impacts of climate change on host–parasite interactions and focus on: (I) the direct temperature effects on parasites; (II) the importance of considering the intricacies of host and parasite ecology for anticipating climate change impacts; and (III) the effect of shifting ecological barriers and corridors. Insights gained from studying the history and ecology of host–parasite systems in the Arctic will be central to understanding the role that climate change is playing in these more complex systems. PMID:25180164

Enteral feeding: drug/nutrient interaction.

PubMed

Lourenço, R

2001-04-01

Enteral nutrition support via a feeding tube is the first choice for artificial nutrition. Most patients also require simultaneous drug therapy, with the potential risk for drug-nutrient interactions which may become relevant in clinical practice. During enteral nutrition, drug-nutrient interactions are more likely to occur than in patients fed orally. However, there is a lack of awareness about its clinical significance, which should be recognised and prevented in order to optimise nutritional and pharmacological therapeutic goals of safety and efficacy. To raise the awareness of potential drug-nutrient interactions and influence on clinical outcomes. To identify factors that can promote drug-nutrient interactions and contribute to nutrition and/or therapeutic failure. To be aware of different types of drug-nutrient interactions. To understand complex underlying mechanisms responsible for drug-nutrient interactions. To learn basic rules for the administration of medications during tube-feeding. Copyright 2001 Harcourt Publishers Ltd.

Norovirus translation requires an interaction between the C Terminus of the genome-linked viral protein VPg and eukaryotic translation initiation factor 4G.

PubMed

Chung, Liliane; Bailey, Dalan; Leen, Eoin N; Emmott, Edward P; Chaudhry, Yasmin; Roberts, Lisa O; Curry, Stephen; Locker, Nicolas; Goodfellow, Ian G

2014-08-01

Viruses have evolved a variety of mechanisms to usurp the host cell translation machinery to enable translation of the viral genome in the presence of high levels of cellular mRNAs. Noroviruses, a major cause of gastroenteritis in man, have evolved a mechanism that relies on the interaction of translation initiation factors with the virus-encoded VPg protein covalently linked to the 5' end of the viral RNA. To further characterize this novel mechanism of translation initiation, we have used proteomics to identify the components of the norovirus translation initiation factor complex. This approach revealed that VPg binds directly to the eIF4F complex, with a high affinity interaction occurring between VPg and eIF4G. Mutational analyses indicated that the C-terminal region of VPg is important for the VPg-eIF4G interaction; viruses with mutations that alter or disrupt this interaction are debilitated or non-viable. Our results shed new light on the unusual mechanisms of protein-directed translation initiation. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

High level theoretical study of benzene-halide adducts: the importance of C-H-anion hydrogen bonding.

PubMed

Coletti, Cecilia; Re, Nazzareno

2009-02-26

High level ab initio calculations were performed on the interaction of halide anions (F(-), Cl(-), Br(-), and I(-)) to benzene. For these systems recent experimental and theoretical data are rather scarce, in spite of their growingly acknowledged importance for binding in complex biological systems. We have thus explored the complete basis set limit and the effect of counterpoise basis set superposition error corrections on the minimum geometries and energies of benzene-halide adducts in their possible interaction modes. The binding energy and enthalpy values (ranging from -15.3 kcal/mol for fluoride to -6.1 kcal/mol for iodide) show that the hydrogen bonding occurring in these complexes cannot be described as a weak interaction. We have furthermore investigated the topology of the minima and of other selected sections of the potential energy surface, so to gain further insight on the nature of the halide-benzene interaction. In particular, the geometry corresponding to the C(6v) symmetry, although being overall repulsive, has displayed the unprecedented presence of a small flex (a minimum in C(6v) symmetry) with interaction energy close to zero or slightly attractive.

Interactions between dorsal and ventral streams for controlling skilled grasp

PubMed Central

van Polanen, Vonne; Davare, Marco

2015-01-01

The two visual systems hypothesis suggests processing of visual information into two distinct routes in the brain: a dorsal stream for the control of actions and a ventral stream for the identification of objects. Recently, increasing evidence has shown that the dorsal and ventral streams are not strictly independent, but do interact with each other. In this paper, we argue that the interactions between dorsal and ventral streams are important for controlling complex object-oriented hand movements, especially skilled grasp. Anatomical studies have reported the existence of direct connections between dorsal and ventral stream areas. These physiological interconnections appear to be gradually more active as the precision demands of the grasp become higher. It is hypothesised that the dorsal stream needs to retrieve detailed information about object identity, stored in ventral stream areas, when the object properties require complex fine-tuning of the grasp. In turn, the ventral stream might receive up to date grasp-related information from dorsal stream areas to refine the object internal representation. Future research will provide direct evidence for which specific areas of the two streams interact, the timing of their interactions and in which behavioural context they occur. PMID:26169317

Preparation, characterization and stability of curcumin-loaded zein-shellac composite colloidal particles.

PubMed

Sun, Cuixia; Xu, Chenqi; Mao, Like; Wang, Di; Yang, Jie; Gao, Yanxiang

2017-08-01

Curcumin-loaded zein-shellac composite particles were prepared by the antisolvent co-precipitation method. The encapsulation efficiency of curcumin was significantly improved from 82.7% in zein particles to 93.2% in zein-shellac complex particles. The result of differential scanning calorimetry suggested that curcumin in the polymeric matrix was in an amorphous state. Fourier transform infrared spectroscopy analysis revealed that curcumin had non-covalently interacted with zein and shellac, mainly through hydrogen bonding and hydrophobic interaction. Aggregates in irregular shapes, with large sizes, were found by atomic force microscopy, and conglutination, integration or fusion of different entities into network structures occurred at a high level of shellac. At the mass ratio of zein to shellac of 1:1, curcumin in the complex particles exhibited improved photochemical and thermal stability. Curcumin-loaded zein-shellac complex particles allowed the controlled release of curcumin in both PBS medium and simulated gastrointestinal fluids. Copyright © 2017 Elsevier Ltd. All rights reserved.

User's guide for ENSAERO: A multidisciplinary program for fluid/structural/control interaction studies of aircraft (release 1)

NASA Technical Reports Server (NTRS)

Guruswamy, Guru P.

1994-01-01

Strong interactions can occur between the flow about an aerospace vehicle and its structural components resulting in several important aeroelastic phenomena. These aeroelastic phenomena can significantly influence the performance of the vehicle. At present, closed-form solutions are available for aeroelastic computations when flows are in either the linear subsonic or supersonic range. However, for aeroelasticity involving complex nonlinear flows with shock waves, vortices, flow separations, and aerodynamic heating, computational methods are still under development. These complex aeroelastic interactions can be dangerous and limit the performance of aircraft. Examples of these detrimental effects are aircraft with highly swept wings experiencing vortex-induced aeroelastic oscillations, transonic regime at which the flutter speed is low, aerothermoelastic loads that play a critical role in the design of high-speed vehicles, and flow separations that often lead to buffeting with undesirable structural oscillations. The simulation of these complex aeroelastic phenomena requires an integrated analysis of fluids and structures. This report presents a summary of the development, applications, and procedures to use the multidisciplinary computer code ENSAERO. This code is based on the Euler/Navier-Stokes flow equations and modal/finite-element structural equations.

A social–ecological perspective for riverscape management in the Columbia River Basin

USGS Publications Warehouse

Hand, Brian K.; Flint, Courtney G.; Frissell, Chris A.; Muhlfeld, Clint C.; Devlin, Shawn P.; Kennedy, Brian P.; Crabtree, Robert L.; McKee, W. Arthur; Luikart, Gordon; Stanford, Jack A.

2018-01-01

Riverscapes are complex, landscape-scale mosaics of connected river and stream habitats embedded in diverse ecological and socioeconomic settings. Social–ecological interactions among stakeholders often complicate natural-resource conservation and management of riverscapes. The management challenges posed by the conservation and restoration of wild salmonid populations in the Columbia River Basin (CRB) of western North America are one such example. Because of their ecological, cultural, and socioeconomic importance, salmonids present a complex management landscape due to interacting environmental factors (eg climate change, invasive species) as well as socioeconomic and political factors (eg dams, hatcheries, land-use change, transboundary agreements). Many of the problems in the CRB can be linked to social–ecological interactions occurring within integrated ecological, human–social, and regional–climatic spheres. Future management and conservation of salmonid populations therefore depends on how well the issues are understood and whether they can be resolved through effective communication and collaboration among ecologists, social scientists, stakeholders, and policy makers.

System Analysis of LWDH Related Genes Based on Text Mining in Biological Networks

PubMed Central

Miao, Yingbo; Zhang, Liangcai; Wang, Yang; Feng, Rennan; Yang, Lei; Zhang, Shihua; Jiang, Yongshuai; Liu, Guiyou

2014-01-01

Liuwei-dihuang (LWDH) is widely used in traditional Chinese medicine (TCM), but its molecular mechanism about gene interactions is unclear. LWDH genes were extracted from the existing literatures based on text mining technology. To simulate the complex molecular interactions that occur in the whole body, protein-protein interaction networks (PPINs) were constructed and the topological properties of LWDH genes were analyzed. LWDH genes have higher centrality properties and may play important roles in the complex biological network environment. It was also found that the distances within LWDH genes are smaller than expected, which means that the communication of LWDH genes during the biological process is rapid and effectual. At last, a comprehensive network of LWDH genes, including the related drugs and regulatory pathways at both the transcriptional and posttranscriptional levels, was constructed and analyzed. The biological network analysis strategy used in this study may be helpful for the understanding of molecular mechanism of TCM. PMID:25243143

Nitrogenase of Klebsiella pneumoniae. Interaction of the component proteins studied by ultracentrifugation

PubMed Central

Eady, Robert R.

1973-01-01

Sedimentation-velocity analyses of mixtures of the component proteins of nitrogenase of Klebsiella pneumoniae at a 1:1 molar ratio, showed a single peak of sedimentation coefficient (12.4S) considerably greater than that obtained for the larger (Fe+Mo-containing) protein centrifuged alone (10.4S). When the ratio exceeded 1:1 (the smaller Fe-containing protein in excess) an additional peak corresponding in sedimentation coefficient (about 4.5S) to free Fe-containing protein appeared. When proteins, which had been inactivated by exposure to air were used, no interaction occurred. Na2S2O4 at 2mm both reversed and prevented interaction between the two proteins; sedimentation coefficients corresponded to those of the proteins when centrifuged alone. These results demonstrate the formation of a complex between the nitrogenase proteins, and, together with data of activity titration curves, are consistent with the formulation of the nitrogenase complex of K. pneumoniae as (Fe-containing protein)–(Fe+Mo-containing protein). ImagesFig. 1. PMID:4589392

LIM Protein Ajuba associates with the RPA complex through direct cell cycle-dependent interaction with the RPA70 subunit.

PubMed

Fowler, Sandy; Maguin, Pascal; Kalan, Sampada; Loayza, Diego

2018-06-22

DNA damage response pathways are essential for genome stability and cell survival. Specifically, the ATR kinase is activated by DNA replication stress. An early event in this activation is the recruitment and phosphorylation of RPA, a single stranded DNA binding complex composed of three subunits, RPA70, RPA32 and RPA14. We have previously shown that the LIM protein Ajuba associates with RPA, and that depletion of Ajuba leads to potent activation of ATR. In this study, we provide evidence that the Ajuba-RPA interaction occurs through direct protein contact with RPA70, and that their association is cell cycle-regulated and is reduced upon DNA replication stress. We propose a model in which Ajuba negatively regulates the ATR pathway by directly interacting with RPA70, thereby preventing inappropriate ATR activation. Our results provide a framework to further our understanding of the mechanism of ATR regulation in human cells in the context of cellular transformation.

Endogenous Versus Exogenous Shocks in Complex Networks: An Empirical Test Using Book Sale Rankings

NASA Astrophysics Data System (ADS)

Sornette, D.; Deschâtres, F.; Gilbert, T.; Ageon, Y.

2004-11-01

We study the precursory and recovery signatures accompanying shocks in complex networks, that we test on a unique database of the Amazon.com ranking of book sales. We find clear distinguishing signatures classifying two types of sales peaks. Exogenous peaks occur abruptly and are followed by a power law relaxation, while endogenous peaks occur after a progressively accelerating power law growth followed by an approximately symmetrical power law relaxation which is slower than for exogenous peaks. These results are rationalized quantitatively by a simple model of epidemic propagation of interactions with long memory within a network of acquaintances. The observed relaxation of sales implies that the sales dynamics is dominated by cascades rather than by the direct effects of news or advertisements, indicating that the social network is close to critical.

Endogenous versus exogenous shocks in complex networks: an empirical test using book sale rankings.

PubMed

Sornette, D; Deschâtres, F; Gilbert, T; Ageon, Y

2004-11-26

We study the precursory and recovery signatures accompanying shocks in complex networks, that we test on a unique database of the Amazon.com ranking of book sales. We find clear distinguishing signatures classifying two types of sales peaks. Exogenous peaks occur abruptly and are followed by a power law relaxation, while endogenous peaks occur after a progressively accelerating power law growth followed by an approximately symmetrical power law relaxation which is slower than for exogenous peaks. These results are rationalized quantitatively by a simple model of epidemic propagation of interactions with long memory within a network of acquaintances. The observed relaxation of sales implies that the sales dynamics is dominated by cascades rather than by the direct effects of news or advertisements, indicating that the social network is close to critical.

Contributions of ignitions, fuels, and weather to the spatial patterns of burn probability of a boreal landscape

Treesearch

Marc-Andre Parisien; Sean A. Parks; Carol Miller; Meg A. Krawchuck; Mark Heathcott; Max A. Moritz

2011-01-01

The spatial pattern of fire observed across boreal landscapes is the outcome of complex interactions among components of the fire environment. We investigated how the naturally occurring patterns of ignitions, fuels, and weather generate spatial pattern of burn probability (BP) in a large and highly fireprone boreal landscape of western Canada, Wood Buffalo National...

Trichodiene production in a Trichoderma harzianum erg1-silenced strain provides evidence of the importance of the sterol biosynthetic pathway in inducing plant defense-related gene expression

USDA-ARS?s Scientific Manuscript database

Trichoderma species are often used as biocontrol agents against plant-pathogenic fungi. A complex molecular interaction occurs among the biocontrol agent, the antagonistic fungus, and the plant. Terpenes and sterols produced by the biocontrol fungus have been found to affect gene expression in both ...

Beneath the Tip of the Iceberg: Exploring the Multiple Forms of University-Industry Linkages

ERIC Educational Resources Information Center

Ramos-Vielba, Irene; Fernandez-Esquinas, Manuel

2012-01-01

This article focuses on the wide variety of channels through which the process of knowledge transfer occurs. The overall objective is to show the complexity of relationships between researchers and firms in a university system, and to identify some specific factors that influence such interactions. Our case study involves a face-to-face survey of…

Impurity and Defect Interactions in GaAs.

DTIC Science & Technology

1982-09-30

motivated :* 1. The actual transport of Cr occurs interstitially. The * diffusion and drift of the substitutional and complexed Cr are negligible. This is...of impurity 3 for the growth I case listed in Table 1, after 1, 5, and 10 minutes. Ps4 C 2- U I3 Nmil I Figur ~0i . . , 0 O20 30 4 5 O 60 080 90

On the Unsteady Shock Wave Interaction with a Backward-Facing Step: Viscous Analysis

NASA Astrophysics Data System (ADS)

Mendoza, N.; Bowersox, R. D. W.

Unsteady shock propagation through ducts with varying cross-sectional area occurs in many engineering applications, such as explosions in underground tunnels, blast shelter design, engine exhaust systems, and high-speed propulsion systems. These complex, transient flows are rich in fundamental fluid-dynamic phenomena and are excellent testbeds for improving our understanding of unsteady fluid dynamics

Influence of host resistance on the genetic structure of the white pine blister rust fungus in the western United States

Treesearch

B. A. Richardson; N. B. Klopfenstein; P. J. Zambino; G. I. McDonald; B. W. Geils; L. M. Carris

2008-01-01

Cronartium ribicola, the causal agent of white pine blister rust, has been devastating to five-needled white pines in North America since its introduction nearly a century ago. However, dynamic and complex interactions occur among C. ribicola, five-needled white pines, and the environment. To examine potential evolutionary...

RNA and RNP as Building Blocks for Nanotechnology and Synthetic Biology.

PubMed

Ohno, Hirohisa; Saito, Hirohide

2016-01-01

Recent technologies that aimed to elucidate cellular function have revealed essential roles for RNA molecules in living systems. Our knowledge concerning functional and structural information of naturally occurring RNA and RNA-protein (RNP) complexes is increasing rapidly. RNA and RNP interaction motifs are structural units that function as building blocks to constitute variety of complex structures. RNA-central synthetic biology and nanotechnology are constructive approaches that employ the accumulated information and build synthetic RNA (RNP)-based circuits and nanostructures. Here, we describe how to design and construct synthetic RNA (RNP)-based devices and structures at the nanometer-scale for biological and future therapeutic applications. RNA/RNP nanostructures can also be utilized as the molecular scaffold to control the localization or interactions of target molecule(s). Moreover, RNA motifs recognized by RNA-binding proteins can be applied to make protein-responsive translational "switches" that can turn gene expression "on" or "off" depending on the intracellular environment. This "synthetic RNA and RNP world" will expand tools for nanotechnology and synthetic biology. In addition, these reconstructive approaches would lead to a greater understanding of building principle in naturally occurring RNA/RNP molecules and systems. Copyright © 2016 Elsevier Inc. All rights reserved.

Fluid flow in the osteocyte mechanical environment: a fluid-structure interaction approach.

PubMed

Verbruggen, Stefaan W; Vaughan, Ted J; McNamara, Laoise M

2014-01-01

Osteocytes are believed to be the primary sensor of mechanical stimuli in bone, which orchestrate osteoblasts and osteoclasts to adapt bone structure and composition to meet physiological loading demands. Experimental studies to quantify the mechanical environment surrounding bone cells are challenging, and as such, computational and theoretical approaches have modelled either the solid or fluid environment of osteocytes to predict how these cells are stimulated in vivo. Osteocytes are an elastic cellular structure that deforms in response to the external fluid flow imposed by mechanical loading. This represents a most challenging multi-physics problem in which fluid and solid domains interact, and as such, no previous study has accounted for this complex behaviour. The objective of this study is to employ fluid-structure interaction (FSI) modelling to investigate the complex mechanical environment of osteocytes in vivo. Fluorescent staining of osteocytes was performed in order to visualise their native environment and develop geometrically accurate models of the osteocyte in vivo. By simulating loading levels representative of vigorous physiological activity ([Formula: see text] compression and 300 Pa pressure gradient), we predict average interstitial fluid velocities [Formula: see text] and average maximum shear stresses [Formula: see text] surrounding osteocytes in vivo. Interestingly, these values occur in the canaliculi around the osteocyte cell processes and are within the range of stimuli known to stimulate osteogenic responses by osteoblastic cells in vitro. Significantly our results suggest that the greatest mechanical stimulation of the osteocyte occurs in the cell processes, which, cell culture studies have indicated, is the most mechanosensitive area of the cell. These are the first computational FSI models to simulate the complex multi-physics mechanical environment of osteocyte in vivo and provide a deeper understanding of bone mechanobiology.

Molecular Mechanisms, Thermodynamics, and Dissociation Kinetics of Knob-Hole Interactions in Fibrin*

PubMed Central

Kononova, Olga; Litvinov, Rustem I.; Zhmurov, Artem; Alekseenko, Andrey; Cheng, Chia Ho; Agarwal, Silvi; Marx, Kenneth A.; Weisel, John W.; Barsegov, Valeri

2013-01-01

Polymerization of fibrin, the primary structural protein of blood clots and thrombi, occurs through binding of knobs ‘A’ and ‘B’ in the central nodule of fibrin monomer to complementary holes ‘a’ and ‘b’ in the γ- and β-nodules, respectively, of another monomer. We characterized the A:a and B:b knob-hole interactions under varying solution conditions using molecular dynamics simulations of the structural models of fibrin(ogen) fragment D complexed with synthetic peptides GPRP (knob ‘A’ mimetic) and GHRP (knob ‘B’ mimetic). The strength of A:a and B:b knob-hole complexes was roughly equal, decreasing with pulling force; however, the dissociation kinetics were sensitive to variations in acidity (pH 5–7) and temperature (T = 25–37 °C). There were similar structural changes in holes ‘a’ and ‘b’ during forced dissociation of the knob-hole complexes: elongation of loop I, stretching of the interior region, and translocation of the moveable flap. The disruption of the knob-hole interactions was not an “all-or-none” transition as it occurred through distinct two-step or single step pathways with or without intermediate states. The knob-hole bonds were stronger, tighter, and more brittle at pH 7 than at pH 5. The B:b knob-hole bonds were weaker, looser, and more compliant than the A:a knob-hole bonds at pH 7 but stronger, tighter, and less compliant at pH 5. Surprisingly, the knob-hole bonds were stronger, not weaker, at elevated temperature (T = 37 °C) compared with T = 25 °C due to the helix-to-coil transition in loop I that helps stabilize the bonds. These results provide detailed qualitative and quantitative characteristics underlying the most significant non-covalent interactions involved in fibrin polymerization. PMID:23720752

Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences.

PubMed

Pitre, S; North, C; Alamgir, M; Jessulat, M; Chan, A; Luo, X; Green, J R; Dumontier, M; Dehne, F; Golshani, A

2008-08-01

Protein-protein interaction (PPI) maps provide insight into cellular biology and have received considerable attention in the post-genomic era. While large-scale experimental approaches have generated large collections of experimentally determined PPIs, technical limitations preclude certain PPIs from detection. Recently, we demonstrated that yeast PPIs can be computationally predicted using re-occurring short polypeptide sequences between known interacting protein pairs. However, the computational requirements and low specificity made this method unsuitable for large-scale investigations. Here, we report an improved approach, which exhibits a specificity of approximately 99.95% and executes 16,000 times faster. Importantly, we report the first all-to-all sequence-based computational screen of PPIs in yeast, Saccharomyces cerevisiae in which we identify 29,589 high confidence interactions of approximately 2 x 10(7) possible pairs. Of these, 14,438 PPIs have not been previously reported and may represent novel interactions. In particular, these results reveal a richer set of membrane protein interactions, not readily amenable to experimental investigations. From the novel PPIs, a novel putative protein complex comprised largely of membrane proteins was revealed. In addition, two novel gene functions were predicted and experimentally confirmed to affect the efficiency of non-homologous end-joining, providing further support for the usefulness of the identified PPIs in biological investigations.

BSA binding and antimicrobial studies of branched polyethyleneimine-copper(II)bipyridine/phenanthroline complexes

NASA Astrophysics Data System (ADS)

Vignesh, Gopalaswamy; Arunachalam, Sankaralingam; Vignesh, Sivanandham; James, Rathinam Arthur

2012-10-01

The interaction of two water soluble branched polyethyleneimine-copper(II) complexes containing bipyridine/phenanthroline with bovine serum albumin (BSA) was studied by, UV-Visible absorption, fluorescence, lifetime measurements and circular dichroism spectroscopic techniques. The polymer-copper(II) complexes strongly quench the intrinsic fluorescence of BSA is the static quenching mechanism through hydrogen bonds and van der Waal's attraction. The distance r, between the BSA and the complexes seems to be less than 2 nm indicating that the energy transfer between the donor and acceptor occurs with high probability. Synchronous fluorescence studies indicate the binding of polymer-copper(II) complexes with BSA mostly changes the polarity around tryptophan residues rather than tyrosine residues. The circular dichroism studies indicate that the binding has induced considerable amount of conformational changes in the protein. The complexes also show some antibacterial and antifungal properties.

Respiratory chain supercomplexes associate with the cysteine desulfurase complex of the iron–sulfur cluster assembly machinery

PubMed Central

Böttinger, Lena; Mårtensson, Christoph U.; Song, Jiyao; Zufall, Nicole; Wiedemann, Nils; Becker, Thomas

2018-01-01

Mitochondria are the powerhouses of eukaryotic cells. The activity of the respiratory chain complexes generates a proton gradient across the inner membrane, which is used by the F1FO-ATP synthase to produce ATP for cellular metabolism. In baker’s yeast, Saccharomyces cerevisiae, the cytochrome bc1 complex (complex III) and cytochrome c oxidase (complex IV) associate in respiratory chain supercomplexes. Iron–sulfur clusters (ISC) form reactive centers of respiratory chain complexes. The assembly of ISC occurs in the mitochondrial matrix and is essential for cell viability. The cysteine desulfurase Nfs1 provides sulfur for ISC assembly and forms with partner proteins the ISC-biogenesis desulfurase complex (ISD complex). Here, we report an unexpected interaction of the active ISD complex with the cytochrome bc1 complex and cytochrome c oxidase. The individual deletion of complex III or complex IV blocks the association of the ISD complex with respiratory chain components. We conclude that the ISD complex binds selectively to respiratory chain supercomplexes. We propose that this molecular link contributes to coordination of iron–sulfur cluster formation with respiratory activity. PMID:29386296

Charge transfer complexes of adenosine-5‧-monophosphate and cytidine-5‧-monophosphate with water-soluble cobalt(II) Schiff base complexes in aqueous solution

NASA Astrophysics Data System (ADS)

Boghaei, Davar M.; Gharagozlou, Mehrnaz

2006-01-01

Water-soluble cobalt(II) tetradentate Schiff base complexes have been shown to form charge transfer (CT) complexes with a series of nucleoside monophosphates including adenosine-5‧-monophosphate (AMP) and cytidine-5‧-monophosphate (CMP). The investigated water-soluble cobalt(II) Schiff base complexes are (i) disodium[{bis(5-sulfo-salicylaldehyde)-o-phenylenediiminato}cobalt(II)], Na2[Co(SO3-salophen)] (1); (ii) disodium[{bis(5-sulfo-salicylaldehyde)-4,5-dimethyl-o-phenylenediiminato}cobalt(II)], Na2[Co(SO3-sal-4,5-dmophen)] (2) and (iii) disodium[{bis(4-methoxy-5-sulfo-salicylaldehyde)-4,5-dimethyl-o-phenylenediiminato}cobalt(II)], Na2[Co(SO3-4-meosal-4,5-dmophen)] (3). The formation constant and thermodynamic parameters for charge transfer complex formation of water-soluble cobalt(II) Schiff base complexes with nucleoside monophosphates were determined spectrophotometrically in aqueous solution at constant ionic strength (I = 0.2 mol dm-3 KNO3) under physiological condition (pH 7.0) and at various temperatures between 288 and 308 K. The stoichiometry has been found to be 1:1 (water-soluble cobalt(II) Schiff base complex: nucleoside monophosphate) in each case. Our spectroscopic and thermodynamic results show that the interaction of water-soluble cobalt(II) Schiff base complexes with the investigated nucleoside monophosphates occurs mainly through the phosphate group. The trend of the interaction according to the cobalt(II) Schiff base complexes due to electronic and steric factors is as follows: Na2[Co(SO3-salophen)] > Na2[Co(SO3-sal-4,5-dmophen)] > Na2[Co(SO3-4-meosal-4,5-dmophen)]. Also the trend of the interaction of a given cobalt(II) Schiff base complex according to the nucleoside monophosphate is as follows: CMP > AMP.

Adaptive iterative design (AID): a novel approach for evaluating the interactive effects of multiple stressors on aquatic organisms.

PubMed

Glaholt, Stephen P; Chen, Celia Y; Demidenko, Eugene; Bugge, Deenie M; Folt, Carol L; Shaw, Joseph R

2012-08-15

The study of stressor interactions by eco-toxicologists using nonlinear response variables is limited by required amounts of a priori knowledge, complexity of experimental designs, the use of linear models, and the lack of use of optimal designs of nonlinear models to characterize complex interactions. Therefore, we developed AID, an adaptive-iterative design for eco-toxicologist to more accurately and efficiently examine complex multiple stressor interactions. AID incorporates the power of the general linear model and A-optimal criteria with an iterative process that: 1) minimizes the required amount of a priori knowledge, 2) simplifies the experimental design, and 3) quantifies both individual and interactive effects. Once a stable model is determined, the best fit model is identified and the direction and magnitude of stressors, individually and all combinations (including complex interactions) are quantified. To validate AID, we selected five commonly co-occurring components of polluted aquatic systems, three metal stressors (Cd, Zn, As) and two water chemistry parameters (pH, hardness) to be tested using standard acute toxicity tests in which Daphnia mortality is the (nonlinear) response variable. We found after the initial data input of experimental data, although literature values (e.g. EC-values) may also be used, and after only two iterations of AID, our dose response model was stable. The model ln(Cd)*ln(Zn) was determined the best predictor of Daphnia mortality response to the combined effects of Cd, Zn, As, pH, and hardness. This model was then used to accurately identify and quantify the strength of both greater- (e.g. As*Cd) and less-than additive interactions (e.g. Cd*Zn). Interestingly, our study found only binary interactions significant, not higher order interactions. We conclude that AID is more efficient and effective at assessing multiple stressor interactions than current methods. Other applications, including life-history endpoints commonly used by regulators, could benefit from AID's efficiency in assessing water quality criteria. Copyright © 2012 Elsevier B.V. All rights reserved.

High Pressure Optical Studies of the Thallous Halides and of Charge-Transfer Complexes

NASA Astrophysics Data System (ADS)

Jurgensen, Charles Willard

High pressure was used to study the insulator -to-metal transition in sulfur and the thallous halides and to study the intermolecular interactions in charge -transfer complexes. The approach to the band overlap insulator -to-metal transition was studied in three thallous halides and sulfur by optical absorption measurements of the band gap as a function of pressure. The band gap of sulfur continuously decreases with pressure up to the insulator -to-metal transition which occurs between 450 and 485 kbars. The results on the thallous halides indicate that the indirect gap decreases more rapidly than the direct gap; the closing of the indirect gap is responsible for the observed insulator -to-metal transitions. High pressure electronic and vibrational spectroscopic measurements on the solid-state complexes of HMB-TCNE were used to study the intermolecular interactions of charge -transfer complexes. The vibrational frequency shifts indicate that the degree of charge transfer increases with pressure which is independently confirmed by an increase in the molar absorptivity of the electronic charge-transfer peak. Induction and dispersion forces contribute towards a red shift of the charge-transfer peak; however, charge-transfer resonance contributes toward a blue shift and this effect is dominant for the HMB-TCNE complexes. High pressure electronic spectra were used to study the effect of intermolecular interactions on the electronic states of TCNQ and its complexes. The red shifts with pressure of the electronic spectra of TCNQ and (TCNQ)(' -) in polymer media and of crystalline TCNQ can be understood in terms of Van der Waals interactions. None of the calculations which considered intradimer distance obtained the proper behavior for either the charge-transfer of the locally excited states of the complexes. The qualitative behavior of both states can be interpreted as the effect of increased mixing of the locally excited and charge transfer states.

An Intrinsically Disordered APLF Links Ku, DNA-PKcs, and XRCC4-DNA Ligase IV in an Extended Flexible Non-homologous End Joining Complex

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

Hammel, Michal; Yu, Yaping; Radhakrishnan, Sarvan K.

DNA double-strand break (DSB) repair by non-homologous end joining (NHEJ) in human cells is initiated by Ku heterodimer binding to a DSB, followed by recruitment of core NHEJ factors including DNA-dependent protein kinase catalytic subunit (DNA-PKcs), XRCC4-like factor (XLF), and XRCC4 (X4)-DNA ligase IV (L4). Ku also interacts with accessory factors such as aprataxin and polynucleotide kinase/phosphatase-like factor (APLF). But, how these factors interact to tether, process, and ligate DSB ends while allowing regulation and chromatin interactions remains enigmatic. Here, small angle X-ray scattering (SAXS) and mutational analyses show APLF is largely an intrinsically disordered protein that binds Ku, Ku/DNA-PKcsmore » (DNA-PK), and X4L4 within an extended flexible NHEJ core complex. X4L4 assembles with Ku heterodimers linked to DNA-PKcs via flexible Ku80 C-terminal regions (Ku80CTR) in a complex stabilized through APLF interactions with Ku, DNA-PK, and X4L4. Our collective results unveil the solution architecture of the six-protein complex and suggest cooperative assembly of an extended flexible NHEJ core complex that supports APLF accessibility while possibly providing flexible attachment of the core complex to chromatin. The resulting dynamic tethering furthermore, provides geometric access of L4 catalytic domains to the DNA ends during ligation and of DNA-PKcs for targeted phosphorylation of other NHEJ proteins as well as trans-phosphorylation of DNA-PKcs on the opposing DSB without disrupting the core ligation complex. Overall the results shed light on evolutionary conservation of Ku, X4, and L4 activities, while explaining the observation that Ku80CTR and DNA-PKcs only occur in a subset of higher eukaryotes.« less

An Intrinsically Disordered APLF Links Ku, DNA-PKcs, and XRCC4-DNA Ligase IV in an Extended Flexible Non-homologous End Joining Complex

DOE PAGES

Hammel, Michal; Yu, Yaping; Radhakrishnan, Sarvan K.; ...

2016-11-14

DNA double-strand break (DSB) repair by non-homologous end joining (NHEJ) in human cells is initiated by Ku heterodimer binding to a DSB, followed by recruitment of core NHEJ factors including DNA-dependent protein kinase catalytic subunit (DNA-PKcs), XRCC4-like factor (XLF), and XRCC4 (X4)-DNA ligase IV (L4). Ku also interacts with accessory factors such as aprataxin and polynucleotide kinase/phosphatase-like factor (APLF). But, how these factors interact to tether, process, and ligate DSB ends while allowing regulation and chromatin interactions remains enigmatic. Here, small angle X-ray scattering (SAXS) and mutational analyses show APLF is largely an intrinsically disordered protein that binds Ku, Ku/DNA-PKcsmore » (DNA-PK), and X4L4 within an extended flexible NHEJ core complex. X4L4 assembles with Ku heterodimers linked to DNA-PKcs via flexible Ku80 C-terminal regions (Ku80CTR) in a complex stabilized through APLF interactions with Ku, DNA-PK, and X4L4. Our collective results unveil the solution architecture of the six-protein complex and suggest cooperative assembly of an extended flexible NHEJ core complex that supports APLF accessibility while possibly providing flexible attachment of the core complex to chromatin. The resulting dynamic tethering furthermore, provides geometric access of L4 catalytic domains to the DNA ends during ligation and of DNA-PKcs for targeted phosphorylation of other NHEJ proteins as well as trans-phosphorylation of DNA-PKcs on the opposing DSB without disrupting the core ligation complex. Overall the results shed light on evolutionary conservation of Ku, X4, and L4 activities, while explaining the observation that Ku80CTR and DNA-PKcs only occur in a subset of higher eukaryotes.« less

Fluorescence correlation spectroscopy study of the complexation of DNA hybrids, IgG antibody, and a chimeric protein of IgG-binding ZZ domains fused with a carbohydrate binding module.

PubMed

Rosa, A M M; Prazeres, D M F; Paulo, P M R

2017-06-28

Fluorescence correlation spectroscopy (FCS) was used to characterize the molecular interactions between the four components of a DNA recognition system. A fluorescent DNA probe was used to assess: (i) the hybridization with a complementary biotin-labeled target, (ii) the complexation of the resulting hybrid and an anti-biotin antibody, and (iii) the binding of the latter complex to a ZZ-CBM fusion protein that combines small synthetic IgG Fc-binding Z domains with a carbohydrate binding module (CBM). These binding interactions were monitored by exposing the fluorescent DNA probe to different amounts and combinations of the other molecules in solution. Through the analysis of FCS autocorrelation curves, an association constant (K a ) of 2.9 × 10 7 M -1 was estimated for DNA·DNA hybridization, and the presence of (non-) complementary target DNA in solution could be discriminated. The specific capture of biotinylated DNA hybrids by anti-biotin IgG was verified, with an apparent K a of 2.5 × 10 6 M -1 . The increment in the diffusion time measured when the DNA·DNA:antibody complexes were in contact with the ZZ-CBM fusion protein suggested that the binding occurs at a stoichiometric ratio of DNA/antibody complex to fusion larger than 1 : 1. The FCS-derived information obtained is useful to gain insight into molecular interactions involved in diagnostic assays.

Identification of a protein–protein interaction between KCNE1 and the activation gate machinery of KCNQ1

PubMed Central

Lvov, Anatoli; Gage, Steven D.; Berrios, Virla M.

2010-01-01

KCNQ1 channels assemble with KCNE1 transmembrane (TM) peptides to form voltage-gated K+ channel complexes with slow activation gate opening. The cytoplasmic C-terminal domain that abuts the KCNE1 TM segment has been implicated in regulating KCNQ1 gating, yet its interaction with KCNQ1 has not been described. Here, we identified a protein–protein interaction between the KCNE1 C-terminal domain and the KCNQ1 S6 activation gate and S4–S5 linker. Using cysteine cross-linking, we biochemically screened over 300 cysteine pairs in the KCNQ1–KCNE1 complex and identified three residues in KCNQ1 (H363C, P369C, and I257C) that formed disulfide bonds with cysteine residues in the KCNE1 C-terminal domain. Statistical analysis of cross-link efficiency showed that H363C preferentially reacted with KCNE1 residues H73C, S74C, and D76C, whereas P369C showed preference for only D76C. Electrophysiological investigation of the mutant K+ channel complexes revealed that the KCNQ1 residue, H363C, formed cross-links not only with KCNE1 subunits, but also with neighboring KCNQ1 subunits in the complex. Cross-link formation involving the H363C residue was state dependent, primarily occurring when the KCNQ1–KCNE1 complex was closed. Based on these biochemical and electrophysiological data, we generated a closed-state model of the KCNQ1–KCNE1 cytoplasmic region where these protein–protein interactions are poised to slow activation gate opening. PMID:20479109

Shock wave/turbulent boundary layer interaction in the flow field of a tri-dimension wind tunnel

NASA Technical Reports Server (NTRS)

Benay, R.; Pot, T.

1986-01-01

The first results of a thorough experimental analysis of a strong three-dimensional shock-wave/turbulent boundary-layer interaction occurring in a three dimensional transonic channel are presented. The aim of this experiment is to help in the physical understanding of a complex field, including several separations, and to provide a well documented case to test computational methods. The flowfield has been probed in many points by means of a three-component laser Doppler velocimeter. The results presented relate only to the mean velocity field. They clearly show the formation in the flow of a strong vortical motion resulting from the shock wave interaction.

Transport behaviors of locally fractional coupled Brownian motors with fluctuating interactions

NASA Astrophysics Data System (ADS)

Wang, Huiqi; Ni, Feixiang; Lin, Lifeng; Lv, Wangyong; Zhu, Hongqiang

2018-09-01

In some complex viscoelastic mediums, it is ubiquitous that absorbing and desorbing surrounding Brownian particles randomly occur in coupled systems. The conventional method is to model a variable-mass system driven by both multiplicative and additive noises. In this paper, an improved mathematical model is created based on generalized Langevin equations (GLE) to characterize the random interaction with locally fluctuating number of coupled particles in the elastically coupled factional Brownian motors (FBM). By the numerical simulations, the effect of fluctuating interactions on collective transport behaviors is investigated, and some abnormal phenomena, such as cooperative behaviors, stochastic resonance (SR) and anomalous transport, are observed in the regime of sub-diffusion.

Characteristics of aperiodic sequence of slip events caused by interaction between seismic patches and that caused be self-organized stress heterogeneity

NASA Astrophysics Data System (ADS)

Kato, N.

2017-12-01

Numerical simulations of earthquake cycles are conducted to investigate the origin of complexity of earthquake recurrence. There are two main causes of the complexity. One is self-organized stress heterogeneity due to dynamical effect. The other is the effect of interaction between some fault patches. In the model, friction on the fault is assumed to obey a rate- and state-dependent friction law. Circular patches of velocity-weakening frictional property are assumed on the fault. On the remaining areas of the fault, velocity-strengthening friction is assumed. We consider three models: Single patch model, two-patch model, and three-patch model. In the first model, the dynamical effect is mainly examined. The latter two models take into consideration the effect of interaction as well as the dynamical effect. Complex multiperiodic or aperiodic sequences of slip events occur when slip behavior changes from the seismic to aseismic, and when the degree of interaction between seismic patches is intermediate. The former is observed in all the models, and the latter is observed in the two-patch model and the three-patch model. Evolution of spatial distribution of shear stress on the fault suggests that aperiodicity at the transition from seismic to aseismic slip is caused by self-organized stress heterogeneity. The iteration maps of recurrence intervals of slip events in aperiodic sequences are examined, and they are approximately expressed by simple curves for aperiodicity at the transition from seismic to aseismic slip. In contrast, the iteration maps for aperiodic sequences caused by interaction between seismic patches are scattered and they are not expressed by simple curves. This result suggests that complex sequences caused by different mechanisms may be distinguished.

Glucosylated polyethylenimine as a tumor-targeting gene carrier.

PubMed

Park, In-Kyu; Cook, Seung-Eun; Kim, You-Kyoung; Kim, Hyun-Woo; Cho, Myung-Haing; Jeong, Hwan-Jeong; Kim, Eun-Mi; Nah, Jae-Woon; Bom, Hee-Seung; Cho, Chong-Su

2005-11-01

Glucosylated polyethylenimine (GPEI) was synthesized as a tumor-targeting gene carrier through facilitative glucose metabolism by tumor glucose transporter. Particle sizes of GPEI/DNA complex increased in proportion to glucose content of GPEI, whereas surface charge of the complex was not dependent on glucosylation, partially due to inefficient shielding of the short hydrophilic group introduced. GPEI with higher glucosylation (36 mol-%) had no cytotoxic effect on cells even at polymer concentrations higher than 200 microg/mL. Compared to unglucosylated PEI, glucosylation induced less than one-order decrease of transfection efficiency. Transfection of GPEI/DNA complex into tumor cells possibly occurred through specific interaction between glucose-related cell receptors and glucose moiety of GPEI. Gamma imaging technique revealed GPEI/DNA complex was distributed in liver, spleen, and tumors.

The importance of α-CT and Salt bridges in the Formation of Insulin and its Receptor Complex by Computational Simulation.

PubMed

Dehghan-Shasaltaneh, Marzieh; Lanjanian, Hossein; Riazi, Gholam Hossein; Masoudi-Nejad, Ali

2018-01-01

Insulin hormone is an important part of the endocrine system. It contains two polypeptide chains and plays a pivotal role in regulating carbohydrate metabolism. Insulin receptors (IR) located on cell surface interacts with insulin to control the intake of glucose. Although several studies have tried to clarify the interaction between insulin and its receptor, the mechanism of this interaction remains elusive because of the receptor's structural complexity and structural changes during the interaction. In this work, we tried to fractionate the interactions. Therefore, sequential docking method utilization of HADDOCK was used to achieve the mentioned goal, so the following processes were done: the first, two pdb files of IR i.e., 3LOH and 3W11 were concatenated using modeller. The second, flexible regions of IR were predicted by HingeProt. Output files resulting from HingeProt were uploaded into HADDOCK. Our results predict new salt bridges in the complex and emphasize on the role of salt bridges to maintain an inverted V structure of IR. Having an inverted V structure leads to activate intracellular signaling pathway. In addition to presence salt bridges to form a convenient structure of IR, the importance of α-chain of carboxyl terminal (α-CT) to interact with insulin was surveyed and also foretokened new insulin/IR contacts, particularly at site 2 (rigid parts 2 and 3). Finally, several conformational changes in residues Asn711-Val715 of α-CT were occurred, we suggest that α-CT is a suitable situation relative to insulin due to these conformational alterations.

ATM activation and its recruitment to damaged DNA require binding to the C terminus of Nbs1.

PubMed

You, Zhongsheng; Chahwan, Charly; Bailis, Julie; Hunter, Tony; Russell, Paul

2005-07-01

ATM has a central role in controlling the cellular responses to DNA damage. It and other phosphoinositide 3-kinase-related kinases (PIKKs) have giant helical HEAT repeat domains in their amino-terminal regions. The functions of these domains in PIKKs are not well understood. ATM activation in response to DNA damage appears to be regulated by the Mre11-Rad50-Nbs1 (MRN) complex, although the exact functional relationship between the MRN complex and ATM is uncertain. Here we show that two pairs of HEAT repeats in fission yeast ATM (Tel1) interact with an FXF/Y motif at the C terminus of Nbs1. This interaction resembles nucleoporin FXFG motif binding to HEAT repeats in importin-beta. Budding yeast Nbs1 (Xrs2) appears to have two FXF/Y motifs that interact with Tel1 (ATM). In Xenopus egg extracts, the C terminus of Nbs1 recruits ATM to damaged DNA, where it is subsequently autophosphorylated. This interaction is essential for ATM activation. A C-terminal 147-amino-acid fragment of Nbs1 that has the Mre11- and ATM-binding domains can restore ATM activation in an Nbs1-depleted extract. We conclude that an interaction between specific HEAT repeats in ATM and the C-terminal FXF/Y domain of Nbs1 is essential for ATM activation. We propose that conformational changes in the MRN complex that occur upon binding to damaged DNA are transmitted through the FXF/Y-HEAT interface to activate ATM. This interaction also retains active ATM at sites of DNA damage.

Electrostatic Steering Accelerates C3d:CR2 Association.

PubMed

Mohan, Rohith R; Huber, Gary A; Morikis, Dimitrios

2016-08-25

Electrostatic effects are ubiquitous in protein interactions and are found to be pervasive in the complement system as well. The interaction between complement fragment C3d and complement receptor 2 (CR2) has evolved to become a link between innate and adaptive immunity. Electrostatic interactions have been suggested to be the driving factor for the association of the C3d:CR2 complex. In this study, we investigate the effects of ionic strength and mutagenesis on the association of C3d:CR2 through Brownian dynamics simulations. We demonstrate that the formation of the C3d:CR2 complex is ionic strength-dependent, suggesting the presence of long-range electrostatic steering that accelerates the complex formation. Electrostatic steering occurs through the interaction of an acidic surface patch in C3d and the positively charged CR2 and is supported by the effects of mutations within the acidic patch of C3d that slow or diminish association. Our data are in agreement with previous experimental mutagenesis and binding studies and computational studies. Although the C3d acidic patch may be locally destabilizing because of unfavorable Coulombic interactions of like charges, it contributes to the acceleration of association. Therefore, acceleration of function through electrostatic steering takes precedence to stability. The site of interaction between C3d and CR2 has been the target for delivery of CR2-bound nanoparticle, antibody, and small molecule biomarkers, as well as potential therapeutics. A detailed knowledge of the physicochemical basis of C3d:CR2 association may be necessary to accelerate biomarker and drug discovery efforts.

Dissecting the Calcium-Induced Differentiation of Human Primary Keratinocytes Stem Cells by Integrative and Structural Network Analyses

PubMed Central

Toufighi, Kiana; Yang, Jae-Seong; Luis, Nuno Miguel; Aznar Benitah, Salvador; Lehner, Ben; Serrano, Luis; Kiel, Christina

2015-01-01

The molecular details underlying the time-dependent assembly of protein complexes in cellular networks, such as those that occur during differentiation, are largely unexplored. Focusing on the calcium-induced differentiation of primary human keratinocytes as a model system for a major cellular reorganization process, we look at the expression of genes whose products are involved in manually-annotated protein complexes. Clustering analyses revealed only moderate co-expression of functionally related proteins during differentiation. However, when we looked at protein complexes, we found that the majority (55%) are composed of non-dynamic and dynamic gene products (‘di-chromatic’), 19% are non-dynamic, and 26% only dynamic. Considering three-dimensional protein structures to predict steric interactions, we found that proteins encoded by dynamic genes frequently interact with a common non-dynamic protein in a mutually exclusive fashion. This suggests that during differentiation, complex assemblies may also change through variation in the abundance of proteins that compete for binding to common proteins as found in some cases for paralogous proteins. Considering the example of the TNF-α/NFκB signaling complex, we suggest that the same core complex can guide signals into diverse context-specific outputs by addition of time specific expressed subunits, while keeping other cellular functions constant. Thus, our analysis provides evidence that complex assembly with stable core components and competition could contribute to cell differentiation. PMID:25946651

Wine microbiome: A dynamic world of microbial interactions.

PubMed

Liu, Youzhong; Rousseaux, Sandrine; Tourdot-Maréchal, Raphaëlle; Sadoudi, Mohand; Gougeon, Régis; Schmitt-Kopplin, Philippe; Alexandre, Hervé

2017-03-04

Most fermented products are generated by a mixture of microbes. These microbial consortia perform various biological activities responsible for the nutritional, hygienic, and aromatic qualities of the product. Wine is no exception. Substantial yeast and bacterial biodiversity is observed on grapes, and in both must and wine. The diverse microorganisms present interact throughout the winemaking process. The interactions modulate the hygienic and sensorial properties of the wine. Many studies have been conducted to elucidate the nature of these interactions, with the aim of establishing better control of the two fermentations occurring during wine processing. However, wine is a very complex medium making such studies difficult. In this review, we present the current state of research on microbial interactions in wines. We consider the different kinds of interactions between different microorganisms together with the consequences of these interactions. We underline the major challenges to obtaining a better understanding of how microbes interact. Finally, strategies and methodologies that may help unravel microbe interactions in wine are suggested.

Insight into ethylene interactions with molybdenum suboxide cluster anions from photoelectron spectra of chemifragments

NASA Astrophysics Data System (ADS)

Schaugaard, Richard N.; Topolski, Josey E.; Ray, Manisha; Raghavachari, Krishnan; Jarrold, Caroline Chick

2018-02-01

Recent studies on reactions between MoxOy- cluster anions and H2O/C2H4 mixtures revealed a complex web of addition, hydrogen evolution, and chemifragmentation reactions, with chemifragments unambiguously connected to cluster reactions with C2H4. To gain insight into the molecular-scale interactions along the chemifragmentation pathways, the anion photoelectron (PE) spectra of MoC2H2-, MoC4H4-, MoOC2H2-, and MoO2C2H2- formed directly in MoxOy- + C2H4 (x > 1; y ≥ x) reactions, along with supporting CCSD(T) and density functional theory calculations, are presented and analyzed. The complexes have spectra that are all consistent with η2-acetylene complexes, though for all but MoC4H4-, the possibility that vinylidene complexes are also present cannot be definitively ruled out. Structures that are consistent with the PE spectrum of MoC2H2- differ from the lowest energy structure, suggesting that the fragment formation is under kinetic control. The PE spectrum of MoO2C2H2- additionally exhibits evidence that photodissociation to MoO2- + C2H2 may be occurring. The results suggest that oxidative dehydrogenation of ethylene is initiated by Lewis acid/base interactions between the Mo centers in larger clusters and the π orbitals in ethylene.

The IκBα/NF-κB complex has two hot spots, one at either end of the interface

PubMed Central

Bergqvist, Simon; Ghosh, Gourisankar; Komives, Elizabeth A.

2008-01-01

IκBα binds to and inhibits the transcriptional activity of NF-κB family members via its ankyrin repeat (AR) domain. The binding affinity of IκBα with NF-κB(p50/p65) heterodimers and NF-κB(p65/65) homodimers is in the picomolar range, and in the cell, this results in long half-lives of the complexes. Direct binding experiments have been performed using surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) on a series of truncations and mutations in order to understand what regions of the interface are most important for the tight binding affinity of this complex. We previously showed that interactions between residues 305 and 321 of NF-κB(p65) with the first AR of IκBα are critical for the binding energy. Interactions in this region are responsible for more than 7 kcal/mol of the binding energy. Here we show equally drastic consequences for the binding energy occur upon truncation of even a few residues at the C terminus of IκBα. Thus, the interface actually has two hot spots, one at either end of the elongated and large surface of interaction. These results suggest a “squeeze” mechanism that leads to the extremely high affinity of the IκBα•NF-κB complex through stabilization of the ankyrin repeat domain. PMID:18824506

Interactions between N-acetyl-L-cysteine protected CdTe quantum dots and doxorubicin through spectroscopic method

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

Yang, Xiupei, E-mail: xiupeiyang@163.com; College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637000; Lin, Jia

2015-06-15

Highlights: • CdTe quantum dots with the diameter of 3–5 nm were synthesized in aqueous solution. • The modified CdTe quantum dots showed well fluorescence properties. • The interaction between the CdTe quantum dots and doxorubicin (DR) was investigated. - Abstract: N-acetyl-L-cysteine protected cadmium telluride quantum dots with a diameter of 3–5 nm were synthesized in aqueous solution. The interaction between N-acetyl-L-cysteine/cadmium telluride quantum dots and doxorubicin was investigated by ultraviolet–visible absorption and fluorescence spectroscopy at physiological conditions (pH 7.2, 37 °C). The results indicate that electron transfer has occurred between N-acetyl-L-cysteine/cadmium telluride quantum dots and doxorubicin under light illumination.more » The quantum dots react readily with doxorubicin to form a N-acetyl-L-cysteine/cadmium telluride-quantum dots/doxorubicin complex via electrostatic attraction between the −NH{sub 3}{sup +} moiety of doxorubicin and the −COO{sup −} moiety of N-acetyl-L-cysteine/cadmium telluride quantum dots. The interaction of N-acetyl-L-cysteine/cadmium telluride-quantum dots/doxorubicin complex with bovine serum albumin was studied as well, showing that the complex might induce the conformation change of bovine serum due to changes in microenvironment of bovine serum.« less

A Role for USP7 in DNA Replication

PubMed Central

Jagannathan, Madhav; Nguyen, Tin; Gallo, David; Luthra, Niharika; Brown, Grant W.; Saridakis, Vivian

2014-01-01

The minichromosome maintenance (MCM) complex, which plays multiple important roles in DNA replication, is loaded onto chromatin following mitosis, remains on chromatin until the completion of DNA synthesis, and then is unloaded by a poorly defined mechanism that involves the MCM binding protein (MCM-BP). Here we show that MCM-BP directly interacts with the ubiquitin-specific protease USP7, that this interaction occurs predominantly on chromatin, and that MCM-BP can tether USP7 to MCM proteins. Detailed biochemical and structure analyses of the USP7–MCM-BP interaction showed that the 155PSTS158 MCM-BP sequence mediates critical interactions with the TRAF domain binding pocket of USP7. Analysis of the effects of USP7 knockout on DNA replication revealed that lack of USP7 results in slowed progression through late S phase without globally affecting the fork rate or origin usage. Lack of USP7 also resulted in increased levels of MCM proteins on chromatin, and investigation of the cause of this increase revealed a defect in the dissociation of MCM proteins from chromatin in mid- to late S phase. This role of USP7 mirrors the previously described role for MCM-BP in MCM complex unloading and suggests that USP7 works with MCM-BP to unload MCM complexes from chromatin at the end of S phase. PMID:24190967

Evolution of specificity in cartilaginous fish glycoprotein hormones and receptors.

PubMed

Buechi, Hanna B; Bridgham, Jamie T

2017-05-15

Glycoprotein hormones (GpH) interact very specifically with their receptors to mediate hypothalamic-pituitary-peripheral gland endocrine signaling. Vertebrates typically have three functionally distinct GpH endocrine signaling complexes: follicle-stimulating hormone, luteinizing hormone, and thyroid-stimulating hormone, and their receptors. Each hormone consists of a common α subunit bound to one of three different β subunits. Individual hormone subunits and receptors are present in genomes of early metazoans, and a subset of hormone subunits and receptors has been recently characterized in sea lamprey. However, it remains unclear when the full complement of hormone and receptor protein families first appeared, and when specificity of interactions between GpH hormones and receptors first evolved. Here we present phylogenetic analyses showing that the elephant shark (Callorhinchus milii) genome contains sequences representing the current diversity of all hormone subunits and receptors in these co-evolving protein families. We examined specificity of hormone and receptor interactions using functional assays testing reporter gene activation by elephant shark follicle-stimulating hormone, luteinizing hormone, and thyroid-stimulating hormone receptors. We show highly specific, dose-responsive hormone interactions for all three complexes. Our results suggest that co-evolution of specificity between proteins in these endocrine signaling complexes occurred prior to the divergence of Chondrichthyes from the chordate lineage. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Chromatin loops as allosteric modulators of enhancer-promoter interactions.

PubMed

Doyle, Boryana; Fudenberg, Geoffrey; Imakaev, Maxim; Mirny, Leonid A

2014-10-01

The classic model of eukaryotic gene expression requires direct spatial contact between a distal enhancer and a proximal promoter. Recent Chromosome Conformation Capture (3C) studies show that enhancers and promoters are embedded in a complex network of looping interactions. Here we use a polymer model of chromatin fiber to investigate whether, and to what extent, looping interactions between elements in the vicinity of an enhancer-promoter pair can influence their contact frequency. Our equilibrium polymer simulations show that a chromatin loop, formed by elements flanking either an enhancer or a promoter, suppresses enhancer-promoter interactions, working as an insulator. A loop formed by elements located in the region between an enhancer and a promoter, on the contrary, facilitates their interactions. We find that different mechanisms underlie insulation and facilitation; insulation occurs due to steric exclusion by the loop, and is a global effect, while facilitation occurs due to an effective shortening of the enhancer-promoter genomic distance, and is a local effect. Consistently, we find that these effects manifest quite differently for in silico 3C and microscopy. Our results show that looping interactions that do not directly involve an enhancer-promoter pair can nevertheless significantly modulate their interactions. This phenomenon is analogous to allosteric regulation in proteins, where a conformational change triggered by binding of a regulatory molecule to one site affects the state of another site.

Enhancer Sharing Promotes Neighborhoods of Transcriptional Regulation Across Eukaryotes

PubMed Central

Quintero-Cadena, Porfirio; Sternberg, Paul W.

2016-01-01

Enhancers physically interact with transcriptional promoters, looping over distances that can span multiple regulatory elements. Given that enhancer–promoter (EP) interactions generally occur via common protein complexes, it is unclear whether EP pairing is predominantly deterministic or proximity guided. Here, we present cross-organismic evidence suggesting that most EP pairs are compatible, largely determined by physical proximity rather than specific interactions. By reanalyzing transcriptome datasets, we find that the transcription of gene neighbors is correlated over distances that scale with genome size. We experimentally show that nonspecific EP interactions can explain such correlation, and that EP distance acts as a scaling factor for the transcriptional influence of an enhancer. We propose that enhancer sharing is commonplace among eukaryotes, and that EP distance is an important layer of information in gene regulation. PMID:27799341

Game theoretical framework in determining house prices

NASA Astrophysics Data System (ADS)

Saiddin, Nor Syuhadah; Zaibidi, Nerda Zura; Sulaiman, Nor Intan Saniah; Abidin, Norhaslinda Zainal

2017-11-01

Housing is a vital component in world's economic development as it provides big contribution of the wealth. The issue of high house prices, worrying several parties, especially middle income buyers in Malaysia. Basically, in housing, there are three main parties involved; buyer, property developer and government. Interaction between those parties will give an impact to the housing market, specifically house prices. The complexity of the interaction has increased due to the differences in each party's preferences and interest. In this research, the main objective is to develop the framework of the interactions among those parties using game theoretical approach. To do so, the preferences and target of each party are investigated and their constraints are established. From the framework, it offers some ideas on how the interaction occurs and how it affect the house prices.

Mechanistic insights into avian reovirus p17-modulated suppression of cell-cycle CDK/cyclin complexes and enhancement of p53 and cyclin H interaction.

PubMed

Chiu, Hung-Chuan; Huang, Wei-Ru; Liao, Tsai-Ling; Chi, Pei-I; Nielsen, Brent L; Liu, Jyung-Hurng; Liu, Hung-Jen

2018-06-15

The avian reovirus (ARV) p17 protein is a nucleocytoplasmic shuttling protein. Although we have demonstrated that p17 causes cell growth retardation via activation of p53, the precise mechanisms remains unclear. This is the first report that ARV p17 possesses broad inhibitory effects on cell-cycle CDKs, cyclins, CDK/cyclin complexes, and CDK activating kinase (CAK) activity in various mammalian, avian, and cancer cell lines. Suppression of CDK activity by p17 occurs by direct binding to CDKs, cyclins, and CDK/cyclin complexes, transcriptional downregulation of CDKs, cytoplasmic retention of CDKs and cyclins, and inhibition of CAK activity by promoting p53/cyclin H interaction. p17 binds to CDK/cyclin except for CDK1/cyclin B1 and CDK7/cyclin H complexes. We have determined that the negatively charged 151 LAVxDxDxE/DDGADPN 165 motif in cyclin B1 interacts with a positively charged region of CDK1. p17 mimics the cyclin B1 sequence to compete for CDK1 binding. The PSTAIRE motif is not required for interaction of CDK1/cyclin B1, but is required for other CDK/cyclin complexes. p17 interacts with cyclins by its cyclin-binding motif 125 RXL 127 Sequence and mutagenic analyses of p17 indicated that a 140 WXFD 143 motif and residues D113 and K122 in p17 are critical for CDK2 and CDK6 binding, leading to their sequestration in the cytoplasm. Exogenous expression of p17 significantly enhanced virus replication while p17 mutants with low binding ability to cell-cycle CDKs have no effect on virus yield, suggesting that p17 inhibits cell growth and the cell cycle benefiting virus replication. An in vivo tumorigenesis assay also showed a significant reduction in tumor size. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

T7 RNA Polymerase Functions In Vitro without Clustering

PubMed Central

Finan, Kieran; Torella, Joseph P.; Kapanidis, Achillefs N.; Cook, Peter R.

2012-01-01

Many nucleic acid polymerases function in clusters known as factories. We investigate whether the RNA polymerase (RNAP) of phage T7 also clusters when active. Using ‘pulldowns’ and fluorescence correlation spectroscopy we find that elongation complexes do not interact in vitro with a Kd<1 µM. Chromosome conformation capture also reveals that genes located 100 kb apart on the E. coli chromosome do not associate more frequently when transcribed by T7 RNAP. We conclude that if clustering does occur in vivo, it must be driven by weak interactions, or mediated by a phage-encoded protein. PMID:22768341

Oak savanna restoration in central Iowa: Assessing indicators of forest health for ecological monitoring (PROJECT NC-F-04-02)

Treesearch

Heidi Asbjornsen; Lars Brudvig

2013-01-01

Savanna ecosystems were once a dominant feature of the Midwestern Corn Belt Plains ecoregion, occurring within the dynamic boundary between prairies to the west and forests to the east, and maintained in the landscape by complex interactions between fire, climate, topography, and human activities (Anderson 1998). Characterized by their continuous understory layer and...

Culture, Structure and Leadership Impacts on Gender Inclusion in the Security Sector

DTIC Science & Technology

2017-09-01

culture were outcomes of structural reform. A guided evolution in security sector culture occurred following persistent social pressure, compliance...brought about a change in national and organizational culture to address socially complex issues. As the orchestrators of large successful corporate...challenges them (Jolly 2002). In the process, we are influenced and shaped as we interact with local, national and international information. Likewise, we

Structure of the dimeric exonuclease TREX1 in complex with DNA displays a proline-rich binding site for WW Domains.

PubMed

Brucet, Marina; Querol-Audí, Jordi; Serra, Maria; Ramirez-Espain, Ximena; Bertlik, Kamila; Ruiz, Lidia; Lloberas, Jorge; Macias, Maria J; Fita, Ignacio; Celada, Antonio

2007-05-11

TREX1 is the most abundant mammalian 3' --> 5' DNA exonuclease. It has been described to form part of the SET complex and is responsible for the Aicardi-Goutières syndrome in humans. Here we show that the exonuclease activity is correlated to the binding preferences toward certain DNA sequences. In particular, we have found three motifs that are selected, GAG, ACA, and CTGC. To elucidate how the discrimination occurs, we determined the crystal structures of two murine TREX1 complexes, with a nucleotide product of the exonuclease reaction, and with a single-stranded DNA substrate. Using confocal microscopy, we observed TREX1 both in nuclear and cytoplasmic subcellular compartments. Remarkably, the presence of TREX1 in the nucleus requires the loss of a C-terminal segment, which we named leucine-rich repeat 3. Furthermore, we detected the presence of a conserved proline-rich region on the surface of TREX1. This observation points to interactions with proline-binding domains. The potential interacting motif "PPPVPRPP" does not contain aromatic residues and thus resembles other sequences that select SH3 and/or Group 2 WW domains. By means of nuclear magnetic resonance titration experiments, we show that, indeed, a polyproline peptide derived from the murine TREX1 sequence interacted with the WW2 domain of the elongation transcription factor CA150. Co-immunoprecipitation studies confirmed this interaction with the full-length TREX1 protein, thereby suggesting that TREX1 participates in more functional complexes than previously thought.

[Arterial media calcification in patients with type 2 diabetes mellitus].

PubMed

Belovici, Maria Isabela; Pandele, G I

2008-01-01

Arterial calcification was previously viewed as an inevitable, passive, and degenerative process that occurred at the end stages of atherosclerosis. Recent studies, however, have demonstrated that calcification of arteries is a complex and regulated process. It may occur in conjunction with atherosclerosis or in an isolated form that is commonly associated with diabetes and renal failure. Higher artery calcium scores are associated with increased cardiovascular events, and some aspects of arterial calcification are similar to the biology of forming bone. Arterial calcification can thus be viewed as a distinct inflammatory arteriopathy, much like atherosclerosis and aneurysms, with its own contribution to cardiovascular morbidity and mortality. Current research involves efforts to define the complex interactions between cellular and molecular mediators of arterial calcification and, in particular, the role of endogenous calcification inhibitors. This review discusses the clinical relevance, cellular events, and suspected molecular pathways that control arterial calcification.

Otolaryngology head and neck surgery: an integrative view of the larynx.

PubMed

McCulloch, Timothy M; Van Daele, Douglas; Ciucci, Michelle R

2011-10-01

The glottis is composed of muscular, cartilaginous, and other viscoelastic tissues which perform some of our most important, complex, coordinated, and life-sustaining functions. Dominated by the thyroarytenoid muscles and associated glottic closure muscles, the larynx is involved in respiration, swallowing, voicing, coughing, valsalva, vomiting, laughing, and crying. With respiration continuing in the background, all other "secondary" laryngeal events seamlessly occur. When the delicate balance of coordinating these events is disrupted by disease or disorder, many of these tasks are compromised. Due to the complex innervation of these volitional and reflexive tasks with brainstem central pattern generators, primary sensorimotor areas and importantly, limbic areas, failure can occur due to disease, anatomic compromise, and even emotional state. Understanding the level of sensorimotor control and interaction among systems that share these laryngeal neuromuscular substrates will improve the diagnostic and therapeutic skill of the clinician when treating compromise of laryngeal function. Copyright © 2011 Wiley Periodicals, Inc.

Activated PLC-γ1 is Catalytically Induced at LAT but Activated PLC-γ1 is Localized at both LAT- and TCR-Containing Complexes

PubMed Central

Cruz-Orcutt, Noemi; Vacaflores, Aldo; Connolly, Sean F.; Bunnell, Stephen C.; Houtman, Jon C.D.

2014-01-01

Phospholipase C-γ1 (PLC-γ1) is a key regulator of T cell receptor (TCR)-induced signaling. Activation of the TCR enhances PLC-γ1 enzymatic function, resulting in calcium influx and the activation of PKC family members and RasGRP. The current model is that phosphorylation of LAT tyrosine 132 facilitates the recruitment of PLC-γ1, leading to its activation and function at the LAT complex. In this study, we examined the phosphorylation kinetics of LAT and PLC-γ1 and the cellular localization of activated PLC-γ1. We observed that commencement of the phosphorylation of LAT tyrosine 132 and PLC-γ1 tyrosine 783 occurred simultaneously, supporting the current model. However, once begun, PLC-γ1 activation occurred more rapidly than LAT tyrosine 132. The association of LAT and PLC-γ1 was more transient than the interaction of LAT and Grb2 and a pool of activated PLC-γ1 translocated away from LAT to cellular structures containing the TCR. These studies demonstrate that LAT and PLC-γ1 form transient interactions that catalyze the activation of PLC-γ1, but that activated PLC-γ1 resides in both LAT and TCR clusters. Together, this work highlights that our current model is incomplete and the activation and function of PLC-γ1 in T cells is highly complex. PMID:24412752

Effect of PEG and mPEG-anthracene on tRNA aggregation and particle formation.

PubMed

Froehlich, E; Mandeville, J S; Arnold, D; Kreplak, L; Tajmir-Riahi, H A

2012-01-09

Poly(ethylene glycol) (PEG) and its derivatives are synthetic polymers with major applications in gene and drug delivery systems. Synthetic polymers are also used to transport miRNA and siRNA in vitro. We studied the interaction of tRNA with several PEGs of different compositions, such as PEG 3350, PEG 6000, and mPEG-anthracene under physiological conditions. FTIR, UV-visible, CD, and fluorescence spectroscopic methods as well as atomic force microscopy (AFM) were used to analyze the PEG binding mode, the binding constant, and the effects of polymer complexation on tRNA stability, aggregation, and particle formation. Structural analysis showed that PEG-tRNA interaction occurs via RNA bases and the backbone phosphate group with both hydrophilic and hydrophobic contacts. The overall binding constants of K(PEG 3350-tRNA)= 1.9 (±0.5) × 10(4) M(-1), K(PEG 6000-tRNA) = 8.9 (±1) × 10(4) M(-1), and K(mPEG-anthracene)= 1.2 (±0.40) × 10(3) M(-1) show stronger polymer-RNA complexation by PEG 6000 and by PEG 3350 than the mPEG-anthracene. AFM imaging showed that PEG complexes contain on average one tRNA with PEG 3350, five tRNA with PEG 6000, and ten tRNA molecules with mPEG-anthracene. tRNA aggregation and particle formation occurred at high polymer concentrations, whereas it remains in A-family structure.

;Host-guest; interactions in Captisol®/Coumestrol inclusion complex: UV-vis, FTIR-ATR and Raman studies

NASA Astrophysics Data System (ADS)

Venuti, Valentina; Stancanelli, Rosanna; Acri, Giuseppe; Crupi, Vincenza; Paladini, Giuseppe; Testagrossa, Barbara; Tommasini, Silvana; Ventura, Cinzia Anna; Majolino, Domenico

2017-10-01

The ability of Captisol® (sulphobutylether-β-cyclodextrin, SBE-β-CD), to form inclusion complexes, both in solution and in the solid state, has been tested in order to improve some unfavorable chemical-physical characteristics, such as poor solubility in water, of a bioflavonoid, Coumestrol (Coum), well known for its anti-oxidant, anti-inflammatory, anti-fungal and anti-viral activity. In pure water, a phase-solubility study was carried out to evaluate the enhancement of the solubility of Coum and, therefore, the occurred complexation with the macrocycle. The stoichiometry and the stability constant of the SBE-β-CD/Coum complex were calculated with the phase solubility method and through the Job's plot. After that, the solid SBE-β-CD/Coum complex was prepared utilizing a kneading method. The spectral changes induced by complexation on characteristic vibrational band of Coum were complementary investigated by Fourier transform infrared spectroscopy in attenuated total reflectance geometry (FTIR-ATR) and Raman spectroscopy, putting into evidence the guest chemical groups involved in the "host-guest" interactions responsible of the formation and stabilization of the complex. Particular attention was paid to the Cdbnd O and Osbnd H stretching vibrations, whose temperature-evolution respectively furnished the enthalpy changes associated to the binding of host and guest in solid phase and to the reorganization of the hydrogen bond scheme upon complexation. From the whole set of results, an inclusion geometry is also proposed.

Modeling uranium(VI) adsorption onto montmorillonite under varying carbonate concentrations: A surface complexation model accounting for the spillover effect on surface potential

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

Tournassat, C.; Tinnacher, R. M.; Grangeon, S.

The prediction of U(VI) adsorption onto montmorillonite clay is confounded by the complexities of: (1) the montmorillonite structure in terms of adsorption sites on basal and edge surfaces, and the complex interactions between the electrical double layers at these surfaces, and (2) U(VI) solution speciation, which can include cationic, anionic and neutral species. Previous U(VI)-montmorillonite adsorption and modeling studies have typically expanded classical surface complexation modeling approaches, initially developed for simple oxides, to include both cation exchange and surface complexation reactions. However, previous models have not taken into account the unique characteristics of electrostatic surface potentials that occur at montmorillonitemore » edge sites, where the electrostatic surface potential of basal plane cation exchange sites influences the surface potential of neighboring edge sites (‘spillover’ effect).« less

Supramolecular reactivity in the gas phase: investigating the intrinsic properties of non-covalent complexes.

PubMed

Cera, Luca; Schalley, Christoph A

2014-03-21

The high vacuum inside a mass spectrometer offers unique conditions to broaden our view on the reactivity of supramolecules. Because dynamic exchange processes between complexes are efficiently suppressed, the intrinsic and intramolecular reactivity of the complexes of interest is observed. Besides this, the significantly higher strength of non-covalent interactions in the absence of competing solvent allows processes to occur that are unable to compete in solution. The present review highlights a series of examples illustrating different aspects of supramolecular gas-phase reactivity ranging from the dissociation and formation of covalent bonds in non-covalent complexes through the reactivity in the restricted inner phase of container molecules and step-by-step mechanistic studies of organocatalytic reaction cycles to cage contraction reactions, processes induced by electron capture, and finally dynamic molecular motion within non-covalent complexes as unravelled by hydrogen-deuterium exchange processes performed in the gas phase.

Modeling uranium(VI) adsorption onto montmorillonite under varying carbonate concentrations: A surface complexation model accounting for the spillover effect on surface potential

DOE PAGES

Tournassat, C.; Tinnacher, R. M.; Grangeon, S.; ...

2017-10-06

The prediction of U(VI) adsorption onto montmorillonite clay is confounded by the complexities of: (1) the montmorillonite structure in terms of adsorption sites on basal and edge surfaces, and the complex interactions between the electrical double layers at these surfaces, and (2) U(VI) solution speciation, which can include cationic, anionic and neutral species. Previous U(VI)-montmorillonite adsorption and modeling studies have typically expanded classical surface complexation modeling approaches, initially developed for simple oxides, to include both cation exchange and surface complexation reactions. However, previous models have not taken into account the unique characteristics of electrostatic surface potentials that occur at montmorillonitemore » edge sites, where the electrostatic surface potential of basal plane cation exchange sites influences the surface potential of neighboring edge sites (‘spillover’ effect).« less

Dense power-law networks and simplicial complexes

NASA Astrophysics Data System (ADS)

Courtney, Owen T.; Bianconi, Ginestra

2018-05-01

There is increasing evidence that dense networks occur in on-line social networks, recommendation networks and in the brain. In addition to being dense, these networks are often also scale-free, i.e., their degree distributions follow P (k ) ∝k-γ with γ ∈(1 ,2 ] . Models of growing networks have been successfully employed to produce scale-free networks using preferential attachment, however these models can only produce sparse networks as the numbers of links and nodes being added at each time step is constant. Here we present a modeling framework which produces networks that are both dense and scale-free. The mechanism by which the networks grow in this model is based on the Pitman-Yor process. Variations on the model are able to produce undirected scale-free networks with exponent γ =2 or directed networks with power-law out-degree distribution with tunable exponent γ ∈(1 ,2 ) . We also extend the model to that of directed two-dimensional simplicial complexes. Simplicial complexes are generalization of networks that can encode the many body interactions between the parts of a complex system and as such are becoming increasingly popular to characterize different data sets ranging from social interacting systems to the brain. Our model produces dense directed simplicial complexes with power-law distribution of the generalized out-degrees of the nodes.

Adsorption of Selenium and Strontium on Goethite: EXAFS Study and Surface Complexation Modeling of the Ternary Systems.

PubMed

Nie, Zhe; Finck, Nicolas; Heberling, Frank; Pruessmann, Tim; Liu, Chunli; Lützenkirchen, Johannes

2017-04-04

Knowledge of the geochemical behavior of selenium and strontium is critical for the safe disposal of radioactive wastes. Goethite, as one of the most thermodynamically stable and commonly occurring natural iron oxy-hydroxides, promisingly retains these elements. This work comprehensively studies the adsorption of Se(IV) and Sr(II) on goethite. Starting from electrokinetic measurements, the binary and ternary adsorption systems are investigated and systematically compared via batch experiments, EXAFS analysis, and CD-MUSIC modeling. Se(IV) forms bidentate inner-sphere surface complexes, while Sr(II) is assumed to form outer-sphere complexes at low and intermediate pH and inner-sphere complexes at high pH. Instead of a direct interaction between Se(IV) and Sr(II), our results indicate an electrostatically driven mutual enhancement of adsorption. Adsorption of Sr(II) is promoted by an average factor of 5 within the typical groundwater pH range from 6 to 8 for the concentration range studied here. However, the interaction between Se(IV) and Sr(II) at the surface is two-sided, Se(IV) promotes Sr(II) outer-sphere adsorption, but competes for inner-sphere adsorption sites at high pH. The complexity of surfaces is highlighted by the inability of adsorption models to predict isoelectric points without additional constraints.

Sequential protein association with nascent 60S ribosomal particles.

PubMed

Saveanu, Cosmin; Namane, Abdelkader; Gleizes, Pierre-Emmanuel; Lebreton, Alice; Rousselle, Jean-Claude; Noaillac-Depeyre, Jacqueline; Gas, Nicole; Jacquier, Alain; Fromont-Racine, Micheline

2003-07-01

Ribosome biogenesis in eukaryotes depends on the coordinated action of ribosomal and nonribosomal proteins that guide the assembly of preribosomal particles. These intermediate particles follow a maturation pathway in which important changes in their protein composition occur. The mechanisms involved in the coordinated assembly of the ribosomal particles are poorly understood. We show here that the association of preribosomal factors with pre-60S complexes depends on the presence of earlier factors, a phenomenon essential for ribosome biogenesis. The analysis of the composition of purified preribosomal complexes blocked in maturation at specific steps allowed us to propose a model of sequential protein association with, and dissociation from, early pre-60S complexes for several preribosomal factors such as Mak11, Ssf1, Rlp24, Nog1, and Nog2. The presence of either Ssf1 or Nog2 in complexes that contain the 27SB pre-rRNA defines novel, distinct pre-60S particles that contain the same pre-rRNA intermediates and that differ only by the presence or absence of specific proteins. Physical and functional interactions between Rlp24 and Nog1 revealed that the assembly steps are, at least in part, mediated by direct protein-protein interactions.

The nucleotide exchange factor MGE exerts a key function in the ATP-dependent cycle of mt-Hsp70-Tim44 interaction driving mitochondrial protein import.

PubMed Central

Schneider, H C; Westermann, B; Neupert, W; Brunner, M

1996-01-01

Import of preproteins into the mitochondrial matrix is driven by the ATP-dependent interaction of mt-Hsp70 with the peripheral inner membrane import protein Tim44 and the preprotein in transit. We show that Mge1p, a co-chaperone of mt-Hsp70, plays a key role in the ATP-dependent import reaction cycle in yeast. Our data suggest a cycle in which the mt-Hsp70-Tim44 complex forms with ATP: Mge1p promotes assembly of the complex in the presence of ATP. Hydrolysis of ATP by mt-Hsp70 occurs in complex with Tim44. Mge1p is then required for the dissociation of the ADP form of mt-Hsp70 from Tim44 after release of inorganic phosphate but before release of ADP. ATP hydrolysis and complex dissociation are accompanied by tight binding of mt-Hsp70 to the preprotein in transit. Subsequently, the release of mt-Hsp70 from the polypeptide chain is triggered by Mge1p which promotes release of ADP from mt-Hsp70. Rebinding of ATP to mt-Hsp70 completes the reaction cycle. Images PMID:8918457

Challenges in network science: Applications to infrastructures, climate, social systems and economics

NASA Astrophysics Data System (ADS)

Havlin, S.; Kenett, D. Y.; Ben-Jacob, E.; Bunde, A.; Cohen, R.; Hermann, H.; Kantelhardt, J. W.; Kertész, J.; Kirkpatrick, S.; Kurths, J.; Portugali, J.; Solomon, S.

2012-11-01

Network theory has become one of the most visible theoretical frameworks that can be applied to the description, analysis, understanding, design and repair of multi-level complex systems. Complex networks occur everywhere, in man-made and human social systems, in organic and inorganic matter, from nano to macro scales, and in natural and anthropogenic structures. New applications are developed at an ever-increasing rate and the promise for future growth is high, since increasingly we interact with one another within these vital and complex environments. Despite all the great successes of this field, crucial aspects of multi-level complex systems have been largely ignored. Important challenges of network science are to take into account many of these missing realistic features such as strong coupling between networks (networks are not isolated), the dynamics of networks (networks are not static), interrelationships between structure, dynamics and function of networks, interdependencies in given networks (and other classes of links, including different signs of interactions), and spatial properties (including geographical aspects) of networks. This aim of this paper is to introduce and discuss the challenges that future network science needs to address, and how different disciplines will be accordingly affected.

The soluble extracellular domain of E-cadherin interferes with EPEC adherence via interaction with the Tir:intimin complex.

PubMed

Login, Frédéric H; Jensen, Helene H; Pedersen, Gitte A; Amieva, Manuel R; Nejsum, Lene N

2018-06-19

Enteropathogenic Escherichia coli (EPEC) causes watery diarrhea when colonizing the surface of enterocytes. The translocated intimin receptor (Tir):intimin receptor complex facilitates tight adherence to epithelial cells and formation of actin pedestals beneath EPEC. We found that the host cell adherens junction protein E-cadherin (Ecad) was recruited to EPEC microcolonies. Live-cell and confocal imaging revealed that Ecad recruitment depends on, and occurs after, formation of the Tir:intimin complex. Combinatorial binding experiments using wild-type EPEC, isogenic mutants lacking Tir or intimin, and E. coli expressing intimin showed that the extracellular domain of Ecad binds the bacterial surface in a Tir:intimin-dependent manner. Finally, addition of the soluble extracellular domain of Ecad to the infection medium or depletion of Ecad extracellular domain from the cell surface reduced EPEC adhesion to host cells. Thus, the soluble extracellular domain of Ecad may be used in the design of intervention strategies targeting EPEC adherence to host cells.-Login, F. H., Jensen, H. H., Pedersen, G. A., Amieva, M. R., Nejsum, L. N. The soluble extracellular domain of E-cadherin interferes with EPEC adherence via interaction with the Tir:intimin complex.

Slater-Pauling behavior within quaternary intermetallic borides of the Ti{sub 3}Co{sub 5}B{sub 2} structure-type

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

Burghaus, Jens; Dronskowski, Richard, E-mail: drons@HAL9000.ac.rwth-aachen.d; Miller, Gordon J.

2009-10-15

First-principles, density-functional studies of several intermetallic borides of the general type M{sub 2}M'Ru{sub 5-n}Rh{sub n}B{sub 2} (n=0-5; M=Sc, Ti, Nb; M'=Fe, Co) show that the variation in saturation magnetic moment with valence-electron count follows a Slater-Pauling curve, with a maximum moment occurring typically at 66 valence electrons. The magnetic moments in these compounds occur primarily from the 3d electrons of the magnetically active M' sites, with some contribution from the Ru/Rh sites via magnetic polarization. Electronic DOS curves reveal that a rigid-band approach is a reasonable approximation for the estimation of saturation moments and the analysis of orbital interactions inmore » this family of complex borides. COHP analyses of the M'-M' orbital interactions indicate optimized interactions in the minority spin states for Co-containing phases, but strong bonding interactions remaining in Fe-containing phases. - Graphical abstract: Theoretically determined (spin-polarized LMTO-GGA) local magnetic moments as a function of the chemical valence Z for various intermetallic borides.« less

Toward an Integrative Understanding of Social Behavior: New Models and New Opportunities

PubMed Central

Blumstein, Daniel T.; Ebensperger, Luis A.; Hayes, Loren D.; Vásquez, Rodrigo A.; Ahern, Todd H.; Burger, Joseph Robert; Dolezal, Adam G.; Dosmann, Andy; González-Mariscal, Gabriela; Harris, Breanna N.; Herrera, Emilio A.; Lacey, Eileen A.; Mateo, Jill; McGraw, Lisa A.; Olazábal, Daniel; Ramenofsky, Marilyn; Rubenstein, Dustin R.; Sakhai, Samuel A.; Saltzman, Wendy; Sainz-Borgo, Cristina; Soto-Gamboa, Mauricio; Stewart, Monica L.; Wey, Tina W.; Wingfield, John C.; Young, Larry J.

2010-01-01

Social interactions among conspecifics are a fundamental and adaptively significant component of the biology of numerous species. Such interactions give rise to group living as well as many of the complex forms of cooperation and conflict that occur within animal groups. Although previous conceptual models have focused on the ecological causes and fitness consequences of variation in social interactions, recent developments in endocrinology, neuroscience, and molecular genetics offer exciting opportunities to develop more integrated research programs that will facilitate new insights into the physiological causes and consequences of social variation. Here, we propose an integrative framework of social behavior that emphasizes relationships between ultimate-level function and proximate-level mechanism, thereby providing a foundation for exploring the full diversity of factors that underlie variation in social interactions, and ultimately sociality. In addition to identifying new model systems for the study of human psychopathologies, this framework provides a mechanistic basis for predicting how social behavior will change in response to environmental variation. We argue that the study of non-model organisms is essential for implementing this integrative model of social behavior because such species can be studied simultaneously in the lab and field, thereby allowing integration of rigorously controlled experimental manipulations with detailed observations of the ecological contexts in which interactions among conspecifics occur. PMID:20661457

The interaction of HMGB1 and linker histones occurs through their acidic and basic tails.

PubMed

Cato, Laura; Stott, Katherine; Watson, Matthew; Thomas, Jean O

2008-12-31

H1 and HMGB1 bind to linker DNA in chromatin, in the vicinity of the nucleosome dyad. They appear to have opposing effects on the nucleosome, H1 stabilising it by "sealing" two turns of DNA around the octamer, and HMGB1 destabilising it, probably by bending the adjacent DNA. Their presence in chromatin might be mutually exclusive. Displacement/replacement of one by the other as a result of their highly dynamic binding in vivo might, in principle, involve interactions between them. Chemical cross-linking and gel-filtration show that a 1:1 linker histone/HMGB1 complex is formed, which persists at physiological ionic strength, and that complex formation requires the acidic tail of HMGB1. NMR spectroscopy shows that the linker histone binds, predominantly through its basic C-terminal domain, to the acidic tail of HMGB1, thereby disrupting the interaction of the tail with the DNA-binding faces of the HMG boxes. A potential consequence of this interaction is enhanced DNA binding by HMGB1, and concomitantly lowered affinity of H1 for DNA. In a chromatin context, this might facilitate displacement of H1 by HMGB1.

Solvation of o-hydroxybenzoic acid in pure and modified supercritical carbon dioxide, according to numerical modeling data

NASA Astrophysics Data System (ADS)

Antipova, M. L.; Gurina, D. L.; Odintsova, E. G.; Petrenko, V. E.

2015-08-01

The dissolution of an elementary fragment of crystal structure (an o-hydroxybenzoic acid ( o-HBA) dimer) in both pure and modified supercritical (SC) carbon dioxide by adding methanol (molar fraction, 0.035) at T = 318 K, ρ = 0.7 g/cm3 is simulated. Features of the solvation mechanism in each solvent are revealed. The solvation of o-HBA in pure SC CO2 is shown to occur via electron donor-acceptor interactions. o-HBA forms a solvate complex in modified SC CO2 through hydrogen bonds between the carboxyl group and methanol. The hydroxyl group of o-HBA participates in the formation of an intramolecular hydrogen bond, and not in interactions with the solvent. It is concluded that the o-HBA-methanol complex is a stable molecular structure, and its lifetime is one order of magnitude higher than those of other hydrogen bonds in fluids.

Spectroscopic study of the charge-transfer complexes TiCl4/styrene and TiCl4/polystyrene

NASA Astrophysics Data System (ADS)

Gonçalves, Norberto S.; Noda, Lúcia. K.

2017-10-01

In this work, solutions of TiCl4/styrene and TiCl4/polystyrene charge-transfer complexes in CHCl3 or CDCl3 were investigated by UV-vis, resonance Raman and 1H NMR spectroscopies in order to study their molecular and electronic structures. Both show a yellow colour due to absorption in the 400 nm region, related to a charge-transfer transition. In Raman spectra, as the excitation approaches the resonance region, the primary enhancement of aromatic ring modes was mainly observed, rather than intensification of the vinylic double-bond stretch. Under the experimental conditions it was observed that formation of polystyrene takes place, as showed by 1H NMR spectra, and the most significant interaction occurs at the aromatic ring, as supported by the results from interaction of TiCl4 with polystyrene, as indicated by the charge-transfer band and resonant intensification of the aromatic ring modes.

Complex Pathologic Roles of RIPK1 and RIPK3: Moving Beyond Necroptosis

PubMed Central

Wegner, Kelby W.; Saleh, Danish; Degterev, Alexei

2017-01-01

A process of regulated necrosis, termed necroptosis, has been recognized as a major contributor to cell death and inflammation occurring under a wide range of pathologic settings. The core event in necroptosis is the formation of the detergent-insoluble “necrosome” complex of homologous Ser/Thr kinases Receptor Interacting Kinase 1 (RIPK1) and Receptor Interacting Kinase 3 (RIPK3), which promotes phosphorylation of a key pro-death effector Mixed Lineage Kinase Domain-like (MLKL) by RIPK3. Core necroptosis mediators are under multiple controls, which have been a subject of intense investigation. Additional, non-necroptotic functions of these factors, primarily in controlling apoptosis and inflammatory responses, have also begun to emerge. This review will provide an overview of the current understanding of the human disease relevance of this pathway, and potential therapeutic strategies, targeting necroptosis mediators in various pathologies. PMID:28126382

Interaction of the iron(II) cage complexes with proteins: protein fluorescence quenching study.

PubMed

Losytskyy, Mykhaylo Y; Kovalska, Vladyslava B; Varzatskii, Oleg A; Sergeev, Alexander M; Yarmoluk, Sergiy M; Voloshin, Yan Z

2013-09-01

Interaction of the iron(II) mono- and bis-clathrochelates with bovine serum albumin (BSA), β-lactoglobulin, lysozyme and insulin was studied by the steady-state and time-resolved fluorescent spectroscopies. These cage complexes do not make significant impact on fluorescent properties of β-lactoglobulin, lysozyme and insulin. At the same time, the monoclathrochelates strongly quench a fluorescence intensity of BSA and substantially decrease its excited state lifetime due to their binding to this protein. This occurs due to the excitation energy transfer from a tryptophan residue to a cage molecule or/and to the change of the tryptophan nearest environment caused by either clathrochelate binding or an alteration of the BSA conformation. The effect of the iron(II) bis-clathrochelate on BSA fluorescence is much weaker as compared to its monomacrobicyclic analogs as a result of an increase in its size.

The mechanism of linkage-specific ubiquitin chain elongation by a single-subunit E2

PubMed Central

Wickliffe, Katherine E.; Lorenz, Sonja; Wemmer, David E.; Kuriyan, John; Rape, Michael

2011-01-01

Ubiquitin chains of different topologies trigger distinct functional consequences, including protein degradation and reorganization of complexes. The assembly of most ubiquitin chains is promoted by E2s, yet how these enzymes achieve linkage specificity is poorly understood. We have discovered that the K11-specific Ube2S orients the donor ubiquitin through an essential non-covalent interaction that occurs in addition to the thioester bond at the E2 active site. The E2-donor ubiquitin complex transiently recognizes the acceptor ubiquitin, primarily through electrostatic interactions. The recognition of the acceptor ubiquitin surface around Lys11, but not around other lysines, generates a catalytically competent active site, which is composed of residues of both Ube2S and ubiquitin. Our studies suggest that monomeric E2s promote linkage-specific ubiquitin chain formation through substrate-assisted catalysis. PMID:21376237

Eliminating the mystery from the concept of emergence

PubMed Central

2010-01-01

While some branches of complexity theory are advancing rapidly, the same cannot be said for our understanding of emergence. Despite a complete knowledge of the rules underlying the interactions between the parts of many systems, we are often baffled by their sudden transitions from simple to complex. Here I propose a solution to this conceptual problem. Given that emergence is often the result of many interactions occurring simultaneously in time and space, an ability to intuitively grasp it would require the ability to consciously think in parallel. A simple exercise is used to demonstrate that we do not possess this ability. Our surprise at the behaviour of cellular automata models, and the natural cases of pattern formation they mimic, is then explained from this perspective. This work suggests that the cognitive limitations of the mind can be as significant a barrier to scientific progress as the limitations of our senses. PMID:21212824

A complex of cardiac cytochrome c1 and cytochrome c.

PubMed

Chiang, Y L; Kaminsky, L S; King, T E

1976-01-10

The interactions of cytochrome c1 and cytochrome c from bovine cardiac mitochondria were investigated. Cytochrome c1 and cytochrome c formed a 1:1 molecular complex in aqueous solutions of low ionic strength. The complex was stable to Sephadex G-75 chromatography. The formation and stability of the complex were independent of the oxidation state of the cytochrome components as far as those reactions studied were concerned. The complex was dissociated in solutions of ionic strength higher than 0.07 or pH exceeding 10 and only partially dissociated in 8 M urea. No complexation occurred when cytochrome c was acetylated on 64% of its lysine residues or photooxidized on its 2 methionine residues. Complexes with molecular ratios of less than 1:1 (i.e. more cytochrome c) were obtained when polymerized cytochrome c, or cytochrome c with all lysine residues guanidinated, or a "1-65 heme peptide" from cyanogen bromide cleavage of cytochrome c was used. These results were interpreted to imply that the complex was predominantly maintained by ionic interactions probably involving some of the lysine residues of cytochrome c but with major stabilization dependent on the native conformations of both cytochromes. The reduced complex was autooxidizable with biphasic kinetics with first order rate constants of 6 X 10(-5) and 5 X U0(-5) s-1 but did not react with carbon monoxide. The complex reacted with cyanide and was reduced by ascorbate at about 32% and 40% respectively, of the rates of reaction with cytochrome c alone. The complex was less photoreducible than cytochrome c1 alone. The complex exhibited remarkably different circular dichroic behavior from that of the summation of cytochrome c1 plus cytochrome c. We concluded that when cytochromes c1 and c interacted they underwent dramatic conformational changes resulting in weakening of their heme crevices. All results available would indicate that in the complex cytochrome c1 was bound at the entrance to the heme crevice of cytochrome c on the methionine-80 side of the heme crevice.

FTIR studies of the redox partner interaction in cytochrome P450: the Pdx-P450cam couple.

PubMed

Karyakin, Andrey; Motiejunas, Domantas; Wade, Rebecca C; Jung, Christiane

2007-03-01

Recently we have developed a new approach to study protein-protein interactions using Fourier transform infrared spectroscopy in combination with titration experiments and principal component analysis (FTIR-TPCA). In the present paper we review the FTIR-TPCA results obtained for the interaction between cytochrome P450 and the redox partner protein in two P450 systems, the Pseudomonas putida P450cam (CYP101) with putidaredoxin (P450cam-Pdx), and the Bacillus megaterium P450BM-3 (CYP102) heme domain with the FMN domain (P450BMP-FMND). Both P450 systems reveal similarities in the structural changes that occur upon redox partner complex formation. These involve an increase in beta-sheets and alpha-helix content, a decrease in the population of random coil/3(10)-helix structure, a redistribution of turn structures within the interacting proteins and changes in the protonation states or hydrogen-bonding of amino acid carboxylic side chains. We discuss in detail the P450cam-Pdx interaction in comparison with literature data and conclusions drawn from experiments obtained by other spectroscopic techniques. The results are also interpreted in the context of a 3D structural model of the Pdx-P450cam complex.

Accounting for Intraligand Interactions in Flexible Ligand Docking with a PMF-Based Scoring Function.

PubMed

Lizunov, A Y; Gonchar, A L; Zaitseva, N I; Zosimov, V V

2015-10-26

We analyzed the frequency with which intraligand contacts occurred in a set of 1300 protein-ligand complexes [ Plewczynski et al. J. Comput. Chem. 2011 , 32 , 742 - 755 .]. Our analysis showed that flexible ligands often form intraligand hydrophobic contacts, while intraligand hydrogen bonds are rare. The test set was also thoroughly investigated and classified. We suggest a universal method for enhancement of a scoring function based on a potential of mean force (PMF-based score) by adding a term accounting for intraligand interactions. The method was implemented via in-house developed program, utilizing an Algo_score scoring function [ Ramensky et al. Proteins: Struct., Funct., Genet. 2007 , 69 , 349 - 357 .] based on the Tarasov-Muryshev PMF [ Muryshev et al. J. Comput.-Aided Mol. Des. 2003 , 17 , 597 - 605 .]. The enhancement of the scoring function was shown to significantly improve the docking and scoring quality for flexible ligands in the test set of 1300 protein-ligand complexes [ Plewczynski et al. J. Comput. Chem. 2011 , 32 , 742 - 755 .]. We then investigated the correlation of the docking results with two parameters of intraligand interactions estimation. These parameters are the weight of intraligand interactions and the minimum number of bonds between the ligand atoms required to take their interaction into account.

Design and Mechanical Stability Analysis of the Interaction Region for the Inverse Compton Scattering Gamma-Ray Source Using Finite Element Method

NASA Astrophysics Data System (ADS)

Khizhanok, Andrei

Development of a compact source of high-spectral brilliance and high impulse frequency gamma rays has been in scope of Fermi National Accelerator Laboratory for quite some time. Main goal of the project is to develop a setup to support gamma rays detection test and gamma ray spectroscopy. Potential applications include but not limited to nuclear astrophysics, nuclear medicine, oncology ('gamma knife'). Present work covers multiple interconnected stages of development of the interaction region to ensure high levels of structural strength and vibrational resistance. Inverse Compton scattering is a complex phenomenon, in which charged particle transfers a part of its energy to a photon. It requires extreme precision as the interaction point is estimated to be 20 microm. The slightest deflection of the mirrors will reduce effectiveness of conversion by orders of magnitude. For acceptable conversion efficiency laser cavity also must have >1000 finesse value, which requires a trade-off between size, mechanical stability, complexity, and price of the setup. This work focuses on advantages and weak points of different designs of interaction regions as well as in-depth description of analyses performed. This includes laser cavity amplification and finesse estimates, natural frequency mapping, harmonic analysis. Structural analysis is required as interaction must occur under high vacuum conditions.

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

Klucevsek, K.; Daley, J.; Darshan, M.S.

We have investigated the nuclear import strategies of high-risk HPV18 L2 minor capsid protein. HPV18 L2 interacts with Kap {alpha}{sub 2} adapter, and Kap {beta}{sub 2} and Kap {beta}{sub 3} nuclear import receptors. Moreover, binding of RanGTP to either Kap {beta}{sub 2} or Kap {beta}{sub 3} inhibits their interaction with L2, suggesting that these Kap {beta}/L2 complexes are import competent. Mapping studies show that HPV18 L2 contains two NLSs: in the N-terminus (nNLS) and in the C-terminus (cNLS), both of which can independently mediate nuclear import. Both nNLS and cNLS form a complex with Kap {alpha}{sub 2}{beta}{sub 1} heterodimer andmore » mediate nuclear import via a classical pathway. The nNLS is also essential for the interaction of HPV18 L2 with Kap {beta}{sub 2} and Kap {beta}{sub 3}. Interestingly, both nNLS and cNLS interact with the viral DNA and this DNA binding occurs without nucleotide sequence specificity. Together, the data suggest that HPV18 L2 can interact via its NLSs with several Kaps and the viral DNA and may enter the nucleus via multiple import pathways mediated by Kap {alpha}{sub 2}{beta}{sub 1} heterodimers, Kap {beta}{sub 2} and Kap {beta}{sub 3}.« less

VIV analysis of pipelines under complex span conditions

NASA Astrophysics Data System (ADS)

Wang, James; Steven Wang, F.; Duan, Gang; Jukes, Paul

2009-06-01

Spans occur when a pipeline is laid on a rough undulating seabed or when upheaval buckling occurs due to constrained thermal expansion. This not only results in static and dynamic loads on the flowline at span sections, but also generates vortex induced vibration (VIV), which can lead to fatigue issues. The phenomenon, if not predicted and controlled properly, will negatively affect pipeline integrity, leading to expensive remediation and intervention work. Span analysis can be complicated by: long span lengths, a large number of spans caused by a rough seabed, and multi-span interactions. In addition, the complexity can be more onerous and challenging when soil uncertainty, concrete degradation and unknown residual lay tension are considered in the analysis. This paper describes the latest developments and a ‘state-of-the-art’ finite element analysis program that has been developed to simulate the span response of a flowline under complex boundary and loading conditions. Both VIV and direct wave loading are captured in the analysis and the results are sequentially used for the ultimate limit state (ULS) check and fatigue life calculation.

A protein that interacts with members of the nuclear hormone receptor family: identification and cDNA cloning.

PubMed Central

Zeiner, M; Gehring, U

1995-01-01

In search of proteins which interact with activated steroid hormone receptors, we screened a human liver lambda gt11 expression library with the glucocorticoid receptor. We identified and cloned a cDNA sequence of 1322 bp that encodes a protein of 274 aa. This protein consists predominantly of hydrophilic amino acids and contains a putative bipartite nuclear localization signal. The in vitro translated receptor-associating protein runs in SDS/polyacrylamide gels with an apparent molecular mass of 46 kDa. By use of the bacterially expressed fusion protein with glutathione S-transferase we have found that interaction is not limited to the glucocorticoid receptor but included other nuclear receptors--most notably, the estrogen and thyroid receptors. Binding also occurs with the glucocorticoid receptor complexed with the antiglucocorticoid RU 38486, with the estrogen receptor complexed with the antiestrogen 4-hydroxytamoxifen or ICI 164,384, and even with receptors not complexed with ligand. Association with steroid hormone receptors depends on prior receptor activation--i.e., release from heat shock proteins. The sequence identified here appears to be a general partner protein for nuclear hormone receptors, with the gene being expressed in a variety of mammalian tissues. Images Fig. 2 Fig. 3 Fig. 4 PMID:8524784

Using Biomolecules to Separate Plutonium

NASA Astrophysics Data System (ADS)

Gogolski, Jarrod

Used nuclear fuel has traditionally been treated through chemical separations of the radionuclides for recycle or disposal. This research considers a biological approach to such separations based on a series of complex and interdependent interactions that occur naturally in the human body with plutonium. These biological interactions are mediated by the proteins serum transferrin and the transferrin receptor. Transferrin to plutonium in vivo and can deposit plutonium into cells after interacting with the transferrin receptor protein at the cell surface. Using cerium as a non-radioactive surrogate for plutonium, it was found that cerium(IV) required multiple synergistic anions to bind in the N-lobe of the bilobal transferrin protein, creating a conformation of the cerium-loaded protein that would be unable to interact with the transferrin receptor protein to achieve a separation. The behavior of cerium binding to transferrin has contributed to understanding how plutonium(IV)-transferrin interacts in vivo and in biological separations.

Cross-scale interactions: Quantifying multi-scaled cause–effect relationships in macrosystems

USGS Publications Warehouse

Soranno, Patricia A.; Cheruvelil, Kendra S.; Bissell, Edward G.; Bremigan, Mary T.; Downing, John A.; Fergus, Carol E.; Filstrup, Christopher T.; Henry, Emily N.; Lottig, Noah R.; Stanley, Emily H.; Stow, Craig A.; Tan, Pang-Ning; Wagner, Tyler; Webster, Katherine E.

2014-01-01

Ecologists are increasingly discovering that ecological processes are made up of components that are multi-scaled in space and time. Some of the most complex of these processes are cross-scale interactions (CSIs), which occur when components interact across scales. When undetected, such interactions may cause errors in extrapolation from one region to another. CSIs, particularly those that include a regional scaled component, have not been systematically investigated or even reported because of the challenges of acquiring data at sufficiently broad spatial extents. We present an approach for quantifying CSIs and apply it to a case study investigating one such interaction, between local and regional scaled land-use drivers of lake phosphorus. Ultimately, our approach for investigating CSIs can serve as a basis for efforts to understand a wide variety of multi-scaled problems such as climate change, land-use/land-cover change, and invasive species.

Agent-based modeling: a new approach for theory building in social psychology.

PubMed

Smith, Eliot R; Conrey, Frederica R

2007-02-01

Most social and psychological phenomena occur not as the result of isolated decisions by individuals but rather as the result of repeated interactions between multiple individuals over time. Yet the theory-building and modeling techniques most commonly used in social psychology are less than ideal for understanding such dynamic and interactive processes. This article describes an alternative approach to theory building, agent-based modeling (ABM), which involves simulation of large numbers of autonomous agents that interact with each other and with a simulated environment and the observation of emergent patterns from their interactions. The authors believe that the ABM approach is better able than prevailing approaches in the field, variable-based modeling (VBM) techniques such as causal modeling, to capture types of complex, dynamic, interactive processes so important in the social world. The article elaborates several important contrasts between ABM and VBM and offers specific recommendations for learning more and applying the ABM approach.

Optical micromanipulation of nanoparticles and cells inside living zebrafish.

PubMed

Johansen, Patrick Lie; Fenaroli, Federico; Evensen, Lasse; Griffiths, Gareth; Koster, Gerbrand

2016-03-21

Regulation of biological processes is often based on physical interactions between cells and their microenvironment. To unravel how and where interactions occur, micromanipulation methods can be used that offer high-precision control over the duration, position and magnitude of interactions. However, lacking an in vivo system, micromanipulation has generally been done with cells in vitro, which may not reflect the complex in vivo situation inside multicellular organisms. Here using optical tweezers we demonstrate micromanipulation throughout the transparent zebrafish embryo. We show that different cells, as well as injected nanoparticles and bacteria can be trapped and that adhesion properties and membrane deformation of endothelium and macrophages can be analysed. This non-invasive micromanipulation inside a whole-organism gives direct insights into cell interactions that are not accessible using existing approaches. Potential applications include screening of nanoparticle-cell interactions for cancer therapy or tissue invasion studies in cancer and infection biology.

Analysis of compaction shock interactions during DDT of low density HMX

NASA Astrophysics Data System (ADS)

Rao, Pratap T.; Gonthier, Keith A.

2017-01-01

Deflagration-to-Detonation Transition (DDT) in confined, low density granular HMX occurs by a complex mechanism that involves compaction shock interactions within the material. Piston driven DDT experiments indicate that detonation is abruptly triggered by the interaction of a strong combustion-supported secondary shock and a piston-supported primary (input) shock, where the nature of the interaction depends on initial packing density and primary shock strength. These interactions influence transition by affecting dissipative heating within the microstructure during pore collapse. Inert meso-scale simulations of successive shock loading of low density HMX are performed to examine how dissipation and hot-spot formation are affected by the initial density, and the primary and secondary shock strengths. This information is used to formulate an ignition and burn model for low density HMX that accounts for the effect of shock densensitization on burn. Preliminary DDT predictions are presented that illustrate how primary shock strength affects the transition mechanism.

Acceleration of electrons in strong beam-plasma interactions

NASA Technical Reports Server (NTRS)

Wilhelm, K.; Bernstein, W.; Kellogg, P. J.; Whalen, B. A.

1984-01-01

The effects of strong beam-plasma interactions on the electron population of the upper atmosphere have been investigated in an electron acceleration experiment performed with a sounding rocket. The rocket carried the Several Complex Experiments (SCEX) payload which included an electron accelerator, three disposable 'throwaway' detectors (TADs), and a stepped electron energy analyzer. The payload was launched in an auroral arc over the rocket at altitudes of 157 and 178 km, respectively. The performance characteristics of the instruments are discussed in detail. The data are combined with the results of laboratory measurements and show that electrons with energies of at least two and probably four times the injection energy of 2 keV were observed during strong beam-plasma interaction events. The interaction events occurred at pitch angles of 54 and 126 degrees. On the basis of the data it is proposed that the superenergization of the electrons is correlated with the length of the beam-plasma interaction region.

A novel germ cell protein, SPIF (sperm PKA interacting factor), is essential for the formation of a PKA/TCP11 complex that undergoes conformational and phosphorylation changes upon capacitation.

PubMed

Stanger, Simone J; Law, Estelle A; Jamsai, Duangporn; O'Bryan, Moira K; Nixon, Brett; McLaughlin, Eileen A; Aitken, R John; Roman, Shaun D

2016-08-01

Spermatozoa require the process of capacitation to enable them to fertilize an egg. PKA is crucial to capacitation and the development of hyperactivated motility. Sperm PKA is activated by cAMP generated by the germ cell-enriched adenylyl cyclase encoded by Adcy10 Male mice lacking Adcy10 are sterile, because their spermatozoa are immotile. The current study was designed to identify binding partners of the sperm-specific (Cα2) catalytic subunit of PKA (PRKACA) by using it as the "bait" in a yeast 2-hybrid system. This approach was used to identify a novel germ cell-enriched protein, sperm PKA interacting factor (SPIF), in 25% of the positive clones. Homozygous Spif-null mice were embryonically lethal. SPIF was coexpressed and coregulated with PRKACA and with t-complex protein (TCP)-11, a protein associated with PKA signaling. We established that these 3 proteins form part of a novel complex in mouse spermatozoa. Upon capacitation, the SPIF protein becomes tyrosine phosphorylated in >95% of sperm. An apparent molecular rearrangement in the complex occurs, bringing PRKACA and TCP11 into proximity. Taken together, these results suggest a role for the novel complex of SPIF, PRKACA, and TCP11 during sperm capacitation, fertilization, and embryogenesis.-Stanger, S. J., Law, E. A., Jamsai, D., O'Bryan, M. K., Nixon, B., McLaughlin, E. A., Aitken, R. J., Roman, S. D. A novel germ cell protein, SPIF (sperm PKA interacting factor), is essential for the formation of a PKA/TCP11 complex that undergoes conformational and phosphorylation changes upon capacitation. © FASEB.

Low-Energy Collisions of Protonated Enantiopure Amino Acids with Chiral Target Gases

NASA Astrophysics Data System (ADS)

Kulyk, K.; Rebrov, O.; Ryding, M.; Thomas, R. D.; Uggerud, E.; Larsson, M.

2017-12-01

Here we report on the gas-phase interactions between protonated enantiopure amino acids ( l- and d-enantiomers of Met, Phe, and Trp) and chiral target gases [( R)- and ( S)-2-butanol, and ( S)-1-phenylethanol] in 0.1-10.0 eV low-energy collisions. Two major processes are seen to occur over this collision energy regime, collision-induced dissociation and ion-molecule complex formation. Both processes were found to be independent of the stereo-chemical composition of the interacting ions and targets. These data shed light on the currently debated mechanisms of gas-phase chiral selectivity by demonstrating the inapplicability of the three-point model to these interactions, at least under single collision conditions. [Figure not available: see fulltext.

Computational pathology: Exploring the spatial dimension of tumor ecology.

PubMed

Nawaz, Sidra; Yuan, Yinyin

2016-09-28

Tumors are evolving ecosystems where cancer subclones and the microenvironment interact. This is analogous to interaction dynamics between species in their natural habitats, which is a prime area of study in ecology. Spatial statistics are frequently used in ecological studies to infer complex relations including predator-prey, resource dependency and co-evolution. Recently, the emerging field of computational pathology has enabled high-throughput spatial analysis by using image processing to identify different cell types and their locations within histological tumor samples. We discuss how these data may be analyzed with spatial statistics used in ecology to reveal patterns and advance our understanding of ecological interactions occurring among cancer cells and their microenvironment. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Bioactive Molecules in Soil Ecosystems: Masters of the Underground

PubMed Central

Zhuang, Xuliang; Gao, Jie; Ma, Anzhou; Fu, Shenglei; Zhuang, Guoqiang

2013-01-01

Complex biological and ecological processes occur in the rhizosphere through ecosystem-level interactions between roots, microorganisms and soil fauna. Over the past decade, studies of the rhizosphere have revealed that when roots, microorganisms and soil fauna physically contact one another, bioactive molecular exchanges often mediate these interactions as intercellular signal, which prepare the partners for successful interactions. Despite the importance of bioactive molecules in sustainable agriculture, little is known of their numerous functions, and improving plant health and productivity by altering ecological processes remains difficult. In this review, we describe the major bioactive molecules present in below-ground ecosystems (i.e., flavonoids, exopolysaccharides, antibiotics and quorum-sensing signals), and we discuss how these molecules affect microbial communities, nutrient availability and plant defense responses. PMID:23615474

a System Dynamics Approach for Looking at the Human and Environmental Interactions of Community-Based Irrigation Systems in New Mexico

NASA Astrophysics Data System (ADS)

Ochoa, C. G.; Tidwell, V. C.

2012-12-01

In the arid southwestern United States community water management systems have adapted to cope with climate variability and with socio-cultural and economic changes that have occurred since the establishment of these systems more than 300 years ago. In New Mexico, the community-based irrigation systems were established by Spanish settlers and have endured climate variability in the form of low levels of precipitation and have prevailed over important socio-political changes including the transfer of territory between Spain and Mexico, and between Mexico and the United States. Because of their inherent nature of integrating land and water use with society involvement these community-based systems have multiple and complex economic, ecological, and cultural interactions. Current urban population growth and more variable climate conditions are adding pressure to the survival of these systems. We are conducting a multi-disciplinary research project that focuses on characterizing these intrinsically complex human and natural interactions in three community-based irrigation systems in northern New Mexico. We are using a system dynamics approach to integrate different hydrological, ecological, socio-cultural and economic aspects of these three irrigation systems. Coupled with intensive field data collection, we are building a system dynamics model that will enable us to simulate important linkages and interactions between environmental and human elements occurring in each of these water management systems. We will test different climate variability and population growth scenarios and the expectation is that we will be able to identify critical tipping points of these systems. Results from this model can be used to inform policy recommendations relevant to the environment and to urban and agricultural land use planning in the arid southwestern United States.

Electrostatic roles in electron transfer from [NiFe] hydrogenase to cytochrome c3 from Desulfovibrio vulgaris Miyazaki F.

PubMed

Sugimoto, Yu; Kitazumi, Yuki; Shirai, Osamu; Nishikawa, Koji; Higuchi, Yoshiki; Yamamoto, Masahiro; Kano, Kenji

2017-05-01

Electrostatic interactions between proteins are key factors that govern the association and reaction rate. We spectroscopically determine the second-order reaction rate constant (k) of electron transfer from [NiFe] hydrogenase (H 2 ase) to cytochrome (cyt) c 3 at various ionic strengths (I). The k value decreases with I. To analyze the results, we develop a semi-analytical formula for I dependence of k based on the assumptions that molecules are spherical and the reaction proceeds via a transition state. Fitting of the formula to the experimental data reveals that the interaction occurs in limited regions with opposite charges and with radii much smaller than those estimated from crystal structures. This suggests that local charges in H 2 ase and cyt c 3 play important roles in the reaction. Although the crystallographic data indicate a positive electrostatic potential over almost the entire surface of the proteins, there exists a small region with negative potential on H 2 ase at which the electron transfer from H 2 ase to cyt c 3 may occur. This local negative potential region is identical to the hypothetical interaction sphere predicted by the analysis. Furthermore, I dependence of k is predicted by the Adaptive Poisson-Boltzmann Solver considering all charges of the amino acids in the proteins and the configuration of H 2 ase/cyt c 3 complex. The calculation reproduces the experimental results except at extremely low I. These results indicate that the stabilization derived from the local electrostatic interaction in the H 2 ase/cyt c 3 complex overcomes the destabilization derived from the electrostatic repulsion of the overall positive charge of both proteins. Copyright © 2017 Elsevier B.V. All rights reserved.

Straining and wrinkling processes during turbulence-premixed flame interaction measured using temporally-resolved diagnostics

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

Steinberg, Adam M.; Driscoll, James F.

2009-12-15

The dynamical processes of flame surface straining and wrinkling that occur as turbulence interacts with a premixed flame were measured using cinema-stereoscopic PIV (CS-PIV) and orthogonal-plane cinema-stereoscopic PIV (OPCS-PIV). These diagnostics provided temporally resolved measurements of turbulence-flame interaction at frame rates of up to 3 kHz and spatial resolutions as small as 280{mu} m. Previous descriptions of flame straining and wrinkling have typically been derived based on a canonical interaction between a pair of counter-rotating vortices and a planar flame surface. However, it was found that this configuration did not properly represent real turbulence-flame interaction. Interactions resembling the canonical configurationmore » were observed in less than 10% of the recorded frames. Instead, straining and wrinkling were generally caused more geometrically complex turbulence, consisting of large groups of structures that could be multiply curved and intertwined. The effect of the interaction was highly dependent on the interaction geometry. Furthermore, even when the turbulence did exist in the canonical geometry, the straining and wrinkling of the flame surface were not well characterized by the vortical structures. A new mechanistic description of the turbulence-flame interaction was therefore identified and confirmed by the measurements. In this description, flame surface straining is caused by coherent structures of fluid-dynamic strain-rate (strain-rate structures). The role of vortical structures is to curve existing flame surface, creating wrinkles. By simultaneously considering both forms of turbulent structure, turbulence-flame interactions in both the canonical configuration and more complex geometries could be understood. (author)« less

Proton NMR spectroscopic characterization of binary and ternary complexes of cobalt(II) carboxypeptidase A with inhibitors

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

Bertini, I.; Luchinat, C.; Messori, L.

The binding of L- and D-phenylalanine and carboxylate inhibitors to cobalt(II)-substituted carboxypeptidase A, Co(II)CPD (E), in the presence and absence of pseudohalogens (X = N/sub 3//sup -/, NCO/sup -/, and NCS/sup -/) has been studied by /sup 1/H NMR spectroscopy. This technique monitors the proton signals of histidine residues bound to cobalt(II) and is therefore sensitive to the interactions of inhibitors that perturb the coordination sphere of the metal. Enzyme-inhibitor complexes, E/times/I, E/times/I/sub 2/, and E/times/I/times/X, each with characteristic NMR features, have been identified. The NMR data suggest that when the carboxylate group of a substrate of inhibitor binds atmore » the active site, a conformational change occurs that allows a second ligand molecule to bind to the metal ion, altering its coordination sphere and thereby attenuating the bidentate behavior of Glu-72. The /sup 1/H NMR signals also reflect alterations in the histidine interactions with the metal upon inhibitor binding. Isotropic shifts in the signals for the C-4 (c) and N protons (a) of one of the histidine ligands are readily observed in all of these complexes. These signals are relatively constant for all E/times/I and E/times/I/times/X complexes, indicating that this ligand is in a relatively fixed or buried conformation. However in the 2:1 carboxylate inhibitor (E/times/I/sub 2/) complexes, both signals are shifted upfield, suggesting a disturbance in the interaction of this histidine with the metal.« less

Novel self-assembled mesalamine-sucralfate complexes: preparation, characterization, and formulation aspects.

PubMed

Ispas-Szabo, Pompilia; Friciu, Mihaela Maria; Nguyen, Phuong; Dumoulin, Yves; Mateescu, Mircea Alexandru

2016-01-01

Two well-known active agents, mesalamine (MES) and sucralfate (SUC), were investigated for possible utilization as fixed-dose combination product. The anti-inflammatory action of MES in association with bioadhesiveness and mucosal healing properties of SUC were considered promising for the development of a new compound containing both molecules, aimed as an improved treatment of ulcerative colitis. The present study investigates the capacity of the two active agents to interact and generate a new and stable entity via self-assembling. Spray-drying was used to co-process the two active principles from an aqueous mixture where the ratio MES:SUC was in the range 25:75, 50:50, and 75:25. The structural data (X-Ray, FTIR, SEM, DSC, and (1)H NMR) have shown that MES and SUC are interacting leading to complexes with properties differing from those of each separate active agent and from their physical blends. (1)H NMR results indicated that complexation occurred when the aqueous suspensions of drugs were mixed, prior to spray-drying. Drug-drug self-assembling was the driving mechanism in the formation of the new entity. Based on the structural data, a hypothetical structure of the complex was proposed. Co-processing of MES and SUC represents a simple and useful procedure to prepare new self-assembled compounds by valorizing the ionic interactions between the two entities. Preliminary studies with oral solid dosage forms based on MES-SUC complexes tested in vitro have shown a controlled MES release, opening the perspective of a new colon-targeted delivery system and a novel class of compounds with therapeutic application in inflammatory bowel diseases.

Beyond Control Panels: Direct Manipulation for Visual Analytics

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

Endert, Alexander; Bradel, Lauren; North, Chris

2013-07-19

Information Visualization strives to provide visual representations through which users can think about and gain insight into information. By leveraging the visual and cognitive systems of humans, complex relationships and phenomena occurring within datasets can be uncovered by exploring information visually. Interaction metaphors for such visualizations are designed to enable users direct control over the filters, queries, and other parameters controlling how the data is visually represented. Through the evolution of information visualization, more complex mathematical and data analytic models are being used to visualize relationships and patterns in data – creating the field of Visual Analytics. However, the expectationsmore » for how users interact with these visualizations has remained largely unchanged – focused primarily on the direct manipulation of parameters of the underlying mathematical models. In this article we present an opportunity to evolve the methodology for user interaction from the direct manipulation of parameters through visual control panels, to interactions designed specifically for visual analytic systems. Instead of focusing on traditional direct manipulation of mathematical parameters, the evolution of the field can be realized through direct manipulation within the visual representation – where users can not only gain insight, but also interact. This article describes future directions and research challenges that fundamentally change the meaning of direct manipulation with regards to visual analytics, advancing the Science of Interaction.« less

Complexity in pH-Dependent Ribozyme Kinetics: Dark pKa Shifts and Wavy Rate-pH Profiles.

PubMed

Frankel, Erica A; Bevilacqua, Philip C

2018-02-06

Charged bases occur in RNA enzymes, or ribozymes, where they play key roles in catalysis. Cationic bases donate protons and perform electrostatic catalysis, while anionic bases accept protons. We previously published simulations of rate-pH profiles for ribozymes in terms of species plots for the general acid and general base that have been useful for understanding how ribozymes respond to pH. In that study, we did not consider interaction between the general acid and general base or interaction with other species on the RNA. Since that report, diverse small ribozyme classes have been discovered, many of which have charged nucleobases or metal ions in the active site that can either directly interact and participate in catalysis or indirectly interact as "influencers". Herein, we simulate experimental rate-pH profiles in terms of species plots in which reverse protonated charged nucleobases interact. These analyses uncover two surprising features of pH-dependent enzyme kinetics. (1) Cooperativity between the general acid and general base enhances population of the functional forms of a ribozyme and manifests itself as hidden or "dark" pK a shifts, real pK a shifts that accelerate the reaction but are not readily observed by standard experimental approaches, and (2) influencers favorably shift the pK a s of proton-transferring nucleobases and manifest themselves as "wavy" rate-pH profiles. We identify parallels with the protein enzyme literature, including reverse protonation and wavelike behavior, while pointing out that RNA is more prone to reverse protonation. The complexities uncovered, which arise from simple pairwise interactions, should aid deconvolution of complex rate-pH profiles for RNA and protein enzymes and suggest veiled catalytic devices for promoting catalysis that can be tested by experiment and calculation.

Electrostatic Steering Accelerates C3d:CR2 Association

PubMed Central

2016-01-01

Electrostatic effects are ubiquitous in protein interactions and are found to be pervasive in the complement system as well. The interaction between complement fragment C3d and complement receptor 2 (CR2) has evolved to become a link between innate and adaptive immunity. Electrostatic interactions have been suggested to be the driving factor for the association of the C3d:CR2 complex. In this study, we investigate the effects of ionic strength and mutagenesis on the association of C3d:CR2 through Brownian dynamics simulations. We demonstrate that the formation of the C3d:CR2 complex is ionic strength-dependent, suggesting the presence of long-range electrostatic steering that accelerates the complex formation. Electrostatic steering occurs through the interaction of an acidic surface patch in C3d and the positively charged CR2 and is supported by the effects of mutations within the acidic patch of C3d that slow or diminish association. Our data are in agreement with previous experimental mutagenesis and binding studies and computational studies. Although the C3d acidic patch may be locally destabilizing because of unfavorable Coulombic interactions of like charges, it contributes to the acceleration of association. Therefore, acceleration of function through electrostatic steering takes precedence to stability. The site of interaction between C3d and CR2 has been the target for delivery of CR2-bound nanoparticle, antibody, and small molecule biomarkers, as well as potential therapeutics. A detailed knowledge of the physicochemical basis of C3d:CR2 association may be necessary to accelerate biomarker and drug discovery efforts. PMID:27092816

Studies of interaction of emodin and DNA in the presence of ethidium bromide by spectroscopic method

NASA Astrophysics Data System (ADS)

Bi, Shuyun; Zhang, Hanqi; Qiao, Chunyu; Sun, Ying; Liu, Chunming

2008-01-01

Emodin interacting with deoxyribonucleic acid (DNA) has been studied by different spectroscopic techniques, such as fluorescence, ultraviolet and visible (UV-vis), and fourier transform infared (FT-IR) spectroscopies, using ethidium bromide (EB) as a fluorescence probe of DNA. The decrease in the fluorescence of DNA-EB system on addition of emodin shows that the fluorescence quenching of DNA-EB complex by emodin occurs. The binding constants of emodin with DNA in the presence of EB are 6.02 × 10 4, 9.20 × 10 4 and 1.17 × 10 5 L mol -1 at 20, 35 and 50 °C, respectively. FT-IR spectrum further suggests that both the phosphate groups and the bases of DNA react with emodin. The reaction of DNA with emodin in the presence of EB is affected by ionic strength and temperature. The values of melting temperature ( Tm) of DNA-EB complex and emodin-DNA-EB complexes were determined, respectively. From the experiment evidences, the major binding mode of emodin with DNA should be the groove binding.

Impact of environment on dynamics of exciton complexes in a WS2 monolayer

NASA Astrophysics Data System (ADS)

Jakubczyk, Tomasz; Nogajewski, Karol; Molas, Maciej R.; Bartos, Miroslav; Langbein, Wolfgang; Potemski, Marek; Kasprzak, Jacek

2018-07-01

Scientific curiosity to uncover original optical properties and functionalities of atomically thin semiconductors, stemming from unusual Coulomb interactions in the two-dimensional geometry and multi-valley band structure, drives the research on monolayers of transition metal dichalcogenides (TMDs). While recent works ascertained the exotic energetic schemes of exciton complexes in TMDs, we here infer their unusual coherent dynamics occurring on subpicosecond time scale. The dynamics is largely affected by the disorder landscape on the submicron scale, thus can be uncovered using four-wave mixing in the frequency domain, which enables microscopic investigations and imaging. Focusing on a WS2 monolayer, we observe that exciton coherence is lost primarily due to interaction with phonons and relaxation processes towards optically dark excitonic states. Notably, when temperature is low and disorder weak, excitons large coherence volume results in enhanced oscillator strength, allowing to reach the regime of radiatively limited dephasing. Additionally, we observe long valley coherence for the negatively charged exciton complex. We therefore elucidate the crucial role of exciton environment in the TMDs on its dynamics and show that revealed mechanisms are ubiquitous within this family.

Interaction of plasticity and circuit organization during the acquisition of cerebellum-dependent motor learning

PubMed Central

Yang, Yan; Lisberger, Stephen G

2013-01-01

Motor learning occurs through interactions between the cerebellar circuit and cellular plasticity at different sites. Previous work has established plasticity in brain slices and suggested plausible sites of behavioral learning. We now reveal what actually happens in the cerebellum during short-term learning. We monitor the expression of plasticity in the simple-spike firing of cerebellar Purkinje cells during trial-over-trial learning in smooth pursuit eye movements of monkeys. Our findings imply that: 1) a single complex-spike response driven by one instruction for learning causes short-term plasticity in a Purkinje cell’s mossy fiber/parallel-fiber input pathways; 2) complex-spike responses and simple-spike firing rate are correlated across the Purkinje cell population; and 3) simple-spike firing rate at the time of an instruction for learning modulates the probability of a complex-spike response, possibly through a disynaptic feedback pathway to the inferior olive. These mechanisms may participate in long-term motor learning. DOI: http://dx.doi.org/10.7554/eLife.01574.001 PMID:24381248

Free-Energy Landscape of Protein-Ligand Interactions Coupled with Protein Structural Changes.

PubMed

Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

2017-02-02

Protein-ligand interactions are frequently coupled with protein structural changes. Focusing on the coupling, we present the free-energy surface (FES) of the ligand-binding process for glutamine-binding protein (GlnBP) and its ligand, glutamine, in which glutamine binding accompanies large-scale domain closure. All-atom simulations were performed in explicit solvents by multiscale enhanced sampling (MSES), which adopts a multicopy and multiscale scheme to achieve enhanced sampling of systems with a large number of degrees of freedom. The structural ensemble derived from the MSES simulation yielded the FES of the coupling, described in terms of both the ligand's and protein's degrees of freedom at atomic resolution, and revealed the tight coupling between the two degrees of freedom. The derived FES led to the determination of definite structural states, which suggested the dominant pathways of glutamine binding to GlnBP: first, glutamine migrates via diffusion to form a dominant encounter complex with Arg75 on the large domain of GlnBP, through strong polar interactions. Subsequently, the closing motion of GlnBP occurs to form ligand interactions with the small domain, finally completing the native-specific complex structure. The formation of hydrogen bonds between glutamine and the small domain is considered to be a rate-limiting step, inducing desolvation of the protein-ligand interface to form the specific native complex. The key interactions to attain high specificity for glutamine, the "door keeper" existing between the two domains (Asp10-Lys115) and the "hydrophobic sandwich" formed between the ligand glutamine and Phe13/Phe50, have been successfully mapped on the pathway derived from the FES.

Structural analysis of intermolecular interactions in the kinesin adaptor complex fasciculation and elongation protein zeta 1/ short coiled-coil protein (FEZ1/SCOCO).

PubMed

Alborghetti, Marcos Rodrigo; Furlan, Ariane da Silva; da Silva, Júlio César; Sforça, Maurício Luís; Honorato, Rodrigo Vargas; Granato, Daniela Campos; dos Santos Migueleti, Deivid Lucas; Neves, Jorge L; de Oliveira, Paulo Sergio Lopes; Paes-Leme, Adriana Franco; Zeri, Ana Carolina de Mattos; de Torriani, Iris Concepcion Linares; Kobarg, Jörg

2013-01-01

Cytoskeleton and protein trafficking processes, including vesicle transport to synapses, are key processes in neuronal differentiation and axon outgrowth. The human protein FEZ1 (fasciculation and elongation protein zeta 1 / UNC-76, in C. elegans), SCOCO (short coiled-coil protein / UNC-69) and kinesins (e.g. kinesin heavy chain / UNC116) are involved in these processes. Exploiting the feature of FEZ1 protein as a bivalent adapter of transport mediated by kinesins and FEZ1 protein interaction with SCOCO (proteins involved in the same path of axonal growth), we investigated the structural aspects of intermolecular interactions involved in this complex formation by NMR (Nuclear Magnetic Resonance), cross-linking coupled with mass spectrometry (MS), SAXS (Small Angle X-ray Scattering) and molecular modelling. The topology of homodimerization was accessed through NMR (Nuclear Magnetic Resonance) studies of the region involved in this process, corresponding to FEZ1 (92-194). Through studies involving the protein in its monomeric configuration (reduced) and dimeric state, we propose that homodimerization occurs with FEZ1 chains oriented in an anti-parallel topology. We demonstrate that the interaction interface of FEZ1 and SCOCO defined by MS and computational modelling is in accordance with that previously demonstrated for UNC-76 and UNC-69. SAXS and literature data support a heterotetrameric complex model. These data provide details about the interaction interfaces probably involved in the transport machinery assembly and open perspectives to understand and interfere in this assembly and its involvement in neuronal differentiation and axon outgrowth.

Structural Analysis of Intermolecular Interactions in the Kinesin Adaptor Complex Fasciculation and Elongation Protein Zeta 1/ Short Coiled-Coil Protein (FEZ1/SCOCO)

PubMed Central

da Silva, Júlio César; Sforça, Maurício Luís; Honorato, Rodrigo Vargas; Granato, Daniela Campos; dos Santos Migueleti, Deivid Lucas; Neves, Jorge L.; de Oliveira, Paulo Sergio Lopes; Paes-Leme, Adriana Franco; Zeri, Ana Carolina de Mattos; de Torriani, Iris Concepcion Linares; Kobarg, Jörg

2013-01-01

Cytoskeleton and protein trafficking processes, including vesicle transport to synapses, are key processes in neuronal differentiation and axon outgrowth. The human protein FEZ1 (fasciculation and elongation protein zeta 1 / UNC-76, in C. elegans), SCOCO (short coiled-coil protein / UNC-69) and kinesins (e.g. kinesin heavy chain / UNC116) are involved in these processes. Exploiting the feature of FEZ1 protein as a bivalent adapter of transport mediated by kinesins and FEZ1 protein interaction with SCOCO (proteins involved in the same path of axonal growth), we investigated the structural aspects of intermolecular interactions involved in this complex formation by NMR (Nuclear Magnetic Resonance), cross-linking coupled with mass spectrometry (MS), SAXS (Small Angle X-ray Scattering) and molecular modelling. The topology of homodimerization was accessed through NMR (Nuclear Magnetic Resonance) studies of the region involved in this process, corresponding to FEZ1 (92-194). Through studies involving the protein in its monomeric configuration (reduced) and dimeric state, we propose that homodimerization occurs with FEZ1 chains oriented in an anti-parallel topology. We demonstrate that the interaction interface of FEZ1 and SCOCO defined by MS and computational modelling is in accordance with that previously demonstrated for UNC-76 and UNC-69. SAXS and literature data support a heterotetrameric complex model. These data provide details about the interaction interfaces probably involved in the transport machinery assembly and open perspectives to understand and interfere in this assembly and its involvement in neuronal differentiation and axon outgrowth. PMID:24116125

The social life of laughter

PubMed Central

Scott, Sophie; Lavan, Nadine; Chen, Sinead; McGettigan, Carolyn

2014-01-01

Laughter is often considered to be the product of humour. However laughter is a social emotion, occurring most often in interactions, where it is associated with bonding, agreement, affection and emotional regulation. Laughter is underpinned by complex neural systems, allowing it to be used flexibly: in humans and chimpanzees, social (voluntary) laughter is distinctly different from evoked (involuntary) laughter, a distinction which is also seen in brain imaging studies of laughter. PMID:25439499

A Study on Run Time Assurance for Complex Cyber Physical Systems

DTIC Science & Technology

2013-04-18

safety verification approach was applied to synchronization of distributed local clocks of the nodes on a CAN bus by Jiang et al. [36]. The class of...mode of interaction between the instrumented system and the checker, we distin- guish between synchronous and asynchronous monitoring. In synchronous ...occurred. Synchronous monitoring may deliver a higher degree of assurance than the asynchronous one, because it can block a dangerous action. However

Altered Astrocyte-Neuron Interactions and Epileptogenesis in Tuberous Sclerosis Complex Disorder

DTIC Science & Technology

2014-06-01

Epileptogenesis in non-tuber neural tissue in TS may thus arise by an imbalance of decreased inhibitory and increased excitatory synaptic transmission...generation in TSC. Epileptogenesis in non-tuber neural tissue in TS may thus arise by an imbalance of decreased inhibitory and increased excitatory synaptic...synaptic damage induced by spontaneous seizures F) increased spine density on pyramidal neuron dendrites occurs before the onset of spontaneous seizures

Nuclear assortment of eIF4E coincides with shut-off of host protein synthesis upon poliovirus infection.

PubMed

Sukarieh, R; Sonenberg, N; Pelletier, J

2010-05-01

Eukaryotic initiation factor (eIF) 4E is a subunit of the cap-binding protein complex, eIF4F, which recognizes the cap structure of cellular mRNAs to facilitate translation initiation. eIF4E is assembled into the eIF4F complex via its interaction with eIF4G, an event that is under Akt/mTOR regulation. The eIF4E-eIF4G interaction is regulated by the eIF4E binding partners, eIF4E-binding proteins and eIF4E-transporter. Cleavage of eIF4G occurs upon poliovirus infection and is responsible for the shut-off of host-cell protein synthesis observed early in infection. Here, we document that relocalization of eIF4E to the nucleus occurs concomitantly with cleavage of eIF4G upon poliovirus infection. This event is not dependent upon virus replication, but is dependent on eIF4G cleavage. We postulate that eIF4E nuclear relocalization may contribute to the shut-off of host protein synthesis that is a hallmark of poliovirus infection by perturbing the circular status of actively translating mRNAs.

Enhanced hydrogenation activity and diastereomeric interactions of methyl pyruvate co-adsorbed with R-1-(1-naphthyl)ethylamine on Pd(111)

DOE PAGES

Mahapatra, Mausumi; Burkholder, Luke; Garvey, Michael; ...

2016-08-04

Unmodified racemic sites on heterogeneous chiral catalysts reduce their overall enantioselectivity, but this effect is mitigated in the Orito reaction (methyl pyruvate (MP) hydrogenation to methyl lactate) by an increased hydrogenation reactivity. Here, this effect is explored on a R-1-(1-naphthyl)ethylamine (NEA)-modified Pd(111) model catalyst where temperature-programmed desorption experiments reveal that NEA accelerates the rates of both MP hydrogenation and H/D exchange. NEAþMP docking complexes are imaged using scanning tunneling microscopy supplemented by density functional theory calculations to allow the most stable docking complexes to be identified. The results show that diastereomeric interactions between NEA and MP occur predominantly by bindingmore » of the C=C of the enol tautomer of MP to the surface, while simultaneously optimizing C=O...H 2N hydrogen-bonding interactions. In conclusion, the combination of chiral-NEA driven diastereomeric docking with a tautomeric preference enhances the hydrogenation activity since C=C bonds hydrogenate more easily than C=O bonds thus providing a rationale for the catalytic observations.« less

[Research Progress on the Interaction Effects and Its Neural Mechanisms between Physical Fatigue and Mental Fatigue].

PubMed

Zhang, Lixin; Zhang, Chuncui; He, Feng; Zhao, Xin; Qi, Hongzhi; Wan, Baikun; Ming, Dong

2015-10-01

Fatigue is an exhaustion state caused by prolonged physical work and mental work, which can reduce working efficiency and even cause industrial accidents. Fatigue is a complex concept involving both physiological and psychological factors. Fatigue can cause a decline of concentration and work performance and induce chronic diseases. Prolonged fatigue may endanger life safety. In most of the scenarios, physical and mental workloads co-lead operator into fatigue state. Thus, it is very important to study the interaction influence and its neural mechanisms between physical and mental fatigues. This paper introduces recent progresses on the interaction effects and discusses some research challenges and future development directions. It is believed that mutual influence between physical fatigue and mental fatigue may occur in the central nervous system. Revealing the basal ganglia function and dopamine release may be important to explore the neural mechanisms between physical fatigue and mental fatigue. Future effort is to optimize fatigue models, to evaluate parameters and to explore the neural mechanisms so as to provide scientific basis and theoretical guidance for complex task designs and fatigue monitoring.

A literature review of interaction of oxidized uranium species and uranium complexes with soluble organic matter

USGS Publications Warehouse

Jennings, Joan K.; Leventhal, J.S.

1978-01-01

Organic material is commonly found associated with uranium ores in sandstone-type deposits. This review of the literature summarizes the classes and separations of naturally occurring organic material but the emphasis is on soluble organic species. The main class of materials of interest is humic substances which are high-molecular-weight complex molecules that are soluble in alkaline solution. These humic substances are able to solubilize (make soluble) minerals and also to complex [by ion exchange and (or) chelation] many cations. The natural process of soil formation results in both mineral decomposition and element complexing by organic species. Uranium in solution, such as ground water, can form many species with other elements or complexes present depending on Eh and pH. In natural systems (oxidizing Eh, pH 5-9) the uranium is usually present as a complex with hydroxide or carbonate. Thermodynamic data for these species are presented. Interacting metals and organic materials have been observed in nature and studied in the laboratory by many workers in diverse scientific disciplines. The results are not easily compared. Measurements of the degree of complexation are reported as equilibrium stability constant determinations. This type of research has been done for Mn, Fe, Cu, Zn, Pb, Ni, Co, Mg, Ca, Al, and to a limited degree for U. The use of Conditional Stability Constants has given quantitative results in some cases. The methods utilized in experiments and calculations are reviewed.

Roles of mono-ubiquitinated Smad4 in the formation of Smad transcriptional complexes

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

Wang Bei; Suzuki, Hiroyuki; Kato, Mitsuyasu

2008-11-14

TGF-{beta} activates receptor-regulated Smad (R-Smad) through phosphorylation by type I receptors. Activated R-Smad binds to Smad4 and the complex translocates into the nucleus and stimulates the transcription of target genes through association with co-activators including p300. It is not clear, however, how activated Smad complexes are removed from target genes. In this study, we show that TGF-{beta} enhances the mono-ubiquitination of Smad4. Smad4 mono-ubiquitination was promoted by p300 and suppressed by the c-Ski co-repressor. Smad4 mono-ubiquitination disrupted the interaction with Smad2 in the presence of constitutively active TGF-{beta} type I receptor. Furthermore, mono-ubiquitinated Smad4 was not found in DNA-binding Smadmore » complexes. A Smad4-Ubiquitin fusion protein, which mimics mono-ubiquitinated Smad4, enhanced localization to the cytoplasm. These results suggest that mono-ubiquitination of Smad4 occurs in the transcriptional activator complex and facilitates the turnover of Smad complexes at target genes.« less

Roles of mono-ubiquitinated Smad4 in the formation of Smad transcriptional complexes.

PubMed

Wang, Bei; Suzuki, Hiroyuki; Kato, Mitsuyasu

2008-11-14

TGF-beta activates receptor-regulated Smad (R-Smad) through phosphorylation by type I receptors. Activated R-Smad binds to Smad4 and the complex translocates into the nucleus and stimulates the transcription of target genes through association with co-activators including p300. It is not clear, however, how activated Smad complexes are removed from target genes. In this study, we show that TGF-beta enhances the mono-ubiquitination of Smad4. Smad4 mono-ubiquitination was promoted by p300 and suppressed by the c-Ski co-repressor. Smad4 mono-ubiquitination disrupted the interaction with Smad2 in the presence of constitutively active TGF-beta type I receptor. Furthermore, mono-ubiquitinated Smad4 was not found in DNA-binding Smad complexes. A Smad4-Ubiquitin fusion protein, which mimics mono-ubiquitinated Smad4, enhanced localization to the cytoplasm. These results suggest that mono-ubiquitination of Smad4 occurs in the transcriptional activator complex and facilitates the turnover of Smad complexes at target genes.

The mediator complex in genomic and non-genomic signaling in cancer.

PubMed

Weber, Hannah; Garabedian, Michael J

2018-05-01

Mediator is a conserved, multi-subunit macromolecular machine divided structurally into head, middle, and tail modules, along with a transiently associating kinase module. Mediator functions as an integrator of transcriptional regulatory activity by interacting with DNA-bound transcription factors and with RNA polymerase II (Pol II) to both activate and repress gene expression. Mediator has been shown to affect multiple steps in transcription, including chromatin looping between enhancers and promoters, pre-initiation complex formation, transcriptional elongation, and mRNA splicing. Individual Mediator subunits participate in regulation of gene expression by the estrogen and androgen receptors and are altered in a number of endocrine cancers, including breast and prostate cancer. In addition to its role in genomic signaling, MED12 has been implicated in non-genomic signaling by interacting with and activating TGF-beta receptor 2 in the cytoplasm. Recent structural studies have revealed extensive inter-domain interactions and complex architecture of the Mediator-Pol II complex, suggesting that Mediator is capable of reorganizing its conformation and composition to fit cellular needs. We propose that alterations in Mediator subunit expression that occur in various cancers could impact the organization and function of Mediator, resulting in changes in gene expression that promote malignancy. A better understanding of the role of Mediator in cancer could reveal new approaches to the diagnosis and treatment of Mediator-dependent endocrine cancers, especially in settings of therapy resistance. Copyright © 2017 Elsevier Inc. All rights reserved.

Nonlinear evolution of Mack modes in a hypersonic boundary layer

NASA Astrophysics Data System (ADS)

Chokani, Ndaona

2005-01-01

In hypersonic boundary layer flows the nonlinear disturbance evolution occurs relatively slowly over a very long length scale and has a profound effect on boundary layer transition. In the case of low-level freestream disturbances and negligible surface roughness, the transition is due to the modal growth of exponentially growing Mack modes that are destabilized by wall cooling. Cross-bicoherence measurements, derived from hot-wire data acquired in a quiet hypersonic tunnel, are used to identify and quantify phase-locked, quadratic sum and difference interactions involving the Mack modes. In the early stages of the nonlinear disturbance evolution, cross-bicoherence measurements indicate that the energy exchange between the Mack mode and the mean flow first occurs to broaden the sidebands; this is immediately followed by a sum interaction of the Mack mode to generate the first harmonic. In the next stages of the nonlinear disturbance evolution, there is a difference interaction of the first harmonic, which is also thought to contribute to the mean flow distortion. This difference interaction, in the latter stages, is also accompanied by a difference interaction between Mack mode and first harmonic, and a sum interaction, which forces the second harmonic. Analysis using the digital complex demodulation technique, shows that the low-frequency, phase-locked interaction that is identified in the cross bicoherence when the Mack mode and first harmonic have large amplitudes, arises due to the amplitude modulation of Mack mode and first harmonic.

Geo-Distinctive Comorbidity Networks of Pediatric Asthma.

PubMed

Shin, Eun Kyong; Shaban-Nejad, Arash

2018-01-01

Most pediatric asthma cases occur in complex interdependencies, exhibiting complex manifestation of multiple symptoms. Studying asthma comorbidities can help to better understand the etiology pathway of the disease. Albeit such relations of co-expressed symptoms and their interactions have been highlighted recently, empirical investigation has not been rigorously applied to pediatric asthma cases. In this study, we use computational network modeling and analysis to reveal the links and associations between commonly co-observed diseases/conditions with asthma among children in Memphis, Tennessee. We present a novel method for geo-parsed comorbidity network analysis to show the distinctive patterns of comorbidity networks in urban and suburban areas in Memphis.

Prediction of Protein-Protein Interaction Sites Using Electrostatic Desolvation Profiles

PubMed Central

Fiorucci, Sébastien; Zacharias, Martin

2010-01-01

Abstract Protein-protein complex formation involves removal of water from the interface region. Surface regions with a small free energy penalty for water removal or desolvation may correspond to preferred interaction sites. A method to calculate the electrostatic free energy of placing a neutral low-dielectric probe at various protein surface positions has been designed and applied to characterize putative interaction sites. Based on solutions of the finite-difference Poisson equation, this method also includes long-range electrostatic contributions and the protein solvent boundary shape in contrast to accessible-surface-area-based solvation energies. Calculations on a large set of proteins indicate that in many cases (>90%), the known binding site overlaps with one of the six regions of lowest electrostatic desolvation penalty (overlap with the lowest desolvation region for 48% of proteins). Since the onset of electrostatic desolvation occurs even before direct protein-protein contact formation, it may help guide proteins toward the binding region in the final stage of complex formation. It is interesting that the probe desolvation properties associated with residue types were found to depend to some degree on whether the residue was outside of or part of a binding site. The probe desolvation penalty was on average smaller if the residue was part of a binding site compared to other surface locations. Applications to several antigen-antibody complexes demonstrated that the approach might be useful not only to predict protein interaction sites in general but to map potential antigenic epitopes on protein surfaces. PMID:20441756

Preventing Data Ambiguity in Infectious Diseases with Four-Dimensional and Personalized Evaluations

PubMed Central

Iandiorio, Michelle J.; Fair, Jeanne M.; Chatzipanagiotou, Stylianos; Ioannidis, Anastasios; Trikka-Graphakos, Eleftheria; Charalampaki, Nikoletta; Sereti, Christina; Tegos, George P.; Hoogesteijn, Almira L.; Rivas, Ariel L.

2016-01-01

Background Diagnostic errors can occur, in infectious diseases, when anti-microbial immune responses involve several temporal scales. When responses span from nanosecond to week and larger temporal scales, any pre-selected temporal scale is likely to miss some (faster or slower) responses. Hoping to prevent diagnostic errors, a pilot study was conducted to evaluate a four-dimensional (4D) method that captures the complexity and dynamics of infectious diseases. Methods Leukocyte-microbial-temporal data were explored in canine and human (bacterial and/or viral) infections, with: (i) a non-structured approach, which measures leukocytes or microbes in isolation; and (ii) a structured method that assesses numerous combinations of interacting variables. Four alternatives of the structured method were tested: (i) a noise-reduction oriented version, which generates a single (one data point-wide) line of observations; (ii) a version that measures complex, three-dimensional (3D) data interactions; (iii) a non-numerical version that displays temporal data directionality (arrows that connect pairs of consecutive observations); and (iv) a full 4D (single line-, complexity-, directionality-based) version. Results In all studies, the non-structured approach revealed non-interpretable (ambiguous) data: observations numerically similar expressed different biological conditions, such as recovery and lack of recovery from infections. Ambiguity was also found when the data were structured as single lines. In contrast, two or more data subsets were distinguished and ambiguity was avoided when the data were structured as complex, 3D, single lines and, in addition, temporal data directionality was determined. The 4D method detected, even within one day, changes in immune profiles that occurred after antibiotics were prescribed. Conclusions Infectious disease data may be ambiguous. Four-dimensional methods may prevent ambiguity, providing earlier, in vivo, dynamic, complex, and personalized information that facilitates both diagnostics and selection or evaluation of anti-microbial therapies. PMID:27411058

Describing and understanding behavioral responses to multiple stressors and multiple stimuli.

PubMed

Hale, Robin; Piggott, Jeremy J; Swearer, Stephen E

2017-01-01

Understanding the effects of environmental change on natural ecosystems is a major challenge, particularly when multiple stressors interact to produce unexpected "ecological surprises" in the form of complex, nonadditive effects that can amplify or reduce their individual effects. Animals often respond behaviorally to environmental change, and multiple stressors can have both population-level and community-level effects. However, the individual, not combined, effects of stressors on animal behavior are commonly studied. There is a need to understand how animals respond to the more complex combinations of stressors that occur in nature, which requires a systematic and rigorous approach to quantify the various potential behavioral responses to the independent and interactive effects of stressors. We illustrate a robust, systematic approach for understanding behavioral responses to multiple stressors based on integrating schemes used to quantitatively classify interactions in multiple-stressor research and to qualitatively view interactions between multiple stimuli in behavioral experiments. We introduce and unify the two frameworks, highlighting their conceptual and methodological similarities, and use four case studies to demonstrate how this unification could improve our interpretation of interactions in behavioral experiments and guide efforts to manage the effects of multiple stressors. Our unified approach: (1) provides behavioral ecologists with a more rigorous and systematic way to quantify how animals respond to interactions between multiple stimuli, an important theoretical advance, (2) helps us better understand how animals behave when they encounter multiple, potentially interacting stressors, and (3) contributes more generally to the understanding of "ecological surprises" in multiple stressors research.

A spectroscopic study of phenylbutazone and aspirin bound to serum albumin in rheumatoid diseases

NASA Astrophysics Data System (ADS)

Maciążek-Jurczyk, M.; Sułkowska, A.; Bojko, B.; Równicka-Zubik, J.; Sułkowski, W. W.

2011-11-01

Interaction of phenylbutazone (PBZ) and aspirin (ASA), two drugs recommended in rheumatoid diseases (RDs), when binding to human (HSA) and bovine (BSA) serum albumins, has been studied by quenching of fluorescence and proton nuclear magnetic resonance ( 1HNMR) techniques. On the basis of spectrofluorescence measurements high affinity binding sites of PBZ and ASA on albumin as well as their interaction within the binding sites were described. A low affinity binding site has been studied by proton nuclear magnetic resonance spectroscopy. Using fluorescence spectroscopy the location of binding site in serum albumin (SA) for PBZ and ASA was found. Association constants Ka were determined for binary (i.e. PBZ-SA and ASA-SA) and ternary complexes (i.e. PBZ-[ASA]-SA and ASA-[PBZ]-SA). PBZ and ASA change the affinity of each other to the binding site in serum albumin (SA). The presence of ASA causes the increase of association constants KaI of PBZ-SA complex. Similarly, PBZ influences KaI of ASA-SA complex. This phenomenon shows that the strength of binding and the stability of the complexes increase in the presence of the second drug. The decrease of KaII values suggests that the competition between PBZ and ASA in binding to serum albumin in the second class of binding sites occurs. The analysis of 1HNMR spectral parameters i.e. changes of chemical shifts and relaxation times of the drug indicate that the presence of ASA weakens the interaction of PBZ with albumin. Similarly PBZ weakens the interaction of ASA with albumin. This conclusion points to the necessity of using a monitoring therapy owning to the possible increase of uncontrolled toxic effects.

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

PubMed

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

2014-12-10

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

[Influence of human gastrointestinal tract bacterial pathogens on host cell apoptosis].

PubMed

Wronowska, Weronika; Godlewska, Renata; Jagusztyn-Krynicka, Elzbieta Katarzyna

2005-01-01

Several pathogenic bacteria are able to trigger apoptosis in the host cell, but the mechanisms by which it occurs differ, and the resulting pathology can take different courses. Induction and/or blockage of programmed cell death upon infection is a result of complex interaction of bacterial proteins with cellular proteins involved in signal transduction and apoptosis. In this review we focus on pro/anti-apoptotic activities exhibited by two enteric pathogens Salmonella enterica, Yersinia spp. and gastric pathogen Helicobacter pylori. We present current knowledge on how interaction between mammalian and bacterial cell relates to the molecular pathways of apoptosis, and what is the role of apoptosis in pathogenesis.

Inside out: Speed-dependent barriers to reactive mixing

NASA Astrophysics Data System (ADS)

Kelley, Douglas; Nevins, Thomas

2015-11-01

Reactive mixing occurs wherever fluid flow and chemical or biological growth interact over time and space. Those interactions often lead to steep gradients in reactant and product concentration, arranged in complex spatial structures that can cause wide variation in the global reaction rate and concentrations. By simultaneously measuring fluid velocity and reaction front locations in laboratory experiments with the Belousov-Zhabotinsky reaction, we find that the barriers defining those structures vary dramatically with speed. In particular, we find that increasing flow speed causes reacted regions to move from vortex edges to vortex cores, thus turning the barriers ``inside out''. This observation has implications for reactive mixing of phytoplankton in global oceans.

Formation of Polyelectrolyte Complex Colloid Particles between Chitosan and Pectin with Different Degree of Esterification

NASA Astrophysics Data System (ADS)

Wang, Hui; Sun, Hongyuan; He, Jieyu

2017-12-01

The effects of degree of esterification, pectin/chitosan ratio and pH on the formation of polyelectrolyte complex colloid particles between chitosan (CS) and pectin (PE) were investigated. Low methoxyl pectin (LPE) was achieved by de-esterifying high methoxyl pectin (HPE) with pectin methyl esterase. Turbidity titration and colorimetric method was used to determine the stability of complex colloid particles. The structure and morphology of complex particles were characterized by FTIR and TEM. When pectin solution was dropped into chitosan solution, complex colloidal dispersion was stable as PE/CS mass ratio was no more than 3:2. Colloidal particles of HPE-CS complex coagulated at larger ratio of PE/CS than LPE-CS. The maximum complex occurred at pH 6.1 for HPE-CS and pH 5.7 for LPE-CS, and decreasing pH leaded to the dissociation of complex particles. Electrostatic interactions between carboxyl groups on pectin and amino groups on chitosan were confirmed by FTIR. Colloidal particle sizes ranged from about 100 nm to 400 nm with spherical shape.

PLC-γ directly binds activated c-Src, which is necessary for carbachol-mediated inhibition of NHE3 activity in Caco-2/BBe cells

PubMed Central

Lee, Luke J.; Kovbasnjuk, Olga; Li, Xuhang; Donowitz, Mark

2013-01-01

Elevated levels of intracellular Ca2+ ([Ca2+]i) inhibit Na+/H+ exchanger 3 (NHE3) activity in the intact intestine. We previously demonstrated that PLC-γ directly binds NHE3, an interaction that is necessary for [Ca2+]i inhibition of NHE3 activity, and that PLC-γ Src homology 2 (SH2) domains may scaffold Ca2+ signaling proteins necessary for regulation of NHE3 activity. [Ca2+]i regulation of NHE3 activity is also c-Src dependent; however, the mechanism by which c-Src is involved is undetermined. We hypothesized that the SH2 domains of PLC-γ might link c-Src to NHE3-containing complexes to mediate [Ca2+]i inhibition of NHE3 activity. In Caco-2/BBe cells, carbachol (CCh) decreased NHE3 activity by ∼40%, an effect abolished with the c-Src inhibitor PP2. CCh treatment increased the amount of active c-Src as early as 1 min through increased Y416 phosphorylation. Coimmunoprecipitation demonstrated that c-Src associated with PLC-γ, but not NHE3, under basal conditions, an interaction that increased rapidly after CCh treatment and occurred before the dissociation of PLC-γ and NHE3 that occurred 10 min after CCh treatment. Finally, direct binding to c-Src only occurred through the PLC-γ SH2 domains, an interaction that was prevented by blocking the PLC-γ SH2 domain. This study demonstrated that c-Src 1) activity is necessary for [Ca2+]i inhibition of NHE3 activity, 2) activation occurs rapidly (∼1 min) after CCh treatment, 3) directly binds PLC-γ SH2 domains and associates dynamically with PLC-γ under elevated [Ca2+]i conditions, and 4) does not directly bind NHE3. Under elevated [Ca2+]i conditions, PLC-γ scaffolds c-Src into NHE3-containing multiprotein complexes before dissociation of PLC-γ from NHE3 and subsequent endocytosis of NHE3. PMID:23703528

PLC-γ directly binds activated c-Src, which is necessary for carbachol-mediated inhibition of NHE3 activity in Caco-2/BBe cells.

PubMed

Zachos, Nicholas C; Lee, Luke J; Kovbasnjuk, Olga; Li, Xuhang; Donowitz, Mark

2013-08-01

Elevated levels of intracellular Ca(2+) ([Ca(2+)]i) inhibit Na(+)/H(+) exchanger 3 (NHE3) activity in the intact intestine. We previously demonstrated that PLC-γ directly binds NHE3, an interaction that is necessary for [Ca(2+)]i inhibition of NHE3 activity, and that PLC-γ Src homology 2 (SH2) domains may scaffold Ca(2+) signaling proteins necessary for regulation of NHE3 activity. [Ca(2+)]i regulation of NHE3 activity is also c-Src dependent; however, the mechanism by which c-Src is involved is undetermined. We hypothesized that the SH2 domains of PLC-γ might link c-Src to NHE3-containing complexes to mediate [Ca(2+)]i inhibition of NHE3 activity. In Caco-2/BBe cells, carbachol (CCh) decreased NHE3 activity by ∼40%, an effect abolished with the c-Src inhibitor PP2. CCh treatment increased the amount of active c-Src as early as 1 min through increased Y(416) phosphorylation. Coimmunoprecipitation demonstrated that c-Src associated with PLC-γ, but not NHE3, under basal conditions, an interaction that increased rapidly after CCh treatment and occurred before the dissociation of PLC-γ and NHE3 that occurred 10 min after CCh treatment. Finally, direct binding to c-Src only occurred through the PLC-γ SH2 domains, an interaction that was prevented by blocking the PLC-γ SH2 domain. This study demonstrated that c-Src 1) activity is necessary for [Ca(2+)]i inhibition of NHE3 activity, 2) activation occurs rapidly (∼1 min) after CCh treatment, 3) directly binds PLC-γ SH2 domains and associates dynamically with PLC-γ under elevated [Ca(2+)]i conditions, and 4) does not directly bind NHE3. Under elevated [Ca(2+)]i conditions, PLC-γ scaffolds c-Src into NHE3-containing multiprotein complexes before dissociation of PLC-γ from NHE3 and subsequent endocytosis of NHE3.

Attributions of guilt and punishment as functions of physical attractiveness and smiling.

PubMed

Abel, Millicent H; Watters, Heather

2005-12-01

The authors found an interaction between sex of participant and sex of defendant in the leniency bias toward a smiling defendant. Differences occurred for male participants when levying punishment for a smiling male defendant vs. a smiling female defendant and for a smiling male defendant vs. a nonsmiling male defendant, whereas differences did not occur for female participants. The authors found moderating effects of physical attractiveness and smiling between guilt and punishment. The only significant positive relationship between guilt and punishment occurred for the defendant whom participants rated low in physical attractiveness and who was not smiling. When guilty, the smiling and unattractive defendant received less punishment than did the smiling and attractive defendant. The authors discussed complex relationships between physical attractiveness, smiling, guilt, and punishment.

Study on molecular structure, spectroscopic properties (FTIR and UV-Vis), NBO, QTAIM, HOMO-LUMO energies and docking studies of 5-fluorouracil, a substance used to treat cancer

NASA Astrophysics Data System (ADS)

Almeida, Michell O.; Barros, Daiane A. S.; Araujo, Sheila C.; Faria, Sergio H. D. M.; Maltarollo, Vinicius G.; Honorio, Kathia M.

2017-09-01

Cancer cells can expand to other parts of body through blood system and nodes from a mechanism known as metastasis. Due to the large annual growth of cancer cases, various biological targets have been studied and related to this disorder. A very interesting target related to cancer is human epidermal growth factor receptor 2 (HER2). In this study, we analyzed the main intermolecular interactions between a drug used in the cancer treatment (5-fluorouracil) and HER2. Molecular modeling methods were also employed to assess the molecular structure, spectroscopic properties (FTIR and UV-Vis), NBO, QTAIM and HOMO-LUMO energies of 5-FU. From the docking simulations it was possible to analyze the interactions that occur between some residues in the binding site of HER2 and 5-FU. To validate the choice of basis set that was used in the NBO and QTAIM analyses, theoretical calculations were performed to obtain FT-IR and UV/Vis spectra, and the theoretical results are consistent with the experimental data, showing that the basis set chosen is suitable. For the maximum λ from the theoretical calculation (254.89 nm) of UV/Vis, the electronic transition from HOMO to LUMO occurs at 4.89 eV. From NBO analyses, we observed interactions between Asp863 and 5-FU, i.e. the orbitals with high transfer of electrons are LP O15 (donor NBO) and BD* (π) N1-H10 (acceptor NBO), being that the value of this interaction is 7.72 kcal/mol. Results from QTAIM indicate one main intermolecular H bond, which is necessary to stabilize the complex formed between the ligands and the biological target. Therefore, this study allowed a careful evaluation on the main structural, spectroscopic and electronic properties involved in the interaction between 5-FU and HER2, an important biological complex related to the cancer treatment.

Plasmon-controlled fluorescence: a new paradigm in fluorescence spectroscopy

PubMed Central

Lakowicz, Joseph R.; Ray, Krishanu; Chowdhury, Mustafa; Szmacinski, Henryk; Fu, Yi; Zhang, Jian; Nowaczyk, Kazimierz

2009-01-01

Fluorescence spectroscopy is widely used in biological research. Until recently, essentially all fluorescence experiments were performed using optical energy which has radiated to the far-field. By far-field we mean at least several wavelengths from the fluorophore, but propagating far-field radiation is usually detected at larger macroscopic distances from the sample. In recent years there has been a growing interest in the interactions of fluorophores with metallic surfaces or particles. Near-field interactions are those occurring within a wavelength distance of an excited fluorophore. The spectral properties of fluorophores can be dramatically altered by near-field interactions with the electron clouds present in metals. These interactions modify the emission in ways not seen in classical fluorescence experiments. In this review we provide an intuitive description of the complex physics of plasmons and near-field interactions. Additionally, we summarize the recent work on metal–fluorophore interactions and suggest how these effects will result in new classes of experimental procedures, novel probes, bioassays and devices. PMID:18810279

Molecular Mechanistic Insights into the Endothelial Receptor Mediated Cytoadherence of Plasmodium falciparum-Infected Erythrocytes

PubMed Central

Li, Ang; Lim, Tong Seng; Shi, Hui; Yin, Jing; Tan, Swee Jin; Li, Zhengjun; Low, Boon Chuan; Tan, Kevin Shyong Wei; Lim, Chwee Teck

2011-01-01

Cytoadherence or sequestration is essential for the pathogenesis of the most virulent human malaria species, Plasmodium falciparum (P. falciparum). Similar to leukocyte-endothelium interaction in response to inflammation, cytoadherence of P. falciparum infected red blood cells (IRBCs) to endothelium occurs under physiological shear stresses in blood vessels and involves an array of molecule complexes which cooperate to form stable binding. Here, we applied single-molecule force spectroscopy technique to quantify the dynamic force spectra and characterize the intrinsic kinetic parameters for specific ligand-receptor interactions involving two endothelial receptor proteins: thrombospondin (TSP) and CD36. It was shown that CD36 mediated interaction was much more stable than that mediated by TSP at single molecule level, although TSP-IRBC interaction appeared stronger than CD36-IRBC interaction in the high pulling rate regime. This suggests that TSP-mediated interaction may initiate cell adhesion by capturing the fast flowing IRBCs whereas CD36 functions as the ‘holder’ for providing stable binding. PMID:21437286

Electronic structure of the [MNH2]+ (M = Sc-Cu) complexes.

PubMed

Hendrickx, Marc F A; Clima, Sergiu

2006-11-23

B3LYP geometry optimizations for the [MNH2]+ complexes of the first-row transition metal cations (Sc+-Cu+) were performed. Without any exception the ground states of these unsaturated amide complexes were calculated to possess planar geometries. CASPT2 binding energies that were corrected for zero-point energies and including relativistic effects show a qualitative trend across the series that closely resembles the experimental observations. The electronic structures for the complexes of the early and middle transition metal cations (Sc+-Co+) differ from the electronic structures derived for the complexes of the late transition metal cations (Ni+ and Cu+). For the former complexes the relative higher position of the 3d orbitals above the singly occupied 2p(pi) HOMO of the uncoordinated NH2 induces an electron transfer from the 3d shell to 2p(pi). The stabilization of the 3d orbitals from the left to the right along the first-row transition metal series causes these orbitals to become situated below the HOMO of the NH2 ligand for Ni+ and Cu+, preventing a transfer from occurring in the [MNH2]+ complexes of these metal cations. Analysis of the low-lying states of the amide complexes revealed a rather unique characteristic of their electronic structures that was found across the entire series. Rather exceptionally for the whole of chemistry, pi-type interactions were calculated to be stronger than the corresponding sigma-type interactions. The origin of this extraordinary behavior can be ascribed to the low-lying sp2 lone pair orbital of the NH2 ligand with respect to the 3d level.

Study on the mechanism of copper-ammonia complex decomposition in struvite formation process and enhanced ammonia and copper removal.

PubMed

Peng, Cong; Chai, Liyuan; Tang, Chongjian; Min, Xiaobo; Song, Yuxia; Duan, Chengshan; Yu, Cheng

2017-01-01

Heavy metals and ammonia are difficult to remove from wastewater, as they easily combine into refractory complexes. The struvite formation method (SFM) was applied for the complex decomposition and simultaneous removal of heavy metal and ammonia. The results indicated that ammonia deprivation by SFM was the key factor leading to the decomposition of the copper-ammonia complex ion. Ammonia was separated from solution as crystalline struvite, and the copper mainly co-precipitated as copper hydroxide together with struvite. Hydrogen bonding and electrostatic attraction were considered to be the main surface interactions between struvite and copper hydroxide. Hydrogen bonding was concluded to be the key factor leading to the co-precipitation. In addition, incorporation of copper ions into the struvite crystal also occurred during the treatment process. Copyright © 2016. Published by Elsevier B.V.

Regulation of microtubule nucleation mediated by γ-tubulin complexes.

PubMed

Sulimenko, Vadym; Hájková, Zuzana; Klebanovych, Anastasiya; Dráber, Pavel

2017-05-01

The microtubule cytoskeleton is critically important for spatio-temporal organization of eukaryotic cells. The nucleation of new microtubules is typically restricted to microtubule organizing centers (MTOCs) and requires γ-tubulin that assembles into multisubunit complexes of various sizes. γ-Tubulin ring complexes (TuRCs) are efficient microtubule nucleators and are associated with large number of targeting, activating and modulating proteins. γ-Tubulin-dependent nucleation of microtubules occurs both from canonical MTOCs, such as spindle pole bodies and centrosomes, and additional sites such as Golgi apparatus, nuclear envelope, plasma membrane-associated sites, chromatin and surface of pre-existing microtubules. Despite many advances in structure of γ-tubulin complexes and characterization of γTuRC interacting factors, regulatory mechanisms of microtubule nucleation are not fully understood. Here, we review recent work on the factors and regulatory mechanisms that are involved in centrosomal and non-centrosomal microtubule nucleation.

Interaction between fault systems in a complex tectonic setting: Insights from InSAR and Teleseismic analysis of the 2015 Lake Saurez and 2016 Muji fault earthquake sequence

NASA Astrophysics Data System (ADS)

Nanjundiah, P.; Barbot, S.; Wei, S.; Tapponnier, P.; Feng, W.; Wang, T.

2017-12-01

The Pamir Plateau is a complex and important component of the India-Eurasia Collision zone. Despite being similar to the Tibetan plateau in elevation and collision processes, quite a bit is still unknown about the structure and the tectonic processes occurring in this region. We aim to better understand the structure, stress and deformation patterns in the northern and central Pamir plateau by analysing InSAR, teleseismic, and optical data for two large earthquakes that occurred in this region between December 2015 (Mw 7.2, Lake Saurez) and November 2016 (Mw 6.6 Muji Fault). We constrain the fault geometry by precisely relocating aftershocks using the double difference technique implemented in HypoDD (Waldhauser & Ellsworth 2000). We used Okada's (1992) Green Functions to invert for slip on the fault with a rectangular dislocation and edgreen to numerically invert for the slip in a layered medium (Wang et al. 2005). The combined datasets highlight the existence of an oblique fault between two major thrust fault systems i.e. the Darwas & the Karakoram faults. The December 2015 event highlights complexity in this fault system. The combination of data sets used in this study highlights the existence of a seismic gap south of Lake Karakul as well as coupling between the Muji and Darwas-Karakoram fault systems. We emphasise the role of smaller faults and their interactions in accommodating the overall strain and tectonics in the Pamir region and their effect on estimating local seismic hazard.

Before the Endless Forms: Embodied Model of Transition from Single Cells to Aggregates to Ecosystem Engineering

PubMed Central

Solé, Ricard V.; Valverde, Sergi

2013-01-01

The emergence of complex multicellular systems and their associated developmental programs is one of the major problems of evolutionary biology. The advantages of cooperation over individuality seem well known but it is not clear yet how such increase of complexity emerged from unicellular life forms. Current multicellular systems display a complex cell-cell communication machinery, often tied to large-scale controls of body size or tissue homeostasis. Some unicellular life forms are simpler and involve groups of cells cooperating in a tissue-like fashion, as it occurs with biofilms. However, before true gene regulatory interactions were widespread and allowed for controlled changes in cell phenotypes, simple cellular colonies displaying adhesion and interacting with their environments were in place. In this context, models often ignore the physical embedding of evolving cells, thus leaving aside a key component. The potential for evolving pre-developmental patterns is a relevant issue: how far a colony of evolving cells can go? Here we study these pre-conditions for morphogenesis by using CHIMERA, a physically embodied computational model of evolving virtual organisms in a pre-Mendelian world. Starting from a population of identical, independent cells moving in a fluid, the system undergoes a series of changes, from spatial segregation, increased adhesion and the development of generalism. Eventually, a major transition occurs where a change in the flow of nutrients is triggered by a sub-population. This ecosystem engineering phenomenon leads to a subsequent separation of the ecological network into two well defined compartments. The relevance of these results for evodevo and its potential ecological triggers is discussed. PMID:23596506

Predicting Physical Interactions between Protein Complexes*

PubMed Central

Clancy, Trevor; Rødland, Einar Andreas; Nygard, Ståle; Hovig, Eivind

2013-01-01

Protein complexes enact most biochemical functions in the cell. Dynamic interactions between protein complexes are frequent in many cellular processes. As they are often of a transient nature, they may be difficult to detect using current genome-wide screens. Here, we describe a method to computationally predict physical interactions between protein complexes, applied to both humans and yeast. We integrated manually curated protein complexes and physical protein interaction networks, and we designed a statistical method to identify pairs of protein complexes where the number of protein interactions between a complex pair is due to an actual physical interaction between the complexes. An evaluation against manually curated physical complex-complex interactions in yeast revealed that 50% of these interactions could be predicted in this manner. A community network analysis of the highest scoring pairs revealed a biologically sensible organization of physical complex-complex interactions in the cell. Such analyses of proteomes may serve as a guide to the discovery of novel functional cellular relationships. PMID:23438732

Phasic heart rate responses and cardiac cycle time in auditory choice reaction time.

PubMed

van der Molen, M W; Somsen, R J; Orlebeke, J F

1983-01-01

This study investigated the cardiovascular-behavioral interaction under short and long stimulus interval conditions. In addition, the cardiovascular-behavioral interaction was studied as affected by cardiac cycle duration. Fourteen subjects performed a choice reaction time (RT) task employing a mixed speed-accuracy tradeoff design in which reactions were paced to coincide with a signal that occurs randomly at either 200 or 500 msec after the reaction stimulus. The preparatory interval between a warning stimulus and a lead-reaction stimulus complex was also varied (2 vs. 4.5 sec). Anticipatory deceleration occurred within the 4.5 sec interval but not in the 2 sec interval. The depth of anticipatory deceleration did not discriminate between fast and slow reactions; but an earlier shift from deceleration to acceleration was associated with fast reactions. The effect of stimulus timing relative to the R-wave of the electrocardiogram was also analysed. Meaningful stimuli tended to produce cardiac slowing as previously described in the literature. Early occurring stimuli prolong the cycle of their occurrence more than late occurring stimuli. The later prolong the subsequent cycle. Cardiac cycle time effects were absent for unattended stimuli. The results of anticipatory deceleration suggested that the depth of deceleration was regulated by time-uncertainty and speed-accuracy criterion.

Potential risks resulting from fruit/vegetable-drug interactions: effects on drug-metabolizing enzymes and drug transporters.

PubMed

Rodríguez-Fragoso, Lourdes; Martínez-Arismendi, José Luis; Orozco-Bustos, Danae; Reyes-Esparza, Jorge; Torres, Eliseo; Burchiel, Scott W

2011-05-01

It has been well established that complex mixtures of phytochemicals in fruits and vegetables can be beneficial for human health. Moreover, it is becoming increasingly apparent that phytochemicals can influence the pharmacological activity of drugs by modifying their absorption characteristics through interactions with drug transporters as well as drug-metabolizing enzyme systems. Such effects are more likely to occur in the intestine and liver, where high concentrations of phytochemicals may occur. Alterations in cytochrome P450 and other enzyme activities may influence the fate of drugs subject to extensive first-pass metabolism. Although numerous studies of nutrient-drug interactions have been published and systematic reviews and meta-analyses of these studies are available, no generalizations on the effect of nutrient-drug interactions on drug bioavailability are currently available. Several publications have highlighted the unintended consequences of the combined use of nutrients and drugs. Many phytochemicals have been shown to have pharmacokinetic interactions with drugs. The present review is limited to commonly consumed fruits and vegetables with significant beneficial effects as nutrients and components in folk medicine. Here, we discuss the phytochemistry and pharmacokinetic interactions of the following fruit and vegetables: grapefruit, orange, tangerine, grapes, cranberry, pomegranate, mango, guava, black raspberry, black mulberry, apple, broccoli, cauliflower, watercress, spinach, tomato, carrot, and avocado. We conclude that our knowledge of the potential risk of nutrient-drug interactions is still limited. Therefore, efforts to elucidate potential risks resulting from food-drug interactions should be intensified in order to prevent undesired and harmful clinical consequences. © 2011 Institute of Food Technologists®

Multiple-stressor effects of sediment, phosphorus and nitrogen on stream macroinvertebrate communities.

PubMed

Davis, Stephen J; Ó hUallacháin, Daire; Mellander, Per-Erik; Kelly, Ann-Marie; Matthaei, Christoph D; Piggott, Jeremy J; Kelly-Quinn, Mary

2018-05-10

Multiple stressors affect stream ecosystems worldwide and their interactions are of particular concern, with gaps existing in understanding stressor impacts on stream communities. Addressing these knowledge gaps will aid in targeting and designing of appropriate mitigation measures. In this study, the agricultural stressors fine sediment (ambient, low, medium, high), phosphorus (ambient, enriched) and nitrogen (ambient, enriched) were manipulated simultaneously in 64 streamside mesocosms to determine their individual and combined effects on the macroinvertebrate community (benthos and drift). Stressor levels were chosen to reflect those typically observed in European agricultural streams. A 21-day colonisation period was followed by a 14-day manipulative period. Results indicate that added sediment had the most pervasive effects, significantly reducing total macroinvertebrate abundance, total EPT abundance and abundances of three common EPT taxa. The greatest effect was at high sediment cover (90%), with decreasing negative impacts at medium (50%) and low (30%) covers. Added sediment also led to higher drift propensities for nine of the twelve drift variables. The effects of nitrogen and phosphorus were relatively weak compared to sediment. Several complex and unpredictable 2-way or 3-way interactions among stressors were observed. While sediment addition generally reduced total abundance at high levels, this decrease was amplified by P enrichment at low sediment, whereas the opposite effect occurred at medium sediment and little effect at high sediment. These results have direct implications for water management as they highlight the importance of managing sediment inputs while also considering the complex interactions which can occur between sediment and nutrient stressors. Copyright © 2018 Elsevier B.V. All rights reserved.

Ductile to Brittle Shear Localization in the Upper Crust During Thermal Anomaly: the Calamita Complex (Elba Island, Italy)

NASA Astrophysics Data System (ADS)

Papeschi, S.

2016-12-01

A field and microstructural study of contemporaneous pluton-related thermal anomaly and thrust faulting highlights the mutual interaction between active regional tectonics, magma emplacement and contact metamorphism. The Calamita Complex is composed of highly strained HT/LP schists, metarenites and metacarbonates. HT metamorphism was caused by the emplacement of the buried Porto Azzurro intrusion occurred at pressures below 0.2 GPa. Thermal anomaly was associated to top-to-NE shearing that produced multiple mylonitic shear zones, a HT/LP W-dipping foliation and E-W trending lineations. Strain markers provided by metaconglomerates suggest that deformation occurred in a constrictional regime, independent from the geometry of the magmatic system. Pluton emplacement and shearing were not caused by each other but they interacted producing an entirely new fabric that transposed the previous regional features. Deformation outlasted cooling causing the progressive localization of shearing along a main cataclastic zone localized at the contact between mylonitic metacarbonates and schists. The interaction between shearing and the emplacement of late leucogranitic sills caused also the development of mylonitic to cataclastic fabrics within the sills, depending on temperature and strain rate at the time of emplacement. At the microscale synkinematic blastesis of andalusite plus cordierite and the progressive switch from GBM- to SGR- to BLG- microstructures of quartz, locally overprinted by cataclastic fabrics. The analysis of microstructures suggest that in the Calamita Complex regional deformation affected the host rocks and the late magmatic products of the pluton that registered the switch from ductile to brittle conditions. This switch was generally due to the progressive cooling of the system; however multiple microstructures suggest that deformation in the Calamita was heterogeneous in time and space and possibly subject to different strain rates in different portions that may have produced coeval ductile and brittle deformation.

Stoichiometric balance of protein copy numbers is measurable and functionally significant in a protein-protein interaction network for yeast endocytosis

PubMed Central

2018-01-01

Stoichiometric balance, or dosage balance, implies that proteins that are subunits of obligate complexes (e.g. the ribosome) should have copy numbers expressed to match their stoichiometry in that complex. Establishing balance (or imbalance) is an important tool for inferring subunit function and assembly bottlenecks. We show here that these correlations in protein copy numbers can extend beyond complex subunits to larger protein-protein interactions networks (PPIN) involving a range of reversible binding interactions. We develop a simple method for quantifying balance in any interface-resolved PPINs based on network structure and experimentally observed protein copy numbers. By analyzing such a network for the clathrin-mediated endocytosis (CME) system in yeast, we found that the real protein copy numbers were significantly more balanced in relation to their binding partners compared to randomly sampled sets of yeast copy numbers. The observed balance is not perfect, highlighting both under and overexpressed proteins. We evaluate the potential cost and benefits of imbalance using two criteria. First, a potential cost to imbalance is that ‘leftover’ proteins without remaining functional partners are free to misinteract. We systematically quantify how this misinteraction cost is most dangerous for strong-binding protein interactions and for network topologies observed in biological PPINs. Second, a more direct consequence of imbalance is that the formation of specific functional complexes depends on relative copy numbers. We therefore construct simple kinetic models of two sub-networks in the CME network to assess multi-protein assembly of the ARP2/3 complex and a minimal, nine-protein clathrin-coated vesicle forming module. We find that the observed, imperfectly balanced copy numbers are less effective than balanced copy numbers in producing fast and complete multi-protein assemblies. However, we speculate that strategic imbalance in the vesicle forming module allows cells to tune where endocytosis occurs, providing sensitive control over cargo uptake via clathrin-coated vesicles. PMID:29518071

Stoichiometric balance of protein copy numbers is measurable and functionally significant in a protein-protein interaction network for yeast endocytosis.

PubMed

Holland, David O; Johnson, Margaret E

2018-03-01

Stoichiometric balance, or dosage balance, implies that proteins that are subunits of obligate complexes (e.g. the ribosome) should have copy numbers expressed to match their stoichiometry in that complex. Establishing balance (or imbalance) is an important tool for inferring subunit function and assembly bottlenecks. We show here that these correlations in protein copy numbers can extend beyond complex subunits to larger protein-protein interactions networks (PPIN) involving a range of reversible binding interactions. We develop a simple method for quantifying balance in any interface-resolved PPINs based on network structure and experimentally observed protein copy numbers. By analyzing such a network for the clathrin-mediated endocytosis (CME) system in yeast, we found that the real protein copy numbers were significantly more balanced in relation to their binding partners compared to randomly sampled sets of yeast copy numbers. The observed balance is not perfect, highlighting both under and overexpressed proteins. We evaluate the potential cost and benefits of imbalance using two criteria. First, a potential cost to imbalance is that 'leftover' proteins without remaining functional partners are free to misinteract. We systematically quantify how this misinteraction cost is most dangerous for strong-binding protein interactions and for network topologies observed in biological PPINs. Second, a more direct consequence of imbalance is that the formation of specific functional complexes depends on relative copy numbers. We therefore construct simple kinetic models of two sub-networks in the CME network to assess multi-protein assembly of the ARP2/3 complex and a minimal, nine-protein clathrin-coated vesicle forming module. We find that the observed, imperfectly balanced copy numbers are less effective than balanced copy numbers in producing fast and complete multi-protein assemblies. However, we speculate that strategic imbalance in the vesicle forming module allows cells to tune where endocytosis occurs, providing sensitive control over cargo uptake via clathrin-coated vesicles.

Crystal structures of resorcin[4]arene and pyrogallol[4]arene complexes with DL-pipecolinic acid. Model compounds for the recognition of the pipecolinyl ring, a key fragment of FK506, through C-H⋯π interaction

NASA Astrophysics Data System (ADS)

Fujisawa, Ikuhide; Kitamura, Yuji; Kato, Ryo; Murayama, Kazutaka; Aoki, Katsuyuki

2014-01-01

Resorcin[4]arene (resorcinol cyclic tetramer, abbreviated as RCT) or pyrogallol[4]arene (pyrogallol cyclic tetramer, PCT) form host-guest 1:1 complexes with DL-pipecolinic acid (DL-pipeH), RCT·DL-pipeH·EtOH·8H2O (1), PCT DL-pipeH·EtOH·4H2O (2), and PCT·DL-pipeH·3H2O (3), whose crystal structures have been determined. In each complex, the pipeH ligand is incorporated into the bowl-shaped cavity of the RCT or PCT host molecules through C-H⋯π interactions between alkyl protons of the piperidine ring of pipeH and π-rings of RCT or PCT, forming an [(RCT/PCT)·pipeH] structural fragment. In 1 and 3, two [(RCT/PCT) pipeH] fragments self-associate across an inversion center to form a guest-mediated, obliquely declined dimeric structure [(RCT/PCT)·L-pipeH·D-pipeH (RCT/PCT)]. In 2, each PCT-capped pipeH ligand bridges to two adjacent PCT molecules to form guest-mediated, optically-discrete helical polymers [PCT·L-pipeH]n or [PCT·D-pipeH]n. An 1H NMR experiment shows that the complexation through C-H⋯π interaction between the piperidine ring of pipeH and π-rings of RCT or PCT occurs also in solution, with the binding constants of 9.7 ± 0.6 M-1 for RCT and 26.5 ± 1.5 M-1 for PCT. These complexes provide a synthetic model for the recognition of the pipecolinyl-ring moiety, a key constituent of immunosuppressant drugs such as FK506, FK520 or rapamycin, by their binding proteins through C-H⋯π interaction.

Hormonal Aspects of Epilepsy

PubMed Central

Pennell, Page B.

2009-01-01

Synopsis The interactions between hormones, epilepsy, and the medications used to treat epilepsy are complex, with tridirectional interactions which affect both men and women in various ways. Abnormalities of baseline endocrine status occur more commonly in people with epilepsy, and are most often described for the sex steroid hormone axis. Common symptoms include sexual dysfunction, decreased fertility, premature menopause, and polycystic ovarian syndrome. Antiepileptic drugs and hormones have a bidirectional interaction, with a decrease in the efficacy of hormonal contraceptive agents with some AEDs and a decrease in the concentration and efficacy of other AEDs with hormonal contraceptives. Endogenous hormones can influence seizure severity and frequency, resulting in catamenial patterns of epilepsy. However, this knowledge can be used to develop hormonal strategies to improve seizure control in people with epilepsy. PMID:19853217

Structural insight into the interaction of proteins containing NPF, DPF, and GPF motifs with the C-terminal EH-domain of EHD1

PubMed Central

Kieken, Fabien; Jović, Marko; Tonelli, Marco; Naslavsky, Naava; Caplan, Steve; Sorgen, Paul L

2009-01-01

Eps15 homology (EH)-domain containing proteins are regulators of endocytic membrane trafficking. EH-domain binding to proteins containing the tripeptide NPF has been well characterized, but recent studies have shown that EH-domains are also able to interact with ligands containing DPF or GPF motifs. We demonstrate that the three motifs interact in a similar way with the EH-domain of EHD1, with the NPF motif having the highest affinity due to the presence of an intermolecular hydrogen bond. The weaker affinity for the DPF and GPF motifs suggests that if complex formation occurs in vivo, they may require high ligand concentrations, the presence of successive motifs and/or specific flanking residues. PMID:19798736

Protein-protein interaction networks: unraveling the wiring of molecular machines within the cell.

PubMed

De Las Rivas, Javier; Fontanillo, Celia

2012-11-01

Mapping and understanding of the protein interaction networks with their key modules and hubs can provide deeper insights into the molecular machinery underlying complex phenotypes. In this article, we present the basic characteristics and definitions of protein networks, starting with a distinction of the different types of associations between proteins. We focus the review on protein-protein interactions (PPIs), a subset of associations defined as physical contacts between proteins that occur by selective molecular docking in a particular biological context. We present such definition as opposed to other types of protein associations derived from regulatory, genetic, structural or functional relations. To determine PPIs, a variety of binary and co-complex methods exist; however, not all the technologies provide the same information and data quality. A way of increasing confidence in a given protein interaction is to integrate orthogonal experimental evidences. The use of several complementary methods testing each single interaction assesses the accuracy of PPI data and tries to minimize the occurrence of false interactions. Following this approach there have been important efforts to unify primary databases of experimentally proven PPIs into integrated databases. These meta-databases provide a measure of the confidence of interactions based on the number of experimental proofs that report them. As a conclusion, we can state that integrated information allows the building of more reliable interaction networks. Identification of communities, cliques, modules and hubs by analysing the topological parameters and graph properties of the protein networks allows the discovery of central/critical nodes, which are candidates to regulate cellular flux and dynamics.

Microfluidics-Based in Vivo Mimetic Systems for the Study of Cellular Biology

PubMed Central

2015-01-01

Conspectus The human body is a complex network of molecules, organelles, cells, tissues, and organs: an uncountable number of interactions and transformations interconnect all the system’s components. In addition to these biochemical components, biophysical components, such as pressure, flow, and morphology, and the location of all of these interactions play an important role in the human body. Technical difficulties have frequently limited researchers from observing cellular biology as it occurs within the human body, but some state-of-the-art analytical techniques have revealed distinct cellular behaviors that occur only in the context of the interactions. These types of findings have inspired bioanalytical chemists to provide new tools to better understand these cellular behaviors and interactions. What blocks us from understanding critical biological interactions in the human body? Conventional approaches are often too naïve to provide realistic data and in vivo whole animal studies give complex results that may or may not be relevant for humans. Microfluidics offers an opportunity to bridge these two extremes: while these studies will not model the complexity of the in vivo human system, they can control the complexity so researchers can examine critical factors of interest carefully and quantitatively. In addition, the use of human cells, such as cells isolated from donated blood, captures human-relevant data and limits the use of animals in research. In addition, researchers can adapt these systems easily and cost-effectively to a variety of high-end signal transduction mechanisms, facilitating high-throughput studies that are also spatially, temporally, or chemically resolved. These strengths should allow microfluidic platforms to reveal critical parameters in the human body and provide insights that will help with the translation of pharmacological advances to clinical trials. In this Account, we describe selected microfluidic innovations within the last 5 years that focus on modeling both biophysical and biochemical interactions in cellular communication, such as flow and cell–cell networks. We also describe more advanced systems that mimic higher level biological networks, such as organ on-a-chip and animal on-a-chip models. Since the first papers in the early 1990s, interest in the bioanalytical use of microfluidics has grown significantly. Advances in micro-/nanofabrication technology have allowed researchers to produce miniaturized, biocompatible assay platforms suitable for microfluidic studies in biochemistry and chemical biology. Well-designed microfluidic platforms can achieve quick, in vitro analyses on pico- and femtoliter volume samples that are temporally, spatially, and chemically resolved. In addition, controlled cell culture techniques using a microfluidic platform have produced biomimetic systems that allow researchers to replicate and monitor physiological interactions. Pioneering work has successfully created cell–fluid, cell–cell, cell–tissue, tissue–tissue, even organ-like level interfaces. Researchers have monitored cellular behaviors in these biomimetic microfluidic environments, producing validated model systems to understand human pathophysiology and to support the development of new therapeutics. PMID:24555566

Microfluidics-based in vivo mimetic systems for the study of cellular biology.

PubMed

Kim, Donghyuk; Wu, Xiaojie; Young, Ashlyn T; Haynes, Christy L

2014-04-15

The human body is a complex network of molecules, organelles, cells, tissues, and organs: an uncountable number of interactions and transformations interconnect all the system's components. In addition to these biochemical components, biophysical components, such as pressure, flow, and morphology, and the location of all of these interactions play an important role in the human body. Technical difficulties have frequently limited researchers from observing cellular biology as it occurs within the human body, but some state-of-the-art analytical techniques have revealed distinct cellular behaviors that occur only in the context of the interactions. These types of findings have inspired bioanalytical chemists to provide new tools to better understand these cellular behaviors and interactions. What blocks us from understanding critical biological interactions in the human body? Conventional approaches are often too naïve to provide realistic data and in vivo whole animal studies give complex results that may or may not be relevant for humans. Microfluidics offers an opportunity to bridge these two extremes: while these studies will not model the complexity of the in vivo human system, they can control the complexity so researchers can examine critical factors of interest carefully and quantitatively. In addition, the use of human cells, such as cells isolated from donated blood, captures human-relevant data and limits the use of animals in research. In addition, researchers can adapt these systems easily and cost-effectively to a variety of high-end signal transduction mechanisms, facilitating high-throughput studies that are also spatially, temporally, or chemically resolved. These strengths should allow microfluidic platforms to reveal critical parameters in the human body and provide insights that will help with the translation of pharmacological advances to clinical trials. In this Account, we describe selected microfluidic innovations within the last 5 years that focus on modeling both biophysical and biochemical interactions in cellular communication, such as flow and cell-cell networks. We also describe more advanced systems that mimic higher level biological networks, such as organ on-a-chip and animal on-a-chip models. Since the first papers in the early 1990s, interest in the bioanalytical use of microfluidics has grown significantly. Advances in micro-/nanofabrication technology have allowed researchers to produce miniaturized, biocompatible assay platforms suitable for microfluidic studies in biochemistry and chemical biology. Well-designed microfluidic platforms can achieve quick, in vitro analyses on pico- and femtoliter volume samples that are temporally, spatially, and chemically resolved. In addition, controlled cell culture techniques using a microfluidic platform have produced biomimetic systems that allow researchers to replicate and monitor physiological interactions. Pioneering work has successfully created cell-fluid, cell-cell, cell-tissue, tissue-tissue, even organ-like level interfaces. Researchers have monitored cellular behaviors in these biomimetic microfluidic environments, producing validated model systems to understand human pathophysiology and to support the development of new therapeutics.

Structural Characterisation of Fenchone and its Complexes with Ethanol by Broadband Rotational Spectroscopy

NASA Astrophysics Data System (ADS)

Loru, Donatella; Sanz, M. Eugenia

2016-06-01

Although significant advances in understanding the human olfactory system have taken place over the last two decades, detailed information on how the interactions between odorants and olfactory receptors occur at the molecular level is still lacking. To achieve a better understanding on the molecular mechanisms involved in olfaction, we are investigating several odorants and their interactions with mimics of amino acid residues in olfactory receptors. We present here the structural characterisation of fenchone (C10H16O) and its complexes with ethanol (to mimic the side chain of serine) using a 2-8 GHz chirped-pulse Fourier transform microwave spectrometer built at King's College London. The rotational spectrum of the parent species and all the 13C and 18O isotopologues of fenchone was observed, and from the experimental rotational constants the substitution (r0) and effective (rs) structures of fenchone were determined. The rotational spectrum of fenchone-ethanol was observed by adding ethanol to the carrier gas and passing the mixture through a receptacle with fenchone. Several 1:1 complexes of fenchone-ethanol have been identified in the rotational spectrum. In all the complexes the ethanol molecule binds to the carbonyl group through an O-H· · · O hydrogen bond.

A computationally identified compound antagonizes excess FGF-23 signaling in renal tubules and a mouse model of hypophosphatemia

DOE PAGES

Xiao, Zhousheng; Riccardi, Demian; Velazquez, Hector A.; ...

2016-11-22

Fibroblast growth factor–23 (FGF-23) interacts with a binary receptor complex composed of α-Klotho (α-KL) and FGF receptors (FGFRs) to regulate phosphate and vitamin D metabolism in the kidney. Excess FGF-23 production, which causes hypophosphatemia, is genetically inherited or occurs with chronic kidney disease. Among other symptoms, hypophosphatemia causes vitamin D deficiency and the bone-softening disorder rickets. Current therapeutics that target the receptor complex have limited utility clinically. In this paper, using a computationally driven, structure-based, ensemble docking and virtual high-throughput screening approach, we identified four novel compounds predicted to selectively inhibit FGF-23–induced activation of the FGFR/α-KL complex. Additional modeling andmore » functional analysis found that Zinc13407541 bound to FGF-23 and disrupted its interaction with the FGFR1/α-KL complex; experiments in a heterologous cell expression system showed that Zinc13407541 selectivity inhibited α-KL–dependent FGF-23 signaling. Zinc13407541 also inhibited FGF-23 signaling in isolated renal tubules ex vivo and partially reversed the hypophosphatemic effects of excess FGF-23 in a mouse model. Finally, these chemical probes provide a platform to develop lead compounds to treat disorders caused by excess FGF-23.« less

A computationally identified compound antagonizes excess FGF-23 signaling in renal tubules and a mouse model of hypophosphatemia.

PubMed

Xiao, Zhousheng; Riccardi, Demian; Velazquez, Hector A; Chin, Ai L; Yates, Charles R; Carrick, Jesse D; Smith, Jeremy C; Baudry, Jerome; Quarles, L Darryl

2016-11-22

Fibroblast growth factor-23 (FGF-23) interacts with a binary receptor complex composed of α-Klotho (α-KL) and FGF receptors (FGFRs) to regulate phosphate and vitamin D metabolism in the kidney. Excess FGF-23 production, which causes hypophosphatemia, is genetically inherited or occurs with chronic kidney disease. Among other symptoms, hypophosphatemia causes vitamin D deficiency and the bone-softening disorder rickets. Current therapeutics that target the receptor complex have limited utility clinically. Using a computationally driven, structure-based, ensemble docking and virtual high-throughput screening approach, we identified four novel compounds predicted to selectively inhibit FGF-23-induced activation of the FGFR/α-KL complex. Additional modeling and functional analysis found that Zinc13407541 bound to FGF-23 and disrupted its interaction with the FGFR1/α-KL complex; experiments in a heterologous cell expression system showed that Zinc13407541 selectivity inhibited α-KL-dependent FGF-23 signaling. Zinc13407541 also inhibited FGF-23 signaling in isolated renal tubules ex vivo and partially reversed the hypophosphatemic effects of excess FGF-23 in a mouse model. These chemical probes provide a platform to develop lead compounds to treat disorders caused by excess FGF-23. Copyright © 2016, American Association for the Advancement of Science.

A computationally identified compound antagonizes excess FGF-23 signaling in renal tubules and a mouse model of hypophosphatemia

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

Xiao, Zhousheng; Riccardi, Demian; Velazquez, Hector A.

Fibroblast growth factor–23 (FGF-23) interacts with a binary receptor complex composed of α-Klotho (α-KL) and FGF receptors (FGFRs) to regulate phosphate and vitamin D metabolism in the kidney. Excess FGF-23 production, which causes hypophosphatemia, is genetically inherited or occurs with chronic kidney disease. Among other symptoms, hypophosphatemia causes vitamin D deficiency and the bone-softening disorder rickets. Current therapeutics that target the receptor complex have limited utility clinically. In this paper, using a computationally driven, structure-based, ensemble docking and virtual high-throughput screening approach, we identified four novel compounds predicted to selectively inhibit FGF-23–induced activation of the FGFR/α-KL complex. Additional modeling andmore » functional analysis found that Zinc13407541 bound to FGF-23 and disrupted its interaction with the FGFR1/α-KL complex; experiments in a heterologous cell expression system showed that Zinc13407541 selectivity inhibited α-KL–dependent FGF-23 signaling. Zinc13407541 also inhibited FGF-23 signaling in isolated renal tubules ex vivo and partially reversed the hypophosphatemic effects of excess FGF-23 in a mouse model. Finally, these chemical probes provide a platform to develop lead compounds to treat disorders caused by excess FGF-23.« less

Structural requirements of endopolygalacturonase for the interaction with PGIP (polygalacturonase-inhibiting protein)

PubMed Central

Federici, L.; Caprari, C.; Mattei, B.; Savino, C.; Di Matteo, A.; De Lorenzo, G.; Cervone, F.; Tsernoglou, D.

2001-01-01

To invade a plant tissue, phytopathogenic fungi produce several cell wall-degrading enzymes; among them, endopolygalacturonase (PG) catalyzes the fragmentation and solubilization of homogalacturonan. Polygalacturonase-inhibiting proteins (PGIPs), found in the cell wall of many plants, counteract fungal PGs by forming specific complexes with them. We report the crystal structure at 1.73 Å resolution of PG from the phytopathogenic fungus Fusarium moniliforme (FmPG). The structure of FmPG was useful to study the mode of interaction of the enzyme with PGIP-2 from Phaseolus vulgaris. Several amino acids of FmPG were mutated, and their contribution to the formation of the complex with PGIP-2 was investigated by surface plasmon resonance. The residues Lys-269 and Arg-267, located inside the active site cleft, and His-188, at the edge of the active site cleft, are critical for the formation of the complex, which is consistent with the observed competitive inhibition of the enzyme played by PGIP-2. The replacement of His-188 with a proline or the insertion of a tryptophan after position 270, variations that both occur in plant PGs, interferes with the formation of the complex. We suggest that these variations are important structural requirements of plant PGs to prevent PGIP binding. PMID:11687632

Experimental and theoretical NMR studies of interaction between phenylalanine derivative and egg yolk lecithin.

PubMed

Wałęsa, Roksana; Ptak, Tomasz; Siodłak, Dawid; Kupka, Teobald; Broda, Małgorzata A

2014-06-01

The interaction of phenylalanine diamide (Ac-Phe-NHMe) with egg yolk lecithin (EYL) in chloroform was studied by (1)H and (13)C NMR. Six complexes EYL-Ac-Phe-NHMe, stabilized by N-H···O or/and C-H···O hydrogen bonds, were optimized at M06-2X/6-31G(d,p) level. The assignment of EYL and Ac-Phe-NHMe NMR signals was supported using GIAO (gauge including atomic orbital) NMR calculations at VSXC and B3LYP level of theory combined with STO-3Gmag basis set. Results of our study indicate that the interaction of peptides with lecithin occurs mainly in the polar 'head' of the lecithin. Additionally, the most probable lecithin site of H-bond interaction with Ac-Phe-NHMe is the negatively charged oxygen in phosphate group that acts as proton acceptor. Copyright © 2014 John Wiley & Sons, Ltd.

Multisensory integration in Lepidoptera: Insights into flower-visitor interactions.

PubMed

Kinoshita, Michiyo; Stewart, Finlay J; Ômura, Hisashi

2017-04-01

As most work on flower foraging focuses on bees, studying Lepidoptera can offer fresh perspectives on how sensory capabilities shape the interaction between flowers and insects. Through a combination of innate preferences and learning, many Lepidoptera persistently visit particular flower species. Butterflies tend to rely on their highly developed sense of colour to locate rewarding flowers, while moths have evolved sophisticated olfactory systems towards the same end. However, these modalities can interact in complex ways; for instance, butterflies' colour preference can shift depending on olfactory context. The mechanisms by which such cross-modal interaction occurs are poorly understood, but the mushroom bodies appear to play a central role. Because of the diversity seen within Lepidoptera in terms of their sensory capabilities and the nature of their relationships with flowers, they represent a fruitful avenue for comparative studies to shed light on the co-evolution of flowers and flower-visiting insects. © 2017 WILEY Periodicals, Inc.

Structural dissection of an interaction between transcription initiation and termination factors implicated in promoter-terminator cross-talk.

PubMed

Bratkowski, Matthew; Unarta, Ilona Christy; Zhu, Lizhe; Shubbar, Murtada; Huang, Xuhui; Liu, Xin

2018-02-02

Functional cross-talk between the promoter and terminator of a gene has long been noted. Promoters and terminators are juxtaposed to form gene loops in several organisms, and gene looping is thought to be involved in transcriptional regulation. The general transcription factor IIB (TFIIB) and the C-terminal domain phosphatase Ssu72, essential factors of the transcription preinitiation complex and the mRNA processing and polyadenylation complex, respectively, are important for gene loop formation. TFIIB and Ssu72 interact both genetically and physically, but the molecular basis of this interaction is not known. Here we present a crystal structure of the core domain of TFIIB in two new conformations that differ in the relative distance and orientation of the two cyclin-like domains. The observed extraordinary conformational plasticity may underlie the binding of TFIIB to multiple transcription factors and promoter DNAs that occurs in distinct stages of transcription, including initiation, reinitiation, and gene looping. We mapped the binding interface of the TFIIB-Ssu72 complex using a series of systematic, structure-guided in vitro binding and site-specific photocross-linking assays. Our results indicate that Ssu72 competes with acidic activators for TFIIB binding and that Ssu72 disrupts an intramolecular TFIIB complex known to impede transcription initiation. We also show that the TFIIB-binding site on Ssu72 overlaps with the binding site of symplekin, a component of the mRNA processing and polyadenylation complex. We propose a hand-off model in which Ssu72 mediates a conformational transition in TFIIB, accounting for the role of Ssu72 in transcription reinitiation, gene looping, and promoter-terminator cross-talk. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

The colloidal state of tannins impacts the nature of their interaction with proteins: the case of salivary proline-rich protein/procyanidins binding.

PubMed

Cala, Olivier; Dufourc, Erick J; Fouquet, Eric; Manigand, Claude; Laguerre, Michel; Pianet, Isabelle

2012-12-18

While the definition of tannins has been historically associated with its propensity to bind proteins in a nonspecific way, it is now admitted that specific interaction also occurs. The case of the astringency perception is a good example to illustrate this phenomenon: astringency is commonly described as a tactile sensation induced by the precipitation of a complex composed of proline-rich proteins present in the human saliva and tannins present in beverages such as tea or red wines. In the present work, the interactions between a human saliva protein segment and three different procyanidins (B1, B3, and C2) were investigated at the atomic level by NMR and molecular dynamics. The data provided evidence for (i) an increase in affinity compared to shortest human saliva peptides, which is accounted for by protein "wraping around" the tannin, (ii) a specificity in the interaction below tannin critical micelle concentration (CMC) of ca. 10 mM, with an affinity scale such that C2 > B1 > B3, and (iii) a nonspecific binding above tannin CMC that conducts irremediably to the precipitation of the tannins/protein complex. Such physicochemical findings describe in accurate terms saliva protein-tannin interactions and provide support for a more subtle description by oenologists of wine astringency perception in the mouth.

When small changes matter: the role of cross-scale interactions between habitat and ecological connectivity in recovery.

PubMed

Thrush, Simon F; Hewitt, Judi E; Lohrer, Andrew M; Chiaroni, Luca D

2013-01-01

Interaction between the diversity of local communities and the degree of connectivity between them has the potential to influence local recovery rates and thus profoundly affect community dynamics in the face of the cumulative impacts that occur across regions. Although such complex interactions have been modeled, field experiments in natural ecosystems to investigate the importance of interactions between local and regional processes are rare, especially so in coastal marine seafloor habitats subjected to many types of disturbance. We conducted a defaunation experiment at eight subtidal sites, incorporating manipulation of habitat structure, to test the relative importance of local habitat features and colonist supply in influencing macrobenthic community recovery rate. Our sites varied in community composition, habitat characteristics, and hydrodynamic conditions, and we conducted the experiment in two phases, exposing defaunated plots to colonists during periods of either high or low larval colonist supply. In both phases of the experiment, five months after disturbance, we were able to develop models that explained a large proportion of variation in community recovery rate between sites. Our results emphasize that the connectivity to the regional species pool influences recovery rate, and although local habitat effects were important, the strength of these effects was affected by broader-scale site characteristics and connectivity. Empirical evidence that cross-scale interactions are important in disturbance-recovery dynamics emphasizes the complex dynamics underlying seafloor community responses to cumulative disturbance.

STAY-GREEN and Chlorophyll Catabolic Enzymes Interact at Light-Harvesting Complex II for Chlorophyll Detoxification during Leaf Senescence in Arabidopsis[C][W

PubMed Central

Sakuraba, Yasuhito; Schelbert, Silvia; Park, So-Yon; Han, Su-Hyun; Lee, Byoung-Doo; Andrès, Céline Besagni; Kessler, Felix; Hörtensteiner, Stefan; Paek, Nam-Chon

2012-01-01

During leaf senescence, plants degrade chlorophyll to colorless linear tetrapyrroles that are stored in the vacuole of senescing cells. The early steps of chlorophyll breakdown occur in plastids. To date, five chlorophyll catabolic enzymes (CCEs), NONYELLOW COLORING1 (NYC1), NYC1-LIKE, pheophytinase, pheophorbide a oxygenase (PAO), and red chlorophyll catabolite reductase, have been identified; these enzymes catalyze the stepwise degradation of chlorophyll to a fluorescent intermediate, pFCC, which is then exported from the plastid. In addition, STAY-GREEN (SGR), Mendel’s green cotyledon gene encoding a chloroplast protein, is required for the initiation of chlorophyll breakdown in plastids. Senescence-induced SGR binds to light-harvesting complex II (LHCII), but its exact role remains elusive. Here, we show that all five CCEs also specifically interact with LHCII. In addition, SGR and CCEs interact directly or indirectly with each other at LHCII, and SGR is essential for recruiting CCEs in senescing chloroplasts. PAO, which had been attributed to the inner envelope, is found to localize in the thylakoid membrane. These data indicate a predominant role for the SGR-CCE-LHCII protein interaction in the breakdown of LHCII-located chlorophyll, likely to allow metabolic channeling of phototoxic chlorophyll breakdown intermediates upstream of nontoxic pFCC. PMID:22366162

Molecular dynamics simulations on interaction between bacterial proteins: Implication on pathogenic activities.

PubMed

Mondal, Manas; Chakrabarti, Jaydeb; Ghosh, Mahua

2018-03-01

We perform molecular dynamics simulation studies on interaction between bacterial proteins: an outer-membrane protein STY3179 and a yfdX protein STY3178 of Salmonella Typhi. STY3179 has been found to be involved in bacterial adhesion and invasion. STY3178 is recently biophysically characterized. It is a soluble protein having antibiotic binding and chaperon activity capabilities. These two proteins co-occur and are from neighboring gene in Salmonella Typhi-occurrence of homologs of both STY3178 and STY3179 are identified in many Gram-negative bacteria. We show using homology modeling, docking followed by molecular dynamics simulation that they can form a stable complex. STY3178 belongs to aqueous phase, while the beta barrel portion of STY3179 remains buried in DPPC bilayer with extra-cellular loops exposed to water. To understand the molecular basis of interaction between STY3178 and STY3179, we compute the conformational thermodynamics which indicate that these two proteins interact through polar and acidic residues belonging to their interfacial region. Conformational thermodynamics results further reveal instability of certain residues in extra-cellular loops of STY3179 upon complexation with STY3178 which is an indication for binding with host cell protein laminin. © 2017 Wiley Periodicals, Inc.

Modeling of intracerebral interictal epileptic discharges: Evidence for network interactions.

PubMed

Meesters, Stephan; Ossenblok, Pauly; Colon, Albert; Wagner, Louis; Schijns, Olaf; Boon, Paul; Florack, Luc; Fuster, Andrea

2018-06-01

The interictal epileptic discharges (IEDs) occurring in stereotactic EEG (SEEG) recordings are in general abundant compared to ictal discharges, but difficult to interpret due to complex underlying network interactions. A framework is developed to model these network interactions. To identify the synchronized neuronal activity underlying the IEDs, the variation in correlation over time of the SEEG signals is related to the occurrence of IEDs using the general linear model. The interdependency is assessed of the brain areas that reflect highly synchronized neural activity by applying independent component analysis, followed by cluster analysis of the spatial distributions of the independent components. The spatiotemporal interactions of the spike clusters reveal the leading or lagging of brain areas. The analysis framework was evaluated for five successfully operated patients, showing that the spike cluster that was related to the MRI-visible brain lesions coincided with the seizure onset zone. The additional value of the framework was demonstrated for two more patients, who were MRI-negative and for whom surgery was not successful. A network approach is promising in case of complex epilepsies. Analysis of IEDs is considered a valuable addition to routine review of SEEG recordings, with the potential to increase the success rate of epilepsy surgery. Copyright © 2018 International Federation of Clinical Neurophysiology. Published by Elsevier B.V. All rights reserved.

Electronic Structure and Magnetic Interactions in the Radical Salt [BEDT-TTF]2[CuCl4].

PubMed

Calzado, Carmen J; Rodríguez-García, Bárbara; Galán Mascarós, José Ramón; Hernández, Norge Cruz

2018-06-07

The magnetic behavior and electric properties of the hybrid radical salt [BEDT-TTF] 2 [CuCl 4 ] have been revisited through extended experimental analyses and DDCI and periodic DFT plane waves calculations. Single crystal X-ray diffraction data have been collected at different temperatures, discovering a phase transition occurring in the 250-300 K range. The calculations indicate the presence of intradimer, interdimer, and organic-inorganic π-d interactions in the crystal, a magnetic pattern much more complex than the Bleaney-Bowers model initially assigned to this material. Although this simple model was good enough to reproduce the magnetic susceptibility data, our calculations demonstrate that the actual magnetic structure is significantly more intricate, with alternating antiferromagnetic 1D chains of the organic BEDT-TTF + radical, connected through weak antiferromagnetic interactions with the CuCl 4 2- ions. Combination of experiment and theory allowed us to unambiguously determine and quantify the leading magnetic interactions in the system. The density-of-states curves confirm the semiconductor nature of the system and the dominant organic contribution of the valence and conduction band edges. This general and combined approach appears to be fundamental in order to properly understand the magnetic structure of these complex materials, where experimental data can actually be fitted from a variety of models and parameters.

Polymer Soft-Landing Isolation of Acetylene on Polystyrene and Poly(vinylpyridine): A Novel Approach to Probing Hydrogen Bonding in Polymers.

PubMed

Li, Yike; Samet, Cindy

2015-09-17

Hydrogen-bonded complexes of acetylene (Ac) with the polymers polystyrene (PS), poly(4-vinylpyridine) (P4VP), and poly(2-vinylpyridine) (P2VP) have been characterized for the first time at 16 K in a "polymer soft-landing isolation" experiment which is being pioneered in our research laboratory. In particular, changes in vibrational modes of Ac provide ample evidence for hydrogen-bonded complexes between Ac and the phenyl groups of PS or the pyridyl groups of P4VP and P2VP. With PS, the proton on the top Ac molecule of the classic T-shaped Ac dimer interacts with the π cloud of the benzene (Bz) ring to form a C-H---π interaction, while the π cloud of the lower Ac forms a second C-H---π interaction with a proton on the Bz ring. An analogous (ring)1-(Ac)2 double interaction occurs between an Ac dimer and the pyridine (Pyr) rings on both P2VP and P4VP, yielding a C-H---N and C-H---π interaction. With P4VP and P2VP a second bridged (ring)2-(Ac)2 product is formed, with the Ac dimer forming nearly collinear C-H---N hydrogen bonds to adjacent Pyr rings. On P2VP this bridged product is the only one after extensive annealing. These complexes in which Ac acts as both proton donor and acceptor have not previously been observed in conventional matrix isolation experiments. This study is the second from our laboratory employing this method, which represents a slight modification of the traditional matrix isolation technique.

Toward the mechanism of eIF4F-mediated ribosomal attachment to mammalian capped mRNAs.

PubMed

Kumar, Parimal; Hellen, Christopher U T; Pestova, Tatyana V

2016-07-01

Ribosomal attachment to mammalian capped mRNAs is achieved through the cap-eukaryotic initiation factor 4E (eIF4E)-eIF4G-eIF3-40S chain of interactions, but the mechanism by which mRNA enters the mRNA-binding channel of the 40S subunit remains unknown. To investigate this process, we recapitulated initiation on capped mRNAs in vitro using a reconstituted translation system. Formation of initiation complexes at 5'-terminal AUGs was stimulated by the eIF4E-cap interaction and followed "the first AUG" rule, indicating that it did not occur by backward scanning. Initiation complexes formed even at the very 5' end of mRNA, implying that Met-tRNAi (Met) inspects mRNA from the first nucleotide and that initiation does not have a "blind spot." In assembled initiation complexes, the cap was no longer associated with eIF4E. Omission of eIF4A or disruption of eIF4E-eIF4G-eIF3 interactions converted eIF4E into a specific inhibitor of initiation on capped mRNAs. Taken together, these results are consistent with the model in which eIF4E-eIF4G-eIF3-40S interactions place eIF4E at the leading edge of the 40S subunit, and mRNA is threaded into the mRNA-binding channel such that Met-tRNAi (Met) can inspect it from the first nucleotide. Before entering, eIF4E likely dissociates from the cap to overcome steric hindrance. We also found that the m(7)G cap specifically interacts with eIF3l. © 2016 Kumar et al.; Published by Cold Spring Harbor Laboratory Press.

Anticoagulant Activity of a Unique Sulfated Pyranosic (1→3)-β-l-Arabinan through Direct Interaction with Thrombin*

PubMed Central

Fernández, Paula V.; Quintana, Irene; Cerezo, Alberto S.; Caramelo, Julio J.; Pol-Fachin, Laercio; Verli, Hugo; Estevez, José M.; Ciancia, Marina

2013-01-01

A highly sulfated 3-linked β-arabinan (Ab1) with arabinose in the pyranose form was obtained from green seaweed Codium vermilara (Bryopsidales). It comprised major amounts of units sulfated on C-2 and C-4 and constitutes the first polysaccharide of this type isolated in the pure form and fully characterized. Ab1 showed anticoagulant activity by global coagulation tests. Less sulfated arabinans obtained from the same seaweed have less or no activity. Ab1 exerts its activity through direct and indirect (antithrombin- and heparin cofactor II-mediated) inhibition of thrombin. Direct thrombin inhibition was studied in detail. By native PAGE, it was possible to detect formation of a complex between Ab1 and human thrombin (HT). Ab1 binding to HT was measured by fluorescence spectroscopy. CD spectra of the Ab1 complex suggested that ligand binding induced a small conformational change on HT. Ab1-thrombin interactions were studied by molecular dynamic simulations using the persulfated octasaccharide as model compound. Most carbohydrate-protein contacts would occur by interaction of sulfate groups with basic amino acid residues on the surface of the enzyme, more than 60% of them being performed by the exosite 2-composing residues. In these interactions, the sulfate groups on C-2 were shown to interact more intensely with the thrombin structure. In contrast, the disulfated oligosaccharide does not promote major conformational modifications at the catalytic site when complexed to exosite 1. These results show that this novel pyranosic sulfated arabinan Ab1 exerts its anticoagulant activity by a mechanism different from those found previously for other sulfated polysaccharides and glycosaminoglycans. PMID:23161548

Gut-associated microbes of Drosophila melanogaster

PubMed Central

Broderick, Nichole; Lemaitre, Bruno

2012-01-01

There is growing interest in using Drosophila melanogaster to elucidate mechanisms that underlie the complex relationships between a host and its microbiota. In addition to the many genetic resources and tools Drosophila provides, its associated microbiota is relatively simple (1–30 taxa), in contrast to the complex diversity associated with vertebrates (> 500 taxa). These attributes highlight the potential of this system to dissect the complex cellular and molecular interactions that occur between a host and its microbiota. In this review, we summarize what is known regarding the composition of gut-associated microbes of Drosophila and their impact on host physiology. We also discuss these interactions in the context of their natural history and ecology and describe some recent insights into mechanisms by which Drosophila and its gut microbiota interact. “Workers with Drosophila have been considered fortunate in that they deal with the first multicellular invertebrate to be cultured monoxenically (Delcourt and Guyenot, 1910); the first to be handled axenically on a semisynthetic diet (Guyenot, 1917); and the first to be grown on a defined diet (Schultz et al., 1946). This list of advantages is somewhat embarrassing, since it implies an interest in nutrition that, in reality, was only secondary. The very first studies were concerned with the reduction of variability in genetic experiments (Delcourt and Guyenot, 1910) and standardization of the nutritional environment.” -James Sang, 1959 Ann NY Acad 1 PMID:22572876

Structural and thermodynamic characterization of doxycycline/β-cyclodextrin supramolecular complex and its bacterial membrane interactions.

PubMed

Suárez, Diego F; Consuegra, Jessika; Trajano, Vivianne C; Gontijo, Sávio M L; Guimarães, Pedro P G; Cortés, Maria E; Denadai, Ângelo L; Sinisterra, Rubén D

2014-06-01

Doxycycline is a semi-synthetic antibiotic commonly used for the treatment of many aerobic and anaerobic bacteria. It inhibits the activity of matrix metalloproteinases (MMPs) and affects cell proliferation. In this study, the structural and thermodynamic parameters of free DOX and a DOX/βCD complex were investigated, as well as their interactions and effects on Staphylococcus aureus cells and cellular cytotoxicity. Complexation of DOX and βCD was confirmed to be an enthalpy- and entropy-driven process, and a low equilibrium constant was obtained. Treatment of S. aureus with higher concentrations of DOX or DOX/βCD resulted in an exponential decrease in S. aureus cell size, as well as a gradual neutralization of zeta potential. These thermodynamic profiles suggest that ion-pairing and hydrogen bonding interactions occur between DOX and the membrane of S. aureus. In addition, the adhesion of βCD to the cell membrane via hydrogen bonding is hypothesized to mediate a synergistic effect which accounts for the higher activity of DOX/βCD against S. aureus compared to pure DOX. Lower cytotoxicity and induction of osteoblast proliferation was also associated with DOX/βCD compared with free DOX. These promising findings demonstrate the potential for DOX/βCD to mediate antimicrobial activity at lower concentrations, and provides a strategy for the development of other antimicrobial formulations. Copyright © 2014. Published by Elsevier B.V.

Aqueous Molecular Dynamics Simulations of the M. tuberculosis Enoyl-ACP Reductase-NADH System and Its Complex with a Substrate Mimic or Diphenyl Ethers Inhibitors

PubMed Central

da Silva Lima, Camilo Henrique; de Alencastro, Ricardo Bicca; Kaiser, Carlos Roland; de Souza, Marcus Vinícius Nora; Rodrigues, Carlos Rangel; Albuquerque, Magaly Girão

2015-01-01

Molecular dynamics (MD) simulations of 12 aqueous systems of the NADH-dependent enoyl-ACP reductase from Mycobacterium tuberculosis (InhA) were carried out for up to 20–40 ns using the GROMACS 4.5 package. Simulations of the holoenzyme, holoenzyme-substrate, and 10 holoenzyme-inhibitor complexes were conducted in order to gain more insight about the secondary structure motifs of the InhA substrate-binding pocket. We monitored the lifetime of the main intermolecular interactions: hydrogen bonds and hydrophobic contacts. Our MD simulations demonstrate the importance of evaluating the conformational changes that occur close to the active site of the enzyme-cofactor complex before and after binding of the ligand and the influence of the water molecules. Moreover, the protein-inhibitor total steric (ELJ) and electrostatic (EC) interaction energies, related to Gly96 and Tyr158, are able to explain 80% of the biological response variance according to the best linear equation, pKi = 7.772 − 0.1885 × Gly96 + 0.0517 × Tyr158 (R2 = 0.80; n = 10), where interactions with Gly96, mainly electrostatic, increase the biological response, while those with Tyr158 decrease. These results will help to understand the structure-activity relationships and to design new and more potent anti-TB drugs. PMID:26457706

Exponential evolution: implications for intelligent extraterrestrial life.

PubMed

Russell, D A

1983-01-01

Some measures of biologic complexity, including maximal levels of brain development, are exponential functions of time through intervals of 10(6) to 10(9) yrs. Biological interactions apparently stimulate evolution but physical conditions determine the time required to achieve a given level of complexity. Trends in brain evolution suggest that other organisms could attain human levels within approximately 10(7) yrs. The number (N) and longevity (L) terms in appropriate modifications of the Drake Equation, together with trends in the evolution of biological complexity on Earth, could provide rough estimates of the prevalence of life forms at specified levels of complexity within the Galaxy. If life occurs throughout the cosmos, exponential evolutionary processes imply that higher intelligence will soon (10(9) yrs) become more prevalent than it now is. Changes in the physical universe become less rapid as time increases from the Big Bang. Changes in biological complexity may be most rapid at such later times. This lends a unique and symmetrical importance to early and late universal times.

Annonalide and derivatives: Semisynthesis, cytotoxic activities and studies on interaction of annonalide with DNA.

PubMed

Marques, Ricardo A; Gomes, Akenaton O C V; de Brito, Maria V; Dos Santos, Ana L P; da Silva, Gladyane S; de Lima, Leandro B; Nunes, Fátima M; de Mattos, Marcos C; de Oliveira, Fátima C E; do Ó Pessoa, Cláudia; de Moraes, Manoel O; de Fátima, Ângelo; Franco, Lucas L; Silva, Marina de M; Dantas, Maria Dayanne de A; Santos, Josué C C; Figueiredo, Isis M; da Silva-Júnior, Edeíldo F; de Aquino, Thiago M; de Araújo-Júnior, João X; de Oliveira, Maria C F; Leslie Gunatilaka, A A

2018-02-01

The cytotoxic activity of the pimarane diterpene annonalide (1) and nine of its semisynthetic derivatives (2-10) was investigated against the human tumor cell lines HL-60 (leukemia), PC-3 (prostate adenocarcinoma), HepG2 (hepatocellular carcinoma), SF-295 (glioblastoma) and HCT-116 (colon cancer), and normal mouse fibroblast (L929) cells. The preparation of 2-10 involved derivatization of the side chain of 1 at C-13. Except for 2, all derivatives are being reported for the first time. Most of the tested compounds presented IC 50 s below 4.0 μM, being considered potential antitumor agents. The structures of all new compounds were elucidated by spectroscopic analyses including 2D NMR and HRMS. Additionally, the interaction of annonalide (1) with ctDNA was evaluated using spectroscopic techniques, and the formation of a supramolecular complex with the macromolecule was confirmed. Competition assays with fluorescent probes (Hoechst and ethidium bromide) and theoretical studies confirmed that 1 interacts preferentially via DNA intercalation with stoichiometric ratio of 1:1 (1:ctDNA). The ΔG value was calculated as -28.24 kJ mol -1 , and indicated that the interaction process occurs spontaneously. Docking studies revealed that van der Walls is the most important interaction in 1-DNA and EB-DNA complexes, and that both ligands (1 and EB) interact with the same DNA residues (DA6, DA17 and DT19). Copyright © 2018. Published by Elsevier B.V.

MRAS: A Close but Understudied Member of the RAS Family.

PubMed

Young, Lucy C; Rodriguez-Viciana, Pablo

2018-01-08

MRAS is the closest relative to the classical RAS oncoproteins and shares most regulatory and effector interactions. However, it also has unique functions, including its ability to function as a phosphatase regulatory subunit when in complex with SHOC2 and protein phosphatase 1 (PP1). This phosphatase complex regulates a crucial step in the activation cycle of RAF kinases and provides a key coordinate input required for efficient ERK pathway activation and transformation by RAS. MRAS mutations rarely occur in cancer but deregulated expression may play a role in tumorigenesis in some settings. Activating mutations in MRAS (as well as SHOC2 and PP1) do occur in the RASopathy Noonan syndrome, underscoring a key role for MRAS within the RAS-ERK pathway. MRAS also has unique roles in cell migration and differentiation and has properties consistent with a key role in the regulation of cell polarity. Further investigations should shed light on what remains a relatively understudied RAS family member. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Electron transport and light-harvesting switches in cyanobacteria

PubMed Central

Mullineaux, Conrad W.

2014-01-01

Cyanobacteria possess multiple mechanisms for regulating the pathways of photosynthetic and respiratory electron transport. Electron transport may be regulated indirectly by controlling the transfer of excitation energy from the light-harvesting complexes, or it may be more directly regulated by controlling the stoichiometry, localization, and interactions of photosynthetic and respiratory electron transport complexes. Regulation of the extent of linear vs. cyclic electron transport is particularly important for controlling the redox balance of the cell. This review discusses what is known of the regulatory mechanisms and the timescales on which they occur, with particular regard to the structural reorganization needed and the constraints imposed by the limited mobility of membrane-integral proteins in the crowded thylakoid membrane. Switching mechanisms requiring substantial movement of integral thylakoid membrane proteins occur on slower timescales than those that require the movement only of cytoplasmic or extrinsic membrane proteins. This difference is probably due to the restricted diffusion of membrane-integral proteins. Multiple switching mechanisms may be needed to regulate electron transport on different timescales. PMID:24478787

'Understanding' as a practical issue in sexual health education for people with intellectual disabilities: a study using two qualitative methods.

PubMed

Finlay, W M L; Rohleder, Poul; Taylor, Natalie; Culfear, Hollie

2015-04-01

Sexual health education is important in addressing the health and social inequalities faced by people with intellectual disabilities. However, provision of health-related advice and education to people with various types and degrees of linguistic and learning difficulties involves addressing complex issues of language and comprehension. This article reports an exploratory study using 2 qualitative methods to examine the delivery of sexual health education to people with intellectual disabilities. Four video-recordings of sexual health education sessions were collected. Conversation analysis was used to examine in detail how such education occurs as a series of interactions between educators and learners. Interviews with 4 educators were carried out and analyzed using thematic analysis. The analysis shows how educators anticipate problems of comprehension and how they respond when there is evidence that a person does not understand the activity or the educational message. This occurs particularly when verbal prompts involve long sentences and abstract concepts. We show a characteristic pattern that arises in these situations, in which both educator and learner jointly produce a superficially correct response. Although interviews allows us some insight into contextual issues, strategy, and aspects of sexual health education that occur outside of the actual teaching sessions, analysis of actual interactions can show us patterns that occur in interactions between educators and learners when comprehension is in question. Addressing how sexual health education is delivered in practice and in detail provides valuable lessons about how such education can be improved. (c) 2015 APA, all rights reserved).

Triggering mechanism and tsunamogenic potential of the Cape Fear Slide complex, U.S. Atlantic margin

USGS Publications Warehouse

Hornbach, Matthew J.; Lavier, Luc L.; Ruppel, Carolyn D.

2007-01-01

Analysis of new multibeam bathymetry data and seismic Chirp data acquired over the Cape Fear Slide complex on the U.S. Atlantic margin suggests that at least 5 major submarine slides have likely occurred there within the past 30,000 years, indicating that repetitive, large-scale mass wasting and associated tsunamis may be more common in this area than previously believed. Gas hydrate deposits and associated free gas as well as salt tectonics have been implicated in previous studies as triggers for the major Cape Fear slide events. Analysis of the interaction of the gas hydrate phase boundary and the various generations of slides indicates that only the most landward slide likely intersected the phase boundary and inferred high gas pressures below it. For much of the region, we believe that displacement along a newly recognized normal fault led to upward migration of salt, oversteepening of slopes, and repeated slope failures. Using new constraints on slide morphology, we develop the first tsunami model for the Cape Fear Slide complex. Our results indicate that if the most seaward Cape Fear slide event occurred today, it could produce waves in excess of 2 m at the present-day 100 m bathymetric contour.

Binding of canonical Wnt ligands to their receptor complexes occurs in ordered plasma membrane environments.

PubMed

Sezgin, Erdinc; Azbazdar, Yagmur; Ng, Xue W; Teh, Cathleen; Simons, Kai; Weidinger, Gilbert; Wohland, Thorsten; Eggeling, Christian; Ozhan, Gunes

2017-08-01

While the cytosolic events of Wnt/β-catenin signaling (canonical Wnt signaling) pathway have been widely studied, only little is known about the molecular mechanisms involved in Wnt binding to its receptors at the plasma membrane. Here, we reveal the influence of the immediate plasma membrane environment on the canonical Wnt-receptor interaction. While the receptors are distributed both in ordered and disordered environments, Wnt binding to its receptors selectively occurs in more ordered membrane environments which appear to cointernalize with the Wnt-receptor complex. Moreover, Wnt/β-catenin signaling is significantly reduced when the membrane order is disturbed by specific inhibitors of certain lipids that prefer to localize at the ordered environments. Similarly, a reduction in Wnt signaling activity is observed in Niemann-Pick Type C disease cells where trafficking of ordered membrane lipid components to the plasma membrane is genetically impaired. We thus conclude that ordered plasma membrane environments are essential for binding of canonical Wnts to their receptor complexes and downstream signaling activity. © 2017 The Authors. The FEBS Journal published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.

Nestedness across biological scales

PubMed Central

Marquitti, Flavia M. D.; Raimundo, Rafael L. G.; Sebastián-González, Esther; Coltri, Patricia P.; Perez, S. Ivan; Brandt, Débora Y. C.; Nunes, Kelly; Daura-Jorge, Fábio G.; Floeter, Sergio R.; Guimarães, Paulo R.

2017-01-01

Biological networks pervade nature. They describe systems throughout all levels of biological organization, from molecules regulating metabolism to species interactions that shape ecosystem dynamics. The network thinking revealed recurrent organizational patterns in complex biological systems, such as the formation of semi-independent groups of connected elements (modularity) and non-random distributions of interactions among elements. Other structural patterns, such as nestedness, have been primarily assessed in ecological networks formed by two non-overlapping sets of elements; information on its occurrence on other levels of organization is lacking. Nestedness occurs when interactions of less connected elements form proper subsets of the interactions of more connected elements. Only recently these properties began to be appreciated in one-mode networks (where all elements can interact) which describe a much wider variety of biological phenomena. Here, we compute nestedness in a diverse collection of one-mode networked systems from six different levels of biological organization depicting gene and protein interactions, complex phenotypes, animal societies, metapopulations, food webs and vertebrate metacommunities. Our findings suggest that nestedness emerge independently of interaction type or biological scale and reveal that disparate systems can share nested organization features characterized by inclusive subsets of interacting elements with decreasing connectedness. We primarily explore the implications of a nested structure for each of these studied systems, then theorize on how nested networks are assembled. We hypothesize that nestedness emerges across scales due to processes that, although system-dependent, may share a general compromise between two features: specificity (the number of interactions the elements of the system can have) and affinity (how these elements can be connected to each other). Our findings suggesting occurrence of nestedness throughout biological scales can stimulate the debate on how pervasive nestedness may be in nature, while the theoretical emergent principles can aid further research on commonalities of biological networks. PMID:28166284

KSC01pd1820

NASA Image and Video Library

2001-12-07

VANDENBERG AIR FORCE BASE, Calif. -- A Delta II rocket launches successfully with the joint NASA/French Space Agency oceanography satellite Jason 1 and Thermosphere Ionosphere Mesosphere Energetics and Dynamics satellite aboard. Liftoff from Launch Complex 2W occurred at 7:07 a.m. PST (10:07 a.m. EST or 15:07 GMT). Jason 1 joins the orbiting Topex/Poseidon satellite to continue observations of the global climate interaction occurring between the sea and the atmosphere as a result of stored solar energy. Instruments on Jason 1 will map variations in ocean surface topography to monitor world ocean circulation, study interactions of the oceans and atmosphere, improve climate predictions and observe events like El Nino. The mission is expected to last three years. The TIMED satellite will study a little-known region above the atmosphere, some 40 to 110 miles from the Earth's surface. Studying this region has been nearly impossible until now because conventional airplanes and balloons cannot reach this high altitude, and it is too low for direct satellite measurements

KSC01pd1822

NASA Image and Video Library

2001-12-07

VANDENBERG AIR FORCE BASE, Calif.. -- A Delta rocket leaps off Launch Complex 2W carrying the joint NASA/French Space Agency oceanography satellite Jason 1 and Thermosphere Ionosphere Mesosphere Energetics and Dynamics satellite aboard. Liftoff occurred at 7:07 a.m. PST (10:07 a.m. EST or 15:07 GMT). Jason 1 joins the orbiting Topex/Poseidon satellite to continue observations of the global climate interaction occurring between the sea and the atmosphere as a result of stored solar energy. Instruments on Jason 1 will map variations in ocean surface topography to monitor world ocean circulation, study interactions of the oceans and atmosphere, improve climate predictions and observe events like El Nino. The mission is expected to last three years. The TIMED satellite will study a little-known region above the atmosphere, some 40 to 110 miles from the Earth's surface. Studying this region has been nearly impossible until now because conventional airplanes and balloons cannot reach this high altitude, and it is too low for direct satellite measurements

The Role of Cancer Stem Cells in the Organ Tropism of Breast Cancer Metastasis: A Mechanistic Balance between the “Seed” and the “Soil”?

PubMed Central

Chu, Jenny E.; Allan, Alison L.

2012-01-01

Breast cancer is a prevalent disease worldwide, and the majority of deaths occur due to metastatic disease. Clinical studies have identified a specific pattern for the metastatic spread of breast cancer, termed organ tropism; where preferential secondary sites include lymph node, bone, brain, lung, and liver. A rare subpopulation of tumor cells, the cancer stem cells (CSCs), has been hypothesized to be responsible for metastatic disease and therapy resistance. Current treatments are highly ineffective against metastatic breast cancer, likely due to the innate therapy resistance of CSCs and the complex interactions that occur between cancer cells and their metastatic microenvironments. A better understanding of these interactions is essential for the development of novel therapeutic targets for metastatic disease. This paper summarizes the characteristics of breast CSCs and their potential metastatic microenvironments. Furthermore, it raises the question of the existence of a CSC niche and highlights areas for future investigation. PMID:22295241

Huntingtin-interacting protein 1-mediated neuronal cell death occurs through intrinsic apoptotic pathways and mitochondrial alterations.

PubMed

Choi, Shin Ae; Kim, Steven J; Chung, Kwang Chul

2006-10-02

Huntingtin interacting protein-1 (Hip1) is known to be associated with the N-terminal domain of huntingtin. Although Hip1 can induce apoptosis, the exact upstream signal transduction pathways have not been clarified yet. In the present study, we examined whether activation of intrinsic and/or extrinsic apoptotic pathways occurs during Hip1-mediated neuronal cell death. Overexpression of Hip1 induced cell death through caspase-3 activation in immortalized hippocampal neuroprogenitor cells. Interestingly, proteolytic processing of Hip1 into partial fragments was observed in response to Hip1 transfection and apoptosis-inducing drugs. Moreover, Hip1 was found to directly bind to and activate caspase-9. This promoted cytosolic release of cytochrome c and apoptosis-inducing factor via mitochondrial membrane perturbation. Furthermore, Hip1 could directly bind to Apaf-1, suggesting that the neurotoxic signals of Hip1 transmit through the intrinsic mitochondrial apoptotic pathways and the formation of apoptosome complex.

Organic bioelectronics probing conformational changes in surface confined proteins

NASA Astrophysics Data System (ADS)

Macchia, Eleonora; Alberga, Domenico; Manoli, Kyriaki; Mangiatordi, Giuseppe F.; Magliulo, Maria; Palazzo, Gerardo; Giordano, Francesco; Lattanzi, Gianluca; Torsi, Luisa

2016-06-01

The study of proteins confined on a surface has attracted a great deal of attention due to its relevance in the development of bio-systems for laboratory and clinical settings. In this respect, organic bio-electronic platforms can be used as tools to achieve a deeper understanding of the processes involving protein interfaces. In this work, biotin-binding proteins have been integrated in two different organic thin-film transistor (TFT) configurations to separately address the changes occurring in the protein-ligand complex morphology and dipole moment. This has been achieved by decoupling the output current change upon binding, taken as the transducing signal, into its component figures of merit. In particular, the threshold voltage is related to the protein dipole moment, while the field-effect mobility is associated with conformational changes occurring in the proteins of the layer when ligand binding occurs. Molecular Dynamics simulations on the whole avidin tetramer in presence and absence of ligands were carried out, to evaluate how the tight interactions with the ligand affect the protein dipole moment and the conformation of the loops surrounding the binding pocket. These simulations allow assembling a rather complete picture of the studied interaction processes and support the interpretation of the experimental results.

Tower Mesonetwork Climatology and Interactive Display Tool

NASA Technical Reports Server (NTRS)

Case, Jonathan L.; Bauman, William H., III

2004-01-01

Forecasters at the 45th Weather Squadron and Spaceflight Meteorology Group use data from the tower network over the Kennedy Space Center (KSC) and Cape Canaveral Air Force Station (CCAFS) to evaluate Launch Commit Criteria, and issue and verify forecasts for ground operations. Systematic biases in these parameters could adversely affect an analysis, forecast, or verification. Also, substantial geographical variations in temperature and wind speed can occur under specific wind directions. To address these concerns, the Applied Meteorology Unit (AMU) developed a climatology of temperatures and winds from the tower network, and identified the geographical variation and significant tower biases. The mesoclimate is largely driven by the complex land-water interfaces across KSC/CCAFS. Towers with close proximity to water typically had much warmer nocturnal temperatures and higher wind speeds throughout the year. The strongest nocturnal wind speeds occurred from October to March whereas the strongest mean daytime wind speeds occurred from February to May. These results of this project can be viewed by forecasters through an interactive graphical user interface developed by the AMU. The web-based interface includes graphical and map displays of mean, standard deviation, bias, and data availability for any combination of towers, variables, months, hours, and wind directions.

Organic bioelectronics probing conformational changes in surface confined proteins

PubMed Central

Macchia, Eleonora; Alberga, Domenico; Manoli, Kyriaki; Mangiatordi, Giuseppe F.; Magliulo, Maria; Palazzo, Gerardo; Giordano, Francesco; Lattanzi, Gianluca; Torsi, Luisa

2016-01-01

The study of proteins confined on a surface has attracted a great deal of attention due to its relevance in the development of bio-systems for laboratory and clinical settings. In this respect, organic bio-electronic platforms can be used as tools to achieve a deeper understanding of the processes involving protein interfaces. In this work, biotin-binding proteins have been integrated in two different organic thin-film transistor (TFT) configurations to separately address the changes occurring in the protein-ligand complex morphology and dipole moment. This has been achieved by decoupling the output current change upon binding, taken as the transducing signal, into its component figures of merit. In particular, the threshold voltage is related to the protein dipole moment, while the field-effect mobility is associated with conformational changes occurring in the proteins of the layer when ligand binding occurs. Molecular Dynamics simulations on the whole avidin tetramer in presence and absence of ligands were carried out, to evaluate how the tight interactions with the ligand affect the protein dipole moment and the conformation of the loops surrounding the binding pocket. These simulations allow assembling a rather complete picture of the studied interaction processes and support the interpretation of the experimental results. PMID:27312768

A novel TPR–BEN domain interaction mediates PICH–BEND3 association

PubMed Central

Pitchai, Ganesha P.; Kaulich, Manuel; Mesa, Pablo; Yao, Qi; Sarlos, Kata; Streicher, Werner W.; Nigg, Erich A.

2017-01-01

Abstract PICH is a DNA translocase required for the maintenance of chromosome stability in human cells. Recent data indicate that PICH co-operates with topoisomerase IIα to suppress pathological chromosome missegregation through promoting the resolution of ultra-fine anaphase bridges (UFBs). Here, we identify the BEN domain-containing protein 3 (BEND3) as an interaction partner of PICH in human cells in mitosis. We have purified full length PICH and BEND3 and shown that they exhibit a functional biochemical interaction in vitro. We demonstrate that the PICH–BEND3 interaction occurs via a novel interface between a TPR domain in PICH and a BEN domain in BEND3, and have determined the crystal structure of this TPR–BEN complex at 2.2 Å resolution. Based on the structure, we identified amino acids important for the TPR–BEN domain interaction, and for the functional interaction of the full-length proteins. Our data reveal a proposed new function for BEND3 in association with PICH, and the first example of a specific protein–protein interaction mediated by a BEN domain. PMID:28977671

An experimental test of a fundamental food web motif.

PubMed

Rip, Jason M K; McCann, Kevin S; Lynn, Denis H; Fawcett, Sonia

2010-06-07

Large-scale changes to the world's ecosystem are resulting in the deterioration of biostructure-the complex web of species interactions that make up ecological communities. A difficult, yet crucial task is to identify food web structures, or food web motifs, that are the building blocks of this baroque network of interactions. Once identified, these food web motifs can then be examined through experiments and theory to provide mechanistic explanations for how structure governs ecosystem stability. Here, we synthesize recent ecological research to show that generalist consumers coupling resources with different interaction strengths, is one such motif. This motif amazingly occurs across an enormous range of spatial scales, and so acts to distribute coupled weak and strong interactions throughout food webs. We then perform an experiment that illustrates the importance of this motif to ecological stability. We find that weak interactions coupled to strong interactions by generalist consumers dampen strong interaction strengths and increase community stability. This study takes a critical step by isolating a common food web motif and through clear, experimental manipulation, identifies the fundamental stabilizing consequences of this structure for ecological communities.

Overdamping by weakly coupled environments

NASA Astrophysics Data System (ADS)

Esposito, Massimiliano; Haake, Fritz

2005-12-01

A quantum system weakly interacting with a fast environment usually undergoes a relaxation with complex frequencies whose imaginary parts are damping rates quadratic in the coupling to the environment in accord with Fermi’s “golden rule.” We show for various models (spin damped by harmonic-oscillator or random-matrix baths, quantum diffusion, and quantum Brownian motion) that upon increasing the coupling up to a critical value still small enough to allow for weak-coupling Markovian master equations, a different relaxation regime can occur. In that regime, complex frequencies lose their real parts such that the process becomes overdamped. Our results call into question the standard belief that overdamping is exclusively a strong coupling feature.

Complexes of horseradish peroxidase with formate, acetate, and carbon monoxide.

PubMed

Carlsson, Gunilla H; Nicholls, Peter; Svistunenko, Dimitri; Berglund, Gunnar I; Hajdu, Janos

2005-01-18

Carbon monoxide, formate, and acetate interact with horseradish peroxidase (HRP) by binding to subsites within the active site. These ligands also bind to catalases, but their interactions are different in the two types of enzymes. Formate (notionally the "hydrated" form of carbon monoxide) is oxidized to carbon dioxide by compound I in catalase, while no such reaction is reported to occur in HRP, and the CO complex of ferrocatalase can only be obtained indirectly. Here we describe high-resolution crystal structures for HRP in its complexes with carbon monoxide and with formate, and compare these with the previously determined HRP-acetate structure [Berglund, G. I., et al. (2002) Nature 417, 463-468]. A multicrystal X-ray data collection strategy preserved the correct oxidation state of the iron during the experiments. Absorption spectra of the crystals and electron paramagnetic resonance data for the acetate and formate complexes in solution correlate electronic states with the structural results. Formate in ferric HRP and CO in ferrous HRP bind directly to the heme iron with iron-ligand distances of 2.3 and 1.8 A, respectively. CO does not bind to the ferric iron in the crystal. Acetate bound to ferric HRP stacks parallel with the heme plane with its carboxylate group 3.6 A from the heme iron, and without an intervening solvent molecule between the iron and acetate. The positions of the oxygen atoms in the bound ligands outline a potential access route for hydrogen peroxide to the iron. We propose that interactions in this channel ensure deprotonation of the proximal oxygen before binding to the heme iron.

Complex fragmentation and silicification structures in fault zones: quartz crystallization and repeated fragmentation in the Rusey fault zone (Cornwall/UK)

NASA Astrophysics Data System (ADS)

Yilmaz, Tim I.; Blenkinsop, Tom; Duschl, Florian; Kruhl, Jörn H.

2015-04-01

Silicified fault rocks typically show structures resulting from various stages of fragmentation and quartz crystallization. Both processes interact episodically and result in complex structures on various scales, which require a wide spectrum of analysis tools. Based on field and microstructural data, the spatial-temporal connection between deformation, quartz crystallization and fluid and material flow along the Rusey fault zone was investigated. The fault can be examined in detail in three dimensions on the north Cornwall coast, UK. It occurs within Carboniferous sandstones, siltstones, mudstones and slates of the Culm basin, and is likely to have had a long history. The fault rocks described here formed during the younger events, possibly due to Tertiary strike-slip reactivation. Frequent fragmentation, flow and crystallization events and their interaction led to various generations of complex-structured quartz units, among them quartz-mantled and partly silicified wall-rock fragments, microcrystalline quartz masses of different compositions and structures, and quartz vein patterns of various ages. Lobate boundaries of quartz masses indicate viscous flow. Fragments are separated by quartz infill, which contains cm-sized open pores, in which quartz crystals have pyramidal terminations. Based on frequent occurrence of feathery textures and the infill geometry, quartz crystallization from chalcedony appears likely, and an origin from silica gel is discussed. Fragmentation structures are generally fractal. This allows differentiation between various processes, such as corrosive wear, wear abrasion and hydraulic brecciation. Material transport along the brittle shear zone, and displacement of the wall-rocks, were at least partly governed by flow of mobile fluid-quartz-particle suspensions. The complex meso- to microstructures were generated by repeated processes of fragmentation, quartz precipitation and grain growth. In general, the brittle Rusey fault zone represents a zone of multiple fragmentation, fluid flow, crystallization and quartz dissolution and precipitation, and is regarded as key example of large-scale cyclic interaction of these processes. The geological evidence of interactions between processes implies that feedbacks and highly non-linear mechanical behaviour generated the complex meso- and microstructures. The fault zone rheology may also therefore have been complex.

Are Interactional Behaviors Exhibited When the Self-Reported Health Question is Asked Associated with Health Status?*

PubMed Central

Garbarski, Dana; Schaeffer, Nora Cate; Dykema, Jennifer

2011-01-01

The self-reported health question summarizes information about health status across several domains of health and is widely used to measure health because it predicts mortality well. We examine whether interactional behaviors produced by respondents and interviewers during the self-reported health question-answer sequence reflect complexities in the respondent’s health history. We observed more problematic interactional behaviors during question-answer sequences in which respondents reported worse health. Furthermore, these behaviors were more likely to occur when there were inconsistencies in the respondent’s health history, even after controlling for the respondent’s answer to the self-reported health question, cognitive ability, and sociodemographic characteristics. We also found that among respondents who reported “excellent” health, and to a lesser extent among those who reported their health was “very good,” problematic interactional behaviors were associated with health inconsistencies. Overall, we find evidence that the interactional behaviors exhibited during the question-answer sequence are associated with respondents’ health status. PMID:21927518

The social life of laughter.

PubMed

Scott, Sophie K; Lavan, Nadine; Chen, Sinead; McGettigan, Carolyn

2014-12-01

Laughter is often considered to be the product of humour. However, laughter is a social emotion, occurring most often in interactions, where it is associated with bonding, agreement, affection, and emotional regulation. Laughter is underpinned by complex neural systems, allowing it to be used flexibly. In humans and chimpanzees, social (voluntary) laughter is distinctly different from evoked (involuntary) laughter, a distinction which is also seen in brain imaging studies of laughter. Copyright © 2014 Elsevier Ltd. All rights reserved.

TRIC: Capturing the direct cellular targets of promoter‐bound transcriptional activators

PubMed Central

Dugan, Amanda; Pricer, Rachel; Katz, Micah

2016-01-01

Abstract Transcriptional activators coordinate the dynamic assembly of multiprotein coactivator complexes required for gene expression to occur. Here we combine the power of in vivo covalent chemical capture with p‐benzoyl‐L‐phenylalanine (Bpa), a genetically incorporated photo‐crosslinking amino acid, and chromatin immunoprecipitation (ChIP) to capture the direct protein interactions of the transcriptional activator VP16 with the general transcription factor TBP at the GAL1 promoter in live yeast. PMID:27213278

Mandible shape in hybrid mice.

PubMed

Renaud, Sabrina; Alibert, Paul; Auffray, Jean-Christophe

2009-09-01

Hybridisation between closely related species is frequently seen as retarding evolutionary divergence and can also promote it by creating novel phenotypes due to new genetic combinations and developmental interactions. We therefore investigated how hybridisation affects the shape of the mouse mandible, a well-known feature in evo-devo studies. Parental groups corresponded to two strains of the European mouse sub-species Mus musculus domesticus and Mus musculus musculus. Parents and hybrids were bred in controlled conditions. The mandibles of F(1) hybrids are mostly intermediate between parental phenotypes as expected for a complex multigenic character. Nevertheless, a transgressive effect as well as an increased phenotypic variance characterise the hybrids. This suggests that hybridisation between the two subspecies could lead to a higher phenotypic variance due to complex interactions among the parental genomes including non-additive genetic effects. The major direction of variance is conserved, however, among hybrids and parent groups. Hybridisation may thus play a role in the production of original transgressive phenotypes occurring following pre-existing patterns of variance.

Methods for Discovery of Novel Cellulosomal Cellulases Using Genomics and Biochemical Tools.

PubMed

Ben-David, Yonit; Dassa, Bareket; Bensoussan, Lizi; Bayer, Edward A; Moraïs, Sarah

2018-01-01

Cell wall degradation by cellulases is extensively explored owing to its potential contribution to biofuel production. The cellulosome is an extracellular multienzyme complex that can degrade the plant cell wall very efficiently, and cellulosomal enzymes are therefore of great interest. The cellulosomal cellulases are defined as enzymes that contain a dockerin module, which can interact with a cohesin module contained in multiple copies in a noncatalytic protein, termed scaffoldin. The assembly of the cellulosomal cellulases into the cellulosomal complex occurs via specific protein-protein interactions. Cellulosome systems have been described initially only in several anaerobic cellulolytic bacteria. However, owing to ongoing genome sequencing and metagenomic projects, the discovery of novel cellulosome-producing bacteria and the description of their cellulosomal genes have dramatically increased in the recent years. In this chapter, methods for discovery of novel cellulosomal cellulases from a DNA sequence by bioinformatics and biochemical tools are described. Their biochemical characterization is also described, including both the enzymatic activity of the putative cellulases and their assembly into mature designer cellulosomes.

Flexible Coordination of Stationary and Mobile Conversations with Gaze: Resource Allocation among Multiple Joint Activities

PubMed Central

Mayor, Eric; Bangerter, Adrian

2016-01-01

Gaze is instrumental in coordinating face-to-face social interactions. But little is known about gaze use when social interactions co-occur with other joint activities. We investigated the case of walking while talking. We assessed how gaze gets allocated among various targets in mobile conversations, whether allocation of gaze to other targets affects conversational coordination, and whether reduced availability of gaze for conversational coordination affects conversational performance and content. In an experimental study, pairs were videotaped in four conditions of mobility (standing still, talking while walking along a straight-line itinerary, talking while walking along a complex itinerary, or walking along a complex itinerary with no conversational task). Gaze to partners was substantially reduced in mobile conversations, but gaze was still used to coordinate conversation via displays of mutual orientation, and conversational performance and content was not different between stationary and mobile conditions. Results expand the phenomena of multitasking to joint activities. PMID:27822189

New insights into saline water evaporation from porous media: Complex interaction between evaporation rates, precipitation, and surface temperature

NASA Astrophysics Data System (ADS)

Shokri-Kuehni, Salomé M. S.; Vetter, Thomas; Webb, Colin; Shokri, Nima

2017-06-01

Understanding salt transport and deposition patterns during evaporation from porous media is important in many engineering and hydrological processes such as soil salinization, ecosystem functioning, and land-atmosphere interaction. As evaporation proceeds, salt concentration increases until it exceeds solubility limits, locally, and crystals precipitate. The interplay between transport processes, crystallization, and evaporation influences where crystallization occurs. During early stages, the precipitated salt creates an evolving porous structure affecting the evaporation kinetics. We conducted a comprehensive series of experiments to investigate how the salt concentration and precipitation influence evaporation dynamics. Our results illustrate the contribution of the evolving salt crust to the evaporative mass losses. High-resolution thermal imaging enabled us to investigate the complex temperature dynamics at the surface of precipitated salt, providing further confirmation of salt crust contribution to the evaporation. We identify different phases of saline water evaporation from porous media with the corresponding dominant mechanisms in each phase and extend the physical understanding of such processes.

Agent-based model of diffusion of N-acyl homoserine lactones in a multicellular environment of Pseudomonas aeruginosa and Candida albicans.

PubMed

Pérez-Rodríguez, Gael; Dias, Sónia; Pérez-Pérez, Martín; Fdez-Riverola, Florentino; Azevedo, Nuno F; Lourenço, Anália

2018-03-08

Experimental incapacity to track microbe-microbe interactions in structures like biofilms, and the complexity inherent to the mathematical modelling of those interactions, raises the need for feasible, alternative modelling approaches. This work proposes an agent-based representation of the diffusion of N-acyl homoserine lactones (AHL) in a multicellular environment formed by Pseudomonas aeruginosa and Candida albicans. Depending on the spatial location, C. albicans cells were variably exposed to AHLs, an observation that might help explain why phenotypic switching of individual cells in biofilms occurred at different time points. The simulation and algebraic results were similar for simpler scenarios, although some statistical differences could be observed (p < 0.05). The model was also successfully applied to a more complex scenario representing a small multicellular environment containing C. albicans and P. aeruginosa cells encased in a 3-D matrix. Further development of this model may help create a predictive tool to depict biofilm heterogeneity at the single-cell level.

Dynamic protein interaction networks and new structural paradigms in signaling

PubMed Central

Csizmok, Veronika; Follis, Ariele Viacava; Kriwacki, Richard W.; Forman-Kay, Julie D.

2017-01-01

Understanding signaling and other complex biological processes requires elucidating the critical roles of intrinsically disordered proteins and regions (IDPs/IDRs), which represent ~30% of the proteome and enable unique regulatory mechanisms. In this review we describe the structural heterogeneity of disordered proteins that underpins these mechanisms and the latest progress in obtaining structural descriptions of ensembles of disordered proteins that are needed for linking structure and dynamics to function. We describe the diverse interactions of IDPs that can have unusual characteristics such as “ultrasensitivity” and “regulated folding and unfolding”. We also summarize the mounting data showing that large-scale assembly and protein phase separation occurs within a variety of signaling complexes and cellular structures. In addition, we discuss efforts to therapeutically target disordered proteins with small molecules. Overall, we interpret the remodeling of disordered state ensembles due to binding and post-translational modifications within an expanded framework for allostery that provides significant insights into how disordered proteins transmit biological information. PMID:26922996

The Saccharomyces cerevisiae MUM2 gene interacts with the DNA replication machinery and is required for meiotic levels of double strand breaks.

PubMed Central

Davis, L; Barbera, M; McDonnell, A; McIntyre, K; Sternglanz, R; Jin , Q; Loidl, J; Engebrecht, J

2001-01-01

The Saccharomyces cerevisiae MUM2 gene is essential for meiotic, but not mitotic, DNA replication and thus sporulation. Genetic interactions between MUM2 and a component of the origin recognition complex and polymerase alpha-primase suggest that MUM2 influences the function of the DNA replication machinery. Early meiotic gene expression is induced to a much greater extent in mum2 cells than in meiotic cells treated with the DNA synthesis inhibitor hydroxyurea. This result indicates that the mum2 meiotic arrest is downstream of the arrest induced by hydroxyurea and suggests that DNA synthesis is initiated in the mutant. Genetic analyses indicate that the recombination that occurs in mum2 mutants is dependent on the normal recombination machinery and on synaptonemal complex components and therefore is not a consequence of lesions created by incompletely replicated DNA. Both meiotic ectopic and allelic recombination are similarly reduced in the mum2 mutant, and the levels are consistent with the levels of meiosis-specific DSBs that are generated. Cytological analyses of mum2 mutants show that chromosome pairing and synapsis occur, although at reduced levels compared to wild type. Given the near-wild-type levels of meiotic gene expression, pairing, and synapsis, we suggest that the reduction in DNA replication is directly responsible for the reduced level of DSBs and meiotic recombination. PMID:11238403

3D microvascular model recapitulates the diffuse large B-cell lymphoma tumor microenvironment in vitro.

PubMed

Mannino, Robert G; Santiago-Miranda, Adriana N; Pradhan, Pallab; Qiu, Yongzhi; Mejias, Joscelyn C; Neelapu, Sattva S; Roy, Krishnendu; Lam, Wilbur A

2017-01-31

Diffuse large B-cell lymphoma (DLBCL) is an aggressive cancer that affects ∼22 000 people in the United States yearly. Understanding the complex cellular interactions of the tumor microenvironment is critical to the success and development of DLBCL treatment strategies. In vitro platforms that successfully model the complex tumor microenvironment without introducing the variability of in vivo systems are vital for understanding these interactions. To date, no such in vitro model exists that can accurately recapitulate the interactions that occur between immune cells, cancer cells, and endothelial cells in the tumor microenvironment of DLBCL. To that end, we developed a lymphoma-on-chip model consisting of a hydrogel based tumor model traversed by a vascularized, perfusable, round microchannel that successfully recapitulates key complexities and interactions of the in vivo tumor microenvironment in vitro. We have shown that the perfusion capabilities of this technique allow us to study targeted treatment strategies, as well as to model the diffusion of infused reagents spatiotemporally. Furthermore, this model employs a novel fabrication technique that utilizes common laboratory materials, and allows for the microfabrication of multiplex microvascular environments without the need for advanced microfabrication facilities. Through our facile microfabrication process, we are able to achieve micro vessels within a tumor model that are highly reliable and precise over the length of the vessel. Overall, we have developed a tool that enables researchers from many diverse disciplines to study previously inaccessible aspects of the DLBCL tumor microenvironment, with profound implications for drug delivery and design.

3D microvascular model recapitulates the diffuse large B-cell lymphoma tumor microenvironment in vitro

PubMed Central

Mannino, Robert G.; Santiago-Miranda, Adriana N.; Pradhan, Pallab; Qiu, Yongzhi; Mejias, Joscelyn C.; Neelapu, Sattva S.; Roy, Krishnendu; Lam, Wilbur A.

2017-01-01

Diffuse large B-cell lymphoma (DLBCL) is an aggressive cancer that affects ~22,000 people in the United States yearly. Understanding the complex cellular interactions of the tumor microenvironment is critical to the success and development of DLBCL treatment strategies. In vitro platforms that successfully model the complex tumor microenvironment without introducing the variability of in vivo systems are vital for understanding these interactions. To date, no such in vitro model exists that can accurately recapitulate the interactions that occur between immune cells, cancer cells, and endothelial cells in the tumor microenvironment of DLBCL. To that end, we developed a lymphoma-on-chip model consisting of a hydrogel based tumor model traversed by a vascularized, perfusable, round microchannel that successfully recapitulates key complexities and interactions of the in vivo tumor microenvironment in vitro. We have shown that the perfusion capabilities of this technique allow us to study targeted treatment strategies, as well as to model the diffusion of infused reagents spatiotemporally. Furthermore, this model employs a novel fabrication technique that utilizes common laboratory materials, and allows for the microfabrication of multiplex microvascular environments without the need for advanced microfabrication facilities. Through our facile microfabrication process, we are able to achieve micro vessels within a tumor model that are highly reliable and precise over the length of the vessel. Overall, we have developed a tool that enables researchers from many diverse disciplines to study previously inaccessible aspects of the DLBCL tumor microenvironment, with profound implications for drug delivery and design. PMID:28054086

Prediction of protein-protein interaction sites using electrostatic desolvation profiles.

PubMed

Fiorucci, Sébastien; Zacharias, Martin

2010-05-19

Protein-protein complex formation involves removal of water from the interface region. Surface regions with a small free energy penalty for water removal or desolvation may correspond to preferred interaction sites. A method to calculate the electrostatic free energy of placing a neutral low-dielectric probe at various protein surface positions has been designed and applied to characterize putative interaction sites. Based on solutions of the finite-difference Poisson equation, this method also includes long-range electrostatic contributions and the protein solvent boundary shape in contrast to accessible-surface-area-based solvation energies. Calculations on a large set of proteins indicate that in many cases (>90%), the known binding site overlaps with one of the six regions of lowest electrostatic desolvation penalty (overlap with the lowest desolvation region for 48% of proteins). Since the onset of electrostatic desolvation occurs even before direct protein-protein contact formation, it may help guide proteins toward the binding region in the final stage of complex formation. It is interesting that the probe desolvation properties associated with residue types were found to depend to some degree on whether the residue was outside of or part of a binding site. The probe desolvation penalty was on average smaller if the residue was part of a binding site compared to other surface locations. Applications to several antigen-antibody complexes demonstrated that the approach might be useful not only to predict protein interaction sites in general but to map potential antigenic epitopes on protein surfaces. Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Local structural ordering in surface-confined liquid crystals

NASA Astrophysics Data System (ADS)

Śliwa, I.; Jeżewski, W.; Zakharov, A. V.

2017-06-01

The effect of the interplay between attractive nonlocal surface interactions and attractive pair long-range intermolecular couplings on molecular structures of liquid crystals confined in thin cells with flat solid surfaces has been studied. Extending the McMillan mean field theory to include finite systems, it has been shown that confining surfaces can induce complex orientational and translational ordering of molecules. Typically, local smectic A, nematic, and isotropic phases have been shown to coexist in certain temperature ranges, provided that confining cells are sufficiently thick, albeit finite. Due to the nonlocality of surface interactions, the spatial arrangement of these local phases can display, in general, an unexpected complexity along the surface normal direction. In particular, molecules located in the vicinity of surfaces can still be organized in smectic layers, even though nematic and/or isotropic order can simultaneously appear in the interior of cells. The resulting surface freezing of smectic layers has been confirmed to occur even for rather weak surface interactions. The surface interactions cannot, however, prevent smectic layers from melting relatively close to system boundaries, even when molecules are still arranged in layers within the central region of the system. The internal interfaces, separating individual liquid-crystal phases, are demonstrated here to form fronts of local finite-size transitions that move across cells under temperature changes. Although the complex molecular ordering in surface confined liquid-crystal systems can essentially be controlled by temperature variations, specific thermal properties of these systems, especially the nature of the local transitions, are argued to be strongly conditioned to the degree of molecular packing.

Metal complexes as DNA intercalators.

PubMed

Liu, Hong-Ke; Sadler, Peter J

2011-05-17

DNA has a strong affinity for many heterocyclic aromatic dyes, such as acridine and its derivatives. Lerman in 1961 first proposed intercalation as the source of this affinity, and this mode of DNA binding has since attracted considerable research scrutiny. Organic intercalators can inhibit nucleic acid synthesis in vivo, and they are now common anticancer drugs in clinical therapy. The covalent attachment of organic intercalators to transition metal coordination complexes, yielding metallointercalators, can lead to novel DNA interactions that influence biological activity. Metal complexes with σ-bonded aromatic side arms can act as dual-function complexes: they bind to DNA both by metal coordination and through intercalation of the attached aromatic ligand. These aromatic side arms introduce new modes of DNA binding, involving mutual interactions of functional groups held in close proximity. The biological activity of both cis- and trans-diamine Pt(II) complexes is dramatically enhanced by the addition of σ-bonded intercalators. We have explored a new class of organometallic "piano-stool" Ru(II) and Os(II) arene anticancer complexes of the type [(η(6)-arene)Ru/Os(XY)Cl](+). Here XY is, for example, ethylenediamine (en), and the arene ligand can take many forms, including tetrahydroanthracene, biphenyl, or p-cymene. Arene-nucleobase stacking interactions can have a significant influence on both the kinetics and thermodynamics of DNA binding. In particular, the cytotoxic activity, conformational distortions, recognition by DNA-binding proteins, and repair mechanisms are dependent on the arene. A major difficulty in developing anticancer drugs is cross-resistance, a phenomenon whereby a cell that is resistant to one drug is also resistant to another drug in the same class. These new complexes are non-cross-resistant with cisplatin towards cancer cells: they constitute a new class of anticancer agents, with a mechanism of action that differs from the anticancer drug cisplatin and its analogs. The Ru-arene complexes with dual functions are more potent towards cancer cells than their nonintercalating analogs. In this Account, we focus on recent studies of dual-function organometallic Ru(II)- and Os(II)-arene complexes and the methods used to detect arene-DNA intercalation. We relate these interactions to the mechanism of anticancer activity and to structure-activity relationships. The interactions between these complexes and DNA show close similarities to those of covalent polycyclic aromatic carcinogens, especially to N7-alkylating intercalation compounds. However, Ru-arene complexes exhibit some new features. Classical intercalation and base extrusion next to the metallated base is observed for {(η(6)-biphenyl)Ru(ethylenediamine)}(2+) adducts of a 14-mer duplex, while penetrating arene intercalation occurs for adducts of the nonaromatic bulky intercalator {(η(6)-tetrahydroanthracene)Ru(ethylenediamine)}(2+) with a 6-mer duplex. The introduction of dual-function Ru-arene complexes introduces new mechanisms of antitumor activity, novel mechanisms for attack on DNA, and new concepts for developing structure- activity relationships. We hope this discussion will stimulate thoughtful and focused research on the design of anticancer chemotherapeutic agents using these unique approaches.

Host Genotype and Microbiota Contribute Asymmetrically to Transcriptional Variation in the Threespine Stickleback Gut

PubMed Central

Small, Clayton M.; Milligan-Myhre, Kathryn; Bassham, Susan; Guillemin, Karen

2017-01-01

Recent studies of interactions between hosts and their resident microbes have revealed important ecological and evolutionary consequences that emerge from these complex interspecies relationships, including diseases that occur when the interactions go awry. Given the preponderance of these interactions, we hypothesized that effects of the microbiota on gene expression in the developing gut—an important aspect of host biology—would be pervasive, and that these effects would be both comparable in magnitude to and contingent on effects of the host genetic background. To evaluate the effects of the microbiota, host genotype, and their interaction on gene expression in the gut of a genetically diverse, gnotobiotic host model, the threespine stickleback (Gasterosteus aculeatus), we compared RNA-seq data among 84 larval fish. Surprisingly, we found that stickleback population and family differences explained substantially more gene expression variation than the presence of microbes. Expression levels of 72 genes, however, were affected by our microbiota treatment. These genes, including many associated with innate immunity, comprise a tractable subset of host genetic factors for precise, systems-level study of host–microbe interactions in the future. Importantly, our data also suggest subtle signatures of a statistical interaction between host genotype and the microbiota on expression patterns of genetic pathways associated with innate immunity, coagulation and complement cascades, focal adhesion, cancer, and peroxisomes. These genotype-by-environment interactions may prove to be important leads to the understanding of host genetic mechanisms commonly at the root of sometimes complex molecular relationships between hosts and their resident microbes. PMID:28391321

Coordination Chemistry of Homoleptic Actinide(IV)-Thiocyanate Complexes

DOE PAGES

Carter, Tyler J.; Wilson, Richard E.

2015-09-10

Here, the synthesis, X-ray crystal structure, vibrational and optical spectroscopy for the eight-coordinate thiocyanate compounds, [Et 4N] 4[Pu IV(NCS) 8], [Et 4N] 4[Th IV(NCS) 8], and [Et 4N] 4[Ce III(NCS) 7(H 2O)] are reported. Thiocyanate was found to rapidly reduce plutonium to Pu III in acidic solutions (pH<1) in the presence of NCS –. The optical spectrum of [Et 4N][SCN] containing Pu III solution was indistinguishable from that of aquated Pu III suggesting that inner-sphere complexation with [Et 4N][SCN] does not occur in water. However, upon concentration, the homoleptic thiocyanate complex [Et 4N] 4[Pu IV(NCS) 8] was crystallized when amore » large excess of [Et 4N][NCS] was present. This compound, along with its U IV analogue, maintains inner-sphere thiocyanate coordination in acetonitrile based on the observation of intense ligand-to-metal charge-transfer bands. Spectroscopic and crystallographic data do not support the interaction of the metal orbitals with the ligand π system, but support an enhanced An IV–NCS interaction, as the Lewis acidity of the metal ion increases from Th to Pu.« less

Variability in the efficacy of psychopharmaceuticals: contributions from pharmacogenomics, ethnopsychopharmacology, and psychological and psychiatric anthropologies.

PubMed

Ninnemann, Kristi M

2012-03-01

Psychological and psychiatric anthropology have long questioned the universality of psychiatric diagnoses, bringing to light the fluidity of mental disorder, and recognizing that the experience and expression of psychopathology is influenced by complex and interacting genetic, environmental, and cultural factors. The majority of our discussions, however, have remained centered around the role of culture in shaping mental illness: drawing attention to subjective experiences of mental illness and culturally patterned modes of symptom presentation, and interrogating the cogency of universal diagnostic rubrics. Psychological and psychiatric anthropology have yet to robustly engage the broadly assumed universal validity of psychiatric medications and the ways in which they are prescribed and experienced. This article provides an introduction into the fields of pharmacogenomics and ethnopsychopharmacology, areas of inquiry seeking to understand the ways in which genetic variability occurring between, and within, large population groups influences individual ability to metabolize psychotropic medications. This piece further addresses the complex issue of psychopharmaceutical efficacy, stressing the ways in which, just as with psychopathology, medications and their outcomes are likewise influenced by the complex interactions of genes, environment, and culture. Lastly, ways in which anthropology can and should engage with the growing fields of pharmacogenomics and ethnopsychopharmacology are suggested.

Effects of surfactants on lipase structure, activity, and inhibition.

PubMed

Delorme, Vincent; Dhouib, Rabeb; Canaan, Stéphane; Fotiadu, Frédéric; Carrière, Frédéric; Cavalier, Jean-François

2011-08-01

Lipase inhibitors are the main anti-obesity drugs prescribed these days, but the complexity of their mechanism of action is making it difficult to develop new molecules for this purpose. The efficacy of these drugs is known to depend closely on the physico-chemistry of the lipid-water interfaces involved and on the unconventional behavior of the lipases which are their target enzymes. The lipolysis reaction which occurs at an oil-water interface involves complex equilibria between adsorption-desorption processes, conformational changes and catalytic mechanisms. In this context, surfactants can induce significant changes in the partitioning of the enzyme and the inhibitor between the water phase and lipid-water interfaces. Surfactants can be found at the oil-water interface where they compete with lipases for adsorption, but also in solution in the form of micellar aggregates and monomers that may interact with hydrophobic parts of lipases in solution. These various interactions, combined with the emulsification and dispersion of insoluble substrates and inhibitors, can either promote or decrease the activity and the inhibition of lipases. Here, we review some examples of the various effects of surfactants on lipase structure, activity and inhibition, which show how complex the various equilibria involved in the lipolysis reaction tend to be.

Streamwise Vorticity Generation in Laminar and Turbulent Jets

NASA Technical Reports Server (NTRS)

Demuren, Aodeji O.; Wilson, Robert V.

1999-01-01

Complex streamwise vorticity fields are observed in the evolution of non-circular jets. Generation mechanisms are investigated via Reynolds-averaged (RANS), large-eddy (LES) and direct numerical (DNS) simulations of laminar and turbulent rectangular jets. Complex vortex interactions are found in DNS of laminar jets, but axis-switching is observed only when a single instability mode is present in the incoming mixing layer. With several modes present, the structures are not coherent and no axis-switching occurs, RANS computations also produce no axis-switching. On the other hand, LES of high Reynolds number turbulent jets produce axis-switching even for cases with several instability modes in the mixing layer. Analysis of the source terms of the mean streamwise vorticity equation through post-processing of the instantaneous results shows that, complex interactions of gradients of the normal and shear Reynolds stresses are responsible for the generation of streamwise vorticity which leads to axis-switching. RANS computations confirm these results. k - epsilon turbulence model computations fail to reproduce the phenomenon, whereas algebraic Reynolds stress model (ASM) computations, in which the secondary normal and shear stresses are computed explicitly, succeeded in reproducing the phenomenon accurately.

“Engineering Substrate Micro- and Nanotopography to Control Cell Function”

PubMed Central

Bettinger, Christopher J; Langer, Robert; Borenstein, Jeffrey T

2010-01-01

Lead-In The interaction of mammalian cells with nanoscale topography has proven to be an important signaling modality in controlling cell function. Naturally occurring nanotopographic structures within the extracellular matrix present surrounding cells with mechanotransductive cues that influence local migration, cell polarization, and other functions. Synthetically nanofabricated topography can also influence cell morphology, alignment, adhesion, migration, proliferation, and cytoskeleton organization. Here we review the use of in vitro synthetic cell-nanotopography interactions to control cell behavior and influence complex cellular processes including stem cell differentiation and tissue organization. Future challenges and opportunities in cell-nanotopography engineering will also be discussed including the elucidation of mechanisms and applications in tissue engineering. PMID:19492373

Technological applications arising from the interactions of DNA bases with metal ions.

PubMed

Park, Ki Soo; Park, Hyun Gyu

2014-08-01

An intense interest has grown in the unique interactions of nucleic acids with metal ions, which lead to the formation of metal-base pairs and the generation of fluorescent nanomaterials. In this review, different types of metal-base pairs, especially those formed from naturally occurring nucleosides, are described with emphasis also being given to recent advances made in employing these complexes to govern enzymatic reactions. The review also contains a comprehensive description of DNA-templated inorganic nanomaterials such as silver nanoclusters which possess excellent fluorescence properties. Finally, a summary is given about how these materials have led to recent advances in the field of nanobiotechnology. Copyright © 2013 Elsevier Ltd. All rights reserved.

Neutrophils establish rapid and robust WAVE complex polarity in an actin-dependent fashion.

PubMed

Millius, Arthur; Dandekar, Sheel N; Houk, Andrew R; Weiner, Orion D

2009-02-10

Asymmetric intracellular signals enable cells to migrate in response to external cues. The multiprotein WAVE (also known as SCAR or WASF) complex activates the actin-nucleating Arp2/3 complex [1-4] and localizes to propagating "waves," which direct actin assembly during neutrophil migration [5, 6]. Here, we observe similar WAVE complex dynamics in other mammalian cells and analyze WAVE complex dynamics during establishment of neutrophil polarity. Earlier models proposed that spatially biased generation [7] or selection of protrusions [8] enables chemotaxis. These models require existing morphological polarity to control protrusions. We show that spatially biased generation and selection of WAVE complex recruitment also occur in morphologically unpolarized neutrophils during development of their first protrusions. Additionally, several mechanisms limit WAVE complex recruitment during polarization and movement: Intrinsic cues restrict WAVE complex distribution during establishment of polarity, and asymmetric intracellular signals constrain it in morphologically polarized cells. External gradients can overcome both intrinsic biases and control WAVE complex localization. After latrunculin-mediated inhibition of actin polymerization, addition and removal of agonist gradients globally recruits and releases the WAVE complex from the membrane. Under these conditions, the WAVE complex no longer polarizes, despite the presence of strong external gradients. Thus, actin polymer and the WAVE complex reciprocally interact during polarization.

A taxonomy of visualization tasks for the analysis of biological pathway data.

PubMed

Murray, Paul; McGee, Fintan; Forbes, Angus G

2017-02-15

Understanding complicated networks of interactions and chemical components is essential to solving contemporary problems in modern biology, especially in domains such as cancer and systems research. In these domains, biological pathway data is used to represent chains of interactions that occur within a given biological process. Visual representations can help researchers understand, interact with, and reason about these complex pathways in a number of ways. At the same time, these datasets offer unique challenges for visualization, due to their complexity and heterogeneity. Here, we present taxonomy of tasks that are regularly performed by researchers who work with biological pathway data. The generation of these tasks was done in conjunction with interviews with several domain experts in biology. These tasks require further classification than is provided by existing taxonomies. We also examine existing visualization techniques that support each task, and we discuss gaps in the existing visualization space revealed by our taxonomy. Our taxonomy is designed to support the development and design of future biological pathway visualization applications. We conclude by suggesting future research directions based on our taxonomy and motivated by the comments received by our domain experts.

An Exquisitely Specific PDZ/Target Recognition Revealed by the Structure of INAD PDZ3 in Complex with TRP Channel Tail.

PubMed

Ye, Fei; Liu, Wei; Shang, Yuan; Zhang, Mingjie

2016-03-01

The vast majority of PDZ domains are known to bind to a few C-terminal tail residues of target proteins with modest binding affinities and specificities. Such promiscuous PDZ/target interactions are not compatible with highly specific physiological functions of PDZ domain proteins and their targets. Here, we report an unexpected PDZ/target binding occurring between the scaffold protein inactivation no afterpotential D (INAD) and transient receptor potential (TRP) channel in Drosophila photoreceptors. The C-terminal 15 residues of TRP are required for the specific interaction with INAD PDZ3. The INAD PDZ3/TRP peptide complex structure reveals that only the extreme C-terminal Leu of TRP binds to the canonical αB/βB groove of INAD PDZ3. The rest of the TRP peptide, by forming a β hairpin structure, binds to a surface away from the αB/βB groove of PDZ3 and contributes to the majority of the binding energy. Thus, the INAD PDZ3/TRP channel interaction is exquisitely specific and represents a new mode of PDZ/target recognitions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Analysis of Power Laws, Shape Collapses, and Neural Complexity: New Techniques and MATLAB Support via the NCC Toolbox.

PubMed

Marshall, Najja; Timme, Nicholas M; Bennett, Nicholas; Ripp, Monica; Lautzenhiser, Edward; Beggs, John M

2016-01-01

Neural systems include interactions that occur across many scales. Two divergent methods for characterizing such interactions have drawn on the physical analysis of critical phenomena and the mathematical study of information. Inferring criticality in neural systems has traditionally rested on fitting power laws to the property distributions of "neural avalanches" (contiguous bursts of activity), but the fractal nature of avalanche shapes has recently emerged as another signature of criticality. On the other hand, neural complexity, an information theoretic measure, has been used to capture the interplay between the functional localization of brain regions and their integration for higher cognitive functions. Unfortunately, treatments of all three methods-power-law fitting, avalanche shape collapse, and neural complexity-have suffered from shortcomings. Empirical data often contain biases that introduce deviations from true power law in the tail and head of the distribution, but deviations in the tail have often been unconsidered; avalanche shape collapse has required manual parameter tuning; and the estimation of neural complexity has relied on small data sets or statistical assumptions for the sake of computational efficiency. In this paper we present technical advancements in the analysis of criticality and complexity in neural systems. We use maximum-likelihood estimation to automatically fit power laws with left and right cutoffs, present the first automated shape collapse algorithm, and describe new techniques to account for large numbers of neural variables and small data sets in the calculation of neural complexity. In order to facilitate future research in criticality and complexity, we have made the software utilized in this analysis freely available online in the MATLAB NCC (Neural Complexity and Criticality) Toolbox.

Protein Flexibility Facilitates Quaternary Structure Assembly and Evolution

PubMed Central

Marsh, Joseph A.; Teichmann, Sarah A.

2014-01-01

The intrinsic flexibility of proteins allows them to undergo large conformational fluctuations in solution or upon interaction with other molecules. Proteins also commonly assemble into complexes with diverse quaternary structure arrangements. Here we investigate how the flexibility of individual protein chains influences the assembly and evolution of protein complexes. We find that flexibility appears to be particularly conducive to the formation of heterologous (i.e., asymmetric) intersubunit interfaces. This leads to a strong association between subunit flexibility and homomeric complexes with cyclic and asymmetric quaternary structure topologies. Similarly, we also observe that the more nonhomologous subunits that assemble together within a complex, the more flexible those subunits tend to be. Importantly, these findings suggest that subunit flexibility should be closely related to the evolutionary history of a complex. We confirm this by showing that evolutionarily more recent subunits are generally more flexible than evolutionarily older subunits. Finally, we investigate the very different explorations of quaternary structure space that have occurred in different evolutionary lineages. In particular, the increased flexibility of eukaryotic proteins appears to enable the assembly of heteromeric complexes with more unique components. PMID:24866000

Origin of attraction in p-benzoquinone complexes with benzene and p-hydroquinone.

PubMed

Tsuzuki, Seiji; Uchimaru, Tadafumi; Ono, Taizo

2017-08-30

The origin of the attraction in charge-transfer complexes (a p-hydroquinone-p-benzoquinone complex and benzene complexes with benzoquinone, tetracyanoethylene and Br 2 ) was analyzed using distributed multipole analysis and symmetry-adapted perturbation theory. Both methods show that the dispersion interactions are the primary source of the attraction in these charge-transfer complexes followed by the electrostatic interactions. The natures of the intermolecular interactions in these complexes are close to the π/π interactions of neutral aromatic molecules. The electrostatic interactions play important roles in determining the magnitude of the attraction. The contribution of charge-transfer interactions to the attraction is not large compared with the dispersion interactions in these complexes.

Macroscopic and microscopic investigation of Ni(II) sequestration on diatomite by batch, XPS, and EXAFS techniques.

PubMed

Sheng, Guodong; Yang, Shitong; Sheng, Jiang; Hu, Jun; Tan, Xiaoli; Wang, Xiangke

2011-09-15

Sequestration of Ni(II) on diatomite as a function of time, pH, and temperature was investigated by batch, XPS, and EXAFS techniques. The ionic strength-dependent sorption at pH < 7.0 was consistent with outer-sphere surface complexation, while the ionic strength-independent sorption at pH = 7.0-8.6 was indicative of inner-sphere surface complexation. EXAFS results indicated that the adsorbed Ni(II) consisted of ∼6 O at R(Ni-O) ≈ 2.05 Å. EXAFS analysis from the second shell suggested that three phenomena occurred at the diatomite/water interface: (1) outer-sphere and/or inner-sphere complexation; (2) dissolution of Si which is the rate limiting step during Ni uptake; and (3) extensive growth of surface (co)precipitates. Under acidic conditions, outer-sphere complexation is the main mechanism controlling Ni uptake, which is in good agreement with the macroscopic results. At contact time of 1 h or 1 day or pH = 7.0-8.0, surface coprecipitates occur concurrently with inner-sphere complexes on diatomite surface, whereas at contact time of 1 month or pH = 10.0, surface (co)precipitates dominate Ni uptake. Furthermore, surface loading increases with temperature increasing, and surface coprecipitates become the dominant mechanism at elevated temperature. The results are important to understand Ni interaction with minerals at the solid-water interface, which is helpful to evaluate the mobility of Ni(II) in the natural environment.

Climate Change, Nutrition, and Bottom-Up and Top-Down Food Web Processes.

PubMed

Rosenblatt, Adam E; Schmitz, Oswald J

2016-12-01

Climate change ecology has focused on climate effects on trophic interactions through the lenses of temperature effects on organismal physiology and phenological asynchronies. Trophic interactions are also affected by the nutrient content of resources, but this topic has received less attention. Using concepts from nutritional ecology, we propose a conceptual framework for understanding how climate affects food webs through top-down and bottom-up processes impacted by co-occurring environmental drivers. The framework integrates climate effects on consumer physiology and feeding behavior with effects on resource nutrient content. It illustrates how studying responses of simplified food webs to simplified climate change might produce erroneous predictions. We encourage greater integrative complexity of climate change research on trophic interactions to resolve patterns and enhance predictive capacities. Copyright © 2016 Elsevier Ltd. All rights reserved.

Selective Plasma Etching of Polymeric Substrates for Advanced Applications

PubMed Central

Puliyalil, Harinarayanan; Cvelbar, Uroš

2016-01-01

In today’s nanoworld, there is a strong need to manipulate and process materials on an atom-by-atom scale with new tools such as reactive plasma, which in some states enables high selectivity of interaction between plasma species and materials. These interactions first involve preferential interactions with precise bonds in materials and later cause etching. This typically occurs based on material stability, which leads to preferential etching of one material over other. This process is especially interesting for polymeric substrates with increasing complexity and a “zoo” of bonds, which are used in numerous applications. In this comprehensive summary, we encompass the complete selective etching of polymers and polymer matrix micro-/nanocomposites with plasma and unravel the mechanisms behind the scenes, which ultimately leads to the enhancement of surface properties and device performance. PMID:28335238

Structural and functional analysis of an essential nucleoporin heterotrimer on the cytoplasmic face of the nuclear pore complex

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

Yoshida, Kimihisa; Seo, Hyuk-Soo; Debler, Erik W.

2012-07-25

So far, only a few of the interactions between the {approx}30 nucleoporins comprising the modular structure of the nuclear pore complex have been defined at atomic resolution. Here we report the crystal structure, at 2.6 {angstrom} resolution, of a heterotrimeric complex, composed of fragments of three cytoplasmically oriented nucleoporins of yeast: Nup82, Nup116, and Nup159. Our data show that the Nup82 fragment, representing more than the N-terminal half of the molecule, folds into an extensively decorated, seven-bladed {beta}-propeller that forms the centerpiece of this heterotrimeric complex and anchors both a C-terminal fragment of Nup116 and the C-terminal tail of Nup159.more » Binding between Nup116 and Nup82 is mutually reinforced via two loops, one emanating from the Nup82 {beta}-propeller and the other one from the {beta}-sandwich fold of Nup116, each contacting binding pockets in their counterparts. The Nup82-Nup159 interaction occurs through an amphipathic {alpha}-helix of Nup159, which is cradled in a large hydrophobic groove that is generated from several large surface decorations of the Nup82 {beta}-propeller. Although Nup159 and Nup116 fragments bind to the Nup82 {beta}-propeller in close vicinity, there are no direct contacts between them, consistent with the noncooperative binding that was detected biochemically. Extensive mutagenesis delineated hot-spot residues for these interactions. We also showed that the Nup82 {beta}-propeller binds to other yeast Nup116 family members, Nup145N, Nup100 and to the mammalian homolog, Nup98. Notably, each of the three nucleoporins contains additional nuclear pore complex binding sites, distinct from those that were defined here in the heterotrimeric Nup82 {center_dot} Nup159 {center_dot} Nup116 complex.« less

Mechanisms and Regulation of Alternative Pre-mRNA Splicing

PubMed Central

Lee, Yeon

2015-01-01

Precursor messenger RNA (pre-mRNA) splicing is a critical step in the posttranscriptional regulation of gene expression, providing significant expansion of the functional proteome of eukaryotic organisms with limited gene numbers. Split eukaryotic genes contain intervening sequences or introns disrupting protein-coding exons, and intron removal occurs by repeated assembly of a large and highly dynamic ribonucleoprotein complex termed the spliceosome, which is composed of five small nuclear ribonucleoprotein particles, U1, U2, U4/U6, and U5. Biochemical studies over the past 10 years have allowed the isolation as well as compositional, functional, and structural analysis of splicing complexes at distinct stages along the spliceosome cycle. The average human gene contains eight exons and seven introns, producing an average of three or more alternatively spliced mRNA isoforms. Recent high-throughput sequencing studies indicate that 100% of human genes produce at least two alternative mRNA isoforms. Mechanisms of alternative splicing include RNA–protein interactions of splicing factors with regulatory sites termed silencers or enhancers, RNA–RNA base-pairing interactions, or chromatin-based effects that can change or determine splicing patterns. Disease-causing mutations can often occur in splice sites near intron borders or in exonic or intronic RNA regulatory silencer or enhancer elements, as well as in genes that encode splicing factors. Together, these studies provide mechanistic insights into how spliceosome assembly, dynamics, and catalysis occur; how alternative splicing is regulated and evolves; and how splicing can be disrupted by cis- and trans-acting mutations leading to disease states. These findings make the spliceosome an attractive new target for small-molecule, antisense, and genome-editing therapeutic interventions. PMID:25784052

Mapping of contact sites in complex formation between transducin and light-activated rhodopsin by covalent crosslinking: Use of a photoactivatable reagent

PubMed Central

Cai, Kewen; Itoh, Yoshiki; Khorana, H. Gobind

2001-01-01

Interaction of light-activated rhodopsin with transducin (T) is the first event in visual signal transduction. We use covalent crosslinking approaches to map the contact sites in interaction between the two proteins. Here we use a photoactivatable reagent, N-[(2-pyridyldithio)-ethyl], 4-azido salicylamide. The reagent is attached to the SH group of cytoplasmic monocysteine rhodopsin mutants by a disulfide-exchange reaction with the pyridylthio group, and the derivatized rhodopsin then is complexed with T by illumination at λ >495 nm. Subsequent irradiation of the complex at λ310 nm generates covalent crosslinks between the two proteins. Crosslinking was demonstrated between T and a number of single cysteine rhodopsin mutants. However, sites of crosslinks were investigated in detail only between T and the rhodopsin mutant S240C (cytoplasmic loop V-VI). Crosslinking occurred predominantly with Tα. For identification of the sites of crosslinks in Tα, the strategy used involved: (i) derivatization of all of the free cysteines in the crosslinked proteins with N-ethylmaleimide; (ii) reduction of the disulfide bond linking the two proteins and isolation of all of the Tα species carrying the crosslinked moiety with a free SH group; (iii) adduct formation of the latter with the N-maleimide moiety of the reagent, maleimido-butyryl-biocytin, containing a biotinyl group; (iv) trypsin degradation of the resulting Tα derivatives and isolation of Tα peptides carrying maleimido-butyryl-biocytin by avidin-agarose chromatography; and (v) identification of the isolated peptides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. We found that crosslinking occurred mainly to two C-terminal peptides in Tα containing the amino acid sequences 310–313 and 342–345. PMID:11320237

Medication Management: The Macrocognitive Workflow of Older Adults With Heart Failure

PubMed Central

2016-01-01

Background Older adults with chronic disease struggle to manage complex medication regimens. Health information technology has the potential to improve medication management, but only if it is based on a thorough understanding of the complexity of medication management workflow as it occurs in natural settings. Prior research reveals that patient work related to medication management is complex, cognitive, and collaborative. Macrocognitive processes are theorized as how people individually and collaboratively think in complex, adaptive, and messy nonlaboratory settings supported by artifacts. Objective The objective of this research was to describe and analyze the work of medication management by older adults with heart failure, using a macrocognitive workflow framework. Methods We interviewed and observed 61 older patients along with 30 informal caregivers about self-care practices including medication management. Descriptive qualitative content analysis methods were used to develop categories, subcategories, and themes about macrocognitive processes used in medication management workflow. Results We identified 5 high-level macrocognitive processes affecting medication management—sensemaking, planning, coordination, monitoring, and decision making—and 15 subprocesses. Data revealed workflow as occurring in a highly collaborative, fragile system of interacting people, artifacts, time, and space. Process breakdowns were common and patients had little support for macrocognitive workflow from current tools. Conclusions Macrocognitive processes affected medication management performance. Describing and analyzing this performance produced recommendations for technology supporting collaboration and sensemaking, decision making and problem detection, and planning and implementation. PMID:27733331

Encapsulation of the Antioxidant R-(+)-α-Lipoic Acid in Permethylated α- and β-Cyclodextrins: Thermal and X-ray Structural Characterization of the 1:1 Inclusion Complexes.

PubMed

Caira, Mino R; Bourne, Susan A; Mzondo, Buntubonke

2017-05-23

The naturally occurring compound α-lipoic acid (ALA) is implicated in manifold critical biological roles and its potent antioxidant properties and potential for treatment of various diseases have led to its widespread use as a dietary supplement. However, shortcomings of poor aqueous solubility and low thermal stability have hampered its development as a medicinal agent, prompting the use of cyclodextrins (CDs) to address these problems. The paucity of published structural data on the nature of the interactions between ALA and CDs motivated the present study, which describes the synthesis and X-ray structural elucidation of crystalline inclusion complexes between the biologically relevant R-(+)-α-lipoic acid (RALA) and the host molecules permethylated α-CD (TMA) and permethylated β-CD (TMB). Single crystal X-ray diffraction of TMA·RALA·6H₂O and TMB·RALA revealed significantly different orientations of the RALA molecule within the TMA and TMB cavities, but in both cases the guest molecule is fully encapsulated by the respective parent host molecules and residues of CD molecules of neighboring complex units. While pure RALA melted at 46-48 °C, combined thermal analysis techniques indicated that on heating the respective complexes, the release of RALA occurred at significantly higher onset temperatures, in the range 150-170 °C.

Medication Management: The Macrocognitive Workflow of Older Adults With Heart Failure.

PubMed

Mickelson, Robin S; Unertl, Kim M; Holden, Richard J

2016-10-12

Older adults with chronic disease struggle to manage complex medication regimens. Health information technology has the potential to improve medication management, but only if it is based on a thorough understanding of the complexity of medication management workflow as it occurs in natural settings. Prior research reveals that patient work related to medication management is complex, cognitive, and collaborative. Macrocognitive processes are theorized as how people individually and collaboratively think in complex, adaptive, and messy nonlaboratory settings supported by artifacts. The objective of this research was to describe and analyze the work of medication management by older adults with heart failure, using a macrocognitive workflow framework. We interviewed and observed 61 older patients along with 30 informal caregivers about self-care practices including medication management. Descriptive qualitative content analysis methods were used to develop categories, subcategories, and themes about macrocognitive processes used in medication management workflow. We identified 5 high-level macrocognitive processes affecting medication management-sensemaking, planning, coordination, monitoring, and decision making-and 15 subprocesses. Data revealed workflow as occurring in a highly collaborative, fragile system of interacting people, artifacts, time, and space. Process breakdowns were common and patients had little support for macrocognitive workflow from current tools. Macrocognitive processes affected medication management performance. Describing and analyzing this performance produced recommendations for technology supporting collaboration and sensemaking, decision making and problem detection, and planning and implementation.

Predicting the Impact of Alternative Splicing on Plant MADS Domain Protein Function

PubMed Central

Severing, Edouard I.; van Dijk, Aalt D. J.; Morabito, Giuseppa; Busscher-Lange, Jacqueline; Immink, Richard G. H.; van Ham, Roeland C. H. J.

2012-01-01

Several genome-wide studies demonstrated that alternative splicing (AS) significantly increases the transcriptome complexity in plants. However, the impact of AS on the functional diversity of proteins is difficult to assess using genome-wide approaches. The availability of detailed sequence annotations for specific genes and gene families allows for a more detailed assessment of the potential effect of AS on their function. One example is the plant MADS-domain transcription factor family, members of which interact to form protein complexes that function in transcription regulation. Here, we perform an in silico analysis of the potential impact of AS on the protein-protein interaction capabilities of MIKC-type MADS-domain proteins. We first confirmed the expression of transcript isoforms resulting from predicted AS events. Expressed transcript isoforms were considered functional if they were likely to be translated and if their corresponding AS events either had an effect on predicted dimerisation motifs or occurred in regions known to be involved in multimeric complex formation, or otherwise, if their effect was conserved in different species. Nine out of twelve MIKC MADS-box genes predicted to produce multiple protein isoforms harbored putative functional AS events according to those criteria. AS events with conserved effects were only found at the borders of or within the K-box domain. We illustrate how AS can contribute to the evolution of interaction networks through an example of selective inclusion of a recently evolved interaction motif in the MADS AFFECTING FLOWERING1-3 (MAF1–3) subclade. Furthermore, we demonstrate the potential effect of an AS event in SHORT VEGETATIVE PHASE (SVP), resulting in the deletion of a short sequence stretch including a predicted interaction motif, by overexpression of the fully spliced and the alternatively spliced SVP transcripts. For most of the AS events we were able to formulate hypotheses about the potential impact on the interaction capabilities of the encoded MIKC proteins. PMID:22295091

Exploring the Human-Nipah Virus Protein-Protein Interactome

PubMed Central

Vera-Velasco, Natalia M.; Mingarro, Ismael

2017-01-01

ABSTRACT Nipah virus is an emerging, highly pathogenic, zoonotic virus of the Paramyxoviridae family. Human transmission occurs by close contact with infected animals, the consumption of contaminated food, or, occasionally, via other infected individuals. Currently, we lack therapeutic or prophylactic treatments for Nipah virus. To develop these agents we must now improve our understanding of the host-virus interactions that underpin a productive infection. This aim led us to perform the present work, in which we identified 101 human-Nipah virus protein-protein interactions (PPIs), most of which (88) are novel. This data set provides a comprehensive view of the host complexes that are manipulated by viral proteins. Host targets include the PRP19 complex and the microRNA (miRNA) processing machinery. Furthermore, we explored the biologic consequences of the interaction with the PRP19 complex and found that the Nipah virus W protein is capable of altering p53 control and gene expression. We anticipate that these data will help in guiding the development of novel interventional strategies to counter this emerging viral threat. IMPORTANCE Nipah virus is a recently discovered virus that infects a wide range of mammals, including humans. Since its discovery there have been yearly outbreaks, and in some of them the mortality rate has reached 100% of the confirmed cases. However, the study of Nipah virus has been largely neglected, and currently we lack treatments for this infection. To develop these agents we must now improve our understanding of the host-virus interactions that underpin a productive infection. In the present work, we identified 101 human-Nipah virus protein-protein interactions using an affinity purification approach coupled with mass spectrometry. Additionally, we explored the cellular consequences of some of these interactions. Globally, this data set offers a comprehensive and detailed view of the host machinery's contribution to the Nipah virus's life cycle. Furthermore, our data present a large number of putative drug targets that could be exploited for the treatment of this infection. PMID:28904190

Exploring the Human-Nipah Virus Protein-Protein Interactome.

PubMed

Martinez-Gil, Luis; Vera-Velasco, Natalia M; Mingarro, Ismael

2017-12-01

Nipah virus is an emerging, highly pathogenic, zoonotic virus of the Paramyxoviridae family. Human transmission occurs by close contact with infected animals, the consumption of contaminated food, or, occasionally, via other infected individuals. Currently, we lack therapeutic or prophylactic treatments for Nipah virus. To develop these agents we must now improve our understanding of the host-virus interactions that underpin a productive infection. This aim led us to perform the present work, in which we identified 101 human-Nipah virus protein-protein interactions (PPIs), most of which (88) are novel. This data set provides a comprehensive view of the host complexes that are manipulated by viral proteins. Host targets include the PRP19 complex and the microRNA (miRNA) processing machinery. Furthermore, we explored the biologic consequences of the interaction with the PRP19 complex and found that the Nipah virus W protein is capable of altering p53 control and gene expression. We anticipate that these data will help in guiding the development of novel interventional strategies to counter this emerging viral threat. IMPORTANCE Nipah virus is a recently discovered virus that infects a wide range of mammals, including humans. Since its discovery there have been yearly outbreaks, and in some of them the mortality rate has reached 100% of the confirmed cases. However, the study of Nipah virus has been largely neglected, and currently we lack treatments for this infection. To develop these agents we must now improve our understanding of the host-virus interactions that underpin a productive infection. In the present work, we identified 101 human-Nipah virus protein-protein interactions using an affinity purification approach coupled with mass spectrometry. Additionally, we explored the cellular consequences of some of these interactions. Globally, this data set offers a comprehensive and detailed view of the host machinery's contribution to the Nipah virus's life cycle. Furthermore, our data present a large number of putative drug targets that could be exploited for the treatment of this infection. Copyright © 2017 American Society for Microbiology.

Influence of diabetes on the pharmacokinetic behavior of natural polyphenols.

PubMed

Xiao, Jianbo; Högger, Petra

2014-01-01

The development of food fortified with polyphenols and polyphenol-rich foods represents a novel approach to prevent or attenuate type 2 diabetes. It has been reported that type 2 diabetes may affect the pharmacokinetics of various drugs in several animal models. There is powerful evidence linking dietary polyphenols consumption with the risk factors defining type 2 diabetes, even if some opposite results occurred. This mini-review summarizes important advances on diabetes-associated changes in pharmacokinetics of natural polyphenols. The pharmacokinetic behavior between drugs and dietary polyphenols probably may be different due to (i) Ingested dose/amount per day. The dietary polyphenol intake per day is much higher than that of clinical drugs; (ii) Complexity of the components. Clinical drugs are well-characterized and typically small molecules. However, the polyphenols in diet are unimaginably complex; (iii) Interaction with food proteins. Although the effects of food proteins on the bioavailability of polyphenols are still not examined in much detail, direct binding interactions of polyphenols to proteins always occur; (iv) The most common polyphenols in the human diet have a low intrinsic activity and are poorly absorbed from the intestine, highly metabolized, or rapidly eliminated. Although there is very limited information available so far, it is proposed that type 2 diabetes influences the pharmacokinetic behavior of dietary polyphenols including: i) competition of glucose with polyphenols regarding binding to plasma proteins; ii) weakened non-covalent interaction affinities of plasma proteins for natural polyphenols due to protein glycation in type II diabetes; iii) the enhanced clearance of polyphenols in type 2 diabetes. An understanding of diabetes-associated changes in absorption, distribution, metabolism, elimination and bioactivities of natural polyphenols as well as the mechanism of the variability should lead to the improvement of the benefits of these polyphenols and clinical outcomes for diabetics.

Electrostatic orientation of the electron-transfer complex between plastocyanin and cytochrome c.

PubMed

Roberts, V A; Freeman, H C; Olson, A J; Tainer, J A; Getzoff, E D

1991-07-15

To understand the specificity and efficiency of protein-protein interactions promoting electron transfer, we evaluated the role of electrostatic forces in precollision orientation by the development of two new methods, computer graphics alignment of protein electrostatic fields and a systematic orientational search of intermolecular electrostatic energies for two proteins at present separation distances. We applied these methods to the plastocyanin/cytochrome c interaction, which is faster than random collision, but too slow for study by molecular dynamics techniques. Significant electrostatic potentials were concentrated on one-fourth (969 A2) of the plastocyanin surface, with the greatest negative potential centered on the Tyr-83 hydroxyl within the acidic patch, and on one-eighth (632 A2) of the cytochrome c surface, with the greatest positive potential centered near the exposed heme edge. Coherent electrostatic fields occurred only over these regions, suggesting that local, rather than global, charge complementarity controls productive recognition. The three energetically favored families of pre-collision orientations all directed the positive region surrounding the heme edge of cytochrome c toward the acidic patch of plastocyanin but differed in heme plane orientation. Analysis of electrostatic fields, electrostatic energies of precollision orientations with 12 and 6 A separation distances, and surface topographies suggested that the favored orientations should converge to productive complexes promoting a single electron-transfer pathway from the cytochrome c heme edge to Tyr-83 of plastocyanin. Direct interactions of the exposed Cu ligand in plastocyanin with the cytochrome c heme edge are not unfavorable sterically or electrostatically but should occur no faster than randomly, indicating that this is not the primary pathway for electron transfer.

Nonlinear effects in evolution - an ab initio study: A model in which the classical theory of evolution occurs as a special case.

PubMed

Clerc, Daryl G

2016-07-21

An ab initio approach was used to study the molecular-level interactions that connect gene-mutation to changes in an organism׳s phenotype. The study provides new insights into the evolutionary process and presents a simplification whereby changes in phenotypic properties may be studied in terms of the binding affinities of the chemical interactions affected by mutation, rather than by correlation to the genes. The study also reports the role that nonlinear effects play in the progression of organs, and how those effects relate to the classical theory of evolution. Results indicate that the classical theory of evolution occurs as a special case within the ab initio model - a case having two attributes. The first attribute: proteins and promoter regions are not shared among organs. The second attribute: continuous limiting behavior exists in the physical properties of organs as well as in the binding affinity of the associated chemical interactions, with respect to displacements in the chemical properties of proteins and promoter regions induced by mutation. Outside of the special case, second-order coupling contributions are significant and nonlinear effects play an important role, a result corroborated by analyses of published activity levels in binding and transactivation assays. Further, gradations in the state of perfection of an organ may be small or large depending on the type of mutation, and not necessarily closely-separated as maintained by the classical theory. Results also indicate that organs progress with varying degrees of interdependence, the likelihood of successful mutation decreases with increasing complexity of the affected chemical system, and differences between the ab initio model and the classical theory increase with increasing complexity of the organism. Copyright © 2016 The Author. Published by Elsevier Ltd.. All rights reserved.

Response of Two Mytilids to a Heatwave: The Complex Interplay of Physiology, Behaviour and Ecological Interactions

PubMed Central

Gestoso, Ignacio; Lima, Fernando P.; Vázquez, Elsa; Comeau, Luc A.; Gomes, Filipa; Seabra, Rui

2016-01-01

Different combinations of behavioural and physiological responses may play a crucial role in the ecological success of species, notably in the context of biological invasions. The invasive mussel Xenostrobus securis has successfully colonised the inner part of the Galician Rias Baixas (NW Spain), where it co-occurs with the commercially-important mussel Mytilus galloprovincialis. This study investigated the effect of a heatwave on the physiological and behavioural responses in monospecific or mixed aggregations of these species. In a mesocosm experiment, mussels were exposed to simulated tidal cycles and similar temperature conditions to those experienced in the field during a heat-wave that occurred in the summer of 2013, when field robo-mussels registered temperatures up to 44.5°C at low tide. The overall responses to stress differed markedly between the two species. In monospecific aggregations M. galloprovincialis was more vulnerable than X. securis to heat exposure during emersion. However, in mixed aggregations, the presence of the invader was associated with lower mortality in M. galloprovincialis. The greater sensitivity of M. galloprovincialis to heat exposure was reflected in a higher mortality level, greater induction of Hsp70 protein and higher rates of respiration and gaping activity, which were accompanied by a lower heart rate (bradycardia). The findings show that the invader enhanced the physiological performance of M. galloprovincialis, highlighting the importance of species interactions in regulating responses to environmental stress. Understanding the complex interactions between ecological factors and physiological and behavioural responses of closely-related species is essential for predicting the impacts of invasions in the context of future climate change. PMID:27736896

Geologic structures related to New Madrid earthquakes near Memphis, Tennessee, based on gravity and magnetic interpretations

USGS Publications Warehouse

Hildenbrand, T.G.; Stuart, W.D.; Talwani, P.

2001-01-01

New inversions of gravity and magnetic data in the region north of memphis. Tennessee, and south of latitude 36?? define boundaries of regional structures and igneous complexes in the upper crust. Microseismicity patterns near interpreted boundaries suggest that igneous complexes influence the locations of microseismicity. A weak seismicity cluster occurs near one intrusion (Covington pluton), at the intersection of the southwest margin of the Missouri batholith and the southeast margin of the Reelfoot rift. A narrow seismicity trend along the Reelfoot rift axis becomes diffuse near a second intrusion (Osceola intrusive complex) and changes direction to an area along the northwest flank of the intrusion. The axial seismicity trend also contains a tight cluster of earthquakes located just outside the Osceola intrusive complex. The mechanical explanation of the two seismicity patterns is uncertain, but the first cluster may be caused by stress concentration due to the high elastic stiffness and strength of the Covington intrusion. The spatially changing seismicity pattern near the Osceola complex may be caused by the preceding factors plus interaction with faulting along the rift axis. The axial seismicity strand itself is one of several connected and interacting active strands that may produce stress concentrations at strand ends and junctions. The microseismicity clusters at the peripheries of the two intrusions lead us to conclude that these stress concentrations or stressed volumes may be locations of future moderate to large earthquakes near Memphis. Published by Elsevier Science B.V.

Coupling functions: Universal insights into dynamical interaction mechanisms

NASA Astrophysics Data System (ADS)

Stankovski, Tomislav; Pereira, Tiago; McClintock, Peter V. E.; Stefanovska, Aneta

2017-10-01

The dynamical systems found in nature are rarely isolated. Instead they interact and influence each other. The coupling functions that connect them contain detailed information about the functional mechanisms underlying the interactions and prescribe the physical rule specifying how an interaction occurs. A coherent and comprehensive review is presented encompassing the rapid progress made recently in the analysis, understanding, and applications of coupling functions. The basic concepts and characteristics of coupling functions are presented through demonstrative examples of different domains, revealing the mechanisms and emphasizing their multivariate nature. The theory of coupling functions is discussed through gradually increasing complexity from strong and weak interactions to globally coupled systems and networks. A variety of methods that have been developed for the detection and reconstruction of coupling functions from measured data is described. These methods are based on different statistical techniques for dynamical inference. Stemming from physics, such methods are being applied in diverse areas of science and technology, including chemistry, biology, physiology, neuroscience, social sciences, mechanics, and secure communications. This breadth of application illustrates the universality of coupling functions for studying the interaction mechanisms of coupled dynamical systems.

Planetary Wave-Tide Interactions in Atmosphere-Ionosphere Coupling, Xiaoli Zhang, Jeffrey M. Forbes, Astrid Maute, and Maura E. Hagan

NASA Astrophysics Data System (ADS)

Zhang, X.; Forbes, J. M.; Maute, A. I.

2017-12-01

Planetary Wave-Tide Interactions in Atmosphere-Ionosphere Coupling Xiaoli Zhang, Jeffrey M. Forbes, Astrid Maute, and Maura E. Hagan The existence of secondary waves in the mesosphere and thermosphere due to nonlinear interactions between atmospheric tides and longer-period waves have been revealed in both satellite data and in the National Center for Atmospheric Research (NCAR) Thermosphere Ionosphere Mesosphere Electrodynamics General Circulation Model (TIME-GCM). The longer-period waves include the quasi-2-day and 6-day westward-propagating "normal modes" of the atmosphere, and eastward-propagating ultra-fast Kelvin waves with periods between 2 and 4 days. The secondary waves add to both the temporal and longitude variability of the atmosphere beyond that associated with the linear superposition of the interacting waves, thus adding "complexity" to the system. Based on our knowledge of the processes governing atmosphere-ionosphere interactions, similar revelations are expected to occur in electric fields, vertical plasma drifts and F-region electron densities. Towards this end, examples of such ionospheric manifestations of wave-wave interactions in TIE-GCM simulations will be presented.

Chabazite and dolomite formation in a dolocrete profile: An example of a complex alkaline paragenesis in Lanzarote, Canary Islands

NASA Astrophysics Data System (ADS)

Alonso-Zarza, Ana M.; Bustamante, Leticia; Huerta, Pedro; Rodríguez-Berriguete, Álvaro; Huertas, María José

2016-05-01

This paper studies the weathering and soil formation processes operating on detrital sediments containing alkaline volcanic rock fragments of the Mirador del Río dolocrete profile. The profile consists of a lower horizon of removilised weathered basalts, an intermediate red sandy mudstones horizon with irregular carbonate layers and a topmost horizon of amalgamated carbonate layers with root traces. Formation occurred in arid to semiarid climates, giving place to a complex mineralogical association, including Mg-carbonates and chabazite, rarely described in cal/dolocretes profiles. Initial vadose weathering processes occurred in the basalts and in directly overlying detrital sediments, producing (Stage 1) red-smectites and dolomicrite. Dominant phreatic (Stage 2) conditions allowed precipitation of coarse-zoned dolomite and chabazite filling porosities. In Stages 3 and 4, mostly pedogenic, biogenic processes played an important role in dolomite and calcite accumulation in the profile. Overall evolution of the profile and its mineralogical association involved initial processes dominated by alteration of host rock, to provide silica and Mg-rich alkaline waters, suitable for chabazite and dolomite formation, without a previous carbonate phase. Dolomite formed both abiogenically and biogenically, but without a previous carbonate precursor and in the absence of evaporites. Dominance of calcite towards the profile top is the result of Mg/Ca decrease in the interstitial meteoric waters due to decreased supply of Mg from weathering, and increased supply of Ca in aeolian dust. Meteoric origin of the water is confirmed by C and O isotope values, which also indicate lack of deep sourced CO2. The dolocrete studied and its complex mineral association reveal the complex interactions that occur at surface during weathering and pedogenesis of basalt-sourced rocks.

Immunodetection of human topoisomerase I-DNA covalent complexes

PubMed Central

Patel, Anand G.; Flatten, Karen S.; Peterson, Kevin L.; Beito, Thomas G.; Schneider, Paula A.; Perkins, Angela L.; Harki, Daniel A.; Kaufmann, Scott H.

2016-01-01

A number of established and investigational anticancer drugs slow the religation step of DNA topoisomerase I (topo I). These agents induce cytotoxicity by stabilizing topo I-DNA covalent complexes, which in turn interact with advancing replication forks or transcription complexes to generate lethal lesions. Despite the importance of topo I-DNA covalent complexes, it has been difficult to detect these lesions within intact cells and tumors. Here, we report development of a monoclonal antibody that specifically recognizes covalent topo I-DNA complexes, but not free topo I or DNA, by immunoblotting, immunofluorescence or flow cytometry. Utilizing this antibody, we demonstrate readily detectable topo I-DNA covalent complexes after treatment with camptothecins, indenoisoquinolines and cisplatin but not nucleoside analogues. Topotecan-induced topo I-DNA complexes peak at 15–30 min after drug addition and then decrease, whereas indotecan-induced complexes persist for at least 4 h. Interestingly, simultaneous staining for covalent topo I-DNA complexes, phospho-H2AX and Rad51 suggests that topotecan-induced DNA double-strand breaks occur at sites distinct from stabilized topo I-DNA covalent complexes. These studies not only provide new insight into the action of topo I-directed agents, but also illustrate a strategy that can be applied to study additional topoisomerases and their inhibitors in vitro and in vivo. PMID:26917015

Magnetic Reconnection at a Thin Current Sheet Separating Two Interlaced Flux Tubes at the Earth's Magnetopause

NASA Astrophysics Data System (ADS)

Kacem, I.; Jacquey, C.; Génot, V.; Lavraud, B.; Vernisse, Y.; Marchaudon, A.; Le Contel, O.; Breuillard, H.; Phan, T. D.; Hasegawa, H.; Oka, M.; Trattner, K. J.; Farrugia, C. J.; Paulson, K.; Eastwood, J. P.; Fuselier, S. A.; Turner, D.; Eriksson, S.; Wilder, F.; Russell, C. T.; Øieroset, M.; Burch, J.; Graham, D. B.; Sauvaud, J.-A.; Avanov, L.; Chandler, M.; Coffey, V.; Dorelli, J.; Gershman, D. J.; Giles, B. L.; Moore, T. E.; Saito, Y.; Chen, L.-J.; Penou, E.

2018-03-01

The occurrence of spatially and temporally variable reconnection at the Earth's magnetopause leads to the complex interaction of magnetic fields from the magnetosphere and magnetosheath. Flux transfer events (FTEs) constitute one such type of interaction. Their main characteristics are (1) an enhanced core magnetic field magnitude and (2) a bipolar magnetic field signature in the component normal to the magnetopause, reminiscent of a large-scale helicoidal flux tube magnetic configuration. However, other geometrical configurations which do not fit this classical picture have also been observed. Using high-resolution measurements from the Magnetospheric Multiscale mission, we investigate an event in the vicinity of the Earth's magnetopause on 7 November 2015. Despite signatures that, at first glance, appear consistent with a classic FTE, based on detailed geometrical and dynamical analyses as well as on topological signatures revealed by suprathermal electron properties, we demonstrate that this event is not consistent with a single, homogenous helicoidal structure. Our analysis rather suggests that it consists of the interaction of two separate sets of magnetic field lines with different connectivities. This complex three-dimensional interaction constructively conspires to produce signatures partially consistent with that of an FTE. We also show that, at the interface between the two sets of field lines, where the observed magnetic pileup occurs, a thin and strong current sheet forms with a large ion jet, which may be consistent with magnetic flux dissipation through magnetic reconnection in the interaction region.

Electrical receptive fields of retinal ganglion cells: Influence of presynaptic neurons

PubMed Central

Apollo, Nicholas V.; Garrett, David J.

2018-01-01

Implantable retinal stimulators activate surviving neurons to restore a sense of vision in people who have lost their photoreceptors through degenerative diseases. Complex spatial and temporal interactions occur in the retina during multi-electrode stimulation. Due to these complexities, most existing implants activate only a few electrodes at a time, limiting the repertoire of available stimulation patterns. Measuring the spatiotemporal interactions between electrodes and retinal cells, and incorporating them into a model may lead to improved stimulation algorithms that exploit the interactions. Here, we present a computational model that accurately predicts both the spatial and temporal nonlinear interactions of multi-electrode stimulation of rat retinal ganglion cells (RGCs). The model was verified using in vitro recordings of ON, OFF, and ON-OFF RGCs in response to subretinal multi-electrode stimulation with biphasic pulses at three stimulation frequencies (10, 20, 30 Hz). The model gives an estimate of each cell’s spatiotemporal electrical receptive fields (ERFs); i.e., the pattern of stimulation leading to excitation or suppression in the neuron. All cells had excitatory ERFs and many also had suppressive sub-regions of their ERFs. We show that the nonlinearities in observed responses arise largely from activation of presynaptic interneurons. When synaptic transmission was blocked, the number of sub-regions of the ERF was reduced, usually to a single excitatory ERF. This suggests that direct cell activation can be modeled accurately by a one-dimensional model with linear interactions between electrodes, whereas indirect stimulation due to summated presynaptic responses is nonlinear. PMID:29432411

Using video-reflexive ethnography to capture the complexity of leadership enactment in the healthcare workplace.

PubMed

Gordon, Lisi; Rees, Charlotte; Ker, Jean; Cleland, Jennifer

2017-12-01

Current theoretical thinking asserts that leadership should be distributed across many levels of healthcare organisations to improve the patient experience and staff morale. However, much healthcare leadership education focusses on the training and competence of individuals and little attention is paid to the interprofessional workplace and how its inherent complexities might contribute to the emergence of leadership. Underpinned by complexity theory, this research aimed to explore how interprofessional healthcare teams enact leadership at a micro-level through influential acts of organising. A whole (interprofessional) team workplace-based study utilising video-reflexive ethnography occurred in two UK clinical sites. Thematic framework analyses of the video data (video-observation and video-reflexivity sessions) were undertaken, followed by in-depth analyses of human-human and human-material interactions. Data analysis revealed a complex interprofessional environment where leadership is a dynamic process, negotiated and renegotiated in various ways throughout interactions (both formal and informal). Being able to "see" themselves at work gave participants the opportunity to discuss and analyse their everyday leadership practices and challenge some of their sometimes deeply entrenched values, beliefs, practices and assumptions about healthcare leadership. These study findings therefore indicate a need to redefine the way that medical and healthcare educators facilitate leadership development and argue for new approaches to research which shifts the focus from leaders to leadership.

The interaction of an ionizing ligand with enzymes having a single ionizing group. Implications for the reaction of folate analogues with dihydrofolate reductase.

PubMed

Stone, S R; Morrison, J F

1983-06-29

Binding theory has been developed for the reaction of an ionizing enzyme with an ionizing ligand. Consideration has been given to the most general scheme in which all possible reactions and interconversions occur as well as to schemes in which certain interactions do not take place. Equations have been derived in terms of the variation of the apparent dissociation constant (Kiapp) as a function of pH. These equations indicate that plots of pKiapp against pH can be wave-, half-bell- or bell-shaped according to the reactions involved. A wave is obtained whenever there is formation of the enzyme-ligand complexes, ionized enzyme . ionized ligand and protonated enzyme . protonated ligand. The additional formation of singly protonated enzyme-ligand complexes does not affect the wave form of the plot, but can influence the shape of the overall curve. The formation of either ionized enzyme . ionized ligand or protonated enzyme . protonated ligand, with or without singly protonated enzyme-ligand species, gives rise to a half-bell-shaped plot. If only singly protonated enzyme-ligand complexes are formed the plots are bell-shaped, but it is not possible to deduce the ionic forms of the reactants that participate in complex formation. Depending on the reaction pathways, true values for the ionization and dissociation constants may or may not be determined.

Biochemical characterization of GM1 micelles-Amphotericin B interaction.

PubMed

Leonhard, Victoria; Alasino, Roxana V; Bianco, Ismael D; Garro, Ariel G; Heredia, Valeria; Beltramo, Dante M

2015-01-01

In this work a thorough characterization of the GM1 micelle-Amphotericin B (AmB) interaction was performed. The micelle formation as well as the drug loading occurs spontaneously, although influenced by the physicochemical conditions, pH and temperature. The chromatographic profile of GM1-AmB complexes at different molar ratios shows the existence of two populations. The differential absorbance of GM1, monomeric and aggregate AmB, allowed us to discriminate the presence of all of them in both fractions. Thus, we noted that at higher proportion of AmB in the complex, increases the larger population which is composed mainly of aggregated AmB. The physical behavior of these micelles shows that both GM1- AmB complexes were stable in solution for at least 30 days. However upon freeze-thawing or lyophilization-solubilization cycles, only the smallest population, enriched in monomeric AmB, showed a complete solubilization. In vitro, GM1-AmB micelles were significantly less toxic on cultured cells than other commercial micellar formulations as Fungizone, but had a similar behavior to liposomal formulations as Ambisome. Regarding the antifungal activity of the new formulation, it was very similar to that of other formulations. The characterization of these GM1-AmB complexes is discussed as a potential new formulation able to improve the antifungal therapeutic efficiency of AmB.

Implementing the LIM code: the structural basis for cell type-specific assembly of LIM-homeodomain complexes

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

Bhati, Mugdha; Lee, Christopher; Nancarrow, Amy L.

2008-09-03

LIM-homeodomain (LIM-HD) transcription factors form a combinatorial 'LIM code' that contributes to the specification of cell types. In the ventral spinal cord, the binary LIM homeobox protein 3 (Lhx3)/LIM domain-binding protein 1 (Ldb1) complex specifies the formation of V2 interneurons. The additional expression of islet-1 (Isl1) in adjacent cells instead specifies the formation of motor neurons through assembly of a ternary complex in which Isl1 contacts both Lhx3 and Ldb1, displacing Lhx3 as the binding partner of Ldb1. However, little is known about how this molecular switch occurs. Here, we have identified the 30-residue Lhx3-binding domain on Isl1 (Isl1{sub LBD}).more » Although the LIM interaction domain of Ldb1 (Ldb1{sub LID}) and Isl1{sub LBD} share low levels of sequence homology, X-ray and NMR structures reveal that they bind Lhx3 in an identical manner, that is, Isl1{sub LBD} mimics Ldb1{sub LID}. These data provide a structural basis for the formation of cell type-specific protein-protein interactions in which unstructured linear motifs with diverse sequences compete to bind protein partners. The resulting alternate protein complexes can target different genes to regulate key biological events.« less

Heating and reduction affect the reaction with tannins of wine protein fractions differing in hydrophobicity.

PubMed

Marangon, Matteo; Vincenzi, Simone; Lucchetta, Marco; Curioni, Andrea

2010-02-15

During the storage, bottled white wines can manifest haziness due to the insolubilisation of the grape proteins that may 'survive' in the fermentation process. Although the exact mechanism of this occurrence is not fully understood, proteins and tannins are considered two of the key factors involved in wine hazing, since their aggregation leads to the formation of insoluble particles. To better understand this complex interaction, proteins and tannins from the same unfined Pinot grigio wine were separated. Wine proteins were then fractionated by hydrophobic interaction chromatography (HIC). A significant correlation between hydrophobicity of the wine protein fractions and the haze formed after reacting with wine tannins was found, with the most reactive fractions revealing (by SDS-PAGE and RP-HPLC analyses) the predominant presence of thaumatin-like proteins. Moreover, the effects of both protein heating and disulfide bonds reduction (with dithiotreithol) on haze formation in the presence of tannins were assessed. These treatments generally resulted in an improved reactivity with tannins, and this phenomenon was related to both the surface hydrophobicity and composition of the protein fractions. Therefore, haze formation in wines seems to be related to hydrophobic interactions occurring among proteins and tannins. These interactions should occur on hydrophobic tannin-binding sites, whose exposition on the proteins can depend on both protein heating and reduction. Copyright 2009 Elsevier B.V. All rights reserved.

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

Hirasaka, Katsuya, E-mail: hirasaka@nagasaki-u.ac.jp; Department of Nutritional Physiology, Institute of Health Biosciences, University of Tokushima, Tokushima; Mills, Edward M.

Uncoupling protein 3 (UCP3) is known to regulate energy dissipation, proton leakage, fatty acid oxidation, and oxidative stress. To identify the putative protein regulators of UCP3, we performed yeast two-hybrid screens. Here we report that UCP3 interacted with HS-1 associated protein X-1 (Hax-1), an anti-apoptotic protein that was localized in the mitochondria, and is involved in cellular responses to Ca{sup 2+}. The hydrophilic sequences within loop 2, and the matrix-localized hydrophilic domain of mouse UCP3, were necessary for binding to Hax-1 at the C-terminal domain, adjacent to the mitochondrial inner membrane. Interestingly, interaction of these proteins occurred in a calcium-dependentmore » manner. Moreover, the NMR spectrum of the C-terminal domain of Hax-1 was dramatically changed by removal of Ca{sup 2+}, suggesting that the C-terminal domain of Hax-1 underwent a Ca{sup 2+}-induced conformational change. In the Ca{sup 2+}-free state, the C-terminal Hax-1 tended to unfold, suggesting that Ca{sup 2+} binding may induce protein folding of the Hax-1 C-terminus. These results suggested that the UCP3-Hax-1 complex may regulate mitochondrial functional changes caused by mitochondrial Ca{sup 2+}. - Highlights: • UCP3 interacts with Hax-1. • The interaction of UCP3 and Hax-1 occurs in a calcium-dependent manner. • The C-terminal domain of Hax-1 undergoes a calcium-induced conformational change.« less

Triadic awareness predicts partner choice in male-infant-male interactions in Barbary macaques.

PubMed

Kubenova, Barbora; Konecna, Martina; Majolo, Bonaventura; Smilauer, Petr; Ostner, Julia; Schülke, Oliver

2017-03-01

Social knowledge beyond one's direct relationships is a key in successfully manoeuvring the social world. Individuals gather information on the quality of social relationships between their group companions, which has been termed triadic awareness. Evidence of the use of triadic awareness in natural contexts is limited mainly to conflict management. Here we investigated triadic awareness in wild Barbary macaques (Macaca sylvanus) in the context of bridging interactions defined as male-infant-male interactions whereby a male (initiator, holder) presents an infant to another male (receiver, non-holder) in order to initiate an affiliative interaction with that male. Analyses based on 1263 h of focal observations on ten infants of one wild social group in Morocco supported the hypothesis that males use their knowledge of the relationship between infants and other adult males when choosing a male as a partner for bridging interactions. Specifically, (i) the number of bridging interactions among holder-infant-receiver triads was positively affected by the strength of the infant-receiver relationship and (ii) when two males were available as bridging partners, a male was more likely to be chosen as the receiver the stronger his social relationship with the infant relative to the other available male. This demonstrates that non-human primates establish triadic awareness of temporary infant-male relationships and use it in a naturally occurring affiliative context. Our results contribute to the discussion about the mechanism underlying the acquisition of triadic awareness and the benefits of its usage, and lend support to hypotheses linking social complexity to the evolution of complex cognition.

An insight into the complex prion-prion interaction network in the budding yeast Saccharomyces cerevisiae.

PubMed

Du, Zhiqiang; Valtierra, Stephanie; Li, Liming

2014-01-01

The budding yeast Saccharomyces cerevisiae is a valuable model system for studying prion-prion interactions as it contains multiple prion proteins. A recent study from our laboratory showed that the existence of Swi1 prion ([SWI(+)]) and overproduction of Swi1 can have strong impacts on the formation of 2 other extensively studied yeast prions, [PSI(+)] and [PIN(+)] ([RNQ(+)]) (Genetics, Vol. 197, 685-700). We showed that a single yeast cell is capable of harboring at least 3 heterologous prion elements and these prions can influence each other's appearance positively and/or negatively. We also showed that during the de novo [PSI(+)] formation process upon Sup35 overproduction, the aggregation patterns of a preexisting inducer ([RNQ(+)] or [SWI(+)]) can undergo significant remodeling from stably transmitted dot-shaped aggregates to aggregates that co-localize with the newly formed Sup35 aggregates that are ring/ribbon/rod- shaped. Such co-localization disappears once the newly formed [PSI(+)] prion stabilizes. Our finding provides strong evidence supporting the "cross-seeding" model for prion-prion interactions and confirms earlier reports that the interactions among different prions and their prion proteins mostly occur at the initiation stages of prionogenesis. Our results also highlight a complex prion interaction network in yeast. We believe that elucidating the mechanism underlying the yeast prion-prion interaction network will not only provide insight into the process of prion de novo generation and propagation in yeast but also shed light on the mechanisms that govern protein misfolding, aggregation, and amyloidogenesis in higher eukaryotes.

Water-mediated protein-fluorophore interactions modulate the affinity of an ABC-ATPase/TNP-ADP complex.

PubMed

Oswald, Christine; Jenewein, Stefan; Smits, Sander H J; Holland, I Barry; Schmitt, Lutz

2008-04-01

TNP-modified nucleotides have been used extensively to study protein-nucleotide interactions. In the case of ABC-ATPases, application of these powerful tools has been greatly restricted due to the significantly higher affinity of the TNP-nucleotide for the corresponding ABC-ATPase in comparison to the non-modified nucleotides. To understand the molecular changes occurring upon binding of the TNP-nucleotide to an ABC-ATPase, we have determined the crystal structure of the TNP-ADP/HlyB-NBD complex at 1.6A resolution. Despite the higher affinity of TNP-ADP, no direct fluorophore-protein interactions were observed. Unexpectedly, only water-mediated interactions were detected between the TNP moiety and Tyr(477), that is engaged in pi-pi stacking with the adenine ring, as well as with two serine residues (Ser(504) and Ser(509)) of the Walker A motif. Interestingly, the side chains of these two serine residues adopt novel conformations that are not observed in the corresponding ADP structure. However, in the crystal structure of the S504A mutant, which binds TNP-ADP with similar affinity to the wild type enzyme, a novel TNP-water interaction compensates for the missing serine side chain. Since this water molecule is not present in the wild type enzyme, these results suggest that only water-mediated interactions provide a structural explanation for the increased affinity of TNP-nucleotides towards ABC-ATPases. However, our results also imply that in silico approaches such as docking or modeling cannot directly be applied to generate 'affinity-adopted' ADP- or ATP-analogs for ABC-ATPases.

Discordant U waves in the setting of hyperkalaemia.

PubMed

Chhabra, Lovely; Spodick, David H

2013-07-04

Physiological U wave genesis occurs likely secondary to either late repolarisation of Purkinje fibres, or late repolarisation of some myocardial cells and/or delayed after depolarisation of the ventricular wall occurring during ventricular filling. Hypokalaemia has a well-known association with pathological 'U wave' which actually combines with the T wave (TU complex) and results from slowing of phase 3 of the action potential with resultant electrical interaction between the three myocardial layers. U waves usually tend to disappear in the setting of hyperkalaemia. We report an unusual case where hyperkalaemia and discordant U waves coexisted. We believe that this may have occurred as a result of partial clinical adaptation of cardiac myocytes to the long-standing effects of hyperkalaemia as the patient had underlying history of chronic kidney disease. We also discuss the possible mechanisms of the U wave genesis and the importance of different U wave morphologies encountered in the real clinical practice.

Characterization of the complex between native and reduced bovine serum albumin with aquacobalamin and evidence of dual tetrapyrrole binding.

PubMed

Dereven'kov, Ilia A; Hannibal, Luciana; Makarov, Sergei V; Makarova, Anna S; Molodtsov, Pavel A; Koifman, Oskar I

2018-05-02

Serum albumin binds to a variety of endogenous ligands and drugs. Human serum albumin (HSA) binds to heme via hydrophobic interactions and axial coordination of the iron center by protein residue Tyr161. Human serum albumin binds to another tetrapyrrole, cobalamin (Cbl), but the structural and functional properties of this complex are poorly understood. Herein, we investigate the reaction between aquacobalamin (H 2 OCbl) and bovine serum albumin (BSA, the bovine counterpart of HSA) using Ultraviolet-Visible and fluorescent spectroscopy, and electron paramagnetic resonance. The reaction between H 2 OCbl and BSA led to the formation of a BSA-Cbl(III) complex consistent with N-axial ligation (amino). Prior to the formation of this complex, the reactants participate in an additional binding event that has been examined by fluorescence spectroscopy. Binding of BSA to Cbl(III) reduced complex formation between the bound cobalamin and free cyanide to form cyanocobalamin (CNCbl), suggesting that the β-axial position of the cobalamin may be occupied by an amino acid residue from the protein. Reaction of BSA containing reduced disulfide bonds with H 2 OCbl produces cob(II)alamin and disulfide with intermediate formation of thiolate Cbl(III)-BSA complex and its decomposition. Finally, in vitro studies showed that cobalamin binds to BSA only in the presence of an excess of protein, which is in contrast to heme binding to BSA that involves a 1:1 stoichiometry. In vitro formation of BSA-Cbl(III) complex does not preclude subsequent heme binding, which occurs without displacement of H 2 OCbl bound to BSA. These data suggest that the two tetrapyrroles interact with BSA in different binding pockets.

Analysis of Power Laws, Shape Collapses, and Neural Complexity: New Techniques and MATLAB Support via the NCC Toolbox

PubMed Central

Marshall, Najja; Timme, Nicholas M.; Bennett, Nicholas; Ripp, Monica; Lautzenhiser, Edward; Beggs, John M.

2016-01-01

Neural systems include interactions that occur across many scales. Two divergent methods for characterizing such interactions have drawn on the physical analysis of critical phenomena and the mathematical study of information. Inferring criticality in neural systems has traditionally rested on fitting power laws to the property distributions of “neural avalanches” (contiguous bursts of activity), but the fractal nature of avalanche shapes has recently emerged as another signature of criticality. On the other hand, neural complexity, an information theoretic measure, has been used to capture the interplay between the functional localization of brain regions and their integration for higher cognitive functions. Unfortunately, treatments of all three methods—power-law fitting, avalanche shape collapse, and neural complexity—have suffered from shortcomings. Empirical data often contain biases that introduce deviations from true power law in the tail and head of the distribution, but deviations in the tail have often been unconsidered; avalanche shape collapse has required manual parameter tuning; and the estimation of neural complexity has relied on small data sets or statistical assumptions for the sake of computational efficiency. In this paper we present technical advancements in the analysis of criticality and complexity in neural systems. We use maximum-likelihood estimation to automatically fit power laws with left and right cutoffs, present the first automated shape collapse algorithm, and describe new techniques to account for large numbers of neural variables and small data sets in the calculation of neural complexity. In order to facilitate future research in criticality and complexity, we have made the software utilized in this analysis freely available online in the MATLAB NCC (Neural Complexity and Criticality) Toolbox. PMID:27445842

Molecular dynamics study of a heteroditopic-calix[4]diquinone-assisted transfer of KCl and dopamine through a water-chloroform liquid-liquid interface.

PubMed

Santos, Sérgio M; Costa, Paulo J; Lankshear, Michael D; Beer, Paul D; Félix, Vítor

2010-09-02

The ability of two heteroditopic calix[4]diquinone receptors to transport a KCl ion-pair and a dopamine zwitterion through a water-chloroform interface was investigated via molecular dynamics (MD) simulations. Gas-phase conformational analysis has been carried on KCl and dopamine receptor binding associations and the lowest energy structures found in both cases show that the recognition of KCl and dopamine zwitterion occurs through multiple and cooperative N-H...anion and O...cation bonding interactions, with the receptor adopting equivalent folded conformations stabilized by pi-stacking interactions. The unconstrained MD simulations performed on KCl and dopamine complexes inserted in either the chloroform or water phase revealed that receptors are preferentially located at the interface with the hydrophobic tert-butyl groups of the calix[4]diquinone moiety immersed in the chloroform bulk while the polar anion binding cavity is directed toward the water phase. When the KCl complex is placed in chloroform, the release of the ion-pair occurs only after the first contact with the water interface, being a nonsimultaneous event, with the chloride anion leaving the receptor before the potassium cation. The dopamine, via the -NH(3)(+) binding entity, remains bound to the receptor during the entire time of the MD simulation (10 ns). In contrast, when both complexes were inserted in the water bulk, the full release of KCl and dopamine are fast events. The potentials of mean force (PMFs), associated with the migration of the complexes from chloroform to water through the interface, were calculated from steered molecular dynamics (SMD) simulations. The PMFs for the free KCl and zwitterionic dopamine migrations were also obtained for comparison purposes. The transport of KCl from water to chloroform (the reverse path) mediated by the receptor has a free energy barrier estimated in 6.50 kcal mol(-1), which is 3.0 kcal mol(-1) smaller than that found for the free KCl. The transport of dopamine complex along the reverse path is characterized by downhill energy profile, with a small free energy barrier of 6.56 kcal mol(-1).

Recognition-Mediated Hydrogel Swelling Controlled by Interaction with a Negative Thermoresponsive LCST Polymer.

PubMed

Belal, Khaled; Stoffelbach, François; Lyskawa, Joël; Fumagalli, Matthieu; Hourdet, Dominique; Marcellan, Alba; Smet, Lieselot De; de la Rosa, Victor R; Cooke, Graeme; Hoogenboom, Richard; Woisel, Patrice

2016-11-02

Most polymeric thermoresponsive hydrogels contract upon heating beyond the lower critical solution temperature (LCST) of the polymers used. Herein, we report a supramolecular hydrogel system that shows the opposite temperature dependence. When the non-thermosesponsive hydrogel NaphtGel, containing dialkoxynaphthalene guest molecules, becomes complexed with the tetra cationic macrocyclic host CBPQT 4+ , swelling occurred as a result of host-guest complex formation leading to charge repulsion between the host units, as well as an osmotic contribution of chloride counter-ions embedded in the network. The immersion of NaphtGel in a solution of poly(N-isopropylacrylamide) with tetrathiafulvalene (TTF) end groups complexed with CBPQT 4+ induced positive thermoresponsive behaviour. The LCST-induced dethreading of the polymer-based pseudorotaxane upon heating led to transfer of the CBPQT 4+ host and a concomitant swelling of NaphtGel. Subsequent cooling led to reformation of the TTF-based host-guest complexes in solution and contraction of the hydrogel. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

HM{sup +} and HM{sup +}‑He (M = Group 2 metal): Chemical or physical interactions?

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

Harris, Joe P.; Dodson, Hannah; Wright, Timothy G., E-mail: Tim.Wright@nottingham.ac.uk

2014-09-07

We investigate the HM{sup +}‑He complexes (M = Group 2 metal) using quantum chemistry. Equilibrium geometries are linear for M = Be and Mg, and bent for M = Ca–Ra; the explanation for this lies in the differing nature of the highest occupied molecular orbitals in the two sets of complexes. The difference primarily occurs as a result of the formation of the H–M{sup +} bond, and so the HM{sup +} diatomics are also studied as part of the present work. The position of the He atom in the complexes is largely determined by the form of the electron density.more » HM{sup +}…He binding energies are obtained and are surprisingly high for a helium complex. The HBe{sup +}…He value is almost 3000 cm{sup −1}, which is high enough to suspect contributions from chemical bonding. This is explored by examining the natural orbital density and by population analyses.« less

Electron and Ion Reactions in Molecular Solids: from astrochemistry to radiobiology

NASA Astrophysics Data System (ADS)

Huels, Michael A.

2001-05-01

Wherever ionizing radiation interacts with matter, it initiates reaction cascades involving ions, radicals, and ballistic secondary electrons; these reactions occur on fs time-scales, and may lead to substantial physical and chemical modifications of a medium. Here I present measurements of 0-80 eV electron and ion reactions in condensed films ranging from simple to complex, and astrophysical to biological in nature. Targets contain either: small molecules, hydrocarbons of increasing complexity (incl. bases, sugars, single/double stranded DNA), molecules on rare gas matrices, or mixed cryogenic films resembling astrophysical or planetary surface ices containing O2, H2O, methane, and aromatic hydrocarbons. The basic electron or ion reaction mechanisms and pathways are found to be fundamentally universal, but are modulated by the physical and chemical nature of the medium; depending on the latter, a reaction cascade may lead to different end-points, e.g. a decrease in molecular complexity via molecular fragmentations, or increases in complexity via secondary ion collision induced synthesis of larger molecules in hydrocarbon rich surface ices.

Cell-microenvironment interactions and architectures in microvascular systems

PubMed Central

Bersini, Simone; Yazdi, Iman K.; Talò, Giuseppe; Shin, Su Ryon; Moretti, Matteo; Khademhosseini, Ali

2016-01-01

In the past decade, significant advances have been made in the design and optimization of novel biomaterials and microfabrication techniques to generate vascularized tissues. Novel microfluidic systems have facilitated the development and optimization of in vitro models for exploring the complex pathophysiological phenomena that occur inside a microvascular environment. To date, most of these models have focused on engineering of increasingly complex systems, rather than analyzing the molecular and cellular mechanisms that drive microvascular network morphogenesis and remodeling. In fact, mutual interactions among endothelial cells (ECs), supporting mural cells and organ-specific cells, as well as between ECs and the extracellular matrix, are key driving forces for vascularization. This review focuses on the integration of materials science, microengineering and vascular biology for the development of in vitro microvascular systems. Various approaches currently being applied to study cell-cell/cell-matrix interactions, as well as biochemical/biophysical cues promoting vascularization and their impact on microvascular network formation, will be identified and discussed. Finally, this review will explore in vitro applications of microvascular systems, in vivo integration of transplanted vascularized tissues, and the important challenges for vascularization and controlling the microcirculatory system within the engineered tissues, especially for microfabrication approaches. It is likely that existing models and more complex models will further our understanding of the key elements of vascular network growth, stabilization and remodeling to translate basic research principles into functional, vascularized tissue constructs for regenerative medicine applications, drug screening and disease models. PMID:27417066

Cell-microenvironment interactions and architectures in microvascular systems.

PubMed

Bersini, Simone; Yazdi, Iman K; Talò, Giuseppe; Shin, Su Ryon; Moretti, Matteo; Khademhosseini, Ali

2016-11-01

In the past decade, significant advances have been made in the design and optimization of novel biomaterials and microfabrication techniques to generate vascularized tissues. Novel microfluidic systems have facilitated the development and optimization of in vitro models for exploring the complex pathophysiological phenomena that occur inside a microvascular environment. To date, most of these models have focused on engineering of increasingly complex systems, rather than analyzing the molecular and cellular mechanisms that drive microvascular network morphogenesis and remodeling. In fact, mutual interactions among endothelial cells (ECs), supporting mural cells and organ-specific cells, as well as between ECs and the extracellular matrix, are key driving forces for vascularization. This review focuses on the integration of materials science, microengineering and vascular biology for the development of in vitro microvascular systems. Various approaches currently being applied to study cell-cell/cell-matrix interactions, as well as biochemical/biophysical cues promoting vascularization and their impact on microvascular network formation, will be identified and discussed. Finally, this review will explore in vitro applications of microvascular systems, in vivo integration of transplanted vascularized tissues, and the important challenges for vascularization and controlling the microcirculatory system within the engineered tissues, especially for microfabrication approaches. It is likely that existing models and more complex models will further our understanding of the key elements of vascular network growth, stabilization and remodeling to translate basic research principles into functional, vascularized tissue constructs for regenerative medicine applications, drug screening and disease models. Copyright © 2016 Elsevier Inc. All rights reserved.

Trophic redundancy reduces vulnerability to extinction cascades

PubMed Central

Sanders, Dirk; Thébault, Elisa; Kehoe, Rachel; Frank van Veen, F. J.

2018-01-01

Current species extinction rates are at unprecedentedly high levels. While human activities can be the direct cause of some extinctions, it is becoming increasingly clear that species extinctions themselves can be the cause of further extinctions, since species affect each other through the network of ecological interactions among them. There is concern that the simplification of ecosystems, due to the loss of species and ecological interactions, increases their vulnerability to such secondary extinctions. It is predicted that more complex food webs will be less vulnerable to secondary extinctions due to greater trophic redundancy that can buffer against the effects of species loss. Here, we demonstrate in a field experiment with replicated plant-insect communities, that the probability of secondary extinctions is indeed smaller in food webs that include trophic redundancy. Harvesting one species of parasitoid wasp led to secondary extinctions of other, indirectly linked, species at the same trophic level. This effect was markedly stronger in simple communities than for the same species within a more complex food web. We show that this is due to functional redundancy in the more complex food webs and confirm this mechanism with a food web simulation model by highlighting the importance of the presence and strength of trophic links providing redundancy to those links that were lost. Our results demonstrate that biodiversity loss, leading to a reduction in redundant interactions, can increase the vulnerability of ecosystems to secondary extinctions, which, when they occur, can then lead to further simplification and run-away extinction cascades. PMID:29467292

Generating Phenotypical Erroneous Human Behavior to Evaluate Human-automation Interaction Using Model Checking

PubMed Central

Bolton, Matthew L.; Bass, Ellen J.; Siminiceanu, Radu I.

2012-01-01

Breakdowns in complex systems often occur as a result of system elements interacting in unanticipated ways. In systems with human operators, human-automation interaction associated with both normative and erroneous human behavior can contribute to such failures. Model-driven design and analysis techniques provide engineers with formal methods tools and techniques capable of evaluating how human behavior can contribute to system failures. This paper presents a novel method for automatically generating task analytic models encompassing both normative and erroneous human behavior from normative task models. The generated erroneous behavior is capable of replicating Hollnagel’s zero-order phenotypes of erroneous action for omissions, jumps, repetitions, and intrusions. Multiple phenotypical acts can occur in sequence, thus allowing for the generation of higher order phenotypes. The task behavior model pattern capable of generating erroneous behavior can be integrated into a formal system model so that system safety properties can be formally verified with a model checker. This allows analysts to prove that a human-automation interactive system (as represented by the model) will or will not satisfy safety properties with both normative and generated erroneous human behavior. We present benchmarks related to the size of the statespace and verification time of models to show how the erroneous human behavior generation process scales. We demonstrate the method with a case study: the operation of a radiation therapy machine. A potential problem resulting from a generated erroneous human action is discovered. A design intervention is presented which prevents this problem from occurring. We discuss how our method could be used to evaluate larger applications and recommend future paths of development. PMID:23105914

Disruption of Specific RNA-RNA Interactions in a Double-Stranded RNA Virus Inhibits Genome Packaging and Virus Infectivity

PubMed Central

Fajardo, Teodoro; Sung, Po-Yu; Roy, Polly

2015-01-01

Bluetongue virus (BTV) causes hemorrhagic disease in economically important livestock. The BTV genome is organized into ten discrete double-stranded RNA molecules (S1-S10) which have been suggested to follow a sequential packaging pathway from smallest to largest segment during virus capsid assembly. To substantiate and extend these studies, we have investigated the RNA sorting and packaging mechanisms with a new experimental approach using inhibitory oligonucleotides. Putative packaging signals present in the 3’untranslated regions of BTV segments were targeted by a number of nuclease resistant oligoribonucleotides (ORNs) and their effects on virus replication in cell culture were assessed. ORNs complementary to the 3’ UTR of BTV RNAs significantly inhibited virus replication without affecting protein synthesis. Same ORNs were found to inhibit complex formation when added to a novel RNA-RNA interaction assay which measured the formation of supramolecular complexes between and among different RNA segments. ORNs targeting the 3’UTR of BTV segment 10, the smallest RNA segment, were shown to be the most potent and deletions or substitution mutations of the targeted sequences diminished the RNA complexes and abolished the recovery of viable viruses using reverse genetics. Cell-free capsid assembly/RNA packaging assay also confirmed that the inhibitory ORNs could interfere with RNA packaging and further substitution mutations within the putative RNA packaging sequence have identified the recognition sequence concerned. Exchange of 3’UTR between segments have further demonstrated that RNA recognition was segment specific, most likely acting as part of the secondary structure of the entire genomic segment. Our data confirm that genome packaging in this segmented dsRNA virus occurs via the formation of supramolecular complexes formed by the interaction of specific sequences located in the 3’ UTRs. Additionally, the inhibition of packaging in-trans with inhibitory ORNs suggests this that interaction is a bona fide target for the design of compounds with antiviral activity. PMID:26646790

Disruption of Specific RNA-RNA Interactions in a Double-Stranded RNA Virus Inhibits Genome Packaging and Virus Infectivity.

PubMed

Fajardo, Teodoro; Sung, Po-Yu; Roy, Polly

2015-12-01

Bluetongue virus (BTV) causes hemorrhagic disease in economically important livestock. The BTV genome is organized into ten discrete double-stranded RNA molecules (S1-S10) which have been suggested to follow a sequential packaging pathway from smallest to largest segment during virus capsid assembly. To substantiate and extend these studies, we have investigated the RNA sorting and packaging mechanisms with a new experimental approach using inhibitory oligonucleotides. Putative packaging signals present in the 3'untranslated regions of BTV segments were targeted by a number of nuclease resistant oligoribonucleotides (ORNs) and their effects on virus replication in cell culture were assessed. ORNs complementary to the 3' UTR of BTV RNAs significantly inhibited virus replication without affecting protein synthesis. Same ORNs were found to inhibit complex formation when added to a novel RNA-RNA interaction assay which measured the formation of supramolecular complexes between and among different RNA segments. ORNs targeting the 3'UTR of BTV segment 10, the smallest RNA segment, were shown to be the most potent and deletions or substitution mutations of the targeted sequences diminished the RNA complexes and abolished the recovery of viable viruses using reverse genetics. Cell-free capsid assembly/RNA packaging assay also confirmed that the inhibitory ORNs could interfere with RNA packaging and further substitution mutations within the putative RNA packaging sequence have identified the recognition sequence concerned. Exchange of 3'UTR between segments have further demonstrated that RNA recognition was segment specific, most likely acting as part of the secondary structure of the entire genomic segment. Our data confirm that genome packaging in this segmented dsRNA virus occurs via the formation of supramolecular complexes formed by the interaction of specific sequences located in the 3' UTRs. Additionally, the inhibition of packaging in-trans with inhibitory ORNs suggests this that interaction is a bona fide target for the design of compounds with antiviral activity.

Complex interactions between diapirs and 4-D subduction driven mantle wedge circulation.

NASA Astrophysics Data System (ADS)

Sylvia, R. T.; Kincaid, C. R.

2015-12-01

Analogue laboratory experiments generate 4-D flow of mantle wedge fluid and capture the evolution of buoyant mesoscale diapirs. The mantle is modeled with viscous glucose syrup with an Arrhenius type temperature dependent viscosity. To characterize diapir evolution we experiment with a variety of fluids injected from multiple point sources. Diapirs interact with kinematically induced flow fields forced by subducting plate motions replicating a range of styles observed in dynamic subduction models (e.g., rollback, steepening, gaps). Data is collected using high definition timelapse photography and quantified using image velocimetry techniques. While many studies assume direct vertical connections between the volcanic arc and the deeper mantle source region, our experiments demonstrate the difficulty of creating near vertical conduits. Results highlight extreme curvature of diapir rise paths. Trench-normal deflection occurs as diapirs are advected downward away from the trench before ascending into wedge apex directed return flow. Trench parallel deflections up to 75% of trench length are seen in all cases, exacerbated by complex geometry and rollback motion. Interdiapir interaction is also important; upwellings with similar trajectory coalesce and rapidly accelerate. Moreover, we observe a new mode of interaction whereby recycled diapir material is drawn down along the slab surface and then initiates rapid fluid migration updip along the slab-wedge interface. Variability in trajectory and residence time leads to complex petrologic inferences. Material from disparate source regions can surface at the same location, mix in the wedge, or become fully entrained in creeping flow adding heterogeneity to the mantle. Active diapirism or any other vertical fluid flux mechanism employing rheological weakening lowers viscosity in the recycling mantle wedge affecting both solid and fluid flow characteristics. Many interesting and insightful results have been presented based upon 2-D, steady-state thermal and flow regimes. We reiterate the importance of 4-D time evolution in subduction models. Analogue experiments allow added feedbacks and complexity improving intuition and providing insight for further investigation.

Modular synchronization in complex networks.

PubMed

Oh, E; Rho, K; Hong, H; Kahng, B

2005-10-01

We study the synchronization transition (ST) of a modified Kuramoto model on two different types of modular complex networks. It is found that the ST depends on the type of intermodular connections. For the network with decentralized (centralized) intermodular connections, the ST occurs at finite coupling constant (behaves abnormally). Such distinct features are found in the yeast protein interaction network and the Internet, respectively. Moreover, by applying the finite-size scaling analysis to an artificial network with decentralized intermodular connections, we obtain the exponent associated with the order parameter of the ST to be beta approximately 1 different from beta(MF) approximately 1/2 obtained from the scale-free network with the same degree distribution but the absence of modular structure, corresponding to the mean field value.

Simple deterministic models and applications. Comment on "Coupled disease-behavior dynamics on complex networks: A review" by Z. Wang et al.

NASA Astrophysics Data System (ADS)

Yang, Hyun Mo

2015-12-01

Currently, discrete modellings are largely accepted due to the access to computers with huge storage capacity and high performance processors and easy implementation of algorithms, allowing to develop and simulate increasingly sophisticated models. Wang et al. [7] present a review of dynamics in complex networks, focusing on the interaction between disease dynamics and human behavioral and social dynamics. By doing an extensive review regarding to the human behavior responding to disease dynamics, the authors briefly describe the complex dynamics found in the literature: well-mixed populations networks, where spatial structure can be neglected, and other networks considering heterogeneity on spatially distributed populations. As controlling mechanisms are implemented, such as social distancing due 'social contagion', quarantine, non-pharmaceutical interventions and vaccination, adaptive behavior can occur in human population, which can be easily taken into account in the dynamics formulated by networked populations.

Climate warming promotes species diversity, but with greater taxonomic redundancy, in complex environments

PubMed Central

Thakur, Madhav P.; Tilman, David; Purschke, Oliver; Ciobanu, Marcel; Cowles, Jane; Isbell, Forest; Wragg, Peter D.; Eisenhauer, Nico

2017-01-01

Climate warming is predicted to alter species interactions, which could potentially lead to extinction events. However, there is an ongoing debate whether the effects of warming on biodiversity may be moderated by biodiversity itself. We tested warming effects on soil nematodes, one of the most diverse and abundant metazoans in terrestrial ecosystems, along a gradient of environmental complexity created by a gradient of plant species richness. Warming increased nematode species diversity in complex (16-species mixtures) plant communities (by ~36%) but decreased it in simple (monocultures) plant communities (by ~39%) compared to ambient temperature. Further, warming led to higher levels of taxonomic relatedness in nematode communities across all levels of plant species richness. Our results highlight both the need for maintaining species-rich plant communities to help offset detrimental warming effects and the inability of species-rich plant communities to maintain nematode taxonomic distinctness when warming occur. PMID:28740868

Self-assembly of a double-helical complex of sodium.

PubMed

Bell, T W; Jousselin, H

1994-02-03

Spontaneous self-organization of helical and multiple-helical molecular structures occurs on several levels in living organisms. Key examples are alpha-helical polypeptides, double-helical nucleic acids and helical protein structures, including F-actin, microtubules and the protein sheath of the tobacco mosaic virus. Although the self-assembly of double-helical transition-metal complexes bears some resemblance to the molecular organization of double-stranded DNA, selection between monohelical, double-helical and triple-helical structures is determined largely by the size and geometrical preference of the tightly bound metal. Here we present an example of double-helical assembly induced by the weaker and non-directional interactions of an alkali-metal ion with an organic ligand that is pre-organized into a coil. We have characterized the resulting complex by two-dimensional NMR and fast-atom-bombardment mass spectrometry. These results provide a step toward the creation of molecular tubes or ion channels consisting of intertwined coils.

Clinical quality needs complex adaptive systems and machine learning.

PubMed

Marsland, Stephen; Buchan, Iain

2004-01-01

The vast increase in clinical data has the potential to bring about large improvements in clinical quality and other aspects of healthcare delivery. However, such benefits do not come without cost. The analysis of such large datasets, particularly where the data may have to be merged from several sources and may be noisy and incomplete, is a challenging task. Furthermore, the introduction of clinical changes is a cyclical task, meaning that the processes under examination operate in an environment that is not static. We suggest that traditional methods of analysis are unsuitable for the task, and identify complexity theory and machine learning as areas that have the potential to facilitate the examination of clinical quality. By its nature the field of complex adaptive systems deals with environments that change because of the interactions that have occurred in the past. We draw parallels between health informatics and bioinformatics, which has already started to successfully use machine learning methods.

Quantum critical point underlying the pseudogap state in underdoped cuprate superconductors

NASA Astrophysics Data System (ADS)

Pepin, Catherine

2014-03-01

Cuprate superconductors rank among the most complex materials that are known in the universe. Faced with this complexity, scientists have adopted two types of approaches. In a bottom up approach, one considers that strong correlations occur at a high energy scale of roughly 1 eV upon very strong Coulomb interactions. In the top down approach one considers that one universal singularity at very low temperatures is responsible for complexity of the phase diagram. In this talk we will argue that the strong quantum fluctuations experienced at the proximity to a anti-ferromagnetic Quantum Critical Point (QCP) is responsible for a cascade of phase transitions in the charge and superconducting channels. We will discuss in this context the emergence of the pseudo-gap and charge order modulations. Symmetries and relations to experimental observations will be addressed. Work done in collaboration with K.B. Efetov (Bochum) and H. Meier (Yale).

An experimental investigation of the impingement of a planar shock wave on an axisymmetric body at Mach 3

NASA Technical Reports Server (NTRS)

Brosh, A.; Kussoy, M. I.

1983-01-01

An experimental study of the flow caused by a planar shock wave impinging obliquely on a cylinder is presented. The complex three dimensional shock wave and boundary layer interaction occurring in practical problems, such as the shock wave impingement from the shuttle nose on an external fuel tank, and store carriage interference on a supersonic tactical aircraft were investigated. A data base for numerical computations of complex flows was also investigated. The experimental techniques included pressure measurements and oil flow patterns on the surface of the cylinder, and shadowgraphs and total and static pressure surveys on the leeward and windward planes of symmetry. The complete data is presented in tabular form. The results reveal a highly complex flow field with two separation zones, regions of high crossflow, and multiple reflected shocks and expansion fans.

Microbiota as a mediator of cancer progression and therapy.

PubMed

Pope, Jillian L; Tomkovich, Sarah; Yang, Ye; Jobin, Christian

2017-01-01

Complex and intricate circuitries regulate cellular proliferation, survival, and growth, and alterations of this network through genetic and epigenetic events result in aberrant cellular behaviors, often leading to carcinogenesis. Although specific germline mutations have been recognized as cancer inducers, the vast majority of neoplastic changes in humans occur through environmental exposure, lifestyle, and diet. An emerging concept in cancer biology implicates the microbiota as a powerful environmental factor modulating the carcinogenic process. For example, the intestinal microbiota influences cancer development or therapeutic responses through specific activities (immune responses, metabolites, microbial structures, and toxins). The numerous effects of microbiota on carcinogenesis, ranging from promoting, preventing, or even influencing therapeutic outcomes, highlight the complex relationship between the biota and the host. In this review, we discuss the latest findings on this complex microbial interaction with the host and highlight potential mechanisms by which the microbiota mediates such a wide impact on carcinogenesis. Copyright © 2016 Elsevier Inc. All rights reserved.

Microbiota as a mediator of cancer progression and therapy

PubMed Central

Pope, Jillian L.; Tomkovich, Sarah; Yang, Ye; Jobin, Christian

2017-01-01

Complex and intricate circuitries regulate cellular proliferation, survival, and growth, and alterations of this network through genetic and epigenetic events result in aberrant cellular behaviors, often leading to carcinogenesis. Although specific germline mutations have been recognized as cancer inducers, the vast majority of neoplastic changes in humans occur through environmental exposure, lifestyle, and diet. An emerging concept in cancer biology implicates the microbiota as a powerful environmental factor modulating the carcinogenic process. For example, the intestinal microbiota influences cancer development or therapeutic responses through specific activities (immune responses, metabolites, microbial structures, and toxins). The numerous effects of microbiota on carcinogenesis, ranging from promoting, preventing, or even influencing therapeutic outcomes, highlight the complex relationship between the biota and the host. In this review, we discuss the latest findings on this complex microbial interaction with the host and highlight potential mechanisms by which the microbiota mediates such a wide impact on carcinogenesis. PMID:27554797

Recent advances in mathematical criminology. Comment on "Statistical physics of crime: A review" by M.R. D'Orsogna and M. Perc

NASA Astrophysics Data System (ADS)

Rodríguez, Nancy

2015-03-01

The use of mathematical tools has long proved to be useful in gaining understanding of complex systems in physics [1]. Recently, many researchers have realized that there is an analogy between emerging phenomena in complex social systems and complex physical or biological systems [4,5,12]. This realization has particularly benefited the modeling and understanding of crime, a ubiquitous phenomena that is far from being understood. In fact, when one is interested in the bulk behavior of patterns that emerge from small and seemingly unrelated interactions as well as decisions that occur at the individual level, the mathematical tools that have been developed in statistical physics, game theory, network theory, dynamical systems, and partial differential equations can be useful in shedding light into the dynamics of these patterns [2-4,6,12].

Iron, ferritin, and nutrition.

PubMed

Theil, Elizabeth C

2004-01-01

Ferritin, a major form of endogenous iron in food legumes such as soybeans, is a novel and natural alternative for iron supplementation strategies where effectiveness is limited by acceptability, cost, or undesirable side effects. A member of the nonheme iron group of dietary iron sources, ferritin is a complex with Fe3+ iron in a mineral (thousands of iron atoms inside a protein cage) protected from complexation. Ferritin illustrates the wide range of chemical and biological properties among nonheme iron sources. The wide range of nonheme iron receptors matched to the structure of the iron complexes that occurs in microorganisms may, by analogy, exist in humans. An understanding of the chemistry and biology of each type of dietary iron source (ferritin, heme, Fe2+ ion, etc.), and of the interactions dependent on food sources, genes, and gender, is required to design diets that will eradicate global iron deficiency in the twenty-first century.

Study of the techniques feasible for food synthesis aboard a spacecraft

NASA Technical Reports Server (NTRS)

Weiss, A. H.

1972-01-01

Synthesis of sugars by Ca(OH)2 catalyzed formaldehyde condensation (the formose reaction) has produced branched carbohydrates that do not occur in nature. The kinetics and mechanisms of the homogeneously catalyzed autocatalytic condensation were studied and analogies between homogeneous and heterogeneous rate laws have been found. Aldol condensations proceed simultaneously with Cannizzaro and crossed-Cannizzaro reactions and Lobry de Bruyn-Van Eckenstein rearrangements. The separate steps as well as the interactions of this highly complex reaction system were elucidated. The system exhibits instabilities, competitive catalytic, mass action, and equilibrium phenomena, complexing, and parallel and consecutive reactions. Specific finding that have been made on the problem will be of interest for synthesizing sugars, both for sustained space flight and for large scale food manufacture. A contribution to methodology for studying complex catalyzed reactions and to understanding control of reaction selectivity was a broad goal of the project.

The Evolution of ICT Markets: An Agent-Based Model on Complex Networks

NASA Astrophysics Data System (ADS)

Zhao, Liangjie; Wu, Bangtao; Chen, Zhong; Li, Li

Information and communication technology (ICT) products exhibit positive network effects.The dynamic process of ICT markets evolution has two intrinsic characteristics: (1) customers are influenced by each others’ purchasing decision; (2) customers are intelligent agents with bounded rationality.Guided by complex systems theory, we construct an agent-based model and simulate on complex networks to examine how the evolution can arise from the interaction of customers, which occur when they make expectations about the future installed base of a product by the fraction of neighbors who are using the same product in his personal network.We demonstrate that network effects play an important role in the evolution of markets share, which make even an inferior product can dominate the whole market.We also find that the intensity of customers’ communication can influence whether the best initial strategy for firms is to improve product quality or expand their installed base.

Respondents, Operants, and Emergents: Toward an Integrated Perspective on Behavior

NASA Technical Reports Server (NTRS)

Rumbaugh, Daune M.; Washburn, David A.; Hillix, William A.

1996-01-01

A triarchic organization of behavior, building on Skinner's description of respondents and operants, is proposed by introducing a third class of behavior called 'emergents.' Emergents are new responses, never specifically reinforced, that require operations more complex than association. Some of these operations occur naturally only in animals above a minimum level of brain complexity, and are developed in an interaction between treatment and organismic variables. (Here complexity is defined in terms of relative levels of hierarchical integration made possible both by the amount of brain, afforded both by brain-body allometric relationships and by encephalization, and, also, the elaboration of dendritic and synaptic connections within the cortex and connections between various parts/regions of the brain.) Examples of emergents are discussed to advance this triarchic view, of behavior. The prime example is language. This triarchic view reflects both the common goals and the cumulative nature of psychological science.

Efficient photosensitized splitting of the thymine dimer/oxetane unit on its modifying beta-cyclodextrin by a binding electron donor.

PubMed

Tang, Wen-Jian; Song, Qin-Hua; Wang, Hong-Bo; Yu, Jing-Yu; Guo, Qing-Xiang

2006-07-07

Two modified beta-cyclodextrins (beta-CDs) with a thymine dimer and a thymine oxetane adduct respectively, TD-CD and Ox-CD, have been prepared, and utilized to bind an electron-rich chromophore, indole or N,N-dimethylaniline (DMA), to form a supramolecular complex. We have examined the photosensitized splitting of the dimer/oxetane unit in TD-CD/Ox-CD by indole or DMA via an electron-transfer pathway, and observed high splitting efficiencies of the dimer/oxetane unit. On the basis of measurements of fluorescence spectra and splitting quantum yields, it is suggested that the splitting reaction occurs in a supramolecular complex by an inclusion interaction between the modified beta-CDs and DMA or indole. The back electron transfer, which leads low splitting efficiencies for the covalently-linked chromophore-dimer/oxetane compounds, is suppressed in the non-covalently-bound complex, and the mechanism has been discussed.

Kinetic and thermodynamic consequences of the substitution of SMe for OMe substituents of cryptophane hosts on the binding of neutral and cationic guests.

PubMed

Garcia, Chantal; Humilière, Delphine; Riva, Nathalie; Collet, André; Dutasta, Jean-Pierre

2003-06-21

To investigate the origin of the high selectivity of cryptophane-E (1) towards Me3NH+, Me4N+, and CHCl3, and particularly to discriminate the different contributions that stabilize the supramolecular complexes, we have synthesized the new cryptophane 2 bearing six MeS groups instead of MeO groups in 1. This led to a decrease of the negative charge density in the equatorial region of 2 without affecting notably the size of the molecular cavity. The binding properties of 1 and 2 towards the three guests were examined in solution and showed a slight decrease of the deltaGa favoring the complexes of 1, accompanied by a significant modification of the deltaHa vs. deltaSa balance. The binding of the ammonium guests to 1 and 2 was strongly entropy driven, while that of CHCl3 was purely enthalpy driven. A combination of spectroscopic and computational techniques was used to assign the main intermolecular interactions that occurred during the inclusion process. The neutral CHCl3 molecule is more stabilized in the less negatively charged CTV cap of 1. The different behavior towards the ammonium cations can be explained in term of interactions with the electronegative heteroatoms and cation-pi interactions. Moreover, this study revealed a considerable slowing down of the guest exchange kinetics with host 2, for which the association and dissociation rates are reduced by a factor 10(3) to 10(4) with respect to 1. For example, at room temperature, the Me4N+@2 complex exhibits a half-life of ca. 2 years, instead of a few hours for the corresponding complex of 1.

Early-Late Heterobimetallic Complexes Linked by Phosphinoamide Ligands. Tuning Redox Potentials and Small Molecule Activation

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

Thomas, Christine M.

2015-08-01

Recent attention in the chemical community has been focused on the energy efficient and environmentally benign conversion of abundant small molecules (CO2, H2O, etc.) to useful liquid fuels. This project addresses these goals by examining fundamental aspects of catalyst design to ultimately access small molecule activation processes under mild conditions. Specifically, Thomas and coworkers have targetted heterobimetallic complexes that feature metal centers with vastly different electronic properties, dictated both by their respective positions on the periodic table and their coordination environment. Unlike homobimetallic complexes featuring identical or similar metals, the bonds between metals in early/late heterobimetallics are more polarized, withmore » the more electron-rich late metal center donating electron density to the more electron-deficient early metal center. While metal-metal bonds pose an interesting strategy for storing redox equivalents and stabilizing reactive metal fragments, the polar character of metal-metal bonds in heterobimetallic complexes renders these molecules ideally poised to react with small molecule substrates via cleavage of energy-rich single and double bonds. In addition, metal-metal interactions have been shown to dramatically affect redox potentials and promote multielectron redox activity, suggesting that metal-metal interactions may provide a mechanism to tune redox potentials and access substrate reduction/activation at mild overpotentials. This research project has provided a better fundamental understanding of how interactions between transition metals can be used as a strategy to promote and/or control chemical transformations related to the clean production of fuels. While this project focused on the study of homogeneous systems, it is anticipated that the broad conclusions drawn from these investigations will be applicable to heterogeneous catalysis as well, particularly on heterogeneous processes that occur at interfaces in multicomponent systems.« less

Study on molecular structure, spectroscopic properties (FTIR and UV-Vis), NBO, QTAIM, HOMO-LUMO energies and docking studies of 5-fluorouracil, a substance used to treat cancer.

PubMed

Almeida, Michell O; Barros, Daiane A S; Araujo, Sheila C; Faria, Sergio H D M; Maltarollo, Vinicius G; Honorio, Kathia M

2017-09-05

Cancer cells can expand to other parts of body through blood system and nodes from a mechanism known as metastasis. Due to the large annual growth of cancer cases, various biological targets have been studied and related to this disorder. A very interesting target related to cancer is human epidermal growth factor receptor 2 (HER2). In this study, we analyzed the main intermolecular interactions between a drug used in the cancer treatment (5-fluorouracil) and HER2. Molecular modeling methods were also employed to assess the molecular structure, spectroscopic properties (FTIR and UV-Vis), NBO, QTAIM and HOMO-LUMO energies of 5-FU. From the docking simulations it was possible to analyze the interactions that occur between some residues in the binding site of HER2 and 5-FU. To validate the choice of basis set that was used in the NBO and QTAIM analyses, theoretical calculations were performed to obtain FT-IR and UV/Vis spectra, and the theoretical results are consistent with the experimental data, showing that the basis set chosen is suitable. For the maximum λ from the theoretical calculation (254.89nm) of UV/Vis, the electronic transition from HOMO to LUMO occurs at 4.89eV. From NBO analyses, we observed interactions between Asp863 and 5-FU, i.e. the orbitals with high transfer of electrons are LP O 15 (donor NBO) and BD* (π) N 1 -H 10 (acceptor NBO), being that the value of this interaction is 7.72kcal/mol. Results from QTAIM indicate one main intermolecular H bond, which is necessary to stabilize the complex formed between the ligands and the biological target. Therefore, this study allowed a careful evaluation on the main structural, spectroscopic and electronic properties involved in the interaction between 5-FU and HER2, an important biological complex related to the cancer treatment. Copyright © 2017 Elsevier B.V. All rights reserved.

An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions

PubMed Central

Sengupta, Raghuvir N.; Van Schie, Sabine N.S.; Giambaşu, George; Dai, Qing; Yesselman, Joseph D.; York, Darrin; Piccirilli, Joseph A.; Herschlag, Daniel

2016-01-01

Biological catalysis hinges on the precise structural integrity of an active site that binds and transforms its substrates and meeting this requirement presents a unique challenge for RNA enzymes. Functional RNAs, including ribozymes, fold into their active conformations within rugged energy landscapes that often contain misfolded conformers. Here we uncover and characterize one such “off-pathway” species within an active site after overall folding of the ribozyme is complete. The Tetrahymena group I ribozyme (E) catalyzes cleavage of an oligonucleotide substrate (S) by an exogenous guanosine (G) cofactor. We tested whether specific catalytic interactions with G are present in the preceding E•S•G and E•G ground-state complexes. We monitored interactions with G via the effects of 2′- and 3′-deoxy (–H) and −amino (–NH2) substitutions on G binding. These and prior results reveal that G is bound in an inactive configuration within E•G, with the nucleophilic 3′-OH making a nonproductive interaction with an active site metal ion termed MA and with the adjacent 2′-OH making no interaction. Upon S binding, a rearrangement occurs that allows both –OH groups to contact a different active site metal ion, termed MC, to make what are likely to be their catalytic interactions. The reactive phosphoryl group on S promotes this change, presumably by repositioning the metal ions with respect to G. This conformational transition demonstrates local rearrangements within an otherwise folded RNA, underscoring RNA's difficulty in specifying a unique conformation and highlighting Nature's potential to use local transitions of RNA in complex function. PMID:26567314

An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions.

PubMed

Sengupta, Raghuvir N; Van Schie, Sabine N S; Giambaşu, George; Dai, Qing; Yesselman, Joseph D; York, Darrin; Piccirilli, Joseph A; Herschlag, Daniel

2016-01-01

Biological catalysis hinges on the precise structural integrity of an active site that binds and transforms its substrates and meeting this requirement presents a unique challenge for RNA enzymes. Functional RNAs, including ribozymes, fold into their active conformations within rugged energy landscapes that often contain misfolded conformers. Here we uncover and characterize one such "off-pathway" species within an active site after overall folding of the ribozyme is complete. The Tetrahymena group I ribozyme (E) catalyzes cleavage of an oligonucleotide substrate (S) by an exogenous guanosine (G) cofactor. We tested whether specific catalytic interactions with G are present in the preceding E•S•G and E•G ground-state complexes. We monitored interactions with G via the effects of 2'- and 3'-deoxy (-H) and -amino (-NH(2)) substitutions on G binding. These and prior results reveal that G is bound in an inactive configuration within E•G, with the nucleophilic 3'-OH making a nonproductive interaction with an active site metal ion termed MA and with the adjacent 2'-OH making no interaction. Upon S binding, a rearrangement occurs that allows both -OH groups to contact a different active site metal ion, termed M(C), to make what are likely to be their catalytic interactions. The reactive phosphoryl group on S promotes this change, presumably by repositioning the metal ions with respect to G. This conformational transition demonstrates local rearrangements within an otherwise folded RNA, underscoring RNA's difficulty in specifying a unique conformation and highlighting Nature's potential to use local transitions of RNA in complex function. © 2015 Sengupta et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Structural basis of recognition of farnesylated and methylated KRAS4b by PDEδ.

PubMed

Dharmaiah, Srisathiyanarayanan; Bindu, Lakshman; Tran, Timothy H; Gillette, William K; Frank, Peter H; Ghirlando, Rodolfo; Nissley, Dwight V; Esposito, Dominic; McCormick, Frank; Stephen, Andrew G; Simanshu, Dhirendra K

2016-11-01

Farnesylation and carboxymethylation of KRAS4b (Kirsten rat sarcoma isoform 4b) are essential for its interaction with the plasma membrane where KRAS-mediated signaling events occur. Phosphodiesterase-δ (PDEδ) binds to KRAS4b and plays an important role in targeting it to cellular membranes. We solved structures of human farnesylated-methylated KRAS4b in complex with PDEδ in two different crystal forms. In these structures, the interaction is driven by the C-terminal amino acids together with the farnesylated and methylated C185 of KRAS4b that binds tightly in the central hydrophobic pocket present in PDEδ. In crystal form II, we see the full-length structure of farnesylated-methylated KRAS4b, including the hypervariable region. Crystal form I reveals structural details of farnesylated-methylated KRAS4b binding to PDEδ, and crystal form II suggests the potential binding mode of geranylgeranylated-methylated KRAS4b to PDEδ. We identified a 5-aa-long sequence motif (Lys-Ser-Lys-Thr-Lys) in KRAS4b that may enable PDEδ to bind both forms of prenylated KRAS4b. Structure and sequence analysis of various prenylated proteins that have been previously tested for binding to PDEδ provides a rationale for why some prenylated proteins, such as KRAS4a, RalA, RalB, and Rac1, do not bind to PDEδ. Comparison of all four available structures of PDEδ complexed with various prenylated proteins/peptides shows the presence of additional interactions due to a larger protein-protein interaction interface in KRAS4b-PDEδ complex. This interface might be exploited for designing an inhibitor with minimal off-target effects.

Effect of homogenisation in formation of thermally induced aggregates in a non- and low- fat milk model system with microparticulated whey proteins.

PubMed

Torres, Isabel Celigueta; Nieto, Gema; Nylander, Tommy; Simonsen, Adam Cohen; Tolkach, Alexander; Ipsen, Richard

2017-05-01

The objective of the research presented in this paper was to investigate how different characteristics of whey protein microparticles (MWP) added to milk as fat replacers influence intermolecular interactions occurring with other milk proteins during homogenisation and heating. These interactions are responsible for the formation of heat-induced aggregates that influence the texture and sensory characteristics of the final product. The formation of heat-induced complexes was studied in non- and low-fat milk model systems, where microparticulated whey protein (MWP) was used as fat replacer. Five MWP types with different particle characteristics were utilised and three heat treatments used: 85 °C for 15 min, 90 °C for 5 min and 95 °C for 2 min. Surface characteristics of the protein aggregates were expressed as the number of available thiol groups and the surface net charge. Intermolecular interactions involved in the formation of protein aggregates were studied by polyacrylamide gel electrophoresis and the final complexes visualised by darkfield microscopy. Homogenisation of non-fat milk systems led to partial adsorption of caseins onto microparticles, independently of the type of microparticle. On the contrary, homogenisation of low-fat milk resulted in preferential adsorption of caseins onto fat globules, rather than onto microparticles. Further heating of the milk, led to the formation of heat induced complexes with different sizes and characteristics depending on the type of MWP and the presence or not of fat. The results highlight the importance of controlling homogenisation and heat processing in yoghurt manufacture in order to induce desired changes in the surface reactivity of the microparticles and thereby promote effective protein interactions.

Leishmania sand fly interaction: progress and challenges.

PubMed

Bates, Paul A

2008-08-01

Complex interactions occurs between Leishmania parasites and their sand fly vectors. Promastigotes of Leishmania live exclusively within the gut, possess flagella and are motile, and kinesins, kinases and G proteins have been described that play a role in regulating flagellar assembly. Movement within the gut is not random: promastigotes can detect gradients of solutes via chemotaxis and osmotaxis. Further they use their flagella to attach to the fly midgut using surface glyconconjugates, a key step in establishment of the infection. Differentiation of mammal-infective stages is characterised by significant biochemical and cellular remodelling. Further, the parasites can manipulate the behaviour of the vector to maximise their transmission, and flies may even deliver altruistic apoptotic forms to aid transmission of infective stages.

Nonradiative Decay Dynamics of METHYL-4-HYDROXYCINNAMATE and its Monohydrated Complex Revealed by Picosecond Pump-Probe Spectroscopy

NASA Astrophysics Data System (ADS)

Ebata, T.; Shimada, D.; Kusaka, R.; Inokuchi, Y.; Ehara, M.

2012-06-01

The lifetimes of methyl 4-hydroxycinnamate (OMpCA) and its mono-hydrated complex (OMpCA-H_2O) in the S_1 state have been measured by picosecond pump-probe spectroscopy in a supersonic beam. For OMpCA, the lifetime of the S_1 - S_0 origin is 8 - 9 ps. On the other hand, the lifetime of OMpCA-H_2O complex at the origin is 930 ps, which is 100 times longer than that. Furthermore, in the complex the S_1 lifetime shows rapid decrease at an energy of 200 cm-1 above the origin and becomes as short as 9 ps at 500 cm-1. Theoretical calculations with symmetry-adapted cluster-configuration interaction (SAC-CI) method suggest that in OMpCA, the trans - cis isomerization occurs smoothly without a barrier on the S_1surface, while in OMpCA-H_2O complex, there exists a barrier along the isomerization coordinate. The calculated barrier height of OMpCA-H_2O is in good agreement with that estimated from the lifetime measurements.

GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking.

PubMed

Heo, Lim; Lee, Hasup; Seok, Chaok

2016-08-18

Protein-protein docking methods have been widely used to gain an atomic-level understanding of protein interactions. However, docking methods that employ low-resolution energy functions are popular because of computational efficiency. Low-resolution docking tends to generate protein complex structures that are not fully optimized. GalaxyRefineComplex takes such low-resolution docking structures and refines them to improve model accuracy in terms of both interface contact and inter-protein orientation. This refinement method allows flexibility at the protein interface and in the overall docking structure to capture conformational changes that occur upon binding. Symmetric refinement is also provided for symmetric homo-complexes. This method was validated by refining models produced by available docking programs, including ZDOCK and M-ZDOCK, and was successfully applied to CAPRI targets in a blind fashion. An example of using the refinement method with an existing docking method for ligand binding mode prediction of a drug target is also presented. A web server that implements the method is freely available at http://galaxy.seoklab.org/refinecomplex.

Managing inherent complexity for sustainable walleye fisheries in Lake Erie

USGS Publications Warehouse

Roseman, Edward F.; Drouin, Richard; Gaden, Marc; Knight, Roger; Tyson, Jeff; Zhao, Yingming; Taylor, William W.; Lynch, Abigail J.; Léonard, Nancy J.

2012-01-01

In Lake Erie, Walleye (Sander vitreus vitreus) is king. The naturally occurring species is the foundation of commercial fishing operations on the Canadian side of the lake and is a much-prized sport fish on the American side. Management of Lake Erie walleye fisheries is complex and takes place in an inter-jurisdictional setting composed of resource agencies from the states of Michigan (MDNR), Ohio (ODNR), Pennsylvania (PFBC), and New York (NYDEC) and the province of Ontario (OMNR). The complexity of walleye management is exacerbated by interactions among environmental and ecological changes in Lake Erie, complex life-history characteristics of the species, public demand for walleye, and cultural/governance differences among managing groups and their respective constituents. Success of future management strategies will largely hinge upon our ability to understand these inherent complexities and to employ tactics that successfully accommodate stock productivity and human demand in a highly dynamic environment. In this report, we review the history of Lake Erie walleye management, outline the multi-jurisdictional process for international management of walleye, and discuss strategies to address challenges facing managers.

Reliability analysis in interdependent smart grid systems

NASA Astrophysics Data System (ADS)

Peng, Hao; Kan, Zhe; Zhao, Dandan; Han, Jianmin; Lu, Jianfeng; Hu, Zhaolong

2018-06-01

Complex network theory is a useful way to study many real complex systems. In this paper, a reliability analysis model based on complex network theory is introduced in interdependent smart grid systems. In this paper, we focus on understanding the structure of smart grid systems and studying the underlying network model, their interactions, and relationships and how cascading failures occur in the interdependent smart grid systems. We propose a practical model for interdependent smart grid systems using complex theory. Besides, based on percolation theory, we also study the effect of cascading failures effect and reveal detailed mathematical analysis of failure propagation in such systems. We analyze the reliability of our proposed model caused by random attacks or failures by calculating the size of giant functioning components in interdependent smart grid systems. Our simulation results also show that there exists a threshold for the proportion of faulty nodes, beyond which the smart grid systems collapse. Also we determine the critical values for different system parameters. In this way, the reliability analysis model based on complex network theory can be effectively utilized for anti-attack and protection purposes in interdependent smart grid systems.

Complex Interaction Mechanisms between Dislocations and Point Defects Studied in Pure Aluminium by a Two-Wave Acoustic Coupling Technique

NASA Astrophysics Data System (ADS)

Bremnes, O.; Progin, O.; Gremaud, G.; Benoit, W.

1997-04-01

Ultrasonic experiments using a two-wave coupling technique were performed on 99.999% pure Al in order to study the interaction mechanisms occurring between dislocations and point defects. The coupling technique consists in measuring the attenuation of ultrasonic waves during low-frequency stress cycles (t). One obtains closed curves () called signatures whose shape and evolution are characteristic of the interaction mechanism controlling the low-frequency dislocation motion. The signatures observed were attributed to the interaction of the dislocations with extrinsic point defects. A new interpretation of the evolution of the signatures measured below 200 K with respect to temperature and stress frequency had to be established: they are linked to depinning of immobile point defects, whereas a thermally activated depinning mechanism does not fit the observations. The signatures measured between 200 and 370 K were interpreted as dragging and depinning of extrinsic point defects which are increasingly mobile with temperature.

Program Predicts Time Courses of Human/Computer Interactions

NASA Technical Reports Server (NTRS)

Vera, Alonso; Howes, Andrew

2005-01-01

CPM X is a computer program that predicts sequences of, and amounts of time taken by, routine actions performed by a skilled person performing a task. Unlike programs that simulate the interaction of the person with the task environment, CPM X predicts the time course of events as consequences of encoded constraints on human behavior. The constraints determine which cognitive and environmental processes can occur simultaneously and which have sequential dependencies. The input to CPM X comprises (1) a description of a task and strategy in a hierarchical description language and (2) a description of architectural constraints in the form of rules governing interactions of fundamental cognitive, perceptual, and motor operations. The output of CPM X is a Program Evaluation Review Technique (PERT) chart that presents a schedule of predicted cognitive, motor, and perceptual operators interacting with a task environment. The CPM X program allows direct, a priori prediction of skilled user performance on complex human-machine systems, providing a way to assess critical interfaces before they are deployed in mission contexts.

Monodisperse self-assembly in a model with protein-like interactions

NASA Astrophysics Data System (ADS)

Wilber, Alex W.; Doye, Jonathan P. K.; Louis, Ard A.; Lewis, Anna C. F.

2009-11-01

We study the self-assembly behavior of patchy particles with "proteinlike" interactions that can be considered as a minimal model for the assembly of viral capsids and other shell-like protein complexes. We thoroughly explore the thermodynamics and dynamics of self-assembly as a function of the parameters of the model and find robust assembly of all target structures considered. Optimal assembly occurs in the region of parameter space where a free energy barrier regulates the rate of nucleation, thus preventing the premature exhaustion of the supply of monomers that can lead to the formation of incomplete shells. The interactions also need to be specific enough to prevent the assembly of malformed shells, but while maintaining kinetic accessibility. Free energy landscapes computed for our model have a funnel-like topography guiding the system to form the target structure and show that the torsional component of the interparticle interactions prevents the formation of disordered aggregates that would otherwise act as kinetic traps.

The President's Day cyclone 17-19 February 1979: An analysis of jet streak interactions prior to cyclogenesis

NASA Technical Reports Server (NTRS)

Uccellini, L. W.; Kocin, P. J.; Walsh, C. H.

1981-01-01

The President's Day cyclone, produced record breaking snowfall along the East Coast of the United States in February 1979. Conventional radiosonde data, SMS GOES infrared imagery and LFM 2 model diagnostics were used to analyze the interaction of upper and lower tropospheric jet streaks prior to cyclogenesis. The analysis reveals that a series of complex scale interactive processes is responsible for the development of the intense cyclone. The evolution of the subsynoptic scale mass and momentum fields prior to and during the period of rapid development of the President's Day cyclone utilizing conventional data and SMS GOES imagery is documented. The interaction between upper and lower tropospheric jet streaks which occurred prior to the onset of cyclogenesis is discussed as well as the possible effects of terrain modified airflow within the precyclogenesis environment. Possible deficiencies in the LFM-2 initial wind fields that could have been responsible, in part, for the poor numerical forecast are examined.