Can Thematic Roles Leave Traces of Their Places?

ERIC Educational Resources Information Center

Chang, Franklin; Bock, Kathryn; Goldberg, Adele E.

2003-01-01

An important question in the study of language production is the nature of the semantic information that speakers use to create syntactic structures. A common answer to this question assumes that thematic roles help to mediate the mapping from messages to syntax. However, research using structural priming has suggested that the construction of…

Biomimetic cellular metals-using hierarchical structuring for energy absorption.

PubMed

Bührig-Polaczek, A; Fleck, C; Speck, T; Schüler, P; Fischer, S F; Caliaro, M; Thielen, M

2016-07-19

Fruit walls as well as nut and seed shells typically perform a multitude of functions. One of the biologically most important functions consists in the direct or indirect protection of the seeds from mechanical damage or other negative environmental influences. This qualifies such biological structures as role models for the development of new materials and components that protect commodities and/or persons from damage caused for example by impacts due to rough handling or crashes. We were able to show how the mechanical properties of metal foam based components can be improved by altering their structure on various hierarchical levels inspired by features and principles important for the impact and/or puncture resistance of the biological role models, rather than by tuning the properties of the bulk material. For this various investigation methods have been established which combine mechanical testing with different imaging methods, as well as with in situ and ex situ mechanical testing methods. Different structural hierarchies especially important for the mechanical deformation and failure behaviour of the biological role models, pomelo fruit (Citrus maxima) and Macadamia integrifolia, were identified. They were abstracted and transferred into corresponding structural principles and thus hierarchically structured bio-inspired metal foams have been designed. A production route for metal based bio-inspired structures by investment casting was successfully established. This allows the production of complex and reliable structures, by implementing and combining different hierarchical structural elements found in the biological concept generators, such as strut design and integration of fibres, as well as by minimising casting defects. To evaluate the structural effects, similar investigation methods and mechanical tests were applied to both the biological role models and the metallic foams. As a result an even deeper quantitative understanding of the form-structure-function relationship of the biological concept generators as well as the bio-inspired metal foams was achieved, on deeper hierarchical levels and overarching different levels.

Structural landscape of base pairs containing post-transcriptional modifications in RNA

PubMed Central

Seelam, Preethi P.; Sharma, Purshotam

2017-01-01

Base pairs involving post-transcriptionally modified nucleobases are believed to play important roles in a wide variety of functional RNAs. Here we present our attempts toward understanding the structural and functional role of naturally occurring modified base pairs using a combination of X-ray crystal structure database analysis, sequence analysis, and advanced quantum chemical methods. Our bioinformatics analysis reveals that despite their presence in all major secondary structural elements, modified base pairs are most prevalent in tRNA crystal structures and most commonly involve guanine or uridine modifications. Further, analysis of tRNA sequences reveals additional examples of modified base pairs at structurally conserved tRNA regions and highlights the conservation patterns of these base pairs in three domains of life. Comparison of structures and binding energies of modified base pairs with their unmodified counterparts, using quantum chemical methods, allowed us to classify the base modifications in terms of the nature of their electronic structure effects on base-pairing. Analysis of specific structural contexts of modified base pairs in RNA crystal structures revealed several interesting scenarios, including those at the tRNA:rRNA interface, antibiotic-binding sites on the ribosome, and the three-way junctions within tRNA. These scenarios, when analyzed in the context of available experimental data, allowed us to correlate the occurrence and strength of modified base pairs with their specific functional roles. Overall, our study highlights the structural importance of modified base pairs in RNA and points toward the need for greater appreciation of the role of modified bases and their interactions, in the context of many biological processes involving RNA. PMID:28341704

Simulation Games and Political Attitudes: The Importance of Role Identification and Game Structure.

ERIC Educational Resources Information Center

Livingston, Samuel A.

In an experiment conducted under classroom conditions with 8th grade students, the simulation game "Democracy" was shown to be effective at teaching that "log-rolling" is an acceptable part of the legislative process. Two aspects of the game--role identification and game structure--were shown to contribute independently to its effectiveness.…

Earthen embankment breaching

USDA-ARS?s Scientific Manuscript database

A large number of embankment structures, including dams, levees, dikes, and barriers, have been built by humans. These structures play a very important role in flood defense, while many are also used for water supply, power generation, transportation, sediment retention, etc. Since these structure...

Role of ice structuring proteins on freezing-thawing cycles of pasta sauces.

PubMed

Calderara, Marianna; Deorsola, Fabio A; Bensaid, Samir; Fino, Debora; Russo, Nunzio; Geobaldo, Francesco

2016-12-01

The freezing of the food is one of the most important technological developments for the storage of food in terms of quality and safety. The aim of this work was to study the role of an ice structuring protein (ISP) on freezing-thawing cycles of different solutions and commercial Italian pasta sauces. Ice structuring proteins were related to the modification of the structure of ice. The results showed that the freezing time of an aqueous solution containing the protein was reduced to about 20% with respect to a pure water solution. The same effect was demonstrated in sugar-containing solutions and in lipid-containing sauces. The study proved a specific role of ISP during thawing, inducing a time decrease similar to that of freezing and even more important in the case of tomato-based sauces. This work demonstrated the role of ISP in the freezing-thawing process, showing a significant reduction of processing in the freezing and thawing phase by adding the protein to pure water and different sugar-, salt- and lipid-containing solutions and commercial sauces, with considerable benefits for the food industry in terms of costs and food quality.

Applying Meta-Analysis to Structural Equation Modeling

ERIC Educational Resources Information Center

Hedges, Larry V.

2016-01-01

Structural equation models play an important role in the social sciences. Consequently, there is an increasing use of meta-analytic methods to combine evidence from studies that estimate the parameters of structural equation models. Two approaches are used to combine evidence from structural equation models: A direct approach that combines…

Corporate Structure Events Involving Regulated Utilities: The Need for a Multidisciplinary, Multijurisdictional Approach

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

Hempling, Scott

2006-08-15

The repeal of PUHCA has occasioned important questions on the appropriate role for regulation in the area of utility corporate structure, including complex process and jurisdictional issues. There is a disproportionality between the importance of these questions and the lack of attention that has been given them by our regulatory and political communities. (author)

Structural Insights into E. coli Porphobilinogen Deaminase during Synthesis and Exit of 1-Hydroxymethylbilane

PubMed Central

Bulusu, Gopalakrishnan

2014-01-01

Porphobilinogen deaminase (PBGD) catalyzes the formation of 1-hydroxymethylbilane (HMB), a crucial intermediate in tetrapyrrole biosynthesis, through a step-wise polymerization of four molecules of porphobilinogen (PBG), using a unique dipyrromethane (DPM) cofactor. Structural and biochemical studies have suggested residues with catalytic importance, but their specific role in the mechanism and the dynamic behavior of the protein with respect to the growing pyrrole chain remains unknown. Molecular dynamics simulations of the protein through the different stages of pyrrole chain elongation suggested that the compactness of the overall protein decreases progressively with addition of each pyrrole ring. Essential dynamics showed that domains move apart while the cofactor turn region moves towards the second domain, thus creating space for the pyrrole rings added at each stage. Residues of the flexible active site loop play a significant role in its modulation. Steered molecular dynamics was performed to predict the exit mechanism of HMB from PBGD at the end of the catalytic cycle. Based on the force profile and minimal structural changes the proposed path for the exit of HMB is through the space between the domains flanking the active site loop. Residues reported as catalytically important, also play an important role in the exit of HMB. Further, upon removal of HMB, the structure of PBGD gradually relaxes to resemble its initial stage structure, indicating its readiness to resume a new catalytic cycle. PMID:24603363

The role of structural parameters in DNA cyclization

DOE PAGES

Alexandrov, Ludmil B.; Bishop, Alan R.; Rasmussen, Kim O.; ...

2016-02-04

The intrinsic bendability of DNA plays an important role with relevance for myriad of essential cellular mechanisms. The flexibility of a DNA fragment can be experimentally and computationally examined by its propensity for cyclization, quantified by the Jacobson-Stockmayer J factor. In this paper, we use a well-established coarse-grained three-dimensional model of DNA and seven distinct sets of experimentally and computationally derived conformational parameters of the double helix to evaluate the role of structural parameters in calculating DNA cyclization.

Systemic Perspectives on Beginning Teacher Programs.

ERIC Educational Resources Information Center

Schlechty, Phillip C.; Whitford, Betty Lou

1989-01-01

Discusses the importance of basing beginning teacher programs in schools where roles are structured to support induction and provide exemplary education for students. Addresses structural and political issues, human resource development, and symbolism. (RJC)

Epidemic spreading on complex networks with overlapping and non-overlapping community structure

NASA Astrophysics Data System (ADS)

Shang, Jiaxing; Liu, Lianchen; Li, Xin; Xie, Feng; Wu, Cheng

2015-02-01

Many real-world networks exhibit community structure where vertices belong to one or more communities. Recent studies show that community structure plays an import role in epidemic spreading. In this paper, we investigate how the extent of overlap among communities affects epidemics. In order to experiment on the characteristic of overlapping communities, we propose a rewiring algorithm that can change the community structure from overlapping to non-overlapping while maintaining the degree distribution of the network. We simulate the Susceptible-Infected-Susceptible (SIS) epidemic process on synthetic scale-free networks and real-world networks by applying our rewiring algorithm. Experiments show that epidemics spread faster on networks with higher level of overlapping communities. Furthermore, overlapping communities' effect interacts with the average degree's effect. Our work further illustrates the important role of overlapping communities in the process of epidemic spreading.

Dust evolution, a global view I. Nanoparticles, nascence, nitrogen and natural selection … joining the dots

NASA Astrophysics Data System (ADS)

Jones, A. P.

2016-12-01

The role and importance of nanoparticles for interstellar chemistry and beyond is explored within the framework of The Heterogeneous dust Evolution Model for Interstellar Solids (THEMIS), focusing on their active surface chemistry, the effects of nitrogen doping and the natural selection of interesting nanoparticle sub-structures. Nanoparticle-driven chemistry, and in particular the role of intrinsic epoxide-type structures, could provide a viable route to the observed gas phase OH in tenuous interstellar clouds en route to becoming molecular clouds. The aromatic-rich moieties present in asphaltenes probably provide a viable model for the structures present within aromatic-rich interstellar carbonaceous grains. The observed doping of such nanoparticle structures with nitrogen, if also prevalent in interstellar dust, could perhaps have important and observable consequences for surface chemistry and the formation of precursor pre-biotic species.

A New Education Scheme for Japan: Importing Education PPP Structures from England and Scotland (Part 1)

ERIC Educational Resources Information Center

Tachioka, Hiroshi; Campbell, Joel R.

2006-01-01

Public Private Partnerships (PPPs) play a very important role in the development of social, health, welfare and education worldwide. Most PPP projects have been in the social, welfare and health fields. However, in recent years, PPP projects also play more active role in education. PPP projects in education have evolved from the mere sponsoring of…

Organizational Role Stress of Secondary School Teachers with Reference to Gender and Management

ERIC Educational Resources Information Center

Mohanty, Sankar Prasad

2017-01-01

Everyone talks on stress. Further, role stress in an organization is very common in the current scenario. The organization has its own structure and goal and an individual plays important role in order to achieve the organisational goals. Individual's unique personality and needs affects his role in any organization. The investigators conducted a…

The role of dispersal mode and habitat specialization for metacommunity structure of shallow beach invertebrates.

PubMed

Rodil, Iván F; Lucena-Moya, Paloma; Jokinen, Henri; Ollus, Victoria; Wennhage, Håkan; Villnäs, Anna; Norkko, Alf

2017-01-01

Metacommunity ecology recognizes the interplay between local and regional patterns in contributing to spatial variation in community structure. In aquatic systems, the relative importance of such patterns depends mainly on the potential connectivity of the specific system. Thus, connectivity is expected to increase in relation to the degree of water movement, and to depend on the specific traits of the study organism. We examined the role of environmental and spatial factors in structuring benthic communities from a highly connected shallow beach network using a metacommunity approach. Both factors contributed to a varying degree to the structure of the local communities suggesting that environmental filters and dispersal-related mechanisms played key roles in determining abundance patterns. We categorized benthic taxa according to their dispersal mode (passive vs. active) and habitat specialization (generalist vs. specialist) to understand the relative importance of environment and dispersal related processes for shallow beach metacommunities. Passive dispersers were predicted by a combination of environmental and spatial factors, whereas active dispersers were not spatially structured and responded only to local environmental factors. Generalists were predicted primarily by spatial factors, while specialists were only predicted by local environmental factors. The results suggest that the role of the spatial component in metacommunity organization is greater in open coastal waters, such as shallow beaches, compared to less-connected environmentally controlled aquatic systems. Our results also reveal a strong environmental role in structuring the benthic metacommunity of shallow beaches. Specifically, we highlight the sensitivity of shallow beach macrofauna to environmental factors related to eutrophication proxies.

The role of dispersal mode and habitat specialization for metacommunity structure of shallow beach invertebrates

PubMed Central

Lucena-Moya, Paloma; Jokinen, Henri; Ollus, Victoria; Wennhage, Håkan; Villnäs, Anna; Norkko, Alf

2017-01-01

Metacommunity ecology recognizes the interplay between local and regional patterns in contributing to spatial variation in community structure. In aquatic systems, the relative importance of such patterns depends mainly on the potential connectivity of the specific system. Thus, connectivity is expected to increase in relation to the degree of water movement, and to depend on the specific traits of the study organism. We examined the role of environmental and spatial factors in structuring benthic communities from a highly connected shallow beach network using a metacommunity approach. Both factors contributed to a varying degree to the structure of the local communities suggesting that environmental filters and dispersal-related mechanisms played key roles in determining abundance patterns. We categorized benthic taxa according to their dispersal mode (passive vs. active) and habitat specialization (generalist vs. specialist) to understand the relative importance of environment and dispersal related processes for shallow beach metacommunities. Passive dispersers were predicted by a combination of environmental and spatial factors, whereas active dispersers were not spatially structured and responded only to local environmental factors. Generalists were predicted primarily by spatial factors, while specialists were only predicted by local environmental factors. The results suggest that the role of the spatial component in metacommunity organization is greater in open coastal waters, such as shallow beaches, compared to less-connected environmentally controlled aquatic systems. Our results also reveal a strong environmental role in structuring the benthic metacommunity of shallow beaches. Specifically, we highlight the sensitivity of shallow beach macrofauna to environmental factors related to eutrophication proxies. PMID:28196112

A Home Economist Speaks Out: Need for a Parenting Course.

ERIC Educational Resources Information Center

Dolny, Candice

1996-01-01

Social trends indicating change in family structure and roles, more single-parent and blended families, and the important role of parents in socialization demonstrate the need for parenting education. A parenting course should include understanding of healthy family life and parental roles, parenting styles, child development, and parenting…

Turbulence production near walls: The role of flow structures with spanwise asymmetry

NASA Technical Reports Server (NTRS)

Alfredsson, P. Henrik; Johansson, Arne V.; Kim, John

1988-01-01

Space-time evolution of near wall flow structures is described by conditional sampling methods, in which conditional averages are formed at various stages of development of shear layer structures. The development of spanwise asymmetry of the structures was found to be important in the creation of the structures and for the process of turbulence production.

Secretaries' role in EHR Documentation and the Implications of Establishing a Structured EHR System.

PubMed

Johansen, Monika Alise; Pedersen, Åse-Merete; Ellingsen, Gunnar

2015-01-01

Secretaries play an important quality assurance role in today's medical record production. This study aimed to identify quality assurance tasks that a future system cannot easily compensate for when developing a new structured EHR in which the physicians do the writing themselves. The study identified two tasks, which we suggest should also be performed by secretaries in the future.

The 2.6 Angstrom Crystal Structure of a Human A[subscript 2A] Adenosine Receptor Bound to an Antagonist

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

Jaakola, Veli-Pekka; Griffith, Mark T.; Hanson, Michael A.

2009-01-15

The adenosine class of heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) mediates the important role of extracellular adenosine in many physiological processes and is antagonized by caffeine. We have determined the crystal structure of the human A{sub 2A} adenosine receptor, in complex with a high-affinity subtype-selective antagonist, ZM241385, to 2.6 angstrom resolution. Four disulfide bridges in the extracellular domain, combined with a subtle repacking of the transmembrane helices relative to the adrenergic and rhodopsin receptor structures, define a pocket distinct from that of other structurally determined GPCRs. The arrangement allows for the binding of the antagonist in an extendedmore » conformation, perpendicular to the membrane plane. The binding site highlights an integral role for the extracellular loops, together with the helical core, in ligand recognition by this class of GPCRs and suggests a role for ZM241385 in restricting the movement of a tryptophan residue important in the activation mechanism of the class A receptors.« less

The Interdependence of the Factors Influencing the Perceived Quality of the Online Learning Experience: A Causal Model

ERIC Educational Resources Information Center

Peltier, James W.; Schibrowsky, John A.; Drago, William

2007-01-01

A structural model of the drivers of online education is proposed and tested. The findings help to identify the interrelated nature of the lectures delivered via technology outside of the traditional classroom, the importance of mentoring, the need to develop course structure, the changing roles for instructors and students, and the importance of…

Hilbert space structure in quantum gravity: an algebraic perspective

DOE PAGES

Giddings, Steven B.

2015-12-16

If quantum gravity respects the principles of quantum mechanics, suitably generalized, it may be that a more viable approach to the theory is through identifying the relevant quantum structures rather than by quantizing classical spacetime. Here, this viewpoint is supported by difficulties of such quantization, and by the apparent lack of a fundamental role for locality. In finite or discrete quantum systems, important structure is provided by tensor factorizations of the Hilbert space. However, even in local quantum field theory properties of the generic type III von Neumann algebras and of long range gauge fields indicate that factorization of themore » Hilbert space is problematic. Instead it is better to focus on the structure of the algebra of observables, and in particular on its subalgebras corresponding to regions. This paper suggests that study of analogous algebraic structure in gravity gives an important perspective on the nature of the quantum theory. Significant departures from the subalgebra structure of local quantum field theory are found, working in the correspondence limit of long-distances/low-energies. Particularly, there are obstacles to identifying commuting algebras of localized operators. In addition to suggesting important properties of the algebraic structure, this and related observations pose challenges to proposals of a fundamental role for entanglement.« less

Hilbert space structure in quantum gravity: an algebraic perspective

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

Giddings, Steven B.

If quantum gravity respects the principles of quantum mechanics, suitably generalized, it may be that a more viable approach to the theory is through identifying the relevant quantum structures rather than by quantizing classical spacetime. Here, this viewpoint is supported by difficulties of such quantization, and by the apparent lack of a fundamental role for locality. In finite or discrete quantum systems, important structure is provided by tensor factorizations of the Hilbert space. However, even in local quantum field theory properties of the generic type III von Neumann algebras and of long range gauge fields indicate that factorization of themore » Hilbert space is problematic. Instead it is better to focus on the structure of the algebra of observables, and in particular on its subalgebras corresponding to regions. This paper suggests that study of analogous algebraic structure in gravity gives an important perspective on the nature of the quantum theory. Significant departures from the subalgebra structure of local quantum field theory are found, working in the correspondence limit of long-distances/low-energies. Particularly, there are obstacles to identifying commuting algebras of localized operators. In addition to suggesting important properties of the algebraic structure, this and related observations pose challenges to proposals of a fundamental role for entanglement.« less

The permeaiblity of fault-zones:the role of stylolites as incipit of dissolution

NASA Astrophysics Data System (ADS)

Magni, Silvana

2017-04-01

Fault zones and fractures play an important role in fluid circulation and then in dissolution, acting as barriers or conductors depending on the distribution of other features associated with them and on the specific conditions (lithological and structural, as well). The fault zone have a high permeability only in the early stages of the movement but shortly after recrystallization and reprecipitation processes greatly reduce the permeability within them. Indeed the dissolution is a complex phenomenon which involves both several factors that lead to the formation of caves and karst systems often complex. Traditionally, in the field of karst , the dissolution is associated with extensional structures such as faults and joints believing that they are more favorable to the water circulation. In this context compressional tectonic structures, as like the stylolites, are never considered. In fact the stylolites play an important role in the fluid circulation (Rawling, 2001) and in particular in the incipit of dissolution and then of the karst. We have so focused our research on the study of permeability of four fault zones in a karst area of Alte Murge (South Italy). Through a detailed structural analysis in the field and using the method of Caine (Caine, 1996), we reconstructed the permeability of the four previous fault zones. Our attention was focused on faults, joints and on stylolites. Contrary to the literature the dissolution and therefore the karst was mainly found along the stylolites and only secondarily along faults. No sign of dissolution was found along the joints. In the context of karst studies, the stylolites, which are structures due to pressure solution has never been taken into account, thinking that in compressional structures is not possible any circulation of water and that therefore there is no fluid-rock interaction. No consideration has been given to the enormous role that the pressure and the microfluidic that are created have in this context. The styololites, the focus of our research open important questions about their exact role as incipit of the dissolution. Through petrophysical analysis and microstructural we are characterizing the porosity and permeability near the stylolites. Recently, fluid-rock interactions and their impact on carbonate rocks is becoming very important because of an increasing interest it the carbonate reservoirs as a consequence of a progressive deterioration of the quantity and quality of the groundwater due to increasing pollution phenomena. In fact the aquifers represent about 40% of the drinking water resources and their importance will increase in coming years. REFERENCESE Caine, J.S.,Evans, J.P., Forster,C.B. (1996). Fault zone architecture and permeability structure. Geology 24, 1025-1032 Rawling,G.C., Goodwin,L.B., Wilson,J.L. (2001). Internal architecture permeability structure and hydrogeologic significance of contrasting fault-zone types. Geology 29, 43-46

Human Milk Oligosaccharides (HMOS): Structure, Function, and Enzyme-Catalyzed Synthesis.

PubMed

Chen, Xi

2015-01-01

The important roles played by human milk oligosaccharides (HMOS), the third major component of human milk, in the health of breast-fed infants have been increasingly recognized, as the structures of more than 100 different HMOS have now been elucidated. Despite the recognition of the various functions of HMOS as prebiotics, antiadhesive antimicrobials, and immunomodulators, the roles and the applications of individual HMOS species are less clear. This is mainly due to the limited accessibility to large amounts of individual HMOS in their pure forms. Current advances in the development of enzymatic, chemoenzymatic, whole-cell, and living-cell systems allow for the production of a growing number of HMOS in increasing amounts. This effort will greatly facilitate the elucidation of the important roles of HMOS and allow exploration into the applications of HMOS both as individual compounds and as mixtures of defined structures with desired functions. The structures, functions, and enzyme-catalyzed synthesis of HMOS are briefly surveyed to provide a general picture about the current progress on these aspects. Future efforts should be devoted to elucidating the structures of more complex HMOS, synthesizing more complex HMOS including those with branched structures, and developing HMOS-based or HMOS-inspired prebiotics, additives, and therapeutics. © 2015 Elsevier Inc. All rights reserved.

Reshaping of Coastlines as the Beginning of Urban Structures Changes in North Poland

NASA Astrophysics Data System (ADS)

Burda, Izabela M.; Nyka, Lucyna; Borodziuk, Adam

2017-10-01

This article discusses the problem of strategies concerning the processes of re-shaping the Baltic Sea southern coastline applied recently in North Poland. The undertaken research is an attempt to identify the relationship between the modifications of coastline forms and the positive changes of urban structures. First of all, it can be seen that these modifications are needed because of the problems of existing shoreline erosion. It can be also observed, that many realized interventions were helpful to save the land but they did not improve the condition of cities situated along the coast. In these cases, it is impossible to connect the sea coastline with the existing grid of public spaces which is a barrier to creating a system that could be perceived as a coherent landscape. The basis for proving the importance of special ways of shoreline modifications are comparative studies and in-field analyses. In facing the problems of coastal cities there is a need to analyse the condition of existing urban structures. Many studies made so far show that there are many problems which have to be identified and solved. Worth noting is the fact that these structures have a unique character because of their location. They play an important role as holiday resorts being an attraction for many inhabitants and visitors from all over the world. Such a role plays, for example, an important part in places such as Jarosławiec, Ustka or Kołobrzeg. However, analysing the strategies applied in recent years, it can be noted that they cannot be the only basis for the strengthening of connections between land and water helping to preserve the land, but they may also play an important role as a factor for initiating urban structures transformations. What is also important, it can be claimed that relationships between sea water and urban structures should be strengthened due to special forms of the coast line. They should be integrated into existing structures making them more comfortable and attractive while also protecting against threats from the water. Playing the role as a protector of land they should use special constructions being at the same time accessible to all users throughout the year and regardless of weather conditions. It is worth emphasizing that special treatment of the coastline helps to establish it as a public domain which is important in achieving high quality urban-water landscapes. Therefore it should be the objective of strategies which are being prepared for parts of coastlines waiting for intervention.

Passenger Value Structure Model

DOT National Transportation Integrated Search

1980-07-01

The objective of this research was to develop a model of the passenger's value structure which would reveal the role and importance of perceived security and other system characteristics on the passenger's evaluation and use of transit systems. The g...

Birefringence of wood at terahertz frequencies

NASA Astrophysics Data System (ADS)

Todoruk, Tara M.; Schneider, Jon; Hartley, Ian D.; Reid, Matthew

2008-06-01

Fibre content of solid wood plays an important role in the wood products industry in terms of value. Additionally, fibre structure in composite wood products such as Oriented Strand Board (OSB) and paper products plays an important role in terms of strength properties. The effect of moisture content on wood properties is important in the manufacturing process and final product performance, and therefore its effect on the birefringence is of considerable interest. Since solid wood exhibits strong birefringence at terahertz frequencies, there may be potential applications of terahertz spectroscopy to fibre content and structure sensing. There are two potential sources for this strong birefringence: (i) form birefringence resulting from the porous structure of solid wood and (ii) intrinsic birefringence resulting from the dielectric properties of the material itself. In this report, the variability of birefringence within and between species, the dependence of the birefringence on moisture content and the relative contributions from form and intrinsic birefringence are examined. In order to clarify the role of these contributions to the measured birefringence, polarized terahertz reflection spectroscopy is examined and compared to the results obtained in a transmission geometry. Comparison of the birefringence measured in transmission and reflection geometries suggests that form birefringence may dominate.

Role of Histone Acetylation in the Assembly and Modulation of Chromatin Structures

PubMed Central

Annunziato, Anthony T.; Hansen, Jeffrey C.

2000-01-01

The acetylation of the core histone N-terminal “tail” domains is now recognized as a highly conserved mechanism for regulating chromatin functional states. The following article examines possible roles of acetylation in two critically important cellular processes: replication-coupled nucleosome assembly, and reversible transitions in chromatin higher order structure. After a description of the acetylation of newly synthesized histones, and of the likely acetyltransferases involved, an overview of histone octamer assembly is presented. Our current understanding of the factors thought to assemble chromatin in vivo is then described. Genetic and biochemical investigations of the function the histone tails, and their acetylation, in nucleosome assembly are detailed, followed by an analysis of the importance of histone deacetylation in the maturation of newly replicated chromatin. In the final section the involvement of the histone tail domains in chromatin higher order structures is addressed, along with the role of histone acetylation in chromatin folding. Suggestions for future research are offered in the concluding remarks. PMID:11097424

Investigating the Predictive Role of Authenticity on Subjective Vitality with Structural Equation Modelling

ERIC Educational Resources Information Center

Akin, Umran; Akin, Ahmet

2014-01-01

Authenticity is a basic personality characteristic that has an important influence on both the psychological and social lives of individuals. Subjective vitality also assumes a facilitative role regarding positive mental health indicators. Therefore, the purpose of this study is to investigate the predictive role of authenticity on subjective…

Structure of synaptophysin: a hexameric MARVEL-domain channel protein.

PubMed

Arthur, Christopher P; Stowell, Michael H B

2007-06-01

Synaptophysin I (SypI) is an archetypal member of the MARVEL-domain family of integral membrane proteins and one of the first synaptic vesicle proteins to be identified and cloned. Most all MARVEL-domain proteins are involved in membrane apposition and vesicle-trafficking events, but their precise role in these processes is unclear. We have purified mammalian SypI and determined its three-dimensional (3D) structure by using electron microscopy and single-particle 3D reconstruction. The hexameric structure resembles an open basket with a large pore and tenuous interactions within the cytosolic domain. The structure suggests a model for Synaptophysin's role in fusion and recycling that is regulated by known interactions with the SNARE machinery. This 3D structure of a MARVEL-domain protein provides a structural foundation for understanding the role of these important proteins in a variety of biological processes.

The roles of biological interactions and pollutant contamination in shaping microbial benthic community structure.

PubMed

Louati, Hela; Said, Olfa Ben; Soltani, Amel; Got, Patrice; Mahmoudi, Ezzeddine; Cravo-Laureau, Cristiana; Duran, Robert; Aissa, Patricia; Pringault, Olivier

2013-11-01

Biological interactions between metazoans and the microbial community play a major role in structuring food webs in aquatic sediments. Pollutants can also strongly affect the structure of meiofauna and microbial communities. This study aims investigating, in a non-contaminated sediment, the impact of meiofauna on bacteria facing contamination by a mixture of three PAHs (fluoranthene, phenanthrene and pyrene). Sediment microcosms were incubated in the presence or absence of meiofauna during 30 days. Bioremediation treatments, nutrient amendment and addition of a hydrocarbon-degrading bacterium, were also tested to enhance PAH biodegradation. Results clearly show the important role of meiofauna as structuring factor for bacterial communities with significant changes observed in the molecular fingerprints. However, these structural changes were not concomitant with changes in biomass or function. PAH contamination had a severe impact on total meiofaunal abundance with a strong decrease of nematodes and the complete disappearance of polychaetes and copepods. In contrast, correspondence analysis, based on T-RFLP fingerprints, showed that contamination by PAH resulted in small shifts in microbial composition, with or without meiofauna, suggesting a relative tolerance of bacteria to the PAH cocktail. The PAH bioremediation treatments were highly efficient with more than 95% biodegradation. No significant difference was observed in presence or absence of meiofauna. Nutrient addition strongly enhanced bacterial and meiofaunal abundances as compared to control and contaminated microcosms, as well as inducing important changes in the bacterial community structure. Nutrients thus were the main structural factor in shaping bacterial community composition, while the role of meiofauna was less evident.

The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery.

PubMed

Papaleo, Elena; Saladino, Giorgio; Lambrughi, Matteo; Lindorff-Larsen, Kresten; Gervasio, Francesco Luigi; Nussinov, Ruth

2016-06-08

Proteins are dynamic entities that undergo a plethora of conformational changes that may take place on a wide range of time scales. These changes can be as small as the rotation of one or a few side-chain dihedral angles or involve concerted motions in larger portions of the three-dimensional structure; both kinds of motions can be important for biological function and allostery. It is becoming increasingly evident that "connector regions" are important components of the dynamic personality of protein structures. These regions may be either disordered loops, i.e., poorly structured regions connecting secondary structural elements, or linkers that connect entire protein domains. Experimental and computational studies have, however, revealed that these regions are not mere connectors, and their role in allostery and conformational changes has been emerging in the last few decades. Here we provide a detailed overview of the structural properties and classification of loops and linkers, as well as a discussion of the main computational methods employed to investigate their function and dynamical properties. We also describe their importance for protein dynamics and allostery using as examples key proteins in cellular biology and human diseases such as kinases, ubiquitinating enzymes, and transcription factors.

Structural classification of proteins using texture descriptors extracted from the cellular automata image.

PubMed

Kavianpour, Hamidreza; Vasighi, Mahdi

2017-02-01

Nowadays, having knowledge about cellular attributes of proteins has an important role in pharmacy, medical science and molecular biology. These attributes are closely correlated with the function and three-dimensional structure of proteins. Knowledge of protein structural class is used by various methods for better understanding the protein functionality and folding patterns. Computational methods and intelligence systems can have an important role in performing structural classification of proteins. Most of protein sequences are saved in databanks as characters and strings and a numerical representation is essential for applying machine learning methods. In this work, a binary representation of protein sequences is introduced based on reduced amino acids alphabets according to surrounding hydrophobicity index. Many important features which are hidden in these long binary sequences can be clearly displayed through their cellular automata images. The extracted features from these images are used to build a classification model by support vector machine. Comparing to previous studies on the several benchmark datasets, the promising classification rates obtained by tenfold cross-validation imply that the current approach can help in revealing some inherent features deeply hidden in protein sequences and improve the quality of predicting protein structural class.

Statistical inference to advance network models in epidemiology.

PubMed

Welch, David; Bansal, Shweta; Hunter, David R

2011-03-01

Contact networks are playing an increasingly important role in the study of epidemiology. Most of the existing work in this area has focused on considering the effect of underlying network structure on epidemic dynamics by using tools from probability theory and computer simulation. This work has provided much insight on the role that heterogeneity in host contact patterns plays on infectious disease dynamics. Despite the important understanding afforded by the probability and simulation paradigm, this approach does not directly address important questions about the structure of contact networks such as what is the best network model for a particular mode of disease transmission, how parameter values of a given model should be estimated, or how precisely the data allow us to estimate these parameter values. We argue that these questions are best answered within a statistical framework and discuss the role of statistical inference in estimating contact networks from epidemiological data. Copyright © 2011 Elsevier B.V. All rights reserved.

An overview of the roles and structure of international high-security veterinary laboratories for infectious animal diseases.

PubMed

Murray, P K

1998-08-01

The unique structure, role and operations of government high-security (HS) laboratories which work on animal diseases are described, with particular reference to the laboratories of nine countries. High-security laboratories provide cost-effective insurance against catastrophic losses which could occur following exotic disease outbreaks. The importance of these laboratories is reflected in the fact that several new laboratories have recently been constructed at considerable expense and older facilities have undergone major renovations. Biosecurity is fundamental to the operation of high-security laboratories, so good facility design and microbiological security practices are very important. High-security laboratories conduct exotic disease diagnosis, certification and surveillance, and also perform research into virology, disease pathogenesis and improvements to diagnostic tests and vaccines. The mandate of these laboratories includes the training of veterinarians in the recognition of exotic diseases. One extremely important role is the provision of expert advice on exotic diseases and participation (both nationally and internationally) in policy decisions regarding animal disease issues.

Cilia-like structures anchor the amphioxus notochord to its sheath.

PubMed

Bočina, Ivana; Ljubešić, Nikola; Saraga-Babić, Mirna

2011-01-01

Body stiffness is important during undulatory locomotion in fish. In amphioxus, the myosepta play an important role in transmission of muscular forces to the notochord. In order to define the specific supporting role of the notochord in amphioxus during locomotion, the ultrastructure of 10 adult amphioxus specimens was analyzed using transmission electron microscopy. Numerous cilia-like structures were found on the surface of each notochordal cell at the sites of their attachment to the notochordal sheath. Ultrastructurally, these structures consisted of the characteristic arrangement of peripheral and central microtubular doublets and were anchored to the inner layer of the notochordal sheath. Immunohistochemically, a positive reaction to applied dynein and β-tubulin antibodies characterized the area of the cilia-like structures. We propose that reduced back-and-forth movements of the cilia-like structures might contribute to the flow of the fluid content inside the notochord, thus modulating the stiffness of the amphioxus body during its undulatory locomotion. Copyright © 2009 Elsevier GmbH. All rights reserved.

Perspective: Role of structure prediction in materials discovery and design

NASA Astrophysics Data System (ADS)

Needs, Richard J.; Pickard, Chris J.

2016-05-01

Materials informatics owes much to bioinformatics and the Materials Genome Initiative has been inspired by the Human Genome Project. But there is more to bioinformatics than genomes, and the same is true for materials informatics. Here we describe the rapidly expanding role of searching for structures of materials using first-principles electronic-structure methods. Structure searching has played an important part in unraveling structures of dense hydrogen and in identifying the record-high-temperature superconducting component in hydrogen sulfide at high pressures. We suggest that first-principles structure searching has already demonstrated its ability to determine structures of a wide range of materials and that it will play a central and increasing part in materials discovery and design.

Network evolution induced by asynchronous stimuli through spike-timing-dependent plasticity.

PubMed

Yuan, Wu-Jie; Zhou, Jian-Fang; Zhou, Changsong

2013-01-01

In sensory neural system, external asynchronous stimuli play an important role in perceptual learning, associative memory and map development. However, the organization of structure and dynamics of neural networks induced by external asynchronous stimuli are not well understood. Spike-timing-dependent plasticity (STDP) is a typical synaptic plasticity that has been extensively found in the sensory systems and that has received much theoretical attention. This synaptic plasticity is highly sensitive to correlations between pre- and postsynaptic firings. Thus, STDP is expected to play an important role in response to external asynchronous stimuli, which can induce segregative pre- and postsynaptic firings. In this paper, we study the impact of external asynchronous stimuli on the organization of structure and dynamics of neural networks through STDP. We construct a two-dimensional spatial neural network model with local connectivity and sparseness, and use external currents to stimulate alternately on different spatial layers. The adopted external currents imposed alternately on spatial layers can be here regarded as external asynchronous stimuli. Through extensive numerical simulations, we focus on the effects of stimulus number and inter-stimulus timing on synaptic connecting weights and the property of propagation dynamics in the resulting network structure. Interestingly, the resulting feedforward structure induced by stimulus-dependent asynchronous firings and its propagation dynamics reflect both the underlying property of STDP. The results imply a possible important role of STDP in generating feedforward structure and collective propagation activity required for experience-dependent map plasticity in developing in vivo sensory pathways and cortices. The relevance of the results to cue-triggered recall of learned temporal sequences, an important cognitive function, is briefly discussed as well. Furthermore, this finding suggests a potential application for examining STDP by measuring neural population activity in a cultured neural network.

Mechanics of vimentin intermediate filaments

NASA Technical Reports Server (NTRS)

Wang, Ning; Stamenovic, Dimitrijie

2002-01-01

It is increasingly evident that the cytoskeleton of living cells plays important roles in mechanical and biological functions of the cells. Here we focus on the contribution of intermediate filaments (IFs) to the mechanical behaviors of living cells. Vimentin, a major structural component of IFs in many cell types, is shown to play an important role in vital mechanical and biological functions such as cell contractility, migration, stiffness, stiffening, and proliferation.

Structural and catalytic effects of an invariant purine substitution in the hammerhead ribozyme: implications for the mechanism of acid–base catalysis

PubMed Central

Schultz, Eric P.; Vasquez, Ernesto E.; Scott, William G.

2014-01-01

The hammerhead ribozyme catalyzes RNA cleavage via acid–base catalysis. Whether it does so by general acid–base catalysis, in which the RNA itself donates and abstracts protons in the transition state, as is typically assumed, or by specific acid–base catalysis, in which the RNA plays a structural role and proton transfer is mediated by active-site water molecules, is unknown. Previous biochemical and crystallographic experiments implicate an invariant purine in the active site, G12, as the general base. However, G12 may play a structural role consistent with specific base catalysis. To better understand the role of G12 in the mechanism of hammerhead catalysis, a 2.2 Å resolution crystal structure of a hammerhead ribozyme from Schistosoma mansoni with a purine substituted for G12 in the active site of the ribozyme was obtained. Comparison of this structure (PDB entry 3zd4), in which A12 is substituted for G, with three previously determined structures that now serve as important experimental controls, allows the identification of structural perturbations that are owing to the purine substitution itself. Kinetic measurements for G12 purine-substituted schistosomal hammerheads confirm a previously observed dependence of rate on the pK a of the substituted purine; in both cases inosine, which is similar to G in pK a and hydrogen-bonding properties, is unexpectedly inactive. Structural comparisons indicate that this may primarily be owing to the lack of the exocyclic 2-amino group in the G12A and G12I substitutions and its structural effect upon both the nucleotide base and phosphate of A9. The latter involves the perturbation of a previously identified and well characterized metal ion-binding site known to be catalytically important in both minimal and full-length hammerhead ribozyme sequences. The results permit it to be suggested that G12 plays an important role in stabilizing the active-site structure. This result, although not inconsistent with the potential role of G12 as a general base, indicates that an alternative hammerhead cleavage mechanism involving specific base catalysis may instead explain the observed rate dependence upon purine substitutions at G12. The crystallographic results, contrary to previous assumptions, therefore cannot be interpreted to favor the general base catalysis mecahnism over the specific base catalysis mechanism. Instead, both of these mutually exclusive mechanistic alternatives must be considered in light of the current structural and biochemical data. PMID:25195740

Structural and catalytic effects of an invariant purine substitution in the hammerhead ribozyme: implications for the mechanism of acid-base catalysis.

PubMed

Schultz, Eric P; Vasquez, Ernesto E; Scott, William G

2014-09-01

The hammerhead ribozyme catalyzes RNA cleavage via acid-base catalysis. Whether it does so by general acid-base catalysis, in which the RNA itself donates and abstracts protons in the transition state, as is typically assumed, or by specific acid-base catalysis, in which the RNA plays a structural role and proton transfer is mediated by active-site water molecules, is unknown. Previous biochemical and crystallographic experiments implicate an invariant purine in the active site, G12, as the general base. However, G12 may play a structural role consistent with specific base catalysis. To better understand the role of G12 in the mechanism of hammerhead catalysis, a 2.2 Å resolution crystal structure of a hammerhead ribozyme from Schistosoma mansoni with a purine substituted for G12 in the active site of the ribozyme was obtained. Comparison of this structure (PDB entry 3zd4), in which A12 is substituted for G, with three previously determined structures that now serve as important experimental controls, allows the identification of structural perturbations that are owing to the purine substitution itself. Kinetic measurements for G12 purine-substituted schistosomal hammerheads confirm a previously observed dependence of rate on the pK(a) of the substituted purine; in both cases inosine, which is similar to G in pK(a) and hydrogen-bonding properties, is unexpectedly inactive. Structural comparisons indicate that this may primarily be owing to the lack of the exocyclic 2-amino group in the G12A and G12I substitutions and its structural effect upon both the nucleotide base and phosphate of A9. The latter involves the perturbation of a previously identified and well characterized metal ion-binding site known to be catalytically important in both minimal and full-length hammerhead ribozyme sequences. The results permit it to be suggested that G12 plays an important role in stabilizing the active-site structure. This result, although not inconsistent with the potential role of G12 as a general base, indicates that an alternative hammerhead cleavage mechanism involving specific base catalysis may instead explain the observed rate dependence upon purine substitutions at G12. The crystallographic results, contrary to previous assumptions, therefore cannot be interpreted to favor the general base catalysis mecahnism over the specific base catalysis mechanism. Instead, both of these mutually exclusive mechanistic alternatives must be considered in light of the current structural and biochemical data.

Caenorhabditis elegans chemical biology: lessons from small molecules

USDA-ARS?s Scientific Manuscript database

How can we complement Caenorhabditis elegans genomics and proteomics with a comprehensive structural and functional annotation of its metabolome? Several lines of evidence indicate that small molecules of largely undetermined structure play important roles in C. elegans biology, including key pathw...

Structural and electronic phase transitions of ThS 2 from first-principles calculations

DOE PAGES

Guo, Yongliang; Wang, Changying; Qiu, Wujie; ...

2016-10-07

Performed a systematic study using first-principles methods of the pressure-induced structural and electronic phase transitions in ThS 2, which may play an important role in the next generation nuclear energy fuel technology.

Teacher Structure as a Predictor of Students' Perceived Competence and Autonomous Motivation: The Moderating Role of Differentiated Instruction

ERIC Educational Resources Information Center

Guay, Frédéric; Roy, Amélie; Valois, Pierre

2017-01-01

Background: An important pedagogical practice is the provision of structure (Farkas & Grolnick, 2010, "Motiv. Emot.," 34, 266). According to self-determination theory (SDT; Deci & Ryan, 1985, "Intrinsic motivation and self-determination in human behavior," Plenum, New York, NY), structure allows students to develop…

The complex roles of space and environment in structuring functional, taxonomic and phylogenetic beta diversity of frogs in the Atlantic Forest

PubMed Central

Luiz, Amom Mendes; Sawaya, Ricardo J.

2018-01-01

Ecological communities are complex entities that can be maintained and structured by niche-based processes such as environmental conditions, and spatial processes such as dispersal. Thus, diversity patterns may be shaped simultaneously at different spatial scales by very distinct processes. Herein we assess whether and how functional, taxonomic, and phylogenetic beta diversities of frog tadpoles are explained by environmental and/or spatial predictors. We implemented a distance–based redundancy analysis to explore variation in components of beta diversity explained by pure environmental and pure spatial predictors, as well as their interactions, at both fine and broad spatial scales. Our results indicated important but complex roles of spatial and environmental predictors in structuring phylogenetic, taxonomic and functional beta diversities. The pure fine-scales spatial fraction was more important in structuring all beta diversity components, especially to functional and taxonomical spatial turnover. Environmental variables such as canopy cover and vegetation structure were important predictors of all components, but especially to functional and taxonomic beta diversity. We emphasize that distinct factors related to environment and space are affecting distinct components of beta diversity in different ways. Although weaker, phylogenetic beta diversity, which is structured more on biogeographical scales, and thus can be represented by spatially structured processes, was more related to broad spatial processes than other components. However, selected fine-scale spatial predictors denoted negative autocorrelation, which may be revealing the existence of differences in unmeasured habitat variables among samples. Although overall important, local environmental-based processes explained better functional and taxonomic beta diversity, as these diversity components carry an important ecological value. We highlight the importance of assessing different components of diversity patterns at different scales by spatially explicit models in order to improve our understanding of community structure and help to unravel the complex nature of biodiversity. PMID:29672575

[Connective tissue and inflammation].

PubMed

Jakab, Lajos

2014-03-23

The author summarizes the structure of the connective tissues, the increasing motion of the constituents, which determine the role in establishing the structure and function of that. The structure and function of the connective tissue are related to each other in the resting as well as inflammatory states. It is emphasized that cellular events in the connective tissue are part of the defence of the organism, the localisation of the damage and, if possible, the maintenance of restitutio ad integrum. The organism responds to damage with inflammation, the non specific immune response, as well as specific, adaptive immunity. These processes are located in the connective tissue. Sterile and pathogenic inflammation are relatively similar processes, but inevitable differences are present, too. Sialic acids and glycoproteins containing sialic acids have important roles, and the role of Siglecs is also highlighted. Also, similarities and differences in damages caused by pathogens and sterile agents are briefly summarized. In addition, the roles of adhesion molecules linked to each other, and the whole event of inflammatory processes are presented. When considering practical consequences it is stressed that the structure (building up) of the organism and the defending function of inflammation both have fundamental importance. Inflammation has a crucial role in maintaining the integrity and the unimpaired somato-psychological state of the organism. Thus, inflammation serves as a tool of organism identical with the natural immune response, inseparably connected with the specific, adaptive immune response. The main events of the inflammatory processes take place in the connective tissue.

Unique structural modulation of a non-native substrate by cochaperone DnaJ.

PubMed

Tiwari, Satyam; Kumar, Vignesh; Jayaraj, Gopal Gunanathan; Maiti, Souvik; Mapa, Koyeli

2013-02-12

The role of bacterial DnaJ protein as a cochaperone of DnaK is strongly appreciated. Although DnaJ unaccompanied by DnaK can bind unfolded as well as native substrate proteins, its role as an individual chaperone remains elusive. In this study, we demonstrate that DnaJ binds a model non-native substrate with a low nanomolar dissociation constant and, more importantly, modulates the structure of its non-native state. The structural modulation achieved by DnaJ is different compared to that achieved by the DnaK-DnaJ complex. The nature of structural modulation exerted by DnaJ is suggestive of a unique unfolding activity on the non-native substrate by the chaperone. Furthermore, we demonstrate that the zinc binding motif along with the C-terminal substrate binding domain of DnaJ is necessary and sufficient for binding and the subsequent binding-induced structural alterations of the non-native substrate. We hypothesize that this hitherto unknown structural alteration of non-native states by DnaJ might be important for its chaperoning activity by removing kinetic traps of the folding intermediates.

Methoxydiphenylamine-substituted fluorene derivatives as hole transporting materials: role of molecular interaction on device photovoltaic performance.

PubMed

Tiazkis, Robertas; Paek, Sanghyun; Daskeviciene, Maryte; Malinauskas, Tadas; Saliba, Michael; Nekrasovas, Jonas; Jankauskas, Vygintas; Ahmad, Shahzada; Getautis, Vytautas; Khaja Nazeeruddin, Mohammad

2017-03-10

The molecular structure of the hole transporting material (HTM) play an important role in hole extraction in a perovskite solar cells. It has a significant influence on the molecular planarity, energy level, and charge transport properties. Understanding the relationship between the chemical structure of the HTM's and perovskite solar cells (PSCs) performance is crucial for the continued development of the efficient organic charge transporting materials. Using molecular engineering approach we have constructed a series of the hole transporting materials with strategically placed aliphatic substituents to investigate the relationship between the chemical structure of the HTMs and the photovoltaic performance. PSCs employing the investigated HTMs demonstrate power conversion efficiency values in the range of 9% to 16.8% highlighting the importance of the optimal molecular structure. An inappropriately placed side group could compromise the device performance. Due to the ease of synthesis and moieties employed in its construction, it offers a wide range of possible structural modifications. This class of molecules has a great potential for structural optimization in order to realize simple and efficient small molecule based HTMs for perovskite solar cells application.

Organization structure as a moderator of the relationship between procedural justice, interactional justice, perceived organizational support, and supervisory trust.

PubMed

Ambrose, Maureen L; Schminke, Marshall

2003-04-01

Organizational justice researchers recognize the important role organization context plays in justice perceptions, yet few studies systematically examine contextual variables. This article examines how 1 aspect of context--organizational structure--affects the relationship between justice perceptions and 2 types of social exchange relationships, organizational and supervisory. The authors suggest that under different structural conditions, procedural and interactional justice will play differentially important roles in determining the quality of organizational social exchange (as evidenced by perceived organizational support [POS]) and supervisory social exchange (as evidenced by supervisory trust). In particular, the authors hypothesized that the relationship between procedural justice and POS would be stronger in mechanistic organizations and that the relationship between interactional justice and supervisory trust would be stronger in organic organizations. The authors' results support these hypotheses.

Processes entangling interactions in communities: forbidden links are more important than abundance in a hummingbird-plant network.

PubMed

Vizentin-Bugoni, Jeferson; Maruyama, Pietro Kiyoshi; Sazima, Marlies

2014-04-07

Understanding the relative importance of multiple processes on structuring species interactions within communities is one of the major challenges in ecology. Here, we evaluated the relative importance of species abundance and forbidden links in structuring a hummingbird-plant interaction network from the Atlantic rainforest in Brazil. Our results show that models incorporating phenological overlapping and morphological matches were more accurate in predicting the observed interactions than models considering species abundance. This means that forbidden links, by imposing constraints on species interactions, play a greater role than species abundance in structuring the ecological network. We also show that using the frequency of interaction as a proxy for species abundance and network metrics to describe the detailed network structure might lead to biased conclusions regarding mechanisms generating network structure. Together, our findings suggest that species abundance can be a less important driver of species interactions in communities than previously thought.

Processes entangling interactions in communities: forbidden links are more important than abundance in a hummingbird–plant network

PubMed Central

Vizentin-Bugoni, Jeferson; Maruyama, Pietro Kiyoshi; Sazima, Marlies

2014-01-01

Understanding the relative importance of multiple processes on structuring species interactions within communities is one of the major challenges in ecology. Here, we evaluated the relative importance of species abundance and forbidden links in structuring a hummingbird–plant interaction network from the Atlantic rainforest in Brazil. Our results show that models incorporating phenological overlapping and morphological matches were more accurate in predicting the observed interactions than models considering species abundance. This means that forbidden links, by imposing constraints on species interactions, play a greater role than species abundance in structuring the ecological network. We also show that using the frequency of interaction as a proxy for species abundance and network metrics to describe the detailed network structure might lead to biased conclusions regarding mechanisms generating network structure. Together, our findings suggest that species abundance can be a less important driver of species interactions in communities than previously thought. PMID:24552835

High Energy Density in Azobenzene-based Materials for Photo-Thermal Batteries via Controlled Polymer Architecture and Polymer-Solvent Interactions.

PubMed

Jeong, Seung Pyo; Renna, Lawrence A; Boyle, Connor J; Kwak, Hyunwook S; Harder, Edward; Damm, Wolfgang; Venkataraman, Dhandapani

2017-12-19

Energy densities of ~510 J/g (max: 698 J/g) have been achieved in azobenzene-based syndiotactic-rich poly(methacrylate) polymers. The processing solvent and polymer-solvent interactions are important to achieve morphologically optimal structures for high-energy density materials. This work shows that morphological changes of solid-state syndiotactic polymers, driven by different solvent processings play an important role in controlling the activation energy of Z-E isomerization as well as the shape of the DSC exotherm. Thus, this study shows the crucial role of processing solvents and thin film structure in achieving higher energy densities.

The Role of Linkers in the Excited-State Dynamic Planarization Processes of Macrocyclic Oligothiophene 12-Mers.

PubMed

Kim, Woojae; Sung, Jooyoung; Park, Kyu Hyung; Shimizu, Hideyuki; Imamura, Mika; Han, Minwoo; Sim, Eunji; Iyoda, Masahiko; Kim, Dongho

2015-11-05

Linkers adjoining chromophores play an important role in modulating the structure of conjugated systems, which is bound up with their photophysical properties. However, to date, the focus of works dealing with linker effects was limited only to linear π-conjugated materials, and there have been no detailed studies on cyclic counterparts. Herein we report the linker effects on the dynamic planarization processes of π-conjugated macrocyclic oligothiophene 12-mers, where the different ratio between ethynylene and vinylene linkers was chosen to control the backbone rigidity. By analyzing transient fluorescence spectra, we demonstrate that the connecting linkers play a crucial role in the excited-state dynamics of cyclic conjugated systems. Faster dynamic planarization, longer exciton delocalization length, and higher degree of planarity were observed in vinylene inserted cyclic oligothiophenes. Molecular dynamics simulations and density functional theory calculations also stress the importance of the role of linkers in modulating the structure of cyclic oligothiophenes.

How do Swedish day center attendees with psychiatric disabilities view their worker role? A structural equation modeling study.

PubMed

Eklund, Mona; Bäckström, Martin; Bejerholm, Ulrika

2018-05-01

To investigate how day center attendees with psychiatric disabilities perceived their worker role and the importance of current work situation and personal factors in that respect. Two-hundred attendees completed the Worker Role Self-assessment and questionnaires addressing possible predictors of the worker role: current employment situation, satisfaction with that situation, and a personal factor (encompassing self-esteem, self-mastery and engagement). Structural equation modeling was used. A model indicated two worker role factors; belief in a future worker role (WR1) and current capacities and routines (WR2). WR1 was positively influenced by having a job, younger age and the personal factor. Satisfaction with current work situation (usually unemployment) was negatively associated with WR1. The personal factor was single predictor of WR2. The attendees rated WR2 more positively than WR1. The personal factor was crucial for both WR1 and WR2. Work-related factors were only important for WR1. The more negative rating of belief in a future worker role may be interpreted as mistrust in the services. The attendees' positive ratings of capacities indicate, however, that they had a rehabilitation potential to develop. Enhancing self-esteem, mastery and engagement may be an avenue for staff in efforts to support the attendee's worker role.

Structural basis for the role of serine-rich repeat proteins from Lactobacillus reuteri in gut microbe–host interactions

PubMed Central

Sequeira, Saannya; Kavanaugh, Devon; MacKenzie, Donald A.; Walpole, Samuel; Leclaire, Charlotte; Gunning, A. Patrick; Latousakis, Dimitrios; Willats, William G. T.; Dong, Changjiang; Juge, Nathalie

2018-01-01

Lactobacillus reuteri, a Gram-positive bacterial species inhabiting the gastrointestinal tract of vertebrates, displays remarkable host adaptation. Previous mutational analyses of rodent strain L. reuteri 100-23C identified a gene encoding a predicted surface-exposed serine-rich repeat protein (SRRP100-23) that was vital for L. reuteri biofilm formation in mice. SRRPs have emerged as an important group of surface proteins on many pathogens, but no structural information is available in commensal bacteria. Here we report the 2.00-Å and 1.92-Å crystal structures of the binding regions (BRs) of SRRP100-23 and SRRP53608 from L. reuteri ATCC 53608, revealing a unique β-solenoid fold in this important adhesin family. SRRP53608-BR bound to host epithelial cells and DNA at neutral pH and recognized polygalacturonic acid (PGA), rhamnogalacturonan I, or chondroitin sulfate A at acidic pH. Mutagenesis confirmed the role of the BR putative binding site in the interaction of SRRP53608-BR with PGA. Long molecular dynamics simulations showed that SRRP53608-BR undergoes a pH-dependent conformational change. Together, these findings provide mechanistic insights into the role of SRRPs in host–microbe interactions and open avenues of research into the use of biofilm-forming probiotics against clinically important pathogens. PMID:29507249

Notochord vacuoles are lysosome-related organelles that function in axis and spine morphogenesis.

PubMed

Ellis, Kathryn; Bagwell, Jennifer; Bagnat, Michel

2013-03-04

The notochord plays critical structural and signaling roles during vertebrate development. At the center of the vertebrate notochord is a large fluid-filled organelle, the notochord vacuole. Although these highly conserved intracellular structures have been described for decades, little is known about the molecular mechanisms involved in their biogenesis and maintenance. Here we show that zebrafish notochord vacuoles are specialized lysosome-related organelles whose formation and maintenance requires late endosomal trafficking regulated by the vacuole-specific Rab32a and H(+)-ATPase-dependent acidification. We establish that notochord vacuoles are required for body axis elongation during embryonic development and identify a novel role in spine morphogenesis. Thus, the vertebrate notochord plays important structural roles beyond early development.

Notochord vacuoles are lysosome-related organelles that function in axis and spine morphogenesis

PubMed Central

Ellis, Kathryn; Bagwell, Jennifer

2013-01-01

The notochord plays critical structural and signaling roles during vertebrate development. At the center of the vertebrate notochord is a large fluid-filled organelle, the notochord vacuole. Although these highly conserved intracellular structures have been described for decades, little is known about the molecular mechanisms involved in their biogenesis and maintenance. Here we show that zebrafish notochord vacuoles are specialized lysosome-related organelles whose formation and maintenance requires late endosomal trafficking regulated by the vacuole-specific Rab32a and H+-ATPase–dependent acidification. We establish that notochord vacuoles are required for body axis elongation during embryonic development and identify a novel role in spine morphogenesis. Thus, the vertebrate notochord plays important structural roles beyond early development. PMID:23460678

Roles of NN-interaction components in shell-structure evolution

NASA Astrophysics Data System (ADS)

Umeya, Atsushi; Muto, Kazuo

2016-11-01

Since the importance of the monopole interaction was first emphasized in 1960s, roles of monopole strengths of two-body nucleon-nucleon interaction in shell structure have been discussed. Through the monopole strengths, we study the roles in shell-structure evolution, starting from explicit forms of the interaction. For the tensor component of the interaction, we show the derivation of the relation, (2j> + 1)Vjj> + (2j< + 1)Vjj< = 0, with a detailed manipulation. We show that one-body spin-orbit term appears in the multipole expansion of two-body spin-orbit interaction. Only the spin-orbit components can affect the spin-orbit energy splitting between spin-orbit partners, when the spin-orbit partner orbits are fully occupied.

Public Interest or Private Agenda? A Meditation on the Role of NGOs in Environmental Policy and Management in Australia

ERIC Educational Resources Information Center

Lane, Marcus B.; Morrison, T. H.

2006-01-01

Non-government organisations (NGOs) have come to assume an important role in environmental policy in Australia. This paper considers the institutional impacts of an enlarged and formal role for NGOs in environmental governance. To foreground the analysis that follows, the paper theorises: (i) the structural democratisation of western societies…

The Role of Feedback in Implicit and Explicit Artificial Grammar Learning: A Comparison between Dyslexic and Non-Dyslexic Adults

ERIC Educational Resources Information Center

Schiff, Rachel; Sasson, Ayelet; Star, Galit; Kahta, Shani

2017-01-01

The importance of feedback for learning has been firmly established over the past few decades. The question of whether feedback plays a significant role in the statistical learning abilities of adults with dyslexia, however, is currently unresolved. Here, we examined the role of feedback in grammaticality judgment, type of structural knowledge,…

MCTBI: a web server for predicting metal ion effects in RNA structures.

PubMed

Sun, Li-Zhen; Zhang, Jing-Xiang; Chen, Shi-Jie

2017-08-01

Metal ions play critical roles in RNA structure and function. However, web servers and software packages for predicting ion effects in RNA structures are notably scarce. Furthermore, the existing web servers and software packages mainly neglect ion correlation and fluctuation effects, which are potentially important for RNAs. We here report a new web server, the MCTBI server (http://rna.physics.missouri.edu/MCTBI), for the prediction of ion effects for RNA structures. This server is based on the recently developed MCTBI, a model that can account for ion correlation and fluctuation effects for nucleic acid structures and can provide improved predictions for the effects of metal ions, especially for multivalent ions such as Mg 2+ effects, as shown by extensive theory-experiment test results. The MCTBI web server predicts metal ion binding fractions, the most probable bound ion distribution, the electrostatic free energy of the system, and the free energy components. The results provide mechanistic insights into the role of metal ions in RNA structure formation and folding stability, which is important for understanding RNA functions and the rational design of RNA structures. © 2017 Sun et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Building Collaborative Structures for Teachers' Autonomy and Self-Efficacy: The Mediating Role of Participative Management and Learning Culture

ERIC Educational Resources Information Center

Lu, Jiafang; Jiang, Xinhui; Yu, Huen; Li, Dongyu

2015-01-01

This study focused on the collaborative structure-building behavior of school principals and examined how such behavior affects teacher empowerment. More important, it tested the mediating effects of participative management and learning culture. By collecting nested data from 104 schools in Hong Kong and adopting multilevel structural equation…

Durability of sealants exposed to outdoor weathering and hot compression cycles

Treesearch

Gregory T. Schueneman; Steven Lacher; Christopher G. Hunt; Christopher C. White; Donald L. Hunston

2011-01-01

Sealants play an important role in weatherproofing structures by filling gaps and preventing air and water intrusion. When incorrectly selected or improperly applied, they may fail quickly, compromising durability of the structure. To ensure reliability and prevent the need for costly repairs to structures, it is necessary to measure durability and predict life...

Teaching Steel Connections Using an Interactive Virtual Steel Sculpture

ERIC Educational Resources Information Center

Moaveni, Saeed; Chou, Karen C.

2015-01-01

Steel connections play important roles in the integrity of a structure, and many structural failures are attributed to connection failures. Connections are the glue that holds a structure together. The failures of the Hartford Coliseum in 1977, the Hyatt Regency Hotel in Kansas City in 1980, and the I-35W Bridge in Minneapolis in 2007 are all…

Total Lightning Observations within Electrified Snowfall using Polarimetric Radar LMA, and NWN Measurements

NASA Technical Reports Server (NTRS)

Schultz, Christopher J.; Bruning, Eric C.; Carey, Lawrence D.; Blakeslee, Richard J.

2013-01-01

Tall structures play and important role in development of winter time lightning flashes.To what extent still needs to be assessed. Tower initiated flashes typically occur as banded structures pass near/overhead. Hi resolution RHI s from polarimetric radar show that the lightning has a tendency to propagate through layered structures within these snowstorms.

The Effect of Riparian Zones in Structuring Small Mammal Communities in the Southern Appalachians

Treesearch

Joshua Laerm; Michael A. Menzel; Dorothy J. Wolf; James R. Welch

1997-01-01

Riparian zones have been shown to be important in structuring vertebrate communities and in maintaining biodiversity. We examined the role of riparian zones in structuring small mammal communities in a southern Appalachian watershed at Coweeta Hydrological Laboratory, Macon County, North Carolina. We established pitfall and live-trap grids in three replicates each of...

CHEMICAL STRUCTURE INDEXING OF TOXICITY DATA ON THE INTERNET: MOVING TOWARDS A FLAT WORLD

EPA Science Inventory

Standardized chemical structure annotation of public toxicity databases and information resources is playing an increasingly important role in the 'flattening' and integration of diverse sets of biological activity data on the Internet. This review discusses public initiatives th...

Home health nursing care agenda based on health policy in Korea.

PubMed

Ryu, Hosihn; An, Jiyoung; Koabyashi, Mia

2005-06-01

Home health nursing care (HHNC) in Korea has taken on an important role under the mandate of the national health care system since 2000. This program was developed to verify the possibility of early discharge of hospitalized patients and cost containment through a research and development project that was conducted with the government from 1994 to 1999. The process of development of HHNC provided an opportunity to realize the advancement and changes in the system into a consumer-focused structure. This is an important turning point for the Korean health care system that suggests certain possibilities for building a foundation for further changes in the service delivery structure. The structure, which had been limited to a supplier-oriented model, is moving to a consumer-oriented structure. Accordingly, the major function and role of nursing policy makers in Korea is to develop an agenda and alternatives for policy-making in a systematic manner and to present implementation strategies clearly.

Importance of Diffuse Metal Ion Binding to RNA

PubMed Central

Tan, Zhi-Jie; Chen, Shi-Jie

2016-01-01

RNAs are highly charged polyanionic molecules. RNA structure and function are strongly correlated with the ionic condition of the solution. The primary focus of this article is on the role of diffusive ions in RNA folding. Due to the long-range nature of electrostatic interactions, the diffuse ions can contribute significantly to RNA structural stability and folding kinetics. We present an overview of the experimental findings as well as the theoretical developments on the diffuse ion effects in RNA folding. This review places heavy emphasis on the effect of magnesium ions. Magnesium ions play a highly efficient role in stabilizing RNA tertiary structures and promoting tertiary structural folding. The highly efficient role goes beyond the mean-field effect such as the ionic strength. In addition to the effects of specific ion binding and ion dehydration, ion-ion correlation for the diffuse ions can contribute to the efficient role of the multivalent ions such as the magnesium ions in RNA folding. PMID:22010269

Importance of diffuse metal ion binding to RNA.

PubMed

Tan, Zhi-Jie; Chen, Shi-Jie

2011-01-01

RNAs are highly charged polyanionic molecules. RNA structure and function are strongly correlated with the ionic condition of the solution. The primary focus of this article is on the role of diffusive ions in RNA folding. Due to the long-range nature of electrostatic interactions, the diffuse ions can contribute significantly to RNA structural stability and folding kinetics. We present an overview of the experimental findings as well as the theoretical developments on the diffuse ion effects in RNA folding. This review places heavy emphasis on the effect of magnesium ions. Magnesium ions play a highly efficient role in stabilizing RNA tertiary structures and promoting tertiary structural folding. The highly efficient role goes beyond the mean-field effect such as the ionic strength. In addition to the effects of specific ion binding and ion dehydration, ion-ion correlation for the diffuse ions can contribute to the efficient role of the multivalent ions such as the magnesium ions in RNA folding.

Exploring Human Diseases and Biological Mechanisms by Protein Structure Prediction and Modeling.

PubMed

Wang, Juexin; Luttrell, Joseph; Zhang, Ning; Khan, Saad; Shi, NianQing; Wang, Michael X; Kang, Jing-Qiong; Wang, Zheng; Xu, Dong

2016-01-01

Protein structure prediction and modeling provide a tool for understanding protein functions by computationally constructing protein structures from amino acid sequences and analyzing them. With help from protein prediction tools and web servers, users can obtain the three-dimensional protein structure models and gain knowledge of functions from the proteins. In this chapter, we will provide several examples of such studies. As an example, structure modeling methods were used to investigate the relation between mutation-caused misfolding of protein and human diseases including epilepsy and leukemia. Protein structure prediction and modeling were also applied in nucleotide-gated channels and their interaction interfaces to investigate their roles in brain and heart cells. In molecular mechanism studies of plants, rice salinity tolerance mechanism was studied via structure modeling on crucial proteins identified by systems biology analysis; trait-associated protein-protein interactions were modeled, which sheds some light on the roles of mutations in soybean oil/protein content. In the age of precision medicine, we believe protein structure prediction and modeling will play more and more important roles in investigating biomedical mechanism of diseases and drug design.

Working Definitions of the Roles and an Organizational Structure in Health Professions Education Scholarship: Initiating an International Conversation.

PubMed

Varpio, Lara; Gruppen, Larry; Hu, Wendy; O'Brien, Bridget; Ten Cate, Olle; Humphrey-Murto, Susan; Irby, David M; van der Vleuten, Cees; Hamstra, Stanley J; Durning, Steven J

2017-02-01

Health professions education scholarship (HPES) is an important and growing field of inquiry. Problematically, consistent use of terminology regarding the individual roles and organizational structures that are active in this field are lacking. This inconsistency impedes the transferability of current and future findings related to the roles and organizational structures of HPES. Based on data collected during interviews with HPES leaders in Canada, Australia, New Zealand, the United States, and the Netherlands, the authors constructed working definitions for some of the professional roles and an organizational structure that support HPES. All authors reviewed the definitions to ensure relevance across multiple countries. The authors define and offer illustrative examples of three professional roles in HPES (clinician educator, HPES research scientist, and HPES administrative leader) and an organizational structure that can support HPES participation (HPES unit). These working definitions are foundational and not all-encompassing and, thus, are offered as stimulus for international dialogue and understanding. With these working definitions, scholars and administrative leaders can examine HPES roles and organizational structures across and between national contexts to decide how lessons learned in other contexts can be applied to their local contexts. Although rigorously constructed, these definitions need to be vetted by the international HPES community. The authors argue that these definitions are sufficiently transferable to support such scholarly investigation and debate.

Aquaporin structure-function relationships: water flow through plant living cells.

PubMed

Zhao, Chang-Xing; Shao, Hong-Bo; Chu, Li-Ye

2008-04-01

Plant aquaporins play an important role in water uptake and movement-an aquaporin that opens and closes a gate that regulates water movement in and out of cells. Some plant aquaporins also play an important role in response to water stress. Since their discovery, advancing knowledge of their structures and properties led to an understanding of the basic features of the water transport mechanism and increased illumination to water relations. Meanwhile, molecular and functional characterization of aquaporins has revealed the significance of their regulation in response to the adverse environments such as salinity and drought. This paper reviews the structure, species diversity, physiology function, regulation of plant aquaporins, and the relations between environmental factors and plant aquaporins. Complete understanding of aquaporin function and regulation is to integrate those mechanisms in time and space and to well regulate the permeation of water across biological membranes under changing environmental and developmental conditions.

Detecting Role Errors in the Gene Hierarchy of the NCI Thesaurus

PubMed Central

Min, Hua; Cohen, Barry; Halper, Michael; Oren, Marc; Perl, Yehoshua

2008-01-01

Gene terminologies are playing an increasingly important role in the ever-growing field of genomic research. While errors in large, complex terminologies are inevitable, gene terminologies are even more susceptible to them due to the rapid growth of genomic knowledge and the nature of its discovery. It is therefore very important to establish quality-assurance protocols for such genomic-knowledge repositories. Different kinds of terminologies oftentimes require auditing methodologies adapted to their particular structures. In light of this, an auditing methodology tailored to the characteristics of the NCI Thesaurus’s (NCIT’s) Gene hierarchy is presented. The Gene hierarchy is of particular interest to the NCIT’s designers due to the primary role of genomics in current cancer research. This multiphase methodology focuses on detecting role-errors, such as missing roles or roles with incorrect or incomplete target structures, occurring within that hierarchy. The methodology is based on two kinds of abstraction networks, called taxonomies, that highlight the role distribution among concepts within the IS-A (subsumption) hierarchy. These abstract views tend to highlight portions of the hierarchy having a higher concentration of errors. The errors found during an application of the methodology are reported. Hypotheses pertaining to the efficacy of our methodology are investigated. PMID:19221606

Capillary Assembly of Colloids: Interactions on Planar and Curved Interfaces

NASA Astrophysics Data System (ADS)

Liu, Iris B.; Sharifi-Mood, Nima; Stebe, Kathleen J.

2018-03-01

In directed assembly, small building blocks are assembled into an organized structure under the influence of guiding fields. Capillary interactions provide a versatile route for structure formation. Colloids adsorbed on fluid interfaces distort the interface, which creates an associated energy field. When neighboring distortions overlap, colloids interact to minimize interfacial area. Contact line pinning, particle shape, and surface chemistry play important roles in structure formation. Interface curvature acts like an external field; particles migrate and assemble in patterns dictated by curvature gradients. We review basic analysis and recent findings in this rapidly evolving literature. Understanding the roles of assembly is essential for tuning the mechanical, physical, and optical properties of the structure.

The Role of Structural Extracellular Matrix Proteins in Urothelial Bladder Cancer (Review)

PubMed Central

Brunner, Andrea; Tzankov, Alexandar

2007-01-01

The extracellular matrix (ECM) plays a key role in the modulation of cancer cell invasion. In urothelial carcinoma of the bladder (UC) the role of ECM proteins has been widely studied. The mechanisms, which are involved in the development of invasion, progression and generalization, are complex, depending on the interaction of ECM proteins with each other as well as with cancer cells. The following review will focus on the pathogenetic role and prognostic value of structural proteins, such as laminins, collagens, fibronectin (FN), tenascin (Tn-C) and thrombospondin 1 (TSP1) in UC. In addition, the role of integrins mediating the interaction of ECM molecules and cancer cells will be addressed, since integrin-mediated FN, Tn-C and TSP1 interactions seem to play an important role during tumor cell invasion and angiogenesis. PMID:19662222

The Structure of Habilitation.

ERIC Educational Resources Information Center

Gibson, David; And Others

1987-01-01

Biographic and program information were related to placement outcomes for 75 mentally retarded adults who had completed a three-year training program and up to three years of subsequent community vocational placement. Results suggested an important role for cognitive variables (symbol management and basic concepts) in the overall structure of…

The Fragrant Chemist

ERIC Educational Resources Information Center

Ward, P.

1973-01-01

The chemist plays an important role in perfumery. There are scientific problems involved in relating odour to structure, including analysis of essential oils, quality control, and synthetic chemistry. (DF)

Clinical managers in the primary care sector: do the benefits stack up?

PubMed

O'Riordan, Chris; McDermott, Aoife

2012-01-01

The purpose of this paper is to explore the nature and value of the clinical management role undertaken by primary care doctors in Ireland. To date, a majority of research has focused on clinical management roles in the acute sector. The paper presents a sub-set of data from a mixed methods study. In total, 14 semi-structured interviews are drawn upon to identify the nature and value of the clinical management role in primary care. Comparison with acute sector research identifies considerable differences in the nature of the clinical management role across sectors--and in the associated value proposition. Structural and role-related contingencies affecting the potential value of clinical management roles in Irish primary care are discussed. Structural influences include the private ownership structure, low complexity and limited requirement for cross-professional coordination. Role-related influences include the primacy of the clinical identity, time constraints and lack of managerial training. The findings provide a limited basis for generalisation, premised on 14 interviews in one national context. However, given the international shift towards the provision of health services in primary care, they provide a research agenda for an important healthcare context. The findings draw attention to the need for policy consideration of the value of the clinical manager role in primary care; how policy can support effective primary care management; and the need for specialised management training, which takes account of the small-firm context. The paper identifies that primary-care clinical-management roles focus on operational management and oversight and discusses the structural and role-related factors which affect their efficacy.

The dual role of fragments in fragment-assembly methods for de novo protein structure prediction

PubMed Central

Handl, Julia; Knowles, Joshua; Vernon, Robert; Baker, David; Lovell, Simon C.

2013-01-01

In fragment-assembly techniques for protein structure prediction, models of protein structure are assembled from fragments of known protein structures. This process is typically guided by a knowledge-based energy function and uses a heuristic optimization method. The fragments play two important roles in this process: they define the set of structural parameters available, and they also assume the role of the main variation operators that are used by the optimiser. Previous analysis has typically focused on the first of these roles. In particular, the relationship between local amino acid sequence and local protein structure has been studied by a range of authors. The correlation between the two has been shown to vary with the window length considered, and the results of these analyses have informed directly the choice of fragment length in state-of-the-art prediction techniques. Here, we focus on the second role of fragments and aim to determine the effect of fragment length from an optimization perspective. We use theoretical analyses to reveal how the size and structure of the search space changes as a function of insertion length. Furthermore, empirical analyses are used to explore additional ways in which the size of the fragment insertion influences the search both in a simulation model and for the fragment-assembly technique, Rosetta. PMID:22095594

Working in a 'third space': a closer look at the hybridity, identity and agency of nurse practitioners.

PubMed

Chulach, Teresa; Gagnon, Marilou

2016-03-01

Nurse practitioners (NPs), as advanced practice nurses, have evolved over the years to become recognized as an important and growing trend in Canada and worldwide. In spite of sound evidence as to the effectiveness of NPs in primary care and other care settings, role implementation and integration continue to pose significant challenges. This article utilizes postcolonial theory, as articulated by Homi Bhabha, to examine and challenge traditional ideologies and structures that have shaped the development, implementation and integration of the NP role to this day. Specifically, we utilize Bhabha's concepts of third space, hybridity, identity and agency in order to further conceptualize the nurse practitioner role, to examine how the role challenges some of the inherent assumptions within the healthcare system and to explore how development of each to these concepts may prove useful in integration of nurse practitioners within the healthcare system. Our analysis casts light on the importance of a broader, power structure analysis and illustrates how colonial assumptions operating within our current healthcare system entrench, expand and re-invent, as well as mask the structures and practices that serve to impede nurse practitioner full integration and contributions. Suggestions are made for future analysis and research. © 2015 John Wiley & Sons Ltd.

Three-dimensional Structure of Saccharomyces Invertase

PubMed Central

Sainz-Polo, M. Angela; Ramírez-Escudero, Mercedes; Lafraya, Alvaro; González, Beatriz; Marín-Navarro, Julia; Polaina, Julio; Sanz-Aparicio, Julia

2013-01-01

Invertase is an enzyme that is widely distributed among plants and microorganisms and that catalyzes the hydrolysis of the disaccharide sucrose into glucose and fructose. Despite the important physiological role of Saccharomyces invertase (SInv) and the historical relevance of this enzyme as a model in early biochemical studies, its structure had not yet been solved. We report here the crystal structure of recombinant SInv at 3.3 Å resolution showing that the enzyme folds into the catalytic β-propeller and β-sandwich domains characteristic of GH32 enzymes. However, SInv displays an unusual quaternary structure. Monomers associate in two different kinds of dimers, which are in turn assembled into an octamer, best described as a tetramer of dimers. Dimerization plays a determinant role in substrate specificity because this assembly sets steric constraints that limit the access to the active site of oligosaccharides of more than four units. Comparative analysis of GH32 enzymes showed that formation of the SInv octamer occurs through a β-sheet extension that seems unique to this enzyme. Interaction between dimers is determined by a short amino acid sequence at the beginning of the β-sandwich domain. Our results highlight the role of the non-catalytic domain in fine-tuning substrate specificity and thus supplement our knowledge of the activity of this important family of enzymes. In turn, this gives a deeper insight into the structural features that rule modularity and protein-carbohydrate recognition. PMID:23430743

Why poverty remains high: the role of income growth, economic inequality, and changes in family structure, 1949-1999.

PubMed

Iceland, John

2003-08-01

After dramatic declines in poverty from 1950 to the early 1970s in the United States, progress stalled. This article examines the association between trends in poverty and income growth, economic inequality, and changes in family structure using three measures of poverty: an absolute measure, a relative measure, and a quasi-relative one. I found that income growth explains most of the trend in absolute poverty, while inequality generally plays the most significant role in explaining trends in relative poverty. Rising inequality in the 1970s and 1980s was especially important in explaining increases in poverty among Hispanics, whereas changes in family structure played a significant role for children and African Americans through 1990. Notably, changes in family structure no longer had a significant association with trends in poverty for any group in the 1990s.

The Role of Human Error in Design, Construction, and Reliability of Marine Structures.

DTIC Science & Technology

1994-10-01

The 1979 Three Mile Island nuclear plant accident was largely a result of a failure to properly sort out and recognize critically important information...determinating the goals and objectives of the program and by evaluating and interpreting the results in terms of structural design, construction, and...67 Checking Models in Structural Design ....................................... 69 Nuclear Power Plants

The importance of the specific Z-DNA structure and polyamines in carcinogenesis: fact or fiction.

PubMed

Juranic, Z; Kidric, M; Tomin, R; Juranić, I; Spuzić, I; Petrović, J

1991-08-01

In this work some aspects of carcinogenesis are given. The importance of the emergence of Z or H DNA structure in the gene, or in the flanking gene sequences for the gene deletion and unusual gene recombination, is discussed. Some considerations on the role of selective pressure (of polyamines, of Mg2+, of the various levels of topoisomerase II, and of ATP) in the process of oncogene amplification, are given too.

Structure-function characterization of the human mitochondrial thiamin pyrophosphate transporter (hMTPPT; SLC25A19): Important roles for Ile(33), Ser(34), Asp(37), His(137) and Lys(291).

PubMed

Sabui, Subrata; Subramanian, Veedamali S; Kapadia, Rubina; Said, Hamid M

2016-08-01

Thiamin plays a critical role in cellular energy metabolism. Mammalian cells obtain the vitamin from their surroundings, converted it to thiamin pyrophosphate (TPP) in the cytoplasm, followed by uptake of TPP by mitochondria via a carrier-mediated process that involves the MTPPT (product of the SLC25A19 gene). Previous studies have characterized different physiological/biological aspects of the human MTPPT (hMTPPT), but less is known about structural features that are important for its function. Here, we used a protein-docking model ("Phyre2" and "DockingServer") to predict residues that may be important for function (substrate recognition) of the hMTPPT; we also examined the role of conserved positively-charged residues predicted ("PRALINE") to be in the trans-membrane domains (TMDs) in uptake of the negatively-charged TPP. Among the six residues predicted by the docking model (i.e., Thr(29), Arg(30), Ile(33), Ser(34), Asp(37) and Phe(298)), only Ile(33), Ser(34) and Asp(37) were found to be critical for function. While no change in translational efficiency/protein stability of the Ser(34) mutant was observed, both the Ile(33) and Asp(37) mutants showed a decrease in this parameter(s); there was also a decrease in the expression of the latter two mutants in mitochondria. A need for a polar residue at position 34 of the hMTPPT was evident. Our findings with the positively-charged residues (i.e., His(82), His(137), Lys(231) and Lys(291)) predicted in the TMD showed that His(137) and Lys(291) are important for function (via a role in proper delivery of the protein to mitochondria). These investigations provide important information about the structure-function relationship of the hMTPPT. Copyright © 2016 Elsevier B.V. All rights reserved.

Kinetic scale structure of low-frequency waves and fluctuations

NASA Astrophysics Data System (ADS)

Lopez Herrera, R. A.; Figueroa-Vinas, A.; Araneda, J. A.; Yoon, P. H.

2017-12-01

The dissipation of solar wind turbulence at kinetic scales is believed to be important for heating the corona and accelerating the wind. Linear Vlasov kinetic theory is a useful tool in identifying various wave modes, including kinetic Alfvén, fast magnetosonic/whistler, ion-acoustic (or kinetic slow mode), and their possible roles in the dissipation. However, kinetic mode structure near the vicinity of ion cyclotron modes is not clearly understood. The present poster aims to further elucidate the structure of these low-frequency waves by introducing discrete particle effects through hybrid simulations and Klimontovich formalism of spontaneous emission theory. The theory and simulation of spontaneously emitted low-frequency fluctuations are employed to identify and distinguish the detailed mode structures associated with ion Bernstein versus quasi modes. The spontaneous emission theory and simulation also confirm the findings of Vlasov theory in that the kinetic Alfvén wave can be defined over a wide range of frequencies, including the proton cyclotron frequency and its harmonics, especially for high beta plasmas. This implies that these low-frequency modes may play predominant roles even in the fully kinetic description of kinetic scale turbulence and dissipation despite the fact that cyclotron harmonic and Bernstein modes may also play important roles in wave-particle interactions.

Disentangling the role of management, vegetation structure, and plant quality for Orthoptera in lowland meadows.

PubMed

Schirmel, Jens; Gerlach, Rebekka; Buhk, Constanze

2017-08-17

Seminatural grasslands provide habitats for various species and are important for biodiversity conservation. The understanding of the diverse responses of species and traits to different grassland management methods is therefore urgently needed. We disentangled the role of grassland management (fertilization and irrigation), vegetation structure (biomass, sward height) and plant quality (protein and fiber content) for Orthoptera communities in lowland hay meadows in Germany. We found vegetation structure to be the most important environmental category in explaining community structure of Orthoptera (species richness, total individuals, functional diversity and species composition). Intensively used meadows (fertilized, irrigated, high plant biomass) were characterized by assemblages with few species, low functional diversity, and low conservation value. Thereby, the relatively moderate fertilizer inputs in our study system of up to ∼75 kg N/ha/year reduced functional diversity of Orthoptera, while this negative effect of fertilization was not detectable when solely considering taxonomic aspects. We found strong support for a prominent role of plant quality in shaping Orthoptera communities and especially the trait composition. Our findings demonstrate the usefulness of considering both taxonomic and functional components (functional diversity) in biodiversity research and we suggest a stronger involvement of plant quality measures in Orthoptera studies. © 2017 Institute of Zoology, Chinese Academy of Sciences.

Structure, and culture of the gut microbiome of the Mormon cricket Anabrus simplex

USDA-ARS?s Scientific Manuscript database

The gut microbiome of insects plays an important role in their ecology and evolution, participating in nutrient acquisition, immunity, and behavior. Microbial community structure within the gut is heavily influenced by differences among gut regions in morphology and physiology, which determine the n...

Bottle Caps as Prekindergarten Mathematical Tools

ERIC Educational Resources Information Center

Raisor, Jill M.; Hudson, Rick A.

2018-01-01

Early childhood provides a time of crucial growth in all developmental domains. Prekindergarten is an optimal time for young children to use objects of play as a medium to explore new cognitive concepts, including mathematical structure. Mathematical structure plays an important role in providing students a means to reason about mathematics,…

The role of perceived classroom goal structures, self-efficacy, and engagement in student science achievement

NASA Astrophysics Data System (ADS)

Uçar, F. Melike; Sungur, Semra

2017-04-01

Background: Numerous studies have been conducted to investigate the factors related to science achievement. In these studies, the classroom goal structure perceptions, engagement, and self-efficacy of the students have emerged as important factors to be examined in relation to students' science achievement.

Ecosystem management and its role in linking science, policy, and management

Treesearch

Matthew Skroch

2005-01-01

The scientific community has recently emphasized the importance of ecological process, structure, and scale in the maintenance of biological diversity. Humans have affected most natural landscapes, and many naturally occurring processes, structures, and species may not rebound to naturally sustaining function without intervention. Ecosystem management relies on science...

Class, paid employment and family roles: making sense of structural disadvantage, gender and health status.

PubMed

Arber, S

1991-01-01

The British tradition of analysing differences in health has been dominated by class, with women belatedly entering this debate. The American tradition has been dominated by role analysis, with women's health considered primarily in terms of their marital, parental and employment roles, with recent research coming to contradictory conclusions. Research in both traditions has reached an impasse. This paper uses a sample of over 25,000 men and women from the 1985 and 1986 British General Household Survey to show how both traditions need to be reformulated and integrated. The ways in which family roles are associated with women's health status is determined by material circumstances, but the material circumstances cannot be captured by occupational class alone. Participation in the labour market and consumption divisions, in the form of housing tenure, are crucial additional indicators of structural disadvantage. Standardised limiting long-standing illness ratios and multivariate logit analysis confirm that occupational class and paid employment are the most important attributes associated with health status for women and men. Family roles are important for women; women without children and previously married women have particularly poor health status especially those not in paid employment and living in local authority housing.

In Silico Analysis for the Study of Botulinum Toxin Structure

NASA Astrophysics Data System (ADS)

Suzuki, Tomonori; Miyazaki, Satoru

2010-01-01

Protein-protein interactions play many important roles in biological function. Knowledge of protein-protein complex structure is required for understanding the function. The determination of protein-protein complex structure by experimental studies remains difficult, therefore computational prediction of protein structures by structure modeling and docking studies is valuable method. In addition, MD simulation is also one of the most popular methods for protein structure modeling and characteristics. Here, we attempt to predict protein-protein complex structure and property using some of bioinformatic methods, and we focus botulinum toxin complex as target structure.

Causal Models of Role Stressor Antecedents and Consequences: The Importance of Occupational Differences.

ERIC Educational Resources Information Center

Bacharach, Samuel; Bamberger, Peter

1992-01-01

Survey data from 215 nurses (10 male) and 430 civil engineers (10 female) supported the plausibility of occupation-specific models (positing direct paths between role stressors, antecedents, and consequences) compared to generic models. A weakness of generic models is the tendency to ignore differences in occupational structure and culture. (SK)

What Has Morality to Do with Religious Education?

ERIC Educational Resources Information Center

Barnes, L. Philip

2011-01-01

The aim of this paper is to provide a positive case for increasing the role and importance of religious morality within the subject of religious education in British schools. The argument is structured in the following way. First, attention is given to the diminished role accorded to moral education within religious education that followed the…

Leaving Home: The Role of Individual and Familial Factors.

ERIC Educational Resources Information Center

Sherrod, Lonnie R.

1996-01-01

Discusses the significance of research on the transition to adulthood, examining social-historical changes that may increase the role of individual and familial factors structuring this phase of the life course. Reviews leaving home in regard to its importance as a factor in late adolescence and the transition to adulthood. (HTH)

The Enigma of the Respiratory Chain Supercomplex.

PubMed

Milenkovic, Dusanka; Blaza, James N; Larsson, Nils-Göran; Hirst, Judy

2017-04-04

Respiratory chain dysfunction plays an important role in human disease and aging. It is now well established that the individual respiratory complexes can be organized into supercomplexes, and structures for these macromolecular assemblies, determined by electron cryo-microscopy, have been described recently. Nevertheless, the reason why supercomplexes exist remains an enigma. The widely held view that they enhance catalysis by channeling substrates is challenged by both structural and biophysical information. Here, we evaluate and discuss data and hypotheses on the structures, roles, and assembly of respiratory-chain supercomplexes and propose a future research agenda to address unanswered questions. Copyright © 2017. Published by Elsevier Inc.

Forging the ring: from fungal septins' divergent roles in morphology, septation and virulence to factors contributing to their assembly into higher order structures.

PubMed

Vargas-Muñiz, Jose M; Juvvadi, Praveen R; Steinbach, William J

2016-09-01

Septins are a conserved family of GTP-binding proteins that are distributed across different lineages of the eukaryotes, with the exception of plants. Septins perform a myriad of functions in fungal cells, ranging from controlling morphogenetic events to contributing to host tissue invasion and virulence. One key attribute of the septins is their ability to assemble into heterooligomeric complexes that organizse into higher order structures. In addition to the established role of septins in the model budding yeast, Saccharomyces cerevisiae, their importance in other fungi recently emerges. While newer roles for septins are being uncovered in these fungi, the mechanism of how septins assemble into a complex and their regulation is only beginning to be comprehended. In this review, we summarize recent findings on the role of septins in different fungi and focus on how the septin complexes of different fungi are organized in vitro and in vivo. Furthermore, we discuss on how phosphorylation/dephosphorylation can serve as an important mechanism of septin complex assembly and regulation.

The mechanics of the primary cilium: an intricate structure with complex function.

PubMed

Hoey, David A; Downs, Matthew E; Jacobs, Christopher R

2012-01-03

The primary cilium is a non-motile singular cellular structure that extends from the surface of nearly every cell in the body. The cilium has been shown to play numerous roles in maintaining tissue homeostasis, through regulating signaling pathways and sensing both biophysical and biochemical changes in the extracellular environment. The structural performance of the cilium is paramount to its function as defective cilia have been linked to numerous pathologies. In particular, the cilium has demonstrated a mechanosensory role in tissues such as the kidney, liver, endothelium and bone, where cilium deflection under mechanical loading triggers a cellular response. Understanding of how cilium structure and subsequent mechanical behavior contributes to the roles that cilium plays in regulating cellular behavior is a compelling question, yet is a relatively untouched research area. Recent advances in biophysical measurements have demonstrated the cilium to be a structurally intricate organelle containing an array of load bearing proteins. Furthermore advances in modeling of this organelle have revealed the importance of these proteins at regulating the cilium's mechanosensitivity. Remarkably, the cilium is capable of adapting its mechanical state, altering its length and possibly it's bending resistance, to regulate its mechanosensitivity demonstrating the importance of cilium mechanics in cellular responses. In this review, we introduce the cilium as a mechanosensor; discuss the advances in the mechanical modeling of cilia; explore the structural features of the cilium, which contribute to its mechanics and finish with possible mechanisms in which alteration in structure may affect ciliary mechanics, consequently affecting ciliary based mechanosensing. Copyright © 2011 Elsevier Ltd. All rights reserved.

Crystal structure of isoflavone reductase from alfalfa (Medicago sativa L.).

PubMed

Wang, Xiaoqiang; He, Xianzhi; Lin, Jianqiao; Shao, Hui; Chang, Zhenzhan; Dixon, Richard A

2006-05-19

Isoflavonoids play important roles in plant defense and exhibit a range of mammalian health-promoting activities. Isoflavone reductase (IFR) specifically recognizes isoflavones and catalyzes a stereospecific NADPH-dependent reduction to (3R)-isoflavanone. The crystal structure of Medicago sativa IFR with deletion of residues 39-47 has been determined at 1.6A resolution. Structural analysis, molecular modeling and docking, and comparison with the structures of other NADPH-dependent enzymes, defined the putative binding sites for co-factor and substrate and potential key residues for enzyme activity and substrate specificity. Further mutagenesis has confirmed the role of Lys144 as a catalytic residue. This study provides a structural basis for understanding the enzymatic mechanism and substrate specificity of IFRs as well as the functions of IFR-like proteins.

G Protein-Coupled Receptor Rhodopsin: A Prospectus

PubMed Central

Filipek, Sławomir; Stenkamp, Ronald E.; Teller, David C.; Palczewski, Krzysztof

2006-01-01

Rhodopsin is a retinal photoreceptor protein of bipartite structure consisting of the transmembrane protein opsin and a light-sensitive chromophore 11-cis-retinal, linked to opsin via a protonated Schiff base. Studies on rhodopsin have unveiled many structural and functional features that are common to a large and pharmacologically important group of proteins from the G protein-coupled receptor (GPCR) superfamily, of which rhodopsin is the best-studied member. In this work, we focus on structural features of rhodopsin as revealed by many biochemical and structural investigations. In particular, the high-resolution structure of bovine rhodopsin provides a template for understanding how GPCRs work. We describe the sensitivity and complexity of rhodopsin that lead to its important role in vision. PMID:12471166

[Genome organization and life cycle of the hepatitis c virus].

PubMed

Kalinina, O V; Dmitriev, A V

2015-01-01

The review summarizes the current data about the hepatitis C viral genome and polyprotein organization. The functional role of the structural and non-structural viral proteins including their interaction with cellular regulatory proteins and cell structural elements is discussed. Specific peculiarities of the life cycle of the hepatitis C virus important for the understanding of the viral hepatitis C pathogenesis are summarized.

Solution structure of CEH-37 homeodomain of the nematode Caenorhabditis elegans

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

Moon, Sunjin; Lee, Yong Woo; Kim, Woo Taek

Highlights: •We have determined solution structures of CEH-37 homedomain. •CEH-37 HD has a compact α-helical structure with HTH DNA binding motif. •Solution structure of CEH-37 HD shares its molecular topology with that of the homeodomain proteins. •Residues in the N-terminal region and HTH motif are important in binding to Caenorhabditis elegans telomeric DNA. •CEH-37 could play an important role in telomere function via DNA binding. -- Abstract: The nematode Caenorhabditis elegans protein CEH-37 belongs to the paired OTD/OTX family of homeobox-containing homeodomain proteins. CEH-37 shares sequence similarity with homeodomain proteins, although it specifically binds to double-stranded C. elegans telomeric DNA,more » which is unusual to homeodomain proteins. Here, we report the solution structure of CEH-37 homeodomain and molecular interaction with double-stranded C. elegans telomeric DNA using nuclear magnetic resonance (NMR) spectroscopy. NMR structure shows that CEH-37 homeodomain is composed of a flexible N-terminal region and three α-helices with a helix-turn-helix (HTH) DNA binding motif. Data from size-exclusion chromatography and fluorescence spectroscopy reveal that CEH-37 homeodomain interacts strongly with double-stranded C. elegans telomeric DNA. NMR titration experiments identified residues responsible for specific binding to nematode double-stranded telomeric DNA. These results suggest that C. elegans homeodomain protein, CEH-37 could play an important role in telomere function via DNA binding.« less

The Dual Role of Vegetation as a Constraint on Mass and Energy Flux into the Critical Zone and as an Emergent Property of Geophysical Critical Zone Structure

NASA Astrophysics Data System (ADS)

Brooks, P. D.; Swetnam, T. L.; Barnard, H. R.; Singha, K.; Harpold, A.; Litvak, M. E.

2017-12-01

Spatial patterns in vegetation long have been used to scale both landsurface-atmosphere exchanges of water and carbon as well as to infer subsurface structure. These pursuits typical proceed in isolation and rarely do inferences gained from one community propagate to related efforts in another. Perhaps more importantly, vegetation often is treated as an emergent property of landscape-climate interactions rather than an active modifier of both critical zone structure and energy fluxes. We posit that vegetation structure and activity are under utilized as a tool towards understanding landscape evolution and present examples that begin to disentangle the role of vegetation as both an emergent property and an active control on critical zone structure and function. As climate change, population growth, and land use changes threaten water resources worldwide, the need for the new insights vegetation can provide becomes not just a basic science priority, but a pressing applied science question with clear societal importance. This presentation will provide an overview of recent efforts to address the dual role of vegetation in both modifying and reflecting critical zone structure in the western North American forests. For example, interactions between topography and stand scale vegetation structure influence both solar radiation and turbulence altering landscape scale partitioning of evaporation vs transpiration with major impacts of surface water supply. Similarly, interactions between topographic shading, lateral redistribution of plant available water, and subsurface storage create a mosaic of drought resistance and resilience across complex terrain. These complex interactions between geophysical and vegetation components of critical zone structure result in predictable patterns in catchment scale hydrologic partitioning within individual watersheds while simultaneously suggesting testable hypotheses for why catchments under similar climate regimes respond so differently to drought stress.

Meteoritics and cosmology among the Aboriginal cultures of Central Australia

NASA Astrophysics Data System (ADS)

Hamacher, Duane W.

2011-03-01

The night sky played an important role in the social structure, oral traditions, and cosmology of the Arrernte and Luritja Aboriginal cultures of Central Australia. A component of this cosmology relates to meteors, meteorites, and impact craters. This paper discusses the role of meteoritic phenomena in Arrernte and Luritja cosmology, showing not only that these groups incorporated this phenomenon in their cultural traditions, but that their oral traditions regarding the relationship between meteors, meteorites and impact structures suggests the Arrernte and Luritja understood that they are directly related.

Invited review article: Photopyroelectric calorimeter for the simultaneous thermal, optical, and structural characterization of samples over phase transitions.

PubMed

Zammit, U; Marinelli, M; Mercuri, F; Paoloni, S; Scudieri, F

2011-12-01

The study of thermophysical properties is of great importance in several scientific fields. Among them, the heat capacity, for example, is related to the microscopic structure of condensed matter and plays an important role in monitoring the changes in the energy content of a system. Calorimetric techniques are thus of fundamental importance for characterizing physical systems, particularly in the vicinity of phase transitions where energy fluctuations can play an important role. In this work, the ability of the Photopyroelctric calorimetry to study the versus temperature behaviour of the specific heat and of the other thermal parameters in the vicinity of phase transitions is outlined. The working principle, the theoretical basis, the experimental configurations, and the advantages of this technique, with respect to the more conventional ones, have been described and discussed in detail. The integrations in the calorimetric setup giving the possibility to perform, simultaneously with the calorimetric studies, complementary kind of characterizations of optical, structural, and electrical properties are also described. A review of the results obtained with this technique, in all its possible configurations, for the high temperature resolution studies of the thermal parameters over several kinds of phase transitions occurring in different systems is presented and discussed.

Detection of driver metabolites in the human liver metabolic network using structural controllability analysis

PubMed Central

2014-01-01

Background Abnormal states in human liver metabolism are major causes of human liver diseases ranging from hepatitis to hepatic tumor. The accumulation in relevant data makes it feasible to derive a large-scale human liver metabolic network (HLMN) and to discover important biological principles or drug-targets based on network analysis. Some studies have shown that interesting biological phenomenon and drug-targets could be discovered by applying structural controllability analysis (which is a newly prevailed concept in networks) to biological networks. The exploration on the connections between structural controllability theory and the HLMN could be used to uncover valuable information on the human liver metabolism from a fresh perspective. Results We applied structural controllability analysis to the HLMN and detected driver metabolites. The driver metabolites tend to have strong ability to influence the states of other metabolites and weak susceptibility to be influenced by the states of others. In addition, the metabolites were classified into three classes: critical, high-frequency and low-frequency driver metabolites. Among the identified 36 critical driver metabolites, 27 metabolites were found to be essential; the high-frequency driver metabolites tend to participate in different metabolic pathways, which are important in regulating the whole metabolic systems. Moreover, we explored some other possible connections between the structural controllability theory and the HLMN, and find that transport reactions and the environment play important roles in the human liver metabolism. Conclusion There are interesting connections between the structural controllability theory and the human liver metabolism: driver metabolites have essential biological functions; the crucial role of extracellular metabolites and transport reactions in controlling the HLMN highlights the importance of the environment in the health of human liver metabolism. PMID:24885538

Physical characteristics of calcium oxalate crystals as determinants in structural defense against chewing insects in Medicago truncatula

USDA-ARS?s Scientific Manuscript database

In addition to the numerous chemical defenses that plants employ to fend off insect herbivores, simple structural components can also play important roles in effective protection. Our investigations have shown that plant crystals of calcium oxalate can function in insect defense. The isolation of ca...

University of Massachusetts Boston: Reconstituting a Continuing Education Division to a Degree-Granting Academic Unit

ERIC Educational Resources Information Center

DiSalvio, Philip

2012-01-01

The ground has shifted in fundamental ways in higher education, and it is becoming increasingly evident that strategic structural reorganization will play an important role in the financial survival of many institutions. Understanding the close links among strategy, structure, and the environment, it makes sense that organizational structure…

Spatial structure of the Mormon cricket gut microbiome and its predicted contribution to nutrition and immune function

USDA-ARS?s Scientific Manuscript database

The gut microbiome of insects plays an important role in their ecology and evolution, participating in nutrient acquisition, immunity, and behavior. Microbial community structure within the gut is heavily influenced by differences among gut regions in morphology and physiology, which determine the n...

Situational and Structural Variation in Youth Perceptions of Maternal Guilt Induction

ERIC Educational Resources Information Center

Rote, Wendy M.; Smetana, Judith G.

2017-01-01

Parental induction of empathy-related guilt plays an important role in children's moral development. However, guilt induction can also be psychologically controlling and detrimental for youth adjustment. This study provided a more nuanced view of parental guilt induction by examining how the nature of a child's misdeed and the structure and…

The Role of Perceived Classroom Goal Structures, Self-Efficacy, and Engagement in Student Science Achievement

ERIC Educational Resources Information Center

Uçar, F. Melike; Sungur, Semra

2017-01-01

Background: Numerous studies have been conducted to investigate the factors related to science achievement. In these studies, the classroom goal structure perceptions, engagement, and self-efficacy of the students have emerged as important factors to be examined in relation to students' science achievement. Purpose: This study examines the…

Obstacle avoidance in social groups: new insights from asynchronous models

PubMed Central

Croft, Simon; Budgey, Richard; Pitchford, Jonathan W.; Wood, A. Jamie

2015-01-01

For moving animals, the successful avoidance of hazardous obstacles is an important capability. Despite this, few models of collective motion have addressed the relationship between behavioural and social features and obstacle avoidance. We develop an asynchronous individual-based model for social movement which allows social structure within groups to be included. We assess the dynamics of group navigation and resulting collision risk in the context of information transfer through the system. In agreement with previous work, we find that group size has a nonlinear effect on collision risk. We implement examples of possible network structures to explore the impact social preferences have on collision risk. We show that any social heterogeneity induces greater obstacle avoidance with further improvements corresponding to groups containing fewer influential individuals. The model provides a platform for both further theoretical investigation and practical application. In particular, we argue that the role of social structures within bird flocks may have an important role to play in assessing the risk of collisions with wind turbines, but that new methods of data analysis are needed to identify these social structures. PMID:25833245

Structure and substrate-binding mechanism of human Ap4A hydrolase.

PubMed

Swarbrick, James D; Buyya, Smrithi; Gunawardana, Dilantha; Gayler, Kenwyn R; McLennan, Alexander G; Gooley, Paul R

2005-03-04

Asymmetric diadenosine 5',5'''-P(1),P(4)-tetraphosphate (Ap(4)A) hydrolases play a major role in maintaining homeostasis by cleaving the metabolite diadenosine tetraphosphate (Ap(4)A) back into ATP and AMP. The NMR solution structures of the 17-kDa human asymmetric Ap(4)A hydrolase have been solved in both the presence and absence of the product ATP. The adenine moiety of the nucleotide predominantly binds in a ring stacking arrangement equivalent to that observed in the x-ray structure of the homologue from Caenorhabditis elegans. The binding site is, however, markedly divergent to that observed in the plant/pathogenic bacteria class of enzymes, opening avenues for the exploration of specific therapeutics. Binding of ATP induces substantial conformational and dynamic changes that were not observed in the C. elegans structure. In contrast to the C. elegans homologue, important side chains that play a major role in substrate binding do not have to reorient to accommodate the ligand. This may have important implications in the mechanism of substrate recognition in this class of enzymes.

Characteristics of the postcounseling reproductive decision-making process: an explorative study.

PubMed

Frets, P G; Verhage, F; Niermeijer, M F

1991-09-01

An in-depth, recorded interview of 30 couples 2-3 years after genetic counseling explored the characteristics of the postcounseling decision-making process, including the role of guilt feelings towards the proband. The study concerned couples with an affected child, sib, or spouse. Results were evaluated by 2 to 4 judges. In contrast to other studies, a generally unstructured decision-making process was found whereby guilt feelings played a significant role in more than half the couples. Guilt feelings were more predominant in couples with an affected sib than in those with an affected spouse. Lack of structure did not seem to complicate the decision-making process. Therefore, authors do not advocate promotion of structuring the decision-making process. Genetic counselors might focus on understanding counselees' feelings concerning the reproductive decision. Acceptance of apparently irrational considerations is particularly important, because these feelings indicate the influence of unconscious motives. Another important aspect of supporting counselees is to understand the role played by guilt feelings toward parents or an affected sib.

Constructing a self: the role of self-structure and self-certainty in social anxiety.

PubMed

Stopa, Lusia; Brown, Mike A; Luke, Michelle A; Hirsch, Colette R

2010-10-01

Current cognitive models stress the importance of negative self-perceptions in maintaining social anxiety, but focus predominantly on content rather than structure. Two studies examine the role of self-structure (self-organisation, self-complexity, and self-concept clarity) in social anxiety. In study one, self-organisation and self-concept clarity were correlated with social anxiety, and a step-wise multiple regression showed that after controlling for depression and self-esteem, which explained 35% of the variance in social anxiety scores, self-concept clarity uniquely predicted social anxiety and accounted for an additional 7% of the variance in social anxiety scores in an undergraduate sample (N=95) and the interaction between self-concept clarity and compartmentalisation (an aspect of evaluative self-organisation) at step 3 of the multiple regression accounted for a further 3% of the variance in social anxiety scores. In study two, high (n=26) socially anxious participants demonstrated less self-concept clarity than low socially anxious participants (n=26) on both self-report (used in study one) and on computerised measures of self-consistency and confidence in self-related judgments. The high socially anxious group had more compartmentalised self-organisation than the low anxious group, but there were no differences between the two groups on any of the other measures of self-organisation. Self-complexity did not contribute to social anxiety in either study, although this may have been due to the absence of a stressor. Overall, the results suggest that self-structure has a potentially important role in understanding social anxiety and that self-concept clarity and other aspects of self-structure such as compartmentalisation interact with each other and could be potential maintaining factors in social anxiety. Cognitive therapy for social phobia might influence self-structure, and understanding the role of structural variables in maintenance and treatment could eventually help to improve treatment outcome. Copyright 2010 Elsevier Ltd. All rights reserved.

Constructing a self: The role of self-structure and self-certainty in social anxiety

PubMed Central

Stopa, Lusia; Brown, Mike A.; Luke, Michelle A.; Hirsch, Colette R.

2010-01-01

Current cognitive models stress the importance of negative self-perceptions in maintaining social anxiety, but focus predominantly on content rather than structure. Two studies examine the role of self-structure (self-organisation, self-complexity, and self-concept clarity) in social anxiety. In study one, self-organisation and self-concept clarity were correlated with social anxiety, and a step-wise multiple regression showed that after controlling for depression and self-esteem, which explained 35% of the variance in social anxiety scores, self-concept clarity uniquely predicted social anxiety and accounted for an additional 7% of the variance in social anxiety scores in an undergraduate sample (N = 95) and the interaction between self-concept clarity and compartmentalisation (an aspect of evaluative self-organisation) at step 3 of the multiple regression accounted for a further 3% of the variance in social anxiety scores. In study two, high (n = 26) socially anxious participants demonstrated less self-concept clarity than low socially anxious participants (n = 26) on both self-report (used in study one) and on computerised measures of self-consistency and confidence in self-related judgments. The high socially anxious group had more compartmentalised self-organisation than the low anxious group, but there were no differences between the two groups on any of the other measures of self-organisation. Self-complexity did not contribute to social anxiety in either study, although this may have been due to the absence of a stressor. Overall, the results suggest that self-structure has a potentially important role in understanding social anxiety and that self-concept clarity and other aspects of self-structure such as compartmentalisation interact with each other and could be potential maintaining factors in social anxiety. Cognitive therapy for social phobia might influence self-structure, and understanding the role of structural variables in maintenance and treatment could eventually help to improve treatment outcome. PMID:20800751

Effects of Vegetation Structure on the Location of Lion Kill Sites in African Thicket.

PubMed

Davies, Andrew B; Tambling, Craig J; Kerley, Graham I H; Asner, Gregory P

2016-01-01

Predator-prey relationships are integral to ecosystem stability and functioning. These relationships are, however, difficult to maintain in protected areas where large predators are increasingly being reintroduced and confined. Where predators make kills has a profound influence on their role in ecosystems, but the relative importance of environmental variables in determining kill sites, and how these might vary across ecosystems is poorly known. We investigated kill sites for lions in South Africa's thicket biome, testing the importance of vegetation structure for kill site locations compared to other environmental variables. Kill sites were located over four years using GPS telemetry and compared to non-kill sites that had been occupied by lions, as well as to random sites within lion ranges. Measurements of 3D vegetation structure obtained from Light Detection and Ranging (LiDAR) were used to calculate the visible area (viewshed) around each site and, along with wind and moonlight data, used to compare kill sites between lion sexes, prey species and prey sexes. Viewshed area was the most important predictor of kill sites (sites in dense vegetation were twice as likely to be kill sites compared to open areas), followed by wind speed and, less so, moonlight. Kill sites for different prey species varied with vegetation structure, and male prey were killed when wind speeds were higher compared to female prey of the same species. Our results demonstrate that vegetation structure is an important component of predator-prey interactions, with varying effects across ecosystems. Such differences require consideration in terms of the ecological roles performed by predators, and in predator and prey conservation.

Structures of EccB 1 and EccD 1 from the core complex of the mycobacterial ESX-1 type VII secretion system

DOE PAGES

Wagner, Jonathan M.; Chan, Sum; Evans, Timothy J.; ...

2016-02-27

The ESX-1 type VII secretion system is an important determinant of virulence in pathogenic mycobacteria, including Mycobacterium tuberculosis. This complicated molecular machine secretes folded proteins through the mycobacterial cell envelope to subvert the host immune response. Despite its important role in disease very little is known about the molecular architecture of the ESX-1 secretion system. This study characterizes the structures of the soluble domains of two conserved core ESX-1 components – EccB 1 and EccD 1. The periplasmic domain of EccB 1 consists of 4 repeat domains and a central domain, which together form a quasi 2-fold symmetrical structure. Themore » repeat domains of EccB 1 are structurally similar to a known peptidoglycan binding protein suggesting a role in anchoring the ESX-1 system within the periplasmic space. The cytoplasmic domain of EccD 1 has a ubiquitin-like fold and forms a dimer with a negatively charged groove. In conclusion, these structures represent a major step towards resolving the molecular architecture of the entire ESX-1 assembly and may contribute to ESX-1 targeted tuberculosis intervention strategies.« less

Structures of EccB 1 and EccD 1 from the core complex of the mycobacterial ESX-1 type VII secretion system

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

Wagner, Jonathan M.; Chan, Sum; Evans, Timothy J.

The ESX-1 type VII secretion system is an important determinant of virulence in pathogenic mycobacteria, including Mycobacterium tuberculosis. This complicated molecular machine secretes folded proteins through the mycobacterial cell envelope to subvert the host immune response. Despite its important role in disease very little is known about the molecular architecture of the ESX-1 secretion system. This study characterizes the structures of the soluble domains of two conserved core ESX-1 components – EccB 1 and EccD 1. The periplasmic domain of EccB 1 consists of 4 repeat domains and a central domain, which together form a quasi 2-fold symmetrical structure. Themore » repeat domains of EccB 1 are structurally similar to a known peptidoglycan binding protein suggesting a role in anchoring the ESX-1 system within the periplasmic space. The cytoplasmic domain of EccD 1 has a ubiquitin-like fold and forms a dimer with a negatively charged groove. In conclusion, these structures represent a major step towards resolving the molecular architecture of the entire ESX-1 assembly and may contribute to ESX-1 targeted tuberculosis intervention strategies.« less

Farmers' perception of the role of veterinary surgeons in vaccination strategies on British dairy farms.

PubMed

Richens, I F; Hobson-West, P; Brennan, M L; Lowton, R; Kaler, J; Wapenaar, W

2015-11-07

There is limited research investigating the motivators and barriers to vaccinating dairy cattle. Veterinary surgeons have been identified as important sources of information for farmers making vaccination and disease control decisions, as well as being farmers' preferred vaccine suppliers. Vets' perception of their own role and communication style can be at odds with farmers' reported preferences. The objective of this study was to investigate how dairy farmers perceived the role of vets in implementing vaccination strategies on their farm. Semi-structured interviews were conducted with 24 dairy farmers from across Britain. The data were analysed using thematic analysis. Analysis revealed that farmers perceive vets to have an important role in facilitating decision-making in all aspects of vaccination, including the aspects of vaccine distribution and advice on implementation. This important role is acknowledged by farmers who have regular veterinary contact, but also farmers with solely emergency veterinary contact. Given this finding, future work should investigate the attitudes of vets towards vaccination and how they perceive their role. Combining this knowledge will enable optimisation of vaccination strategies on British dairy farms. British Veterinary Association.

THE ROLE OF PICKUP IONS ON THE STRUCTURE OF THE VENUSIAN BOW SHOCK AND ITS IMPLICATIONS FOR THE TERMINATION SHOCK

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

Lu Quanming; Shan Lican; Zhang Tielong

2013-08-20

The recent crossing of the termination shock by Voyager 2 has demonstrated the important role of pickup ions (PUIs) in the physics of collisionless shocks. The Venus Express (VEX) spacecraft orbits Venus in a 24 hr elliptical orbit that crosses the bow shock twice a day. VEX provides a unique opportunity to investigate the role of PUIs on the structure of collisionless shocks more generally. Using VEX observations, we find that the strength of the Venusian bow shock is weaker when solar activity is strong. We demonstrate that this surprising anti-correlation is due to PUIs mediating the Venusian bow shock.

Bringing together local culture and rural development: findings from Ireland, Pennsylvania and Alaska

Treesearch

M.A. Brennan; Courtney G. Flint; A.E. Luloff

2009-01-01

The developmental trajectories of communities are routinely explained by reference to economic history, human capital deficits, or the structure of local labour markets. The role of local culture in understanding community development or in interpreting empirical research has received less attention. We believe culture plays an important independent role in shaping...

Opportunities and Outcomes: The Role of Peers in Developing the Oral Academic English Proficiency of Adolescent English Learners

ERIC Educational Resources Information Center

Carhill-Poza, Avary

2015-01-01

Although researchers often acknowledge the importance of linguistically rich interactions in the academic language development of emergent bilingual students, few studies have explicitly examined the role of linguistic peer support and the underlying structure of social relationships in the second language learning experiences and outcomes of…

The Role of Higher Education within Broader Skills Policies, a Comparison of Emerging Scottish and English Approaches

ERIC Educational Resources Information Center

Keep, Ewart

2014-01-01

This article explores the important role played by higher education in broader skills and economic development policies in England and Scotland. It places the often divergent policy experiments and structural developments in these two countries' higher education systems within an international policy context and explains why England and Scotland…

Adolescents' Commitment to Developing Talent: The Role of Peers in Continuing Motivation for Sports and the Arts.

ERIC Educational Resources Information Center

Patrick, Helen; Ryan, Allison M.; Alfeld-Liro, Corinne; Fredericks, Jennifer A.; Hruda, Ludmila Z.; Eccles, Jacquelynne S.

1999-01-01

Conducted semi-structured in-depth interviews with 41 adolescents talented in sports or the arts to study the importance of peer relationships in their continued involvement in their talent activities, sex differences in attitudes, and possible differences by activity domain. Peers generally played a supportive role, although females were more…

Crystallography and Interphase Boundary of Martensite and Bainite in Steels

NASA Astrophysics Data System (ADS)

Furuhara, Tadashi; Chiba, Tadachika; Kaneshita, Takeshi; Wu, Huidong; Miyamoto, Goro

2017-06-01

Grain refinements in lath martensite and bainite structures are crucial for strengthening and toughening of high-strength structural steels. Clearly, crystallography of transformation plays an important role in determining the "grain" sizes in these structures. In the present study, crystallography and intrinsic boundary structure of martensite and bainite are described. Furthermore, various extrinsic factors affecting variant selection and growth kinetics, such as elastic/plastic strain and alloying effects on interphase boundary migration, are discussed.

Characterizing the structural ensemble of γ-secretase using a multiscale molecular dynamics approach† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc00980a Click here for additional data file.

PubMed Central

Aguayo-Ortiz, Rodrigo; Chávez-García, Cecilia; Straub, John E.

2017-01-01

γ-Secretase is an intramembrane-cleaving aspartyl protease that plays an essential role in the processing of a variety of integral membrane proteins. Its role in the ultimate cleavage step in the processing of amyloid precursor protein to form amyloid-β (Aβ) peptide makes it an important therapeutic target in Alzheimer's disease research. Significant recent advances have been made in structural studies of this critical membrane protein complex. However, details of the mechanism of activation of the enzyme complex remain unclear. Using a multiscale computational modeling approach, combining multiple coarse-grained microsecond dynamic trajectories with all-atom models, the structure and two conformational states of the γ-secretase complex were evaluated. The transition between enzymatic state 1 and state 2 is shown to critically depend on the protonation states of the key catalytic residues Asp257 and Asp385 in the active site domain. The active site formation, related to our γ-secretase state 2, is observed to involve a concerted movement of four transmembrane helices from the catalytic subunit, resulting in the required localization of the catalytic residues. Global analysis of the structural ensemble of the enzyme complex was used to identify collective fluctuations important to the mechanism of substrate recognition and demonstrate that the corresponding fluctuations observed were uncorrelated with structural changes associated with enzyme activation. Overall, this computational study provides essential insight into the role of structure and dynamics in the activation and function of γ-secretase. PMID:28970936

The key role of the scaffold on the efficiency of dendrimer nanodrugs

PubMed Central

Caminade, Anne-Marie; Fruchon, Séverine; Turrin, Cédric-Olivier; Poupot, Mary; Ouali, Armelle; Maraval, Alexandrine; Garzoni, Matteo; Maly, Marek; Furer, Victor; Kovalenko, Valeri; Majoral, Jean-Pierre; Pavan, Giovanni M.; Poupot, Rémy

2015-01-01

Dendrimers are well-defined macromolecules whose highly branched structure is reminiscent of many natural structures, such as trees, dendritic cells, neurons or the networks of kidneys and lungs. Nature has privileged such branched structures for increasing the efficiency of exchanges with the external medium; thus, the whole structure is of pivotal importance for these natural networks. On the contrary, it is generally believed that the properties of dendrimers are essentially related to their terminal groups, and that the internal structure plays the minor role of an ‘innocent' scaffold. Here we show that such an assertion is misleading, using convergent information from biological data (human monocytes activation) and all-atom molecular dynamics simulations on seven families of dendrimers (13 compounds) that we have synthesized, possessing identical terminal groups, but different internal structures. This work demonstrates that the scaffold of nanodrugs strongly influences their properties, somewhat reminiscent of the backbone of proteins. PMID:26169490

Do employed and nonemployed Korean mothers experience different levels of psychological well-being in relation to their gender role attitudes and role qualities?

PubMed

Kim, H

1998-06-01

This study explored the association of gender role attitudes (GRAs) and the quality of roles with the psychological well-being among employed and nonemployed mothers in Korea. Evidence supports the thesis that employed mothers with more liberal GRAs will report higher levels of psychological well-being. All role qualities were expected to be related to women's psychological well-being regardless of work status. Maternal role was expected to be more important in determining a working mothers well-being, but wife role was in fact the most important. Among nonemployed mothers, both the maternal and wife role affected well-being. Participants were recruits from a variety of institutional settings in Seoul, Korea, in 1995. The sample included 700 mothers, of whom 263 were working mothers; 295 were nonemployed mothers. Most were highly educated and affluent. The first model included only social structural variables, which were unrelated to the relationship between employment status and well-being. Gender of children was the only significant variable. Nonemployed mothers with a son had greater well-being than those without a son. The model excluding all social structural variables showed that GRA was unrelated to employed mothers' well-being. But, inclusion of the interaction between attitude and group suggests that well-being was related to agreement with whatever their role was. A model that included role qualities found that roles as wife, mother, and employee were positively related to well-being. The role of wife was significantly related to well-being among employed mothers. The wife and mother roles were significantly related to well-being among nonemployed mothers.

Linking nurses' perceptions of patient care quality to job satisfaction: the role of authentic leadership and empowering professional practice environments.

PubMed

Spence Laschinger, Heather K; Fida, Roberta

2015-05-01

A model linking authentic leadership, structural empowerment, and supportive professional practice environments to nurses' perceptions of patient care quality and job satisfaction was tested. Positive work environment characteristics are important for nurses' perceptions of patient care quality and job satisfaction (significant factors for retention). Few studies have examined the mechanism by which these characteristics operate to influence perceptions of patient care quality or job satisfaction. A cross-sectional provincial survey of 723 Canadian nurses was used to test the hypothesized models using structural equation modeling. The model was an acceptable fit and all paths were significant. Authentic leadership had a positive effect on structural empowerment, which had a positive effect on perceived support for professional practice and a negative effect on nurses' perceptions that inadequate unit staffing prevented them from providing high-quality patient care. These workplace conditions predicted job satisfaction. Authentic leaders play an important role in creating empowering professional practice environments that foster high-quality care and job satisfaction.

Non-Structural Proteins of Arthropod-Borne Bunyaviruses: Roles and Functions

PubMed Central

Eifan, Saleh; Schnettler, Esther; Dietrich, Isabelle; Kohl, Alain; Blomström, Anne-Lie

2013-01-01

Viruses within the Bunyaviridae family are tri-segmented, negative-stranded RNA viruses. The family includes several emerging and re-emerging viruses of humans, animals and plants, such as Rift Valley fever virus, Crimean-Congo hemorrhagic fever virus, La Crosse virus, Schmallenberg virus and tomato spotted wilt virus. Many bunyaviruses are arthropod-borne, so-called arboviruses. Depending on the genus, bunyaviruses encode, in addition to the RNA-dependent RNA polymerase and the different structural proteins, one or several non-structural proteins. These non-structural proteins are not always essential for virus growth and replication but can play an important role in viral pathogenesis through their interaction with the host innate immune system. In this review, we will summarize current knowledge and understanding of insect-borne bunyavirus non-structural protein function(s) in vertebrate, plant and arthropod. PMID:24100888

Three-dimensional structure of dominant instabilities in turbulent flow over smooth and rough boundaries

NASA Astrophysics Data System (ADS)

Grass, A. J.; Stuart, R. J.; Mansour-Tehrani, M.

1991-01-01

The current status of knowledge regarding coherent vortical structures in turbulent boundary layers and their role in turbulence generation are reviewed. The investigations reported in the study concentrate attention on rough-wall flows prevailing in the geophysical environment and include an experiment determining the three-dimensional form of the turbulence structures linked to the ejection and inrush events observed over rough walls and an experiment concerned with measuring the actual spanwise scale of the near-wall structures for boundary conditions ranging from hydrodynamically smooth to fully rough. It is demonstrated that horseshoe vortical structures are present and play an important role in rough-wall flows and they increase in scale with increasing wall distance, while a dominant spanwise wavelength occurs in the instantaneous cross-flow distribution of streamwise velocity close to the rough wall.

Experimental demonstration of the importance of competition under disturbance.

PubMed

Violle, Cyrille; Pu, Zhichao; Jiang, Lin

2010-07-20

Ecologists have long recognized the roles of competition and disturbance in shaping ecological communities, and the combinatorial effects of these two factors have been the subject of substantial ecological research. Nevertheless, it is still unclear whether competition remains as an important structuring force in habitats strongly influenced by disturbance. The conventional belief remains that the importance of competition decreases with increasing disturbance, but limited theory suggests otherwise. Using protist communities established in laboratory microcosms, we demonstrate that disturbance does not diminish the importance of competition. Interspecific competition significantly increased rates of species extinction over a broad disturbance gradient, and increasing disturbance intensities increased, rather than decreased, the tempo of competitive exclusion. This community-level pattern is linked to the species-level pattern that interspecific competition led to most frequent extinctions of each species at the highest level of disturbance that the species can tolerate. Consequently, despite a strong tradeoff between competitive ability and disturbance tolerance across the competing species, species diversity generally declined with disturbance. The consistent structuring role of competition throughout the disturbance gradient underscores the need to understand competitive interactions and their consequences even in highly disturbed habitats.

Roles of glutamates and metal ions in a rationally designed nitric oxide reductase based on myoglobin

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

Lin, Y.W.; Robinson, H.; Yeung, N.

2010-05-11

A structural and functional model of bacterial nitric oxide reductase (NOR) has been designed by introducing two glutamates (Glu) and three histidines (His) in sperm whale myoglobin. X-ray structural data indicate that the three His and one Glu (V68E) residues bind iron, mimicking the putative FeB site in NOR, while the second Glu (I107E) interacts with a water molecule and forms a hydrogen bonding network in the designed protein. Unlike the first Glu (V68E), which lowered the heme reduction potential by {approx}110 mV, the second Glu has little effect on the heme potential, suggesting that the negatively charged Glu hasmore » a different role in redox tuning. More importantly, introducing the second Glu resulted in a {approx}100% increase in NOR activity, suggesting the importance of a hydrogen bonding network in facilitating proton delivery during NOR reactivity. In addition, EPR and X-ray structural studies indicate that the designed protein binds iron, copper, or zinc in the FeB site, each with different effects on the structures and NOR activities, suggesting that both redox activity and an intermediate five-coordinate heme-NO species are important for high NOR activity. The designed protein offers an excellent model for NOR and demonstrates the power of using designed proteins as a simpler and more well-defined system to address important chemical and biological issues.« less

Roles of Glutamates and Metal ions in a Rationally Designed Nitric Oxide Reductase Based on Myoglobin

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

Y Lin; N Yeung; Y Gao

2011-12-31

A structural and functional model of bacterial nitric oxide reductase (NOR) has been designed by introducing two glutamates (Glu) and three histidines (His) in sperm whale myoglobin. X-ray structural data indicate that the three His and one Glu (V68E) residues bind iron, mimicking the putative FeB site in NOR, while the second Glu (I107E) interacts with a water molecule and forms a hydrogen bonding network in the designed protein. Unlike the first Glu (V68E), which lowered the heme reduction potential by {approx}110 mV, the second Glu has little effect on the heme potential, suggesting that the negatively charged Glu hasmore » a different role in redox tuning. More importantly, introducing the second Glu resulted in a {approx}100% increase in NOR activity, suggesting the importance of a hydrogen bonding network in facilitating proton delivery during NOR reactivity. In addition, EPR and X-ray structural studies indicate that the designed protein binds iron, copper, or zinc in the FeB site, each with different effects on the structures and NOR activities, suggesting that both redox activity and an intermediate five-coordinate heme-NO species are important for high NOR activity. The designed protein offers an excellent model for NOR and demonstrates the power of using designed proteins as a simpler and more well-defined system to address important chemical and biological issues.« less

Soil resources and topography shape local tree community structure in tropical forests

PubMed Central

Baldeck, Claire A.; Harms, Kyle E.; Yavitt, Joseph B.; John, Robert; Turner, Benjamin L.; Valencia, Renato; Navarrete, Hugo; Davies, Stuart J.; Chuyong, George B.; Kenfack, David; Thomas, Duncan W.; Madawala, Sumedha; Gunatilleke, Nimal; Gunatilleke, Savitri; Bunyavejchewin, Sarayudh; Kiratiprayoon, Somboon; Yaacob, Adzmi; Supardi, Mohd N. Nur; Dalling, James W.

2013-01-01

Both habitat filtering and dispersal limitation influence the compositional structure of forest communities, but previous studies examining the relative contributions of these processes with variation partitioning have primarily used topography to represent the influence of the environment. Here, we bring together data on both topography and soil resource variation within eight large (24–50 ha) tropical forest plots, and use variation partitioning to decompose community compositional variation into fractions explained by spatial, soil resource and topographic variables. Both soil resources and topography account for significant and approximately equal variation in tree community composition (9–34% and 5–29%, respectively), and all environmental variables together explain 13–39% of compositional variation within a plot. A large fraction of variation (19–37%) was spatially structured, yet unexplained by the environment, suggesting an important role for dispersal processes and unmeasured environmental variables. For the majority of sites, adding soil resource variables to topography nearly doubled the inferred role of habitat filtering, accounting for variation in compositional structure that would previously have been attributable to dispersal. Our results, illustrated using a new graphical depiction of community structure within these plots, demonstrate the importance of small-scale environmental variation in shaping local community structure in diverse tropical forests around the globe. PMID:23256196

Can I help you? A qualitative study of pharmacist and pharmacy assistant views on the role of pharmacy assistants in New Zealand.

PubMed

Sheridan, Janie; Kelly, Fiona; Basheer, Mariam; Jan, Reem; Lee, Alice

2011-08-01

To begin to explore the role of PAs more fully in a New Zealand context, through semi-structured interviews with PAs and pharmacists. Semi-structured, qualitative interviews with a convenience sample of pairs of PAs and pharmacists working in a pharmacy together. Pharmacists and PAs both described important roles for PAs. The PAs tended to see themselves as the first point of contact for customers, and that they fulfilled an important healthcare role for the public. Pharmacists agreed that they were the first point of contact yet viewed this more as a gatekeeper role to the pharmacist. Views were also expressed about the difference between PAs and other retail employees. Pharmacists and PAs noted that the 'public' expected PAs to have a basic knowledge of non-prescription medicines and their uses. PAs described difficulties when requesting personal information from customers or asking essential questions where the customer had made a specific product request. Being able to know when to refer to the pharmacist was seen as a key role. Despite being able to describe a number of roles for PAs, these were highly variable. The lack of mandatory training and a clearly articulated role for PAs in New Zealand meant that in some cases PAs might be seen as little more than general retail assistants--a view not in line with their actual roles and practices. Attention to these issues may well help to resolve this, as will public education about the PA's role. © 2011 The Authors. IJPP © 2011 Royal Pharmaceutical Society.

Nursing Competency: Definition, Structure and Development

PubMed Central

Fukada, Mika

2018-01-01

Nursing competency includes core abilities that are required for fulfilling one’s role as a nurse. Therefore, it is important to clearly define nursing competency to establish a foundation for nursing education curriculum. However, while the concepts surrounding nursing competency are important for improving nursing quality, they are still not yet completely developed. Thus, challenges remain in establishing definitions and structures for nursing competency, competency levels necessary for nursing professionals, training methods and so on. In the present study, we reviewed the research on definitions and attributes of nursing competency in Japan as well as competency structure, its elements and evaluation. Furthermore, we investigated training methods to teach nursing competency. PMID:29599616

Nursing Competency: Definition, Structure and Development.

PubMed

Fukada, Mika

2018-03-01

Nursing competency includes core abilities that are required for fulfilling one's role as a nurse. Therefore, it is important to clearly define nursing competency to establish a foundation for nursing education curriculum. However, while the concepts surrounding nursing competency are important for improving nursing quality, they are still not yet completely developed. Thus, challenges remain in establishing definitions and structures for nursing competency, competency levels necessary for nursing professionals, training methods and so on. In the present study, we reviewed the research on definitions and attributes of nursing competency in Japan as well as competency structure, its elements and evaluation. Furthermore, we investigated training methods to teach nursing competency.

Kinetic Scale Structure of Low-frequency Waves and Fluctuations

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

López, Rodrigo A.; Yoon, Peter H.; Viñas, Adolfo F.

The dissipation of solar wind turbulence at kinetic scales is believed to be important for the heating of the corona and for accelerating the wind. The linear Vlasov kinetic theory is a useful tool for identifying various wave modes, including kinetic Alfvén, fast magnetosonic/whistler, and ion-acoustic (or kinetic slow), and their possible roles in the dissipation. However, the kinetic mode structure in the vicinity of ion-cyclotron modes is not clearly understood. The present paper aims to further elucidate the structure of these low-frequency waves by introducing discrete particle effects through hybrid simulations and Klimontovich formalism of spontaneous emission theory. Themore » theory and simulation of spontaneously emitted low-frequency fluctuations are employed to identify and distinguish the detailed mode structures associated with ion-Bernstein modes versus quasi-modes. The spontaneous emission theory and simulation also confirm the findings of the Vlasov theory in that the kinetic Alfvén waves can be defined over a wide range of frequencies, including the proton cyclotron frequency and its harmonics, especially for high-beta plasmas. This implies that these low-frequency modes may play predominant roles even in the fully kinetic description of kinetic scale turbulence and dissipation despite the fact that cyclotron harmonic and Bernstein modes may also play important roles in wave–particle interactions.« less

Implementation of the Interdisciplinary Generalist Curriculum Project: considerations of structure, funding, and design.

PubMed

Wilson, M; Kahn, N; Wartman, S

2001-04-01

Implementation of the Interdisciplinary Generalist Curriculum (IGC) Project involved complex processes that reflect structural, funding, and intervention design considerations. Among structural considerations, the IGC Project benefited from a national structure above the level of the demonstration schools. Governance by committee was highly effective because it harnessed and balanced power. At the national level, governance by committee was enhanced by strong central coordination, and it had a role-modeling effect for governance at the school level. The IGC experience over the seven-year course of the project suggests that it is important to revisit the role of a national advisory committee over time and to revise that role as warranted. Funding considerations, including the importance of funding evaluation for a period of time long enough to measure intended impacts and the length and amount of funding to demonstration schools, are discussed. Prescription of the IGC intervention and the focus on years one and two of medical education are critical design considerations. The authors conclude that the IGC Project used relatively few federal dollars to demonstrate a highly prescribed intervention in a limited number of medical schools toward a clear and limited goal. IGC lessons apply to programs specifically targeting primary care education, but also to other medical school curricular innovations, and perhaps, to a larger framework of multi-site educational interventions.

The roles of plant phenolics in defence and communication during Agrobacterium and Rhizobium infection.

PubMed

Bhattacharya, Amita; Sood, Priyanka; Citovsky, Vitaly

2010-09-01

Phenolics are aromatic benzene ring compounds with one or more hydroxyl groups produced by plants mainly for protection against stress. The functions of phenolic compounds in plant physiology and interactions with biotic and abiotic environments are difficult to overestimate. Phenolics play important roles in plant development, particularly in lignin and pigment biosynthesis. They also provide structural integrity and scaffolding support to plants. Importantly, phenolic phytoalexins, secreted by wounded or otherwise perturbed plants, repel or kill many microorganisms, and some pathogens can counteract or nullify these defences or even subvert them to their own advantage. In this review, we discuss the roles of phenolics in the interactions of plants with Agrobacterium and Rhizobium.

Mechanisms of plant spindle formation.

PubMed

Zhang, Han; Dawe, R Kelly

2011-04-01

In eukaryotes, the formation of a bipolar spindle is necessary for the equal segregation of chromosomes to daughter cells. Chromosomes, microtubules and kinetochores all contribute to spindle morphogenesis and have important roles during mitosis. A unique property of flowering plant cells is that they entirely lack centrosomes, which in animals have a major role in spindle formation. The absence of these important structures suggests that plants have evolved novel mechanisms to assure chromosome segregation. In this review, we highlight some of the recent studies on plant mitosis and argue that plants utilize a variation of "spindle self-organization" that takes advantage of the early polarity of plant cells and accentuates the role of kinetochores in stabilizing the spindle midzone in prometaphase.

The nanoscale organization of signaling domains at the plasma membrane.

PubMed

Griffié, Juliette; Burn, Garth; Owen, Dylan M

2015-01-01

In this chapter, we present an overview of the role of the nanoscale organization of signaling domains in regulating key cellular processes. In particular, we illustrate the importance of protein and lipid nanodomains as triggers and mediators of cell signaling. As particular examples, we summarize the state of the art of understanding the role of nanodomains in the mounting of an immune response, cellular adhesion, intercellular communication, and cell proliferation. Thus, this chapter underlines the essential role the nanoscale organization of key signaling proteins and lipid domains. We will also see how nanodomains play an important role in the lifecycle of many pathogens relevant to human disease and therefore illustrate how these structures may become future therapeutic targets. Copyright © 2015 Elsevier Inc. All rights reserved.

The evolutionary and ecological consequences of animal social networks: emerging issues.

PubMed

Kurvers, Ralf H J M; Krause, Jens; Croft, Darren P; Wilson, Alexander D M; Wolf, Max

2014-06-01

The first generation of research on animal social networks was primarily aimed at introducing the concept of social networks to the fields of animal behaviour and behavioural ecology. More recently, a diverse body of evidence has shown that social fine structure matters on a broader scale than initially expected, affecting many key ecological and evolutionary processes. Here, we review this development. We discuss the effects of social network structure on evolutionary dynamics (genetic drift, fixation probabilities, and frequency-dependent selection) and social evolution (cooperation and between-individual behavioural differences). We discuss how social network structure can affect important coevolutionary processes (host-pathogen interactions and mutualisms) and population stability. We also discuss the potentially important, but poorly studied, role of social network structure on dispersal and invasion. Throughout, we highlight important areas for future research. Copyright © 2014 Elsevier Ltd. All rights reserved.

Brain Structure and Resting-State Functional Connectivity in University Professors with High Academic Achievement

ERIC Educational Resources Information Center

Li, Weiwei; Yang, Wenjing; Li, Wenfu; Li, Yadan; Wei, Dongtao; Li, Huimin; Qiu, Jiang; Zhang, Qinglin

2015-01-01

Creative persons play an important role in technical innovation and social progress. There is little research on the neural correlates with researchers with high academic achievement. We used a combined structural (regional gray matter volume, rGMV) and functional (resting-state functional connectivity analysis, rsFC) approach to examine the…

ROLE OF TYROSINE-SULFATED PROTEINS IN RETINAL STRUCTURE AND FUNCTION

PubMed Central

Kanan, Y.; Al-Ubaidi, M.R.

2014-01-01

The extracellular matrix (ECM) plays a significant role in cellular and retinal health. The study of retinal tyrosine-sulfated proteins is an important first step toward understanding the role of ECM in retinal health and diseases. These secreted proteins are members of the retinal ECM. Tyrosine sulfation was shown to be necessary for the development of proper retinal structure and function. The importance of tyrosine sulfation is further demonstrated by the evolutionary presence of tyrosylprotein sulfotransferases, enzymes that catalyze proteins’ tyrosine sulfation, and the compensatory abilities of these enzymes. Research has identified four tyrosine-sulfated retinal proteins: fibulin 2, vitronectin, complement factor H (CFH), and opticin. Vitronectin and CFH regulate the activation of the complement system and are involved in the etiology of some cases of age-related macular degeneration. Analysis of the role of tyrosine sulfation in fibulin function showed that sulfation influences the protein's ability to regulate growth and migration. Although opticin was recently shown to exhibit anti-angiogenic properties, it is not yet determined what role sulfation plays in that function. Future studies focusing on identifying all of the tyrosine-sulfated retinal proteins would be instrumental in determining the impact of sulfation on retinal protein function in retinal homeostasis and diseases. PMID:25819460

Periostin: a novel prognostic and therapeutic target for genitourinary cancer?

PubMed

Nuzzo, Pier Vitale; Buzzatti, Giulia; Ricci, Francesco; Rubagotti, Alessandra; Argellati, Francesca; Zinoli, Linda; Boccardo, Francesco

2014-10-01

Many of the cellular abnormalities present in solid tumors are structural in nature and involve the proteins of the extracellular matrix (ECM). Periostin is a protein produced and secreted by the fibroblasts as a component of the ECM where it is involved in regulating intercellular adhesion. The expression of periostin has an important physiological role during embryogenesis and growth, namely at the level of bone, dental, and cardiac tissues. Many studies indicate that periostin plays an important role for tumor progression in various types of cancer, such as colon, lung, head and neck, breast, ovarian, and prostate. To the best of our knowledge, a limited number of studies have investigated periostin expression in urogenital cancer, such as prostate, bladder, penile, and renal cancer, and no studies were performed in testis cancer. In this review article, we summarize the most recent knowledge of periostin, its genetic and protein structure, and the role of the different isoforms identified and sequenced so far. In particular, we focus our attention on the role of this protein in genitourinary tumors, trying to emphasize the role not only as a possible prognostic marker, but also as a possible target for the development of future anticancer therapies. Copyright © 2014 Elsevier Inc. All rights reserved.

Genetics Home Reference: dystrophic epidermolysis bullosa

MedlinePlus

... protein that is used to assemble type VII collagen. Collagens are molecules that give structure and strength to ... tendons, and ligaments, throughout the body. Type VII collagen plays an important role in strengthening and stabilizing ...

Environmental Filtering Process Has More Important Roles than Dispersal Limitation in Shaping Large-Scale Prokaryotic Beta Diversity Patterns of Grassland Soils.

PubMed

Cao, Peng; Wang, Jun-Tao; Hu, Hang-Wei; Zheng, Yuan-Ming; Ge, Yuan; Shen, Ju-Pei; He, Ji-Zheng

2016-07-01

Despite the utmost importance of microorganisms in maintaining ecosystem functioning and their ubiquitous distribution, our knowledge of the large-scale pattern of microbial diversity is limited, particularly in grassland soils. In this study, the microbial communities of 99 soil samples spanning over 3000 km across grassland ecosystems in northern China were investigated using high-throughput sequencing to analyze the beta diversity pattern and the underlying ecological processes. The microbial communities were dominated by Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, and Planctomycetes across all the soil samples. Spearman's correlation analysis indicated that climatic factors and soil pH were significantly correlated with the dominant microbial taxa, while soil microbial richness was positively linked to annual precipitation. The environmental divergence-dissimilarity relationship was significantly positive, suggesting the importance of environmental filtering processes in shaping soil microbial communities. Structural equation modeling found that the deterministic process played a more important role than the stochastic process on the pattern of soil microbial beta diversity, which supported the predictions of niche theory. Partial mantel test analysis have showed that the contribution of independent environmental variables has a significant effect on beta diversity, while independent spatial distance has no such relationship, confirming that the deterministic process was dominant in structuring soil microbial communities. Overall, environmental filtering process has more important roles than dispersal limitation in shaping microbial beta diversity patterns in the grassland soils.

[Structural empowerment and work-family fit in nurses].

PubMed

Orłowska, Agnieszka; Łaguna, Mariola

2016-12-22

The goal of the study was to investigate the relationship between structural empowerment and work-family fit in Polish nurses. Structural empowerment is a strategy for managing by providing the employees with opportunities, information, support and resources essential for the effective performance of work duties. Work-family fit takes 2 forms of relationships between these 2 spheres: conflict (functioning in one role is more difficult because of participation in the other role) and facilitation (fulfilling the duties associated with one role enriches filling up the other role). A total of 159 nurses employed in hospitals took part in the study. The Polish versions of the Conditions of Work Effectiveness Questionnaire and the Work-Family Fit Questionnaire were used. Hierarchical linear regression analysis was applied for data analysis. The results show statistically signifficant relationships between structural empowerment and work-family fit in nurses. In the hospital environment, characterized by a high degree of empowerment, nurses experience a lower level of work-family conflict and a higher level of facilitation in both directions. Hospital management strategy based on structural empowerment of nurses favors reconciliation of professional and family roles. Therefore, it is important for hospitals to create appropriate working conditions that allow nurses to effectively deal with demands arising from work and family spheres. Med Pr 2016;67(6):787-800. This work is available in Open Access model and licensed under a CC BY-NC 3.0 PL license.

Enabling professional development in mental health nursing: the role of clinical leadership.

PubMed

Ennis, G; Happell, B; Reid-Searl, K

2015-10-01

Clinical leadership is acknowledged as important to the nursing profession. While studies continue to identify its significance in contributing to positive outcomes for consumers, the role that clinical leadership has in enabling and supporting professional development in mental health nursing is poorly understood. This study utilized a grounded theory methodology to explore the characteristics clinicians consider important for clinical leadership and its significance for mental health nursing in day-to-day clinical practice. Individual face-to-face, semi-structured interviews were conducted with nurses working in mental health settings. Participants described the important role that clinical leaders play in enabling professional development of others through role modelling and clinical teaching. They describe how nurses, whom they perceive as clinical leaders, use role modelling and clinical teaching to influence the professional development of nursing staff and undergraduate nursing students. Attributes such as professionalism and honesty were seen, by participants, as enablers for clinical leaders in effectively and positively supporting the professional development of junior staff and undergraduate nurses in mental health nursing. This paper examines clinical leadership from the perspective of mental health nurses delivering care, and highlights the important role of clinical leaders in supporting professional development in mental health nursing. © 2015 John Wiley & Sons Ltd.

Regulation of Intestinal Epithelial Cells Properties and Functions by Amino Acids.

PubMed

Kong, Shanshan; Zhang, Yanhui H; Zhang, Weiqiang

2018-01-01

Intestinal epithelial cells (IECs) line the surface of intestinal epithelium, where they play important roles in the digestion of food, absorption of nutrients, and protection of the human body from microbial infections, and others. Dysfunction of IECs can cause diseases. The development, maintenance, and functions of IECs are strongly influenced by external nutrition, such as amino acids. Amino acids play important roles in regulating the properties and functions of IECs. In this article, we briefly reviewed the current understanding of the roles of amino acids in the regulation of IECs' properties and functions in physiological state, including in IECs homeostasis (differentiation, proliferation, and renewal), in intestinal epithelial barrier structure and functions, and in immune responses. We also summarized some important findings on the effects of amino acids supplementation (e.g., glutamine and arginine) in restoring IECs' and intestine functions in some diseased states. These findings will further our understanding of the important roles of amino acids in the homeostasis of IECs and could potentially help identify novel targets and reagents for the therapeutic interventions of diseases associated with dysfunctional IECs.

The emerging role of native mass spectrometry in characterizing the structure and dynamics of macromolecular complexes

PubMed Central

Boeri Erba, Elisabetta; Petosa, Carlo

2015-01-01

Mass spectrometry (MS) is a powerful tool for determining the mass of biomolecules with high accuracy and sensitivity. MS performed under so-called “native conditions” (native MS) can be used to determine the mass of biomolecules that associate noncovalently. Here we review the application of native MS to the study of protein−ligand interactions and its emerging role in elucidating the structure of macromolecular assemblies, including soluble and membrane protein complexes. Moreover, we discuss strategies aimed at determining the stoichiometry and topology of subunits by inducing partial dissociation of the holo-complex. We also survey recent developments in "native top-down MS", an approach based on Fourier Transform MS, whereby covalent bonds are broken without disrupting non-covalent interactions. Given recent progress, native MS is anticipated to play an increasingly important role for researchers interested in the structure of macromolecular complexes. PMID:25676284

Initial Vocational Training from a Company Perspective: A Comparison of British and German In-House Training Cultures

ERIC Educational Resources Information Center

Pilz, Matthias

2009-01-01

Vocational training and skills are playing an increasingly important role in the developed economies. However, both the vocational education structure and the underlying philosophy and culture of education and training vary from country to country. What is clear, though, is that employers play a crucial role in all cases; this paper explores the…

Marital Satisfaction among Older Couples: The Role of Satisfaction with Social Networks and Psychological Well-Being

ERIC Educational Resources Information Center

Walker, Ruth; Isherwood, Linda; Burton, Cassandra; Kitwe-Magambo, Katie; Luszcz, Mary

2013-01-01

Marital satisfaction is important for health and well-being, although determinants of satisfaction among older couples are unclear. Much of the marital literature has focused on the role of the spouse, in isolation from satisfaction with broader social relationships. We conducted separate semi-structured interviews with both members of n = 40…

Molecular Architecture of Strictosidine Glucosidase: The Gateway to the Biosynthesis of the Monoterpenoid Indole Alkaloid Family[W

PubMed Central

Barleben, Leif; Panjikar, Santosh; Ruppert, Martin; Koepke, Juergen; Stöckigt, Joachim

2007-01-01

Strictosidine β-d-glucosidase (SG) follows strictosidine synthase (STR1) in the production of the reactive intermediate required for the formation of the large family of monoterpenoid indole alkaloids in plants. This family is composed of ∼2000 structurally diverse compounds. SG plays an important role in the plant cell by activating the glucoside strictosidine and allowing it to enter the multiple indole alkaloid pathways. Here, we report detailed three-dimensional information describing both native SG and the complex of its inactive mutant Glu207Gln with the substrate strictosidine, thus providing a structural characterization of substrate binding and identifying the amino acids that occupy the active site surface of the enzyme. Structural analysis and site-directed mutagenesis experiments demonstrate the essential role of Glu-207, Glu-416, His-161, and Trp-388 in catalysis. Comparison of the catalytic pocket of SG with that of other plant glucosidases demonstrates the structural importance of Trp-388. Compared with all other glucosidases of plant, bacterial, and archaeal origin, SG's residue Trp-388 is present in a unique structural conformation that is specific to the SG enzyme. In addition to STR1 and vinorine synthase, SG represents the third structural example of enzymes participating in the biosynthetic pathway of the Rauvolfia alkaloid ajmaline. The data presented here will contribute to deciphering the structure and reaction mechanism of other higher plant glucosidases. PMID:17890378

Role of theory of mind and executive function in explaining social intelligence: a structural equation modeling approach.

PubMed

Yeh, Zai-Ting

2013-01-01

Social intelligence is the ability to understand others and the social context effectively and thus to interact with people successfully. Research has suggested that the theory of mind (ToM) and executive function may play important roles in explaining social intelligence. The specific aim of the present study was to test with structural equation modeling (SEM) the hypothesis that performance on ToM tasks is more associated with social intelligence in the elderly than is performance on executive functions. One hundred and seventy-seven participants (age 56-96) completed ToM, executive function, and other basic cognition tasks, and were rated with social intelligence scales. The SEM results showed that ToM and executive function were strongly correlated (0.54); however, only the path coefficient from ToM to social intelligence, and not from executive function, was significant (0.37). ToM performance, but not executive function, was strongly correlated with social intelligence among elderly individuals. ToM and executive function might play different roles in social behavior during normal aging; however, based on the present results, it is possible that ToM might play an important role in social intelligence.

Cooperation-Controlled Learning for Explicit Class Structure in Self-Organizing Maps

PubMed Central

Kamimura, Ryotaro

2014-01-01

We attempt to demonstrate the effectiveness of multiple points of view toward neural networks. By restricting ourselves to two points of view of a neuron, we propose a new type of information-theoretic method called “cooperation-controlled learning.” In this method, individual and collective neurons are distinguished from one another, and we suppose that the characteristics of individual and collective neurons are different. To implement individual and collective neurons, we prepare two networks, namely, cooperative and uncooperative networks. The roles of these networks and the roles of individual and collective neurons are controlled by the cooperation parameter. As the parameter is increased, the role of cooperative networks becomes more important in learning, and the characteristics of collective neurons become more dominant. On the other hand, when the parameter is small, individual neurons play a more important role. We applied the method to the automobile and housing data from the machine learning database and examined whether explicit class boundaries could be obtained. Experimental results showed that cooperation-controlled learning, in particular taking into account information on input units, could be used to produce clearer class structure than conventional self-organizing maps. PMID:25309950

Elucidation of Enzymatic Mechanism of Phenazine Biosynthetic Protein PhzF Using QM/MM and MD Simulations

PubMed Central

Liu, Fei; Zhao, Yi-Lei; Wang, Xiaolei; Hu, Hongbo; Peng, Huasong; Wang, Wei; Wang, Jing-Fang; Zhang, Xuehong

2015-01-01

The phenazine biosynthetic pathway is of considerable importance for the pharmaceutical industry. The pathway produces two products: phenazine-1,6-dicarboxylic acid and phenazine-1-carboxylic acid. PhzF is an isomerase that catalyzes trans-2,3-dihydro-3-hydroxyanthranilic acid isomerization and plays an essential role in the phenazine biosynthetic pathway. Although the PhzF crystal structure has been determined recently, an understanding of the detailed catalytic mechanism and the roles of key catalytic residues are still lacking. In this study, a computational strategy using a combination of molecular modeling, molecular dynamics simulations, and quantum mechanics/molecular mechanics simulations was used to elucidate these important issues. The Apo enzyme, enzyme–substrate complexes with negatively charged Glu45, enzyme–transition state analog inhibitor complexes with neutral Glu45, and enzyme–product complexes with negatively charged Glu45 structures were optimized and modeled using a 200 ns molecular dynamics simulation. Residues such as Gly73, His74, Asp208, Gly212, Ser213, and water, which play important roles in ligand binding and the isomerization reaction, were comprehensively investigated. Our results suggest that the Glu45 residue at the active site of PhzF acts as a general base/acid catalyst during proton transfer. This study provides new insights into the detailed catalytic mechanism of PhzF and the results have important implications for PhzF modification. PMID:26414009

Computational Methods in Drug Discovery

PubMed Central

Sliwoski, Gregory; Kothiwale, Sandeepkumar; Meiler, Jens

2014-01-01

Computer-aided drug discovery/design methods have played a major role in the development of therapeutically important small molecules for over three decades. These methods are broadly classified as either structure-based or ligand-based methods. Structure-based methods are in principle analogous to high-throughput screening in that both target and ligand structure information is imperative. Structure-based approaches include ligand docking, pharmacophore, and ligand design methods. The article discusses theory behind the most important methods and recent successful applications. Ligand-based methods use only ligand information for predicting activity depending on its similarity/dissimilarity to previously known active ligands. We review widely used ligand-based methods such as ligand-based pharmacophores, molecular descriptors, and quantitative structure-activity relationships. In addition, important tools such as target/ligand data bases, homology modeling, ligand fingerprint methods, etc., necessary for successful implementation of various computer-aided drug discovery/design methods in a drug discovery campaign are discussed. Finally, computational methods for toxicity prediction and optimization for favorable physiologic properties are discussed with successful examples from literature. PMID:24381236

Endocrine system: part 1.

PubMed

Johnstone, Carolyn; Hendry, Charles; Farley, Alistair; McLafferty, Ella

2014-05-27

This article, which forms part of the life sciences series and is the first of two articles on the endocrine system, examines the structure and function of the organs of the endocrine system. It is important that nurses understand how the endocrine system works and its role in maintaining health. The role of the endocrine system and the types, actions and control of hormones are explored. The gross structure of the pituitary and thyroid glands are described along with relevant physiology. Several disorders of the thyroid gland are outlined. The second article examines growth hormone, the pancreas and adrenal glands.

Emerging battery research in Indonesia: The role of nuclear applications

NASA Astrophysics Data System (ADS)

Kartini, E.

2015-12-01

Development of lithium ion batteries will play an important role in achieving innovative sustainable energy. To reduce the production cost of such batteries, the Indonesian government has instituted a strategy to use local resources. Therefore, this technology is now part of the National Industrial Strategic Plan. One of the most important scientific challenges is to improve performance of lithium batteries. Neutron scattering is a very important technique to investigate crystal structure of electrode materials. The unique properties of neutrons, which allow detection of light elements such as lithium ions, are indispensable. The utilization of neutron scattering facilities at the Indonesian National Nuclear Energy Agency will provide significant contributions to the development of improved lithium ion battery technologies.

Poland's Education and Training: Boosting and Adapting Human Capital. OECD Economics Department Working Papers, No. 495

ERIC Educational Resources Information Center

O'Brien, Paul; Paczynski, Wojciech

2006-01-01

An effective system of education and training is important for both social and economic reasons. Its role in the Polish economy is to provide the current and future labour force with skills to facilitate both continuing productivity growth and reallocation of resources as structural adjustment proceeds. Important reforms to decentralise primary…

Behavior Characteristics Desired in Faculty, by Deans at California Community Colleges: A Delphi Study

ERIC Educational Resources Information Center

Elliott, Alexandria

2016-01-01

Purpose: The community-college system in the United States has evolved tremendously since its beginning in 1901. There have been many changes, but one important aspect of the community college's structure that has continued to remain of utmost importance is the roles and responsibilities of faculty. The faculty has been traditionally hired based…

Deciphering the Role of the Gag-Pol Ribosomal Frameshift Signal in HIV-1 RNA Genome Packaging

PubMed Central

Nikolaitchik, Olga A.

2014-01-01

ABSTRACT A key step of retroviral replication is packaging of the viral RNA genome during virus assembly. Specific packaging is mediated by interactions between the viral protein Gag and elements in the viral RNA genome. In HIV-1, similar to most retroviruses, the packaging signal is located within the 5′ untranslated region and extends into the gag-coding region. A recent study reported that a region including the Gag-Pol ribosomal frameshift signal plays an important role in HIV-1 RNA packaging; deletions or mutations that affect the RNA structure of this signal lead to drastic decreases (10- to 50-fold) in viral RNA packaging and virus titer. We examined here the role of the ribosomal frameshift signal in HIV-1 RNA packaging by studying the RNA packaging and virus titer in the context of proviruses. Three mutants with altered ribosomal frameshift signal, either through direct deletion of the signal, mutation of the 6U slippery sequence, or alterations of the secondary structure were examined. We found that RNAs from all three mutants were packaged efficiently, and they generate titers similar to that of a virus containing the wild-type ribosomal frameshift signal. We conclude that although the ribosomal frameshift signal plays an important role in regulating the replication cycle, this RNA element is not directly involved in regulating RNA encapsidation. IMPORTANCE To generate infectious viruses, HIV-1 must package viral RNA genome during virus assembly. The specific HIV-1 genome packaging is mediated by interactions between the structural protein Gag and elements near the 5′ end of the viral RNA known as packaging signal. In this study, we examined whether the Gag-Pol ribosomal frameshift signal is important for HIV-1 RNA packaging as recently reported. Our results demonstrated that when Gag/Gag-Pol is supplied in trans, none of the tested ribosomal frameshift signal mutants has defects in RNA packaging or virus titer. These studies provide important information on how HIV-1 regulates its genome packaging and generate infectious viruses necessary for transmission to new hosts. PMID:24453371

Effects of Vegetation Structure on the Location of Lion Kill Sites in African Thicket

PubMed Central

Davies, Andrew B.; Tambling, Craig J.; Kerley, Graham I. H.; Asner, Gregory P.

2016-01-01

Predator-prey relationships are integral to ecosystem stability and functioning. These relationships are, however, difficult to maintain in protected areas where large predators are increasingly being reintroduced and confined. Where predators make kills has a profound influence on their role in ecosystems, but the relative importance of environmental variables in determining kill sites, and how these might vary across ecosystems is poorly known. We investigated kill sites for lions in South Africa’s thicket biome, testing the importance of vegetation structure for kill site locations compared to other environmental variables. Kill sites were located over four years using GPS telemetry and compared to non-kill sites that had been occupied by lions, as well as to random sites within lion ranges. Measurements of 3D vegetation structure obtained from Light Detection and Ranging (LiDAR) were used to calculate the visible area (viewshed) around each site and, along with wind and moonlight data, used to compare kill sites between lion sexes, prey species and prey sexes. Viewshed area was the most important predictor of kill sites (sites in dense vegetation were twice as likely to be kill sites compared to open areas), followed by wind speed and, less so, moonlight. Kill sites for different prey species varied with vegetation structure, and male prey were killed when wind speeds were higher compared to female prey of the same species. Our results demonstrate that vegetation structure is an important component of predator-prey interactions, with varying effects across ecosystems. Such differences require consideration in terms of the ecological roles performed by predators, and in predator and prey conservation. PMID:26910832

Inverse Interscale Transport of the Reynolds Shear Stress in Plane Couette Turbulence

NASA Astrophysics Data System (ADS)

Kawata, Takuya; Alfredsson, P. Henrik

2018-06-01

Interscale interaction between small-scale structures near the wall and large-scale structures away from the wall plays an increasingly important role with increasing Reynolds number in wall-bounded turbulence. While the top-down influence from the large- to small-scale structures is well known, it has been unclear whether the small scales near the wall also affect the large scales away from the wall. In this Letter we show that the small-scale near-wall structures indeed play a role to maintain the large-scale structures away from the wall, by showing that the Reynolds shear stress is transferred from small to large scales throughout the channel. This is in contrast to the turbulent kinetic energy transport which is from large to small scales. Such an "inverse" interscale transport of the Reynolds shear stress eventually supports the turbulent energy production at large scales.

Ab-initio atomic level stress and role of d-orbitals in CuZr, CuZn and CuY

NASA Astrophysics Data System (ADS)

Ojha, Madhusudan; Nicholson, Don M.; Egami, Takeshi

2015-03-01

Atomic level stress offers a new tool to characterize materials within the local approximation to density functional theory (DFT). Ab-initio atomic level stresses in B2 structures of CuZr, CuZn and CuY are calculated and results are explained on the basis of d-orbital contributions to Density of States (DOS). The overlap of d-orbital DOS plays an important role in the relative magnitude of atomic level stresses in these structures. The trends in atomic level stresses that we observed in these simple B2 structures are also seen in complex structures such as liquids, glasses and solid solutions. The stresses are however modified by the different coordination and relaxed separation distances in these complex structures. We used the Locally Self-Consistent Multiple Scattering (LSMS) code and Vienna Ab-initio Simulation Package (VASP) for ab-initio calculations.

Recognition of Local DNA Structures by p53 Protein

PubMed Central

Brázda, Václav; Coufal, Jan

2017-01-01

p53 plays critical roles in regulating cell cycle, apoptosis, senescence and metabolism and is commonly mutated in human cancer. These roles are achieved by interaction with other proteins, but particularly by interaction with DNA. As a transcription factor, p53 is well known to bind consensus target sequences in linear B-DNA. Recent findings indicate that p53 binds with higher affinity to target sequences that form cruciform DNA structure. Moreover, p53 binds very tightly to non-B DNA structures and local DNA structures are increasingly recognized to influence the activity of wild-type and mutant p53. Apart from cruciform structures, p53 binds to quadruplex DNA, triplex DNA, DNA loops, bulged DNA and hemicatenane DNA. In this review, we describe local DNA structures and summarize information about interactions of p53 with these structural DNA motifs. These recent data provide important insights into the complexity of the p53 pathway and the functional consequences of wild-type and mutant p53 activation in normal and tumor cells. PMID:28208646

Defining the molecular structure of teixobactin analogues and understanding their role in antibacterial activities.

PubMed

Parmar, Anish; Prior, Stephen H; Iyer, Abhishek; Vincent, Charlotte S; Van Lysebetten, Dorien; Breukink, Eefjan; Madder, Annemieke; Taylor, Edward J; Singh, Ishwar

2017-02-07

The discovery of the highly potent antibiotic teixobactin, which kills the bacteria without any detectable resistance, has stimulated interest in its structure-activity relationship. However, a molecular structure-activity relationship has not been established so far for teixobactin. Moreover, the importance of the individual amino acids in terms of their l/d configuration and their contribution to the molecular structure and biological activity are still unknown. For the first time, we have defined the molecular structure of seven teixobactin analogues through the variation of the d/l configuration of its key residues, namely N-Me-d-Phe, d-Gln, d-allo-Ile and d-Thr. Furthermore, we have established the role of the individual d amino acids and correlated this with the molecular structure and biological activity. Through extensive NMR and structural calculations, including molecular dynamics simulations, we have revealed the residues for maintaining a reasonably unstructured teixobactin which is imperative for biological activity.

CHEMICAL STRUCTURE INDEXING OF TOXICITY DATA ON ...

EPA Pesticide Factsheets

Standardized chemical structure annotation of public toxicity databases and information resources is playing an increasingly important role in the 'flattening' and integration of diverse sets of biological activity data on the Internet. This review discusses public initiatives that are accelerating the pace of this transformation, with particular reference to toxicology-related chemical information. Chemical content annotators, structure locator services, large structure/data aggregator web sites, structure browsers, International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) codes, toxicity data models and public chemical/biological activity profiling initiatives are all playing a role in overcoming barriers to the integration of toxicity data, and are bringing researchers closer to the reality of a mineable chemical Semantic Web. An example of this integration of data is provided by the collaboration among researchers involved with the Distributed Structure-Searchable Toxicity (DSSTox) project, the Carcinogenic Potency Project, projects at the National Cancer Institute and the PubChem database. Standardizing chemical structure annotation of public toxicity databases

The N Domain of Human Angiotensin-I-converting Enzyme

PubMed Central

Anthony, Colin S.; Corradi, Hazel R.; Schwager, Sylva L. U.; Redelinghuys, Pierre; Georgiadis, Dimitris; Dive, Vincent; Acharya, K. Ravi; Sturrock, Edward D.

2010-01-01

Angiotensin-I-converting enzyme (ACE) plays a critical role in the regulation of blood pressure through its central role in the renin-angiotensin and kallikrein-kinin systems. ACE contains two domains, the N and C domains, both of which are heavily glycosylated. Structural studies of ACE have been fraught with severe difficulties because of surface glycosylation of the protein. In order to investigate the role of glycosylation in the N domain and to create suitable forms for crystallization, we have investigated the importance of the 10 potential N-linked glycan sites using enzymatic deglycosylation, limited proteolysis, and mass spectrometry. A number of glycosylation mutants were generated via site-directed mutagenesis, expressed in CHO cells, and analyzed for enzymatic activity and thermal stability. At least eight of 10 of the potential glycan sites are glycosylated; three C-terminal sites were sufficient for expression of active N domain, whereas two N-terminal sites are important for its thermal stability. The minimally glycosylated Ndom389 construct was highly suitable for crystallization studies. The structure in the presence of an N domain-selective phosphinic inhibitor RXP407 was determined to 2.0 Å resolution. The Ndom389 structure revealed a hinge region that may contribute to the breathing motion proposed for substrate binding. PMID:20826823

NARROW-LINE-WIDTH UV BURSTS IN THE TRANSITION REGION ABOVE SUNSPOTS OBSERVED BY IRIS

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

Hou, Zhenyong; Huang, Zhenghua; Xia, Lidong

Various small-scale structures abound in the solar atmosphere above active regions, playing an important role in the dynamics and evolution therein. We report on a new class of small-scale transition region structures in active regions, characterized by strong emissions but extremely narrow Si iv line profiles as found in observations taken with the Interface Region Imaging Spectrograph (IRIS). Tentatively named as narrow-line-width UV bursts (NUBs), these structures are located above sunspots and comprise one or multiple compact bright cores at sub-arcsecond scales. We found six NUBs in two data sets (a raster and a sit-and-stare data set). Among these, fourmore » events are short-lived with a duration of ∼10 minutes, while two last for more than 36 minutes. All NUBs have Doppler shifts of 15–18 km s{sup −1}, while the NUB found in sit-and-stare data possesses an additional component at ∼50 km s{sup −1} found only in the C ii and Mg ii lines. Given that these events are found to play a role in the local dynamics, it is important to further investigate the physical mechanisms that generate these phenomena and their role in the mass transport in sunspots.« less

Key functional role of the optical properties of coral skeletons in coral ecology and evolution.

PubMed

Enríquez, Susana; Méndez, Eugenio R; Hoegh-Guldberg, Ove; Iglesias-Prieto, Roberto

2017-04-26

Multiple scattering of light on coral skeleton enhances light absorption efficiency of coral symbionts and plays a key role in the regulation of their internal diffuse light field. To understand the dependence of this enhancement on skeleton meso- and macrostructure, we analysed the scattering abilities of naked coral skeletons for 74 Indo-Pacific species. Sensitive morphotypes to thermal and light stress, flat-extraplanate and branching corals, showed the most efficient structures, while massive-robust species were less efficient. The lowest light-enhancing scattering abilities were found for the most primitive colonial growth form: phaceloid. Accordingly, the development of highly efficient light-collecting structures versus the selection of less efficient but more robust holobionts to cope with light stress may constitute a trade-off in the evolution of modern symbiotic scleractinian corals, characterizing two successful adaptive solutions. The coincidence of the most important structural modifications with epitheca decline supports the importance of the enhancement of light transmission across coral skeleton in modern scleractinian diversification, and the central role of these symbioses in the design and optimization of coral skeleton. Furthermore, the same ability that lies at the heart of the success of symbiotic corals as coral-reef-builders can also explain the 'Achilles's heel' of these symbioses in a warming ocean. © 2017 The Author(s).

Complementary aspects of diffusion imaging and fMRI; I: structure and function.

PubMed

Mulkern, Robert V; Davis, Peter E; Haker, Steven J; Estepar, Raul San Jose; Panych, Lawrence P; Maier, Stephan E; Rivkin, Michael J

2006-05-01

Studying the intersection of brain structure and function is an important aspect of modern neuroscience. The development of magnetic resonance imaging (MRI) over the last 25 years has provided new and powerful tools for the study of brain structure and function. Two tools in particular, diffusion imaging and functional MRI (fMRI), are playing increasingly important roles in elucidating the complementary aspects of brain structure and function. In this work, we review basic technical features of diffusion imaging and fMRI for studying the integrity of white matter structural components and for determining the location and extent of cortical activation in gray matter, respectively. We then review a growing body of literature in which the complementary aspects of diffusion imaging and fMRI, applied as separate examinations but analyzed in tandem, have been exploited to enhance our knowledge of brain structure and function.

Protein Crystallography in Vaccine Research and Development.

PubMed

Malito, Enrico; Carfi, Andrea; Bottomley, Matthew J

2015-06-09

The use of protein X-ray crystallography for structure-based design of small-molecule drugs is well-documented and includes several notable success stories. However, it is less well-known that structural biology has emerged as a major tool for the design of novel vaccine antigens. Here, we review the important contributions that protein crystallography has made so far to vaccine research and development. We discuss several examples of the crystallographic characterization of vaccine antigen structures, alone or in complexes with ligands or receptors. We cover the critical role of high-resolution epitope mapping by reviewing structures of complexes between antigens and their cognate neutralizing, or protective, antibody fragments. Most importantly, we provide recent examples where structural insights obtained via protein crystallography have been used to design novel optimized vaccine antigens. This review aims to illustrate the value of protein crystallography in the emerging discipline of structural vaccinology and its impact on the rational design of vaccines.

Protein Crystallography in Vaccine Research and Development

PubMed Central

Malito, Enrico; Carfi, Andrea; Bottomley, Matthew J.

2015-01-01

The use of protein X-ray crystallography for structure-based design of small-molecule drugs is well-documented and includes several notable success stories. However, it is less well-known that structural biology has emerged as a major tool for the design of novel vaccine antigens. Here, we review the important contributions that protein crystallography has made so far to vaccine research and development. We discuss several examples of the crystallographic characterization of vaccine antigen structures, alone or in complexes with ligands or receptors. We cover the critical role of high-resolution epitope mapping by reviewing structures of complexes between antigens and their cognate neutralizing, or protective, antibody fragments. Most importantly, we provide recent examples where structural insights obtained via protein crystallography have been used to design novel optimized vaccine antigens. This review aims to illustrate the value of protein crystallography in the emerging discipline of structural vaccinology and its impact on the rational design of vaccines. PMID:26068237

'A civilizing mission'? Austrian medicine and the reform of medical structures in the Ottoman Empire, 1838-1850.

PubMed

Chahrour, Marcel

2007-12-01

During the 1840s, physicians from the Habsburg Empire played a decisive role in the reform of medical structures in the Ottoman Empire. This paper discusses different aspects of this scientific and cultural encounter. It emphasizes the importance of Austrian health care structures as a model for the work of these physicians in the Ottoman Empire and studies the role of the medical school ran by the Austrians as a means of representing, on the one hand, the reformatory efforts of the Ottoman Empire and, on the other hand, the motivations of the Habsburg monarchy for an involvement in Ottoman health care affairs, strongly bound up with its own quarantine politics towards the Ottoman Empire.

Linking morphology with activity through the lifetime of pretreated PtNi nanostructured thin film catalysts

DOE PAGES

Cullen, David A.; Lopez-Haro, Miguel; Bayle-Guillemaud, Pascale; ...

2015-04-10

In this study, the nanoscale morphology of highly active Pt 3Ni 7 nanostructured thin film fuel cell catalysts is linked with catalyst surface area and activity following catalyst pretreatments, conditioning and potential cycling. The significant role of fuel cell conditioning on the structure and composition of these extended surface catalysts is demonstrated by high resolution imaging, elemental mapping and tomography. The dissolution of Ni during fuel cell conditioning leads to highly complex, porous structures which were visualized in 3D by electron tomography. Quantification of the rendered surfaces following catalyst pretreatment, conditioning, and cycling shows the important role pore structure playsmore » in surface area, activity, and durability.« less

The role of detachment and interlayer shear zones in the structural evolution of the southern Espinhaço range, eastern Brazil

NASA Astrophysics Data System (ADS)

Kuchenbecker, Matheus; Sanglard, Júlio Carlos Destro

2018-07-01

Sedimentary rocks usually show a significant mechanical anisotropy due to its layered nature. Because of this, they play an important role controlling rock deformation and the study of the deformation partitioning caused by rheological heterogeneities becomes a crucial step to understand the inversion of sedimentary basins. The detachment and interlayer shear zones, described at southern Espinhaço range, correspond to part of the structural collection that records the compressive deformation which is associated to the Brazilian-Pan African orogeny during Gondwana amalgamation. The mechanical contrast between lithological units is the main parameter of control for the occurrence of these zones which can be found with variable thickness from millimeter interlayer shear zones to regional-sized basement-cover detachment zones. The phyllitic layers are the most incompetent lithotype among metasedimentary rocks and they play an important role in the ductile-brittle regional deformation by accommodating much of the deformation during faulting and/or folding. Even though being a more competent rock, internal interlayer shear zones and other shear structures can be found in quartzite when in contact with weaker rocks. These structures accommodate a significant amount of deformation at the southern Espinhaço range and, because of this, they are of great value in understanding the inversion of the Espinhaço basins during West Gondwana assembly. The focus of the present paper is to discuss the main situations where interlayer shear occurs, to present a brief compendium of the main structures associated to this process and to add parameters to its recognition and interpretation.

[Computational chemistry in structure-based drug design].

PubMed

Cao, Ran; Li, Wei; Sun, Han-Zi; Zhou, Yu; Huang, Niu

2013-07-01

Today, the understanding of the sequence and structure of biologically relevant targets is growing rapidly and researchers from many disciplines, physics and computational science in particular, are making significant contributions to modern biology and drug discovery. However, it remains challenging to rationally design small molecular ligands with desired biological characteristics based on the structural information of the drug targets, which demands more accurate calculation of ligand binding free-energy. With the rapid advances in computer power and extensive efforts in algorithm development, physics-based computational chemistry approaches have played more important roles in structure-based drug design. Here we reviewed the newly developed computational chemistry methods in structure-based drug design as well as the elegant applications, including binding-site druggability assessment, large scale virtual screening of chemical database, and lead compound optimization. Importantly, here we address the current bottlenecks and propose practical solutions.

p-brane actions and higher Roytenberg brackets

NASA Astrophysics Data System (ADS)

Jurčo, Branislav; Schupp, Peter; Vysoký, Jan

2013-02-01

Motivated by the quest to understand the analog of non-geometric flux compactification in the context of M-theory, we study higher dimensional analogs of generalized Poisson sigma models and corresponding dual string and p-brane models. We find that higher generalizations of the algebraic structures due to Dorfman, Roytenberg and Courant play an important role and establish their relation to Nambu-Poisson structures.

The interface of protein structure, protein biophysics, and molecular evolution

PubMed Central

Liberles, David A; Teichmann, Sarah A; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J; de Koning, A P Jason; Dokholyan, Nikolay V; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L; Goldstein, Richard A; Grahnen, Johan A; Holder, Mark T; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C; Naylor, Gavin; Perica, Tina; Pollock, David D; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I; Thorne, Jeffrey L; Thornton, Joseph W; Weinreich, Daniel M; Whelan, Simon

2012-01-01

Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction. PMID:22528593

Comprehensive comparative analysis and identification of RNA-binding protein domains: multi-class classification and feature selection.

PubMed

Jahandideh, Samad; Srinivasasainagendra, Vinodh; Zhi, Degui

2012-11-07

RNA-protein interaction plays an important role in various cellular processes, such as protein synthesis, gene regulation, post-transcriptional gene regulation, alternative splicing, and infections by RNA viruses. In this study, using Gene Ontology Annotated (GOA) and Structural Classification of Proteins (SCOP) databases an automatic procedure was designed to capture structurally solved RNA-binding protein domains in different subclasses. Subsequently, we applied tuned multi-class SVM (TMCSVM), Random Forest (RF), and multi-class ℓ1/ℓq-regularized logistic regression (MCRLR) for analysis and classifying RNA-binding protein domains based on a comprehensive set of sequence and structural features. In this study, we compared prediction accuracy of three different state-of-the-art predictor methods. From our results, TMCSVM outperforms the other methods and suggests the potential of TMCSVM as a useful tool for facilitating the multi-class prediction of RNA-binding protein domains. On the other hand, MCRLR by elucidating importance of features for their contribution in predictive accuracy of RNA-binding protein domains subclasses, helps us to provide some biological insights into the roles of sequences and structures in protein-RNA interactions.

Detecting macroecological patterns in bacterial communities across independent studies of global soils.

PubMed

Ramirez, Kelly S; Knight, Christopher G; de Hollander, Mattias; Brearley, Francis Q; Constantinides, Bede; Cotton, Anne; Creer, Si; Crowther, Thomas W; Davison, John; Delgado-Baquerizo, Manuel; Dorrepaal, Ellen; Elliott, David R; Fox, Graeme; Griffiths, Robert I; Hale, Chris; Hartman, Kyle; Houlden, Ashley; Jones, David L; Krab, Eveline J; Maestre, Fernando T; McGuire, Krista L; Monteux, Sylvain; Orr, Caroline H; van der Putten, Wim H; Roberts, Ian S; Robinson, David A; Rocca, Jennifer D; Rowntree, Jennifer; Schlaeppi, Klaus; Shepherd, Matthew; Singh, Brajesh K; Straathof, Angela L; Bhatnagar, Jennifer M; Thion, Cécile; van der Heijden, Marcel G A; de Vries, Franciska T

2018-02-01

The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential 'indicator' taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.

Mutualistic mimicry and filtering by altitude shape the structure of Andean butterfly communities.

PubMed

Chazot, Nicolas; Willmott, Keith R; Santacruz Endara, Paola G; Toporov, Alexandre; Hill, Ryan I; Jiggins, Chris D; Elias, Marianne

2014-01-01

Both the abiotic environment and abiotic interactions among species contribute to shaping species assemblages. While the roles of habitat filtering and competitive interactions are clearly established, less is known about how positive interactions, whereby species benefit from the presence of one another, affect community structure. Here we assess the importance of positive interactions by studying Andean communities of butterflies that interact mutualistically via Müllerian mimicry. We show that communities at similar altitudes have a similar phylogenetic composition, confirming that filtering by altitude is an important process. We also provide evidence that species that interact mutualistically (i.e., species that share the same mimicry wing pattern) coexist at large scales more often than expected by chance. Furthermore, we detect an association between mimicry structure and altitude that is stronger than expected even when phylogeny is corrected for, indicating adaptive convergence for wing pattern and/or altitudinal range driven by mutualistic interactions. Positive interactions extend far beyond Müllerian mimicry, with many examples in plants and animals, and their role in the evolution and assembly of communities may be more pervasive than is currently appreciated. Our findings have strong implications for the evolution and resilience of community structure in a changing world.

History, anatomical nomenclature, comparative anatomy and functions of the hippocampal formation.

PubMed

El-Falougy, H; Benuska, J

2006-01-01

The complex structures in the cerebral hemispheres is included under one term, the limbic system. Our conception of this system and its special functions rises from the comparative neuroanatomical and neurophysiological studies. The components of the limbic system are the hippocampus, gyrus parahippocampalis, gyrus dentatus, gyrus cinguli, corpus amygdaloideum, nuclei anteriores thalami, hypothalamus and gyrus paraterminalis Because of its unique macroscopic and microscopic structure, the hippocampus is a conspicuous part of the limbic system. During phylogenetic development, the hippocampus developed from a simple cortical plate in amphibians into complex three-dimensional convoluted structure in mammals. In the last few decades, structures of the limbic system were extensively studied. Attention was directed to the physiological functions and pathological changes of the hippocampus. Experimental studies proved that the hippocampus has a very important role in the process of learning and memory. Another important functions of the hippocampus as a part of the limbic system is its role in regulation of sexual and emotional behaviour. The term "hippocampal formation" is defined as the complex of six structures: gyrus dentatus, hippocampus proprius, subiculum proprium, presubiculum, parasubiculum and area entorhinalis In this work we attempt to present a brief review of knowledge about the hippocampus from the point of view of history, anatomical nomenclature, comparative anatomy and functions (Tab. 1, Fig. 2, Ref. 33).

Mechanical Response of Single Filamin A (ABP-280) Molecules and Its Role in the Actin/Filamin A Gel

NASA Astrophysics Data System (ADS)

Sano, Ryoko; Furuike, Shou; Ito, Tadanao; Ohashi, Kazuyo; Yamazaki, Masahito

2004-04-01

Actin/filamin A gel plays important roles in mechanical response of cells. We found a force (50 to 220 pN)-induced unfolding of single filamin A molecules using AFM, and have proposed a hypothesis on the role of single filamin A in the novel property of viscoelasticity of actin/filamin A gel. We also investigated structure and its dynamics of actin/filamin A gel formed in a giant liposome using fluorescence microscopy.

Crystal structure of Gib2, a signal-transducing protein scaffold associated with ribosomes in Cryptococcus neoformans

NASA Astrophysics Data System (ADS)

Ero, Rya; Dimitrova, Valya Tenusheva; Chen, Yun; Bu, Wenting; Feng, Shu; Liu, Tongbao; Wang, Ping; Xue, Chaoyang; Tan, Suet Mien; Gao, Yong-Gui

2015-03-01

The atypical Gβ-like/RACK1 Gib2 protein promotes cAMP signalling that plays a central role in regulating the virulence of Cryptococcus neoformans. Gib2 contains a seven-bladed β transducin structure and is emerging as a scaffold protein interconnecting signalling pathways through interactions with various protein partners. Here, we present the crystal structure of Gib2 at a 2.2-Å resolution. The structure allows us to analyse the association between Gib2 and the ribosome, as well as to identify the Gib2 amino acid residues involved in ribosome binding. Our studies not only suggest that Gib2 has a role in protein translation but also present Gib2 as a physical link at the crossroads of various regulatory pathways important for the growth and virulence of C. neoformans.

Transforming the Delivery of Care in the Post–Health Reform Era: What Role Will Community Health Workers Play?

PubMed Central

Ro, Marguerite; Villa, Normandy William; Powell, Wayne; Knickman, James R.

2011-01-01

The Patient Protection and Affordable Care Act (PPACA) affords opportunities to sustain the role of community health workers (CHWs). Among myriad strategies encouraged by PPACA are prevention and care coordination, particularly for chronic diseases, chief drivers of increased health care costs. Prevention and care coordination are functions that have been performed by CHWs for decades, particularly among underserved populations. The two key delivery models promoted in the PPACA are accountable care organizations and health homes. Both stress the importance of interdisciplinary, interprofessional health care teams, the ideal context for integrating CHWs. Equally important, the payment structures encouraged by PPACA to support these delivery models offer the vehicles to sustain the role of these valued workers. PMID:22021289

Role of NDI in ABDR Assessment, Equipment & Logistics

DTIC Science & Technology

2010-05-01

RTO-EN-AVT-156 6 - 1 Role of NDI in ABDR Assessment, Equipment & Logistics Capt. (Dr.) Ferdinando Dolce Italian Air Force – Flight Test...showing results of NDT techniques applied on composite material structures. 1 . INTRODUCTION Damage assessment is one of the most important step...cured laminates applications (figure 1 ). Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the collection of

The Role of Leadership Practices on Job Stress among Malay Academic Staff: A Structural Equation Modeling Analysis

ERIC Educational Resources Information Center

Safaria, Triantoro; bin Othman, Ahmad; Wahab, Muhammad Nubli Abdul

2011-01-01

Globalization brings change in all aspect of human life, including in how job and organizations operate. These changes create strain and stress not only among employee at business organization, but also among academic staff. The dean of faculty or department at university has important role in prevent the effects of job stress among the academic…

The roles of competition and habitat in the dynamics of populations and species distributions Ecology

Treesearch

Charles B. Yackulic; Janice Reid; James D. Nichols; James E. Hines; Raymond Davis; Eric Forsman

2014-01-01

The role of competition in structuring biotic communities at fine spatial scales is well known from detailed process-based studies. Our understanding of competition’s importance at broader scales is less resolved and mainly based on static species distribution maps. Here, we bridge this gap by examining the joint occupancy dynamics of an invading species (Barred Owl,...

The Role of Biotin in Bacterial Physiology and Virulence: a Novel Antibiotic Target for Mycobacterium tuberculosis.

PubMed

Salaemae, Wanisa; Booker, Grant W; Polyak, Steven W

2016-04-01

Biotin is an essential cofactor for enzymes present in key metabolic pathways such as fatty acid biosynthesis, replenishment of the tricarboxylic acid cycle, and amino acid metabolism. Biotin is synthesized de novo in microorganisms, plants, and fungi, but this metabolic activity is absent in mammals, making biotin biosynthesis an attractive target for antibiotic discovery. In particular, biotin biosynthesis plays important metabolic roles as the sole source of biotin in all stages of the Mycobacterium tuberculosis life cycle due to the lack of a transporter for scavenging exogenous biotin. Biotin is intimately associated with lipid synthesis where the products form key components of the mycobacterial cell membrane that are critical for bacterial survival and pathogenesis. In this review we discuss the central role of biotin in bacterial physiology and highlight studies that demonstrate the importance of its biosynthesis for virulence. The structural biology of the known biotin synthetic enzymes is described alongside studies using structure-guided design, phenotypic screening, and fragment-based approaches to drug discovery as routes to new antituberculosis agents.

Role of Endogenous Sulfur Dioxide in Regulating Vascular Structural Remodeling in Hypertension

PubMed Central

Chen, Selena; Tang, Chaoshu

2016-01-01

Sulfur dioxide (SO2), an emerging gasotransmitter, was discovered to be endogenously generated in the cardiovascular system. Recently, the physiological effects of endogenous SO2 were confirmed. Vascular structural remodeling (VSR), an important pathological change in many cardiovascular diseases, plays a crucial role in the pathogenesis of the diseases. Here, the authors reviewed the research progress of endogenous SO2 in regulating VSR by searching the relevant data from PubMed and Medline. In spontaneously hypertensive rats (SHRs) and pulmonary hypertensive rats, SO2/aspartate aminotransferase (AAT) pathway was significantly altered. SO2 inhibited vascular smooth muscle cell (VSMC) proliferation, promoted apoptosis, inhibited the synthesis of extracellular collagen but promoted its degradation, and enhanced antioxidative capacity, thereby playing a significant role in attenuating VSR. However, the detailed mechanisms needed to be further explored. Further studies in this field would be important for the better understanding of the pathogenesis of systemic hypertension and pulmonary hypertension. Also, clinical trials are needed to demonstrate if SO2 would be a potential therapeutic target in cardiovascular diseases. PMID:27721913

Social roles and the evolution of networks in extreme and isolated environments

NASA Technical Reports Server (NTRS)

Johnson, Jeffrey C.; Boster, James S.; Palinkas, Lawrence A.

2003-01-01

This article reports on the evolution of network structure as it relates to formal and informal social roles in well-bounded, isolated groups. Research was conducted at the Amundsen-Scott South Pole Station. Data were collected on crewmembers' networks of social interaction over each of three winter-over periods, when the station is completely isolated. In addition, data were collected on the informal roles played by crewmembers (e.g., instrumental leadership, expressive leadership). The study found that globally coherent networks in winter-over groups were associated with group consensus on the presence of critically important informal social roles (e.g., expressive leadership) where global coherence is the extent to which a network forms a single group composed of a unitary core and periphery as opposed to being factionalized into two or more subgroups. Conversely, the evolution of multiple subgroups was associated with the absence of consensus on critical informal social roles, above all the critically important role of instrumental leader.

Role of Intramolecular Aromatic π-π Interactions in the Self-Assembly of Di-l-Phenylalanine Dipeptide Driven by Intermolecular Interactions: Effect of Alanine Substitution.

PubMed

Reddy, Samala Murali Mohan; Shanmugam, Ganesh

2016-09-19

Although the role of intermolecular aromatic π-π interactions in the self-assembly of di-l-phenylalanine (l-Phe-l-Phe, FF), a peptide that is known for hierarchical structure, is well established, the influence of intramolecular π-π interactions on the morphology of the self-assembled structure of FF has not been studied. Herein, the role of intramolecular aromatic π-π interactions is investigated for FF and analogous alanine (Ala)-containing dipeptides, namely, l-Phe-l-Ala (FA) and l-Ala-l-Phe (AF). The results reveal that these dipeptides not only form self-assemblies, but also exhibit remarkable differences in structural morphology. The morphological differences between FF and the analogues indicate the importance of intramolecular π-π interactions, and the structural difference between FA and AF demonstrates the crucial role of the nature of intramolecular side-chain interactions (aromatic-aliphatic or aliphatic-aromatic), in addition to intermolecular interactions, in deciding the final morphology of the self-assembled structure. The current results emphasise that intramolecular aromatic π-π interaction may not be essential to induce self-assembly in smaller peptides, and π (aromatic)-alkyl or alkyl-π (aromatic) interactions may be sufficient. This work also illustrates the versatility of aromatic and a combination of aromatic and aliphatic residues in dipeptides in the formation of structurally diverse self-assembled structures. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Does perturbative quantum chromodynamics imply a Regge singularity above unity

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

Bishari, M.

1982-07-15

It is investigated whether perturbative quantum chromodynamics can have some implications on Regge behavior of deep-inelastic structure functions. The possible indirect but important role of unitarity, in constraining the theory, is pointed out.

Shifting Stakes: Understanding the Dynamic Roles of Individuals and Organizations in Social Media Protests.

PubMed

Spiro, Emma S; Monroy-Hernández, Andrés

2016-01-01

In this paper we examine two protests characterized by substantial social media presence and distributed participation frameworks via two core questions: what roles did organizations and individuals play, and how did participants' social interactions change over the course of the protests? To answer these questions, we analyzed a large Twitter activity dataset for the #YoSoy132 student uprising in Mexico and Brazil's "bus rebellion." Results indicate that individuals initially took prominence at the protests but faded in importance as the movements dwindled and organizations took over. Regarding the dynamics and structure of the interactions, we found that key time points with unique social structures often map to exogenous events such as coordinated protests in physical locations. Our results have important consequences for the visibility of such social movements and their ability to attract continued participation by individuals and organizations.

Shifting Stakes: Understanding the Dynamic Roles of Individuals and Organizations in Social Media Protests

PubMed Central

2016-01-01

In this paper we examine two protests characterized by substantial social media presence and distributed participation frameworks via two core questions: what roles did organizations and individuals play, and how did participants’ social interactions change over the course of the protests? To answer these questions, we analyzed a large Twitter activity dataset for the #YoSoy132 student uprising in Mexico and Brazil’s “bus rebellion.” Results indicate that individuals initially took prominence at the protests but faded in importance as the movements dwindled and organizations took over. Regarding the dynamics and structure of the interactions, we found that key time points with unique social structures often map to exogenous events such as coordinated protests in physical locations. Our results have important consequences for the visibility of such social movements and their ability to attract continued participation by individuals and organizations. PMID:27776191

Excited states of protonated DNA/RNA bases.

PubMed

Berdakin, Matias; Féraud, Géraldine; Dedonder-Lardeux, Claude; Jouvet, Christophe; Pino, Gustavo A

2014-06-14

The very fast relaxation of the excited states to the ground state in DNA/RNA bases is a necessary process to ensure the photostability of DNA and its rate is highly sensitive to the tautomeric form of the bases. Protonation of the bases plays a crucial role in many biochemical and mutagenic processes and it can result in alternative tautomeric structures, thus making important the knowledge of the properties of protonated DNA/RNA bases. We report here the photofragmentation spectra of the five protonated DNA/RNA bases. In most of the cases, the spectra exhibit well resolved vibrational structures, with broad bands associated with very short excited state lifetimes. The similarity between the electronic properties, e.g. excitation energy and very short excited state lifetimes for the canonical tautomers of protonated and neutral DNA bases, suggests that the former could also play an important role in the photostability mechanism of DNA.

The Popeye Domain Containing Genes and Their Function as cAMP Effector Proteins in Striated Muscle.

PubMed

Brand, Thomas

2018-03-13

The Popeye domain containing (POPDC) genes encode transmembrane proteins, which are abundantly expressed in striated muscle cells. Hallmarks of the POPDC proteins are the presence of three transmembrane domains and the Popeye domain, which makes up a large part of the cytoplasmic portion of the protein and functions as a cAMP-binding domain. Interestingly, despite the prediction of structural similarity between the Popeye domain and other cAMP binding domains, at the protein sequence level they strongly differ from each other suggesting an independent evolutionary origin of POPDC proteins. Loss-of-function experiments in zebrafish and mouse established an important role of POPDC proteins for cardiac conduction and heart rate adaptation after stress. Loss-of function mutations in patients have been associated with limb-girdle muscular dystrophy and AV-block. These data suggest an important role of these proteins in the maintenance of structure and function of striated muscle cells.

Individuals and populations: the role of long-term, individual-based studies of animals in ecology and evolutionary biology.

PubMed

Clutton-Brock, Tim; Sheldon, Ben C

2010-10-01

Many important questions in ecology and evolutionary biology can only be answered with data that extend over several decades and answering a substantial proportion of questions requires records of the life histories of recognisable individuals. We identify six advantages that long-term, individual based studies afford in ecology and evolution: (i) analysis of age structure; (ii) linkage between life history stages; (iii) quantification of social structure; (iv) derivation of lifetime fitness measures; (v) replication of estimates of selection; (vi) linkage between generations, and we review their impact on studies in six key areas of evolution and ecology. Our review emphasises the unusual opportunities and productivity of long-term, individual-based studies and documents the important role that they play in research on ecology and evolutionary biology as well as the difficulties they face. Copyright © 2010 Elsevier Ltd. All rights reserved.

Structure and Bonding in Heme-Nitrosyl Complexes and Implications for Biology

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

Lehnert, Nicolai; Scheidt, W. Robert; Wolf, Matthew W.

This review summarizes our current understanding of the geometric and electronic structures of ferrous and ferric heme–nitrosyls, which are of key importance for the biological functions and transformations of NO. In-depth correlations are made between these properties and the reactivities of these species. Here, a focus is put on the discoveries that have been made in the last 10 years, but previous findings are also included as necessary. Besides this, ferrous heme–nitroxyl complexes are also considered, which have become of increasing interest recently due to their roles as intermediates in NO and multiheme nitrite reductases, and because of the potentialmore » role of HNO as a signaling molecule in mammals. In recent years, computational methods have received more attention as a means of investigating enzyme reaction mechanisms, and some important findings from these theoretical studies are also highlighted in this chapter.« less

Recombination, Pairing, and Synapsis of Homologs during Meiosis

PubMed Central

Zickler, Denise; Kleckner, Nancy

2015-01-01

Recombination is a prominent feature of meiosis in which it plays an important role in increasing genetic diversity during inheritance. Additionally, in most organisms, recombination also plays mechanical roles in chromosomal processes, most notably to mediate pairing of homologous chromosomes during prophase and, ultimately, to ensure regular segregation of homologous chromosomes when they separate at the first meiotic division. Recombinational interactions are also subject to important spatial patterning at both early and late stages. Recombination-mediated processes occur in physical and functional linkage with meiotic axial chromosome structure, with interplay in both directions, before, during, and after formation and dissolution of the synaptonemal complex (SC), a highly conserved meiosis-specific structure that links homolog axes along their lengths. These diverse processes also are integrated with recombination-independent interactions between homologous chromosomes, nonhomology-based chromosome couplings/clusterings, and diverse types of chromosome movement. This review provides an overview of these diverse processes and their interrelationships. PMID:25986558

Sensitivity of system stability to model structure

USGS Publications Warehouse

Hosack, G.R.; Li, H.W.; Rossignol, P.A.

2009-01-01

A community is stable, and resilient, if the levels of all community variables can return to the original steady state following a perturbation. The stability properties of a community depend on its structure, which is the network of direct effects (interactions) among the variables within the community. These direct effects form feedback cycles (loops) that determine community stability. Although feedback cycles have an intuitive interpretation, identifying how they form the feedback properties of a particular community can be intractable. Furthermore, determining the role that any specific direct effect plays in the stability of a system is even more daunting. Such information, however, would identify important direct effects for targeted experimental and management manipulation even in complex communities for which quantitative information is lacking. We therefore provide a method that determines the sensitivity of community stability to model structure, and identifies the relative role of particular direct effects, indirect effects, and feedback cycles in determining stability. Structural sensitivities summarize the degree to which each direct effect contributes to stabilizing feedback or destabilizing feedback or both. Structural sensitivities prove useful in identifying ecologically important feedback cycles within the community structure and for detecting direct effects that have strong, or weak, influences on community stability. The approach may guide the development of management intervention and research design. We demonstrate its value with two theoretical models and two empirical examples of different levels of complexity. ?? 2009 Elsevier B.V. All rights reserved.

Fish-derived nutrient hotspots shape coral reef benthic communities.

PubMed

Shantz, Andrew A; Ladd, Mark C; Schrack, Elizabeth; Burkepile, Deron E

2015-12-01

Animal-derived nutrients play an important role in structuring nutrient regimes within and between ecosystems. When animals undergo repetitive, aggregating behavior through time, they can create nutrient hotspots where rates of biogeochemical activity are higher than those found in the surrounding environment. In turn, these hotspots can influence ecosystem processes and community structure. We examined the potential for reef fishes from the family Haemulidae (grunts) to create nutrient hotspots and the potential impact of these hotspots on reef communities. To do so, we tracked the schooling locations of diurnally migrating grunts, which shelter at reef sites during the day but forage off reef each night, and measured the impact of these fish schools on benthic communities. We found that grunt schools showed a high degree of site fidelity, repeatedly returning to the same coral heads. These aggregations created nutrient hotspots around coral heads where nitrogen and phosphorus delivery was roughly 10 and 7 times the respective rates of delivery to structurally similar sites that lacked schools of these fishes. In turn, grazing rates of herbivorous fishes at grunt-derived hotspots were approximately 3 times those of sites where grunts were rare. These differences in nutrient delivery and grazing led to distinct benthic communities with higher cover of crustose coralline algae and less total algal abundance at grunt aggregation sites. Importantly, coral growth was roughly 1.5 times greater at grunt hotspots, likely due to the important nutrient subsidy. Our results suggest that schooling reef fish and their nutrient subsidies play an important role in mediating community structure on coral reefs and that overfishing may have important negative consequences on ecosystem functions. As such, management strategies must consider mesopredatory fishes in addition to current protection often offered to herbivores and top-tier predators. Furthermore, our results suggest that restoration strategies may benefit from focusing on providing structure for aggregating fishes on reefs with low topographic complexity or focusing the restoration of nursery raised corals around existing nutrient hotspots.

University Students' Knowledge Structures and Informal Reasoning on the Use of Genetically Modified Foods: Multidimensional Analyses

NASA Astrophysics Data System (ADS)

Wu, Ying-Tien

2013-10-01

This study aims to provide insights into the role of learners' knowledge structures about a socio-scientific issue (SSI) in their informal reasoning on the issue. A total of 42 non-science major university students' knowledge structures and informal reasoning were assessed with multidimensional analyses. With both qualitative and quantitative analyses, this study revealed that those students with more extended and better-organized knowledge structures, as well as those who more frequently used higher-order information processing modes, were more oriented towards achieving a higher-level informal reasoning quality. The regression analyses further showed that the "richness" of the students' knowledge structures explained 25 % of the variation in their rebuttal construction, an important indicator of reasoning quality, indicating the significance of the role of students' sophisticated knowledge structure in SSI reasoning. Besides, this study also provides some initial evidence for the significant role of the "core" concept within one's knowledge structure in one's SSI reasoning. The findings in this study suggest that, in SSI-based instruction, science instructors should try to identify students' core concepts within their prior knowledge regarding the SSI, and then they should try to guide students to construct and structure relevant concepts or ideas regarding the SSI based on their core concepts. Thus, students could obtain extended and well-organized knowledge structures, which would then help them achieve better learning transfer in dealing with SSIs.

Faunal impact on vegetation structure and ecosystem function in mangrove forests: A review

USGS Publications Warehouse

Cannicci, Stefano; Burrows, Damien; Fratini, Sara; Smith, Thomas J.; Offenberg, Joachim; Dahdouh-Guebas, Farid

2008-01-01

The last 20 years witnessed a real paradigm shift concerning the impact of biotic factors on ecosystem functions as well as on vegetation structure of mangrove forests. Before this small scientific revolution took place, structural aspects of mangrove forests were viewed to be the result of abiotic processes acting from the bottom-up, while, at ecosystem level, the outwelling hypothesis stated that mangroves primary production was removed via tidal action and carried to adjacent nearshore ecosystems where it fuelled detrital based food-webs. The sesarmid crabs were the first macrofaunal taxon to be considered a main actor in mangrove structuring processes, thanks to a number of studies carried out in the Indo-Pacific forests in the late 1970s and early 1980s. Following these classical papers, a number of studies on Sesarmidae feeding and burrowing ecology were carried out, which leave no doubts about the great importance of these herbivorous crabs in structuring and functioning Old world ecosystems. Although Sesarmidae are still considered very important in shaping mangrove structure and functioning, recent literature emphasizes the significance of other invertebrates. The Ocypodidae have now been shown to have the same role as Sesarmidae in terms of retention of forest products and organic matter processing in New world mangroves. In both New and Old world mangroves, crabs process large amounts of algal primary production, contribute consistently to retention of mangrove production and as ecosystem engineers, change particle size distribution and enhance soil aeration. Our understanding of the strong impact of gastropods, by means of high intake rates of mangrove products and differential consumption of propagules, has changed only recently. The role of insects must also be stressed. It is now clear that older techniques used to assess herbivory rates by insects strongly underestimate their impact, both in case of leaf eating and wood boring species and that herbivorous insects can potentially play a strong role in many aspects of mangrove ecology. Moreover, researchers only recently realized that ant–plant interactions may form an important contribution to our understanding of insect–plant dynamics in these habitats. Ants seem to be able to relieve mangroves from important herbivores such as many insects and sesarmid crabs. It thus seems likely that ants have positive effects on mangrove performance.

Rclick: a web server for comparison of RNA 3D structures.

PubMed

Nguyen, Minh N; Verma, Chandra

2015-03-15

RNA molecules play important roles in key biological processes in the cell and are becoming attractive for developing therapeutic applications. Since the function of RNA depends on its structure and dynamics, comparing and classifying the RNA 3D structures is of crucial importance to molecular biology. In this study, we have developed Rclick, a web server that is capable of superimposing RNA 3D structures by using clique matching and 3D least-squares fitting. Our server Rclick has been benchmarked and compared with other popular servers and methods for RNA structural alignments. In most cases, Rclick alignments were better in terms of structure overlap. Our server also recognizes conformational changes between structures. For this purpose, the server produces complementary alignments to maximize the extent of detectable similarity. Various examples showcase the utility of our web server for comparison of RNA, RNA-protein complexes and RNA-ligand structures. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

The dynamics of male brooding, mating patterns, and sex roles in pipefishes and seahorses (family Syngnathidae).

PubMed

Wilson, Anthony B; Ahnesjö, Ingrid; Vincent, Amanda C J; Meyer, Axel

2003-06-01

Modern theory predicts that relative parental investment of the sexes in their young is a key factor responsible for sexual selection. Seahorses and pipefishes (family Syngnathidae) are extraordinary among fishes in their remarkable adaptations for paternal care and frequent occurrences of sex-role reversals (i.e., female-female competition for mates), offering exceptional opportunities to test predictions of sexual selection theory. During mating, the female transfers eggs into or onto specialized egg-brooding structures that are located on either the male's abdomen or its tail, where they are osmoregulated, aerated, and nourished by specially adapted structures. All syngnathid males exhibit this form of parental care but the brooding structures vary, ranging from the simple ventral gluing areas of some pipefishes to the completely enclosed pouches found in seahorses. We present a molecular phylogeny that indicates that the diversification of pouch types is positively correlated with the major evolutionary radiation of the group, suggesting that this extreme development and diversification of paternal care may have been an important evolutionary innovation of the Syngnathidae. Based on recent studies that show that the complexity of brooding structures reflects the degree of paternal investment in several syngnathid species, we predicted sex-role reversals to be more common among species with more complex brooding structures. In contrast to this prediction, however, both parsimony- and likelihood-based reconstructions of the evolution of sex-role reversal in pipefishes and seahorses suggest multiple shifts in sex roles in the group, independent from the degree of brood pouch development. At the same time, our data demonstrate that sex-role reversal is positively associated with polygamous mating patterns, whereas most nonreversed species mate monogamously, suggesting that selection for polygamy or monogamy in pipefishes and seahorses may strongly influence sex roles in the wild.

Impact of Machine-Translated Text on Entity and Relationship Extraction

DTIC Science & Technology

2014-12-01

20 1 1. Introduction Using social network analysis tools is an important asset in...semantic modeling software to automatically build detailed network models from unstructured text. Contour imports unstructured text and then maps the text...onto an existing ontology of frames at the sentence level, using FrameNet, a structured language model, and through Semantic Role Labeling ( SRL

Differential deposition of H2A.Z in rice seedling tissue during the day-night cycle.

PubMed

Zhang, Kang; Xu, Wenying; Wang, Chunchao; Yi, Xin; Su, Zhen

2017-03-04

Chromatin structure has an important role in modulating gene expression. The incorporation of histone variants into the nucleosome leads to important changes in the chromatin structure. The histone variant H2A.Z is highly conserved between different species of fungi, animals, and plants. However, dynamic changes to H2A.Z in rice have not been reported during the day-night cycle. In this study, we generated genome wide maps of H2A.Z for day and night time in harvested seedling tissues by combining chromatin immunoprecipitation and high-throughput sequencing. The analysis results for the H2A.Z data sets detected 7099 genes with higher depositions of H2A.Z in seedling tissues harvested at night compared with seedling tissues harvested during the day, whereas 4597 genes had higher H2A.Z depositions in seedlings harvested during the day. The gene expression profiles data suggested that H2A.Z probably negatively regulated gene expression during the day-night cycle and was involved in many important biologic processes. In general, our results indicated that H2A.Z may play an important role in plant responses to the diurnal oscillation process.

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

Marcianò, G.; Huang, D. T., E-mail: d.huang@beatson.gla.ac.uk

The Spt16–SSRP1 heterodimer is a histone chaperone that plays an important role in regulating chromatin assembly. Here, a crystal structure of the N-terminal domain of human Spt16 is presented and it is shown that this domain may contribute to histone binding. The histone chaperone FACT plays an important role in facilitating nucleosome assembly and disassembly during transcription. FACT is a heterodimeric complex consisting of Spt16 and SSRP1. The N-terminal domain of Spt16 resembles an inactive aminopeptidase. How this domain contributes to the histone chaperone activity of FACT remains elusive. Here, the crystal structure of the N-terminal domain (NTD) of humanmore » Spt16 is reported at a resolution of 1.84 Å. The structure adopts an aminopeptidase-like fold similar to those of the Saccharomyces cerevisiae and Schizosaccharomyces pombe Spt16 NTDs. Isothermal titration calorimetry analyses show that human Spt16 NTD binds histones H3/H4 with low-micromolar affinity, suggesting that Spt16 NTD may contribute to histone binding in the FACT complex. Surface-residue conservation and electrostatic analysis reveal a conserved acidic patch that may be involved in histone binding.« less

Biosynthesis, structural, and functional attributes of tocopherols in planta; past, present, and future perspectives.

PubMed

Hussain, Nazim; Irshad, Faiza; Jabeen, Zahra; Shamsi, Imran Haider; Li, Zhilan; Jiang, Lixi

2013-07-03

Tocopherols are lipophilic molecules, ubiquitously synthesized in all photosynthetic organisms. Being a group of vitamin E compounds, they play an essential role in human nutrition and health. Despite their structural and functional attributes as important antioxidants in plants, it would be misleading to ignore the potential roles of tocopherols beyond their antioxidant properties in planta. Detailed characterization of mutants and transgenic plants, including Arabidopsis (vte1, vte2, vte4, and so on), maize (sxd1) mutants, and transgenic potato and tobacco lines altered in tocopherol biosynthesis and contents, has led to surprising outcomes regarding the additional functions of these molecules. Thus, the aim of this review is to highlight the past and present research findings on tocopherols' structural, biosynthesis, and functional properties in plants. Special emphasis is given to their suggested functions in planta, such as cell signaling, hormonal interactions, and coordinated response of tocopherols to other antioxidants under abiotic stresses. Moreover, some important questions about possible new functions of tocopherols will be discussed as future prospects to stimulate further research.

The role of the extracellular matrix in tissue distribution of macromolecules in normal and pathological tissues: potential therapeutic consequences.

PubMed

Wiig, Helge; Gyenge, Christina; Iversen, Per Ole; Gullberg, Donald; Tenstad, Olav

2008-05-01

The interstitial space is a dynamic microenvironment that consists of interstitial fluid and structural molecules of the extracellular matrix, such as glycosaminoglycans (hyaluronan and proteoglycans) and collagen. Macromolecules can distribute in the interstitium only in those spaces unoccupied by structural components, a phenomenon called interstitial exclusion. The exclusion phenomenon has direct consequences for plasma volume regulation. Early studies have assigned a major role to collagen as an excluding agent that accounts for the sterical (geometrical) exclusion. More recently, it has been shown that the contribution of negatively charged glycosaminoglycans might also be significant, resulting in an additional electrostatical exclusion effect. This charge effect may be of importance for drug uptake and suggests that either the glycosaminoglycans or the net charge of macromolecular substances to be delivered may be targeted to increase the available volume and uptake of macromolecular therapeutic agents in tumor tissue. Here, we provide an overview of the structural components of the interstitium and discuss the importance the sterical and electrostatical components have on the dynamics of transcapillary fluid exchange.

Structure-Based Characterization of Multiprotein Complexes

PubMed Central

Wiederstein, Markus; Gruber, Markus; Frank, Karl; Melo, Francisco; Sippl, Manfred J.

2014-01-01

Summary Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies. PMID:24954616

Exploring protein interiors: the role of a buried histidine in the KH module fold.

PubMed

Fraternali, F; Amodeo, P; Musco, G; Nilges, M; Pastore, A

1999-03-01

The K-homology (KH) module is a novel RNA-binding motif. The structures of a representative KH motif from vigilin (vig-KH6) and of the first KH domain of fmr1 have been recently solved by nuclear magnetic resonance (NMR) and automated assignment-refinement techniques (ARIA). While a hydrophobic residue is found at position 21 in most of the KH modules, a buried His is conserved in all the 15 KH repeats of vigilin. This position must therefore have a key structural role in stabilizing the hydrophobic core. In the present work, we have addressed the following questions in order to obtain a detailed description of the role of His 21: i) what is the exact role of the histidine in the hydrophobic core of vig-KH6? ii) can we define the interactions that allow a conserved buried position to be occupied by a histidine both in vig-KH6 and in the whole vigilin KH sub-family? iii) how is the structure and stability of vig-KH6 influenced by the state of protonation of this histidine? To answer these questions, we have carried out an extensive refinement of the vig-KH6 structure using both an improved ARIA protocol starting from different initial structures and successively running restrained and unrestrained trajectories in water. An analysis of the stability of secondary structural elements, solvent accessibility, and hydrogen bonding patterns allows hypothesis on the structural role of residue His 21 and on the interactions that this residue forms with the environment. The importance of the protonation state of His 21 on the stability of the KH fold was addressed and validated by experimental results.

Evolution of Structure in Nuclei: Meditation by Sub-Shell Modifications and Relation to Binding Energies

NASA Astrophysics Data System (ADS)

Casten, R. F.; Cakirli, R. B.

2009-03-01

Understanding the development of configuration mixing, coherence, collectivity, and deformation in nuclei is one of the crucial challenges in nuclear structure physics, and one which has become all the more important with the advent of next generation facilities for the study of exotic nuclei. We will discuss recent work on phase/shape transitional behavior in nuclei, and the role of changes in sub-shell structure in mediating such transitional regions. We will also discuss a newly found, much deeper, link between nuclear structure and nuclear binding energies.

Thermostability of In Vitro Evolved Bacillus subtilis Lipase A: A Network and Dynamics Perspective

PubMed Central

Srivastava, Ashutosh; Sinha, Somdatta

2014-01-01

Proteins in thermophilic organisms remain stable and function optimally at high temperatures. Owing to their important applicability in many industrial processes, such thermostable proteins have been studied extensively, and several structural factors attributed to their enhanced stability. How these factors render the emergent property of thermostability to proteins, even in situations where no significant changes occur in their three-dimensional structures in comparison to their mesophilic counter-parts, has remained an intriguing question. In this study we treat Lipase A from Bacillus subtilis and its six thermostable mutants in a unified manner and address the problem with a combined complex network-based analysis and molecular dynamic studies to find commonality in their properties. The Protein Contact Networks (PCN) of the wild-type and six mutant Lipase A structures developed at a mesoscopic scale were analyzed at global network and local node (residue) level using network parameters and community structure analysis. The comparative PCN analysis of all proteins pointed towards important role of specific residues in the enhanced thermostability. Network analysis results were corroborated with finer-scale molecular dynamics simulations at both room and high temperatures. Our results show that this combined approach at two scales can uncover small but important changes in the local conformations that add up to stabilize the protein structure in thermostable mutants, even when overall conformation differences among them are negligible. Our analysis not only supports the experimentally determined stabilizing factors, but also unveils the important role of contacts, distributed throughout the protein, that lead to thermostability. We propose that this combined mesoscopic-network and fine-grained molecular dynamics approach is a convenient and useful scheme not only to study allosteric changes leading to protein stability in the face of negligible over-all conformational changes due to mutations, but also in other molecular networks where change in function does not accompany significant change in the network structure. PMID:25122499

F-BAR family proteins, emerging regulators for cell membrane dynamic changes-from structure to human diseases.

PubMed

Liu, Suxuan; Xiong, Xinyu; Zhao, Xianxian; Yang, Xiaofeng; Wang, Hong

2015-05-09

Eukaryotic cell membrane dynamics change in curvature during physiological and pathological processes. In the past ten years, a novel protein family, Fes/CIP4 homology-Bin/Amphiphysin/Rvs (F-BAR) domain proteins, has been identified to be the most important coordinators in membrane curvature regulation. The F-BAR domain family is a member of the Bin/Amphiphysin/Rvs (BAR) domain superfamily that is associated with dynamic changes in cell membrane. However, the molecular basis in membrane structure regulation and the biological functions of F-BAR protein are unclear. The pathophysiological role of F-BAR protein is unknown. This review summarizes the current understanding of structure and function in the BAR domain superfamily, classifies F-BAR family proteins into nine subfamilies based on domain structure, and characterizes F-BAR protein structure, domain interaction, and functional relevance. In general, F-BAR protein binds to cell membrane via F-BAR domain association with membrane phospholipids and initiates membrane curvature and scission via Src homology-3 (SH3) domain interaction with its partner proteins. This process causes membrane dynamic changes and leads to seven important cellular biological functions, which include endocytosis, phagocytosis, filopodium, lamellipodium, cytokinesis, adhesion, and podosome formation, via distinct signaling pathways determined by specific domain-binding partners. These cellular functions play important roles in many physiological and pathophysiological processes. We further summarize F-BAR protein expression and mutation changes observed in various diseases and developmental disorders. Considering the structure feature and functional implication of F-BAR proteins, we anticipate that F-BAR proteins modulate physiological and pathophysiological processes via transferring extracellular materials, regulating cell trafficking and mobility, presenting antigens, mediating extracellular matrix degradation, and transmitting signaling for cell proliferation.

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.

High-resolution crystal structures of the photoreceptor glyceraldehyde 3-phosphate dehydrogenase (GAPDH) with three and four-bound NAD molecules

PubMed Central

Baker, Bo Y; Shi, Wuxian; Wang, Benlian; Palczewski, Krzysztof

2014-01-01

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) catalyzes the oxidative phosphorylation of d-glyceraldehyde 3-phosphate (G3P) into 1,3-diphosphoglycerate (BGP) in the presence of the NAD cofactor. GAPDH is an important drug target because of its central role in glycolysis, and nonglycolytic processes such as nuclear RNA transport, DNA replication/repair, membrane fusion and cellular apoptosis. Recent studies found that GAPDH participates in the development of diabetic retinopathy and its progression after the cessation of hyperglycemia. Here, we report two structures for native bovine photoreceptor GAPDH as a homotetramer with differing occupancy by NAD, bGAPDH(NAD)4, and bGAPDH(NAD)3. The bGAPDH(NAD)4 was solved at 1.52 Å, the highest resolution for GAPDH. Structural comparison of the bGAPDH(NAD)4 and bGAPDH(NAD)3 models revealed novel details of conformational changes induced by cofactor binding, including a loop region (residues 54–56). Structure analysis of bGAPDH confirmed the importance of Phe34 in NAD binding, and demonstrated that Phe34 was stabilized in the presence of NAD but displayed greater mobility in its absence. The oxidative state of the active site Cys149 residue is regulated by NAD binding, because this residue was found oxidized in the absence of dinucleotide. The distance between Cys149 and His176 decreased upon NAD binding and Cys149 remained in a reduced state when NAD was bound. These findings provide an important structural step for understanding the mechanism of GAPDH activity in vision and its pathological role in retinopathies. PMID:25176140

Packaging of Mason-Pfizer monkey virus (MPMV) genomic RNA depends upon conserved long-range interactions (LRIs) between U5 and gag sequences

PubMed Central

Kalloush, Rawan M.; Vivet-Boudou, Valérie; Ali, Lizna M.; Mustafa, Farah; Marquet, Roland; Rizvi, Tahir A.

2016-01-01

MPMV has great potential for development as a vector for gene therapy. In this respect, precisely defining the sequences and structural motifs that are important for dimerization and packaging of its genomic RNA (gRNA) are of utmost importance. A distinguishing feature of the MPMV gRNA packaging signal is two phylogenetically conserved long-range interactions (LRIs) between U5 and gag complementary sequences, LRI-I and LRI-II. To test their biological significance in the MPMV life cycle, we introduced mutations into these structural motifs and tested their effects on MPMV gRNA packaging and propagation. Furthermore, we probed the structure of key mutants using SHAPE (selective 2′hydroxyl acylation analyzed by primer extension). Disrupting base-pairing of the LRIs affected gRNA packaging and propagation, demonstrating their significance to the MPMV life cycle. A double mutant restoring a heterologous LRI-I was fully functional, whereas a similar LRI-II mutant failed to restore gRNA packaging and propagation. These results demonstrate that while LRI-I acts at the structural level, maintaining base-pairing is not sufficient for LRI-II function. In addition, in vitro RNA dimerization assays indicated that the loss of RNA packaging in LRI mutants could not be attributed to the defects in dimerization. Our findings suggest that U5-gag LRIs play an important architectural role in maintaining the structure of the 5′ region of the MPMV gRNA, expanding the crucial role of LRIs to the nonlentiviral group of retroviruses. PMID:27095024

The role of religious leaders in health promotion for older Mexicans with diabetes.

PubMed

Rivera-Hernandez, Maricruz

2015-02-01

Clergy in the Mexico play a major role in addressing the health care needs of their congregants. With qualitative semi-structured key-informant interviews, this study explored the views of ten male Mexican religious leaders (mostly Catholic) about their understanding of their role in diabetes health promotion. The major themes from the qualitative interviews emphasized the importance of open communication between church leaders and their parishioners, the role of the church in diabetes programs, and the unique position of religious institutions as a link between physical and spiritual aspects of health. Implications for diabetes interventions are discussed.

Limits to gene flow in a cosmopolitan marine planktonic diatom.

PubMed

Casteleyn, Griet; Leliaert, Frederik; Backeljau, Thierry; Debeer, Ann-Eline; Kotaki, Yuichi; Rhodes, Lesley; Lundholm, Nina; Sabbe, Koen; Vyverman, Wim

2010-07-20

The role of geographic isolation in marine microbial speciation is hotly debated because of the high dispersal potential and large population sizes of planktonic microorganisms and the apparent lack of strong dispersal barriers in the open sea. Here, we show that gene flow between distant populations of the globally distributed, bloom-forming diatom species Pseudo-nitzschia pungens (clade I) is limited and follows a strong isolation by distance pattern. Furthermore, phylogenetic analysis implies that under appropriate geographic and environmental circumstances, like the pronounced climatic changes in the Pleistocene, population structuring may lead to speciation and hence may play an important role in diversification of marine planktonic microorganisms. A better understanding of the factors that control population structuring is thus essential to reveal the role of allopatric speciation in marine microorganisms.

Dawn of the in vivo RNA structurome and interactome.

PubMed

Kwok, Chun Kit

2016-10-15

RNA is one of the most fascinating biomolecules in living systems given its structural versatility to fold into elaborate architectures for important biological functions such as gene regulation, catalysis, and information storage. Knowledge of RNA structures and interactions can provide deep insights into their functional roles in vivo For decades, RNA structural studies have been conducted on a transcript-by-transcript basis. The advent of next-generation sequencing (NGS) has enabled the development of transcriptome-wide structural probing methods to profile the global landscape of RNA structures and interactions, also known as the RNA structurome and interactome, which transformed our understanding of the RNA structure-function relationship on a transcriptomic scale. In this review, molecular tools and NGS methods used for RNA structure probing are presented, novel insights uncovered by RNA structurome and interactome studies are highlighted, and perspectives on current challenges and potential future directions are discussed. A more complete understanding of the RNA structures and interactions in vivo will help illuminate the novel roles of RNA in gene regulation, development, and diseases. © 2016 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

Magnetic structure and local lattice distortion in giant negative thermal expansion material Mn3Cu1-xGexN

NASA Astrophysics Data System (ADS)

Iikubo, S.; Kodama, K.; Takenaka, K.; Takagi, H.; Shamoto, S.

2010-11-01

Magnetic and local structures in an antiperovskite system, Mn3Cu1-xGexN, with a giant negative thermal expansion have been studied by neutron powder diffraction measurement. We discuss (1) an importance of an averaged cubic crystal structure and a ΓG5g antiferromagnetic spin structure for the large magneto-volume effect (MVE) in this itinerant electron system, (2) an unique role of a local lattice distortion well described by the low temperature tetragonal structure of Mn3GeN for the broadening of MVE.

From Structure to Function: A Comprehensive Compendium of Tools to Unveil Protein Domains and Understand Their Role in Cytokinesis.

PubMed

Rincon, Sergio A; Paoletti, Anne

2016-01-01

Unveiling the function of a novel protein is a challenging task that requires careful experimental design. Yeast cytokinesis is a conserved process that involves modular structural and regulatory proteins. For such proteins, an important step is to identify their domains and structural organization. Here we briefly discuss a collection of methods commonly used for sequence alignment and prediction of protein structure that represent powerful tools for the identification homologous domains and design of structure-function approaches to test experimentally the function of multi-domain proteins such as those implicated in yeast cytokinesis.

Emerging battery research in Indonesia: The role of nuclear applications

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

Kartini, E.

2015-12-31

Development of lithium ion batteries will play an important role in achieving innovative sustainable energy. To reduce the production cost of such batteries, the Indonesian government has instituted a strategy to use local resources. Therefore, this technology is now part of the National Industrial Strategic Plan. One of the most important scientific challenges is to improve performance of lithium batteries. Neutron scattering is a very important technique to investigate crystal structure of electrode materials. The unique properties of neutrons, which allow detection of light elements such as lithium ions, are indispensable. The utilization of neutron scattering facilities at the Indonesianmore » National Nuclear Energy Agency will provide significant contributions to the development of improved lithium ion battery technologies.« less

Structure and earthworms

USDA-ARS?s Scientific Manuscript database

Earthworms are an important part of the soil ecosystem and an indicator of soil quality. Sometimes referred to as ecosystem engineers, they play a pivotal role in maintaining soil productivity. Their burrowing, feeding, and casting activities alter the physical, chemical, and biological properties o...

Temporal variation in bat-fruit interactions: Foraging strategies influence network structure over time

NASA Astrophysics Data System (ADS)

Zapata-Mesa, Natalya; Montoya-Bustamante, Sebastián; Murillo-García, Oscar E.

2017-11-01

Mutualistic interactions, such as seed dispersal, are important for the maintenance of structure and stability of tropical communities. However, there is a lack of information about spatial and temporal variation in plant-animal interaction networks. Thus, our goal was to assess the effect of bat's foraging strategies on temporal variation in the structure and robustness of bat-fruit networks in both a dry and a rain tropical forest. We evaluated monthly variation in bat-fruit networks by using seven structure metrics: network size, average path length, nestedness, modularity, complementary specialization, normalized degree and betweenness centrality. Seed dispersal networks showed variations in size, species composition and modularity; did not present nested structures and their complementary specialization was high compared to other studies. Both networks presented short path lengths, and a constantly high robustness, despite their monthly variations. Sedentary bat species were recorded during all the study periods and occupied more central positions than nomadic species. We conclude that foraging strategies are important structuring factors that affect the dynamic of networks by determining the functional roles of frugivorous bats over time; thus sedentary bats are more important than nomadic species for the maintenance of the network structure, and their conservation is a must.

Brain’s DNA Repair Response to Neurotoxicants

DTIC Science & Technology

2005-07-01

it is possible that OTA exposure may impact on this ability of this structure to maintain its functional integrity over time. Indeed it is known...Gordon et al., 2004). In light of the critical role played by hippocampus in cognitive function, and the importance of neurogenesis in this structure ...uncompetitive inhibitorof both succinate-cytochrome c reductase and succinate dehydrogenase while sparing cytochrome oxidase and NADH dehydrogenase

Laboratory Measurements of Charge Transfer on Atomic Hydrogen at Thermal Energies

NASA Technical Reports Server (NTRS)

Havener, C. C.; Vane, C. R.; Krause, H. F.; Stancil, P. C.; Mroczkowski, T.; Savin, D. W.

2002-01-01

We describe our ongoing program to measure velocity dependent charge transfer (CT) cross sections for selected ions on atomic hydrogen using the ion-aloin merged-beams apparatus at Oak Ridge Natioiial Laboralory. Our focus is on those ions for which CT plays an important role in determining the ionization structure, line emis sion, and thermal structure of observed cosmic photoionized plasmas.

Altered structural development and accelerated succession from intermediate-scale wind disturbance in Quercus stands on the Cumberland Plateau, USA

Treesearch

Stephen D White; Justin L. Hart; Callie J. Schweitzer; Daniel C. Dey

2015-01-01

Natural disturbances play important roles in shaping the structure and composition of all forest ecosystems and can be used to inform silvicultural practices. Canopy disturbances are often classified along a gradient ranging from highly localized, gap-scale events to stand-replacing events. Wind storms such as downbursts, derechos, and low intensity tornadoes typically...

Histone H3 Lysine 14 (H3K14) Acetylation Facilitates DNA Repair in a Positioned Nucleosome by Stabilizing the Binding of the Chromatin Remodeler RSC (Remodels Structure of Chromatin)*

PubMed Central

Duan, Ming-Rui; Smerdon, Michael J.

2014-01-01

Histone H3 acetylation is induced by UV damage in yeast and may play an important role in regulating the repair of UV photolesions in nucleosome-loaded genomic loci. However, it remains elusive how H3 acetylation facilitates repair. We generated a strongly positioned nucleosome containing homogeneously acetylated H3 at Lys-14 (H3K14ac) and investigated possible mechanisms by which H3K14 acetylation modulates repair. We show that H3K14ac does not alter nucleosome unfolding dynamics or enhance the repair of UV-induced cyclobutane pyrimidine dimers by UV photolyase. Importantly, however, nucleosomes with H3K14ac have a higher affinity for purified chromatin remodeling complex RSC (Remodels the Structure of Chromatin) and show greater cyclobutane pyrimidine dimer repair compared with unacetylated nucleosomes. Our study indicates that, by anchoring RSC, H3K14 acetylation plays an important role in the unfolding of strongly positioned nucleosomes during repair of UV damage. PMID:24515106

The Aldo-Keto Reductase Superfamily and its Role in Drug Metabolism and Detoxification

PubMed Central

Barski, Oleg A.; Tipparaju, Srinivas M.; Bhatnagar, Aruni

2008-01-01

The Aldo-Keto Reductase (AKR) superfamily comprises of several enzymes that catalyze redox transformations involved in biosynthesis, intermediary metabolism and detoxification. Substrates of the family include glucose, steroids, glycosylation end products, lipid peroxidation products, and environmental pollutants. These proteins adopt a (β/α)8 barrel structural motif interrupted by a number of extraneous loops and helixes that vary between proteins and bring structural identity to individual families. The human AKR family differs from the rodent families. Due to their broad substrate specificity, AKRs play an important role in the Phase II detoxification of a large number of pharmaceuticals, drugs, and xenobiotics. PMID:18949601

The cytoskeleton in cell-autonomous immunity: structural determinants of host defence

PubMed Central

Mostowy, Serge; Shenoy, Avinash R.

2016-01-01

Host cells use antimicrobial proteins, pathogen-restrictive compartmentalization and cell death in their defence against intracellular pathogens. Recent work has revealed that four components of the cytoskeleton — actin, microtubules, intermediate filaments and septins, which are well known for their roles in cell division, shape and movement — have important functions in innate immunity and cellular self-defence. Investigations using cellular and animal models have shown that these cytoskeletal proteins are crucial for sensing bacteria and for mobilizing effector mechanisms to eliminate them. In this Review, we highlight the emerging roles of the cytoskeleton as a structural determinant of cell-autonomous host defence. PMID:26292640

Calcium in the Oxygen-Evolving Complex: Structural and Mechanistic Role Determined by X-ray Spectroscopy

PubMed Central

Yachandra, Vittal K.; Yano, Junko

2011-01-01

This review describes the results from X-ray absorption spectroscopy studies that have contributed to an understanding of the role of Ca in the photosynthetic water oxidation reaction. The results include the first Mn, Ca and Sr X-ray spectroscopy studies using Ca or Sr-substituted PS II samples that established the presence of a MnCa heteronuclear structure and its orientation, and the most recent Sr X-ray spectroscopy study using biosynthetically prepared Sr-containing PS II in the various S-states that provide important insights into the requirement for Ca in the mechanism of the Mn4Ca catalytic center. PMID:21524917

Structural alterations of thin actin filaments in muscle contraction by synchrotron X-ray fiber diffraction.

PubMed

Wakabayashi, Katsuzo; Sugimoto, Yasunobu; Takezawa, Yasunori; Ueno, Yutaka; Minakata, Shiho; Oshima, Kanji; Matsuo, Tatsuhito; Kobayashi, Takakazu

2007-01-01

Strong evidence has been accumulated that the conformational changes of the thin actin filaments are occurring and playing an important role in the entire process of muscle contraction. The conformational changes and the mechanical properties of the thin actin filaments we have found by X-ray fiber diffraction on skeletal muscle contraction are explored. Recent studies on the conformational changes of regulatory proteins bound to actin filaments upon activation and in the force generation process are also described. Finally, the roles of structural alterations and dynamics of the actin filaments are discussed in conjunction with the regulation mechanism and the force generation mechanism.

"I Don't Even Know What Blogging Is": The Role of Digital Media in a Five-Year-Old Girl's Life

ERIC Educational Resources Information Center

Teichert, Laura; Anderson, Ann

2014-01-01

Using a qualitative lens, this study investigated the role of digital media in the life of a five-year-old girl. The study focused on determining what this five-year-old knew about technology, what digital tools was she currently using and how important were these tools in her everyday life. Data collection included semi-structured interviews…

Structure Prediction of the Second Extracellular Loop in G-Protein-Coupled Receptors

PubMed Central

Kmiecik, Sebastian; Jamroz, Michal; Kolinski, Michal

2014-01-01

G-protein-coupled receptors (GPCRs) play key roles in living organisms. Therefore, it is important to determine their functional structures. The second extracellular loop (ECL2) is a functionally important region of GPCRs, which poses significant challenge for computational structure prediction methods. In this work, we evaluated CABS, a well-established protein modeling tool for predicting ECL2 structure in 13 GPCRs. The ECL2s (with between 13 and 34 residues) are predicted in an environment of other extracellular loops being fully flexible and the transmembrane domain fixed in its x-ray conformation. The modeling procedure used theoretical predictions of ECL2 secondary structure and experimental constraints on disulfide bridges. Our approach yielded ensembles of low-energy conformers and the most populated conformers that contained models close to the available x-ray structures. The level of similarity between the predicted models and x-ray structures is comparable to that of other state-of-the-art computational methods. Our results extend other studies by including newly crystallized GPCRs. PMID:24896119

Precambrian Basement Structure Map of the Continental United States - An Interpretation of Geologic and Aeromagnetic Data

USGS Publications Warehouse

Sims, Paul K.; Saltus, Richard W.; Anderson, Eric D.

2008-01-01

The Precambrian basement rocks of the continental United States are largely covered by younger sedimentary and volcanic rocks, and the availability of updated aeromagnetic data (NAMAG, 2002) provides a means to infer major regional basement structures and tie together the scattered, but locally abundant, geologic information. Precambrian basement structures in the continental United States have strongly influenced later Proterozoic and Phanerozoic tectonism within the continent, and there is a growing awareness of the utility of these structures in deciphering major younger tectonic and related episodes. Interest in the role of basement structures in the evolution of continents has been recently stimulated, particularly by publications of the Geological Society of London (Holdsworth and others, 1998; Holdsworth and others, 2001). These publications, as well as others, stress the importance of reactivation of basement structures in guiding the subsequent evolution of continents. Knowledge of basement structures is an important key to understanding the geology of continental interiors.

Genesis of femtosecond-induced nanostructures on solid surfaces.

PubMed

Varlamova, Olga; Martens, Christian; Ratzke, Markus; Reif, Juergen

2014-11-01

The start and evolution of the formation of laser-induced periodic surface structures (LIPSS, ripples) are investigated. The important role of irradiation dose (fluence×number of pulses) for the properties of the generated structures is demonstrated. It is shown how, with an increasing dose, the structures evolve from random surface modification to regular sub-wavelength ripples, then coalesce to broader LIPSS and finally form more complex shapes when ablation produces deep craters. First experiments are presented following this evolution in one single irradiated spot.

Principles of Research Tissue Banking and Specimen Evaluation from the Pathologist's Perspective.

PubMed

McDonald, Sandra A

2010-12-01

Human tissue biorepositories have an increasingly visible and important role within industrial enterprises in supporting biomedical research, including the rapidly advancing fields of proteomics, pharmacogenomics, and molecular epidemiology. Pathologists play a vital but often underrecognized role in the operation of these tissue banks. Besides interpreting studies that arise from banked samples, pathologists are needed to characterize tissues for research, to conduct quality assurance programs, to assist with resource allocation decisions, and to serve an educational role for investigators using the tissues. This article describes these key principles and illustrates examples where pathologist involvement is crucial to biorepository management. Of overarching importance, pathologists play a critical role in helping biorepository users understand the principles of specimen evaluation (histologic and structural composition of tissues, and their limitations) so as to optimize the scientific benefit of the tissues. In conclusion, greater involvement of pathologists in research tissue banking will enhance the scientific utility of biorepositories.

Advances in Homology Protein Structure Modeling

PubMed Central

Xiang, Zhexin

2007-01-01

Homology modeling plays a central role in determining protein structure in the structural genomics project. The importance of homology modeling has been steadily increasing because of the large gap that exists between the overwhelming number of available protein sequences and experimentally solved protein structures, and also, more importantly, because of the increasing reliability and accuracy of the method. In fact, a protein sequence with over 30% identity to a known structure can often be predicted with an accuracy equivalent to a low-resolution X-ray structure. The recent advances in homology modeling, especially in detecting distant homologues, aligning sequences with template structures, modeling of loops and side chains, as well as detecting errors in a model, have contributed to reliable prediction of protein structure, which was not possible even several years ago. The ongoing efforts in solving protein structures, which can be time-consuming and often difficult, will continue to spur the development of a host of new computational methods that can fill in the gap and further contribute to understanding the relationship between protein structure and function. PMID:16787261

Ion-Neutral Coupling in Solar Prominence

NASA Technical Reports Server (NTRS)

Gilbert, H.; DeVore, C. R.; Karpen, J.; Kucera, T.; Antiochos, S.; Kawashima, R.

2011-01-01

Coupling between ions and neutrals in magnetized plasmas is fundamentally important to many aspects of heliophysics, including our ionosphere, the solar chromosphere, the solar wind interaction with planetary atmospheres, and the interface between the heliosphere and the interstellar medium. Ion-neutral coupling also plays a major role in the physics of solar prominences. By combining theory, modeling, and observations we are working toward a better understanding of the structure and dynamics of partially ionized prominence plasma. Two key questions are addressed in the present work: 1) what physical mechanism(s) sets the cross-field scale of prominence threads? 2) Are ion-neutral interactions responsible for the vertical flows and structure in prominences? We present initial results from a study investigating what role ion-neutral interactions play in prominence dynamics and structure. This research was supported by NASA.

Nonequilibrium stabilization of an RNA/protein droplet emulsion by nuclear actin

NASA Astrophysics Data System (ADS)

Brangwynne, Clifford

2013-03-01

Actin plays a structural role in the cytoplasm. However, actin takes on new functions and structures in the nucleus that are poorly understood. The nuclei of the large oocytes of the frog X. laevisspecifically accumulate actin to reach high concentrations; however, it remains unclear if this actin polymerizes into a network, and what, if any, structural role such an actin network might play. Here, we use microrheological and confocal imaging techniques to probe the local architecture and mechanics of the nucleus. Our data show that actin forms a weak network that spatially organizes the nucleus by kinetically stabilizing embedded liquid-like RNA/protein bodies which are important for cell growth. In actin-disrupted nuclei this RNA/protein droplet emulsion is destabilized leading to homotypic coalescence into single large droplets. Our data provide intriguing new insights into why large cell nuclei require an actin-based structural scaffold.

[Insulin-like growth factor-1 (IGF-1) - structure and the role in the human body].

PubMed

Filus, Alicja; Zdrojewicz, Zygmunt

2015-01-01

In the recent years, managed to broadly explore the structure and role of insulin-like growth factors type 1 and 2 (IGF1 I 2). They belong to the structure of polypeptide hormones homologous to proinsulin. They are characterized by a wide range of activities. IGF-1 is a key mediator of most tissue effects of growth hormone (GH). In addition to effects on growth processes of the body, is also an important factor for cell homeostasis, is subject to both endocrine and tissue-specific auto- and paracrine regulation. In this paper, the current, general knowledge on the structure, function and mechanism of biological effects of IGF-1 in the human body was presented. Attention was also drawn to the directions of use of IGf-1 in the treatment of other diseases than the diseases of the hypothalamic-pituitary and growth disorders in children. © Polish Society for Pediatric Endocrinology and Diabetology.

Shadow Labor: Work and Wages among Immigrant Hispanic Women in Durham, North Carolina.

PubMed

Flippen, Chenoa A

2016-07-01

Drawing on data collected in Durham, NC, this paper examines the forces shaping the labor supply and wages of immigrant Hispanic women in new destinations. The analysis evaluates the role of human capital and immigration characteristics (including legal status), family structure, and immigrant-specific labor market conditions, such as subcontracting, in shaping labor market outcomes. Findings indicate that the main determinants of labor supply among immigrant Hispanic women in Durham relate to family structure, with human capital playing a relatively minor role. Important variation is observed, however, in the degree of work-family conflict across occupations. For wages, human capital and immigration characteristics (including documentation) are more determinant than family structure. Results highlight the extremely precarious position of immigrant Hispanic women in Durham's low wage labor market, and multiple, overlapping sources of disadvantage, particularly relating to legal status and family structure.

Role of thermal history in atomic dynamics of chalcogenide glass: A case study on Ge{sub 20}Te{sub 80} glass

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

Sharma, Yashika; Kalra, Geetanjali; Murugavel, Sevi, E-mail: murug@physics.du.ac.in

The non-existence of thermodynamic equilibrium in glasses, their thermal history plays a very crucial role in explaining the relaxation behavior in various time scales and its configurational states. More importantly, the associated relaxation behavior is related mainly to the structural phenomenon of the glasses. Here, we report the dependence of quenching rate on the variation of structural units. The local structures of these glasses are monitored by recording the Raman spectroscopy and related to the different configurational states. The observed variations in structural differences are reflected in the measured density of the corresponding glasses. The quenching rate dependent of themore » relative fractions of edge-shared and corner-shared GeTe{sub 4} tetrahedral units are shown to be consistent with the corresponding variations in the measured density values.« less

Shadow Labor: Work and Wages among Immigrant Hispanic Women in Durham, North Carolina

PubMed Central

Flippen, Chenoa A.

2017-01-01

Drawing on data collected in Durham, NC, this paper examines the forces shaping the labor supply and wages of immigrant Hispanic women in new destinations. The analysis evaluates the role of human capital and immigration characteristics (including legal status), family structure, and immigrant-specific labor market conditions, such as subcontracting, in shaping labor market outcomes. Findings indicate that the main determinants of labor supply among immigrant Hispanic women in Durham relate to family structure, with human capital playing a relatively minor role. Important variation is observed, however, in the degree of work-family conflict across occupations. For wages, human capital and immigration characteristics (including documentation) are more determinant than family structure. Results highlight the extremely precarious position of immigrant Hispanic women in Durham’s low wage labor market, and multiple, overlapping sources of disadvantage, particularly relating to legal status and family structure. PMID:28603290

25th anniversary article: scalable multiscale patterned structures inspired by nature: the role of hierarchy.

PubMed

Bae, Won-Gyu; Kim, Hong Nam; Kim, Doogon; Park, Suk-Hee; Jeong, Hoon Eui; Suh, Kahp-Yang

2014-02-01

Multiscale, hierarchically patterned surfaces, such as lotus leaves, butterfly wings, adhesion pads of gecko lizards are abundantly found in nature, where microstructures are usually used to strengthen the mechanical stability while nanostructures offer the main functionality, i.e., wettability, structural color, or dry adhesion. To emulate such hierarchical structures in nature, multiscale, multilevel patterning has been extensively utilized for the last few decades towards various applications ranging from wetting control, structural colors, to tissue scaffolds. In this review, we highlight recent advances in scalable multiscale patterning to bring about improved functions that can even surpass those found in nature, with particular focus on the analogy between natural and synthetic architectures in terms of the role of different length scales. This review is organized into four sections. First, the role and importance of multiscale, hierarchical structures is described with four representative examples. Second, recent achievements in multiscale patterning are introduced with their strengths and weaknesses. Third, four application areas of wetting control, dry adhesives, selectively filtrating membranes, and multiscale tissue scaffolds are overviewed by stressing out how and why multiscale structures need to be incorporated to carry out their performances. Finally, we present future directions and challenges for scalable, multiscale patterned surfaces. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Highly Heterogeneous Soil Bacterial Communities around Terra Nova Bay of Northern Victoria Land, Antarctica

PubMed Central

Lim, Hyoun Soo; Hong, Soon Gyu; Kim, Ji Hee; Lee, Joohan; Choi, Taejin; Ahn, Tae Seok; Kim, Ok-Sun

2015-01-01

Given the diminished role of biotic interactions in soils of continental Antarctica, abiotic factors are believed to play a dominant role in structuring of microbial communities. However, many ice-free regions remain unexplored, and it is unclear which environmental gradients are primarily responsible for the variations among bacterial communities. In this study, we investigated the soil bacterial community around Terra Nova Bay of Victoria Land by pyrosequencing and determined which environmental variables govern the bacterial community structure at the local scale. Six bacterial phyla, Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes, were dominant, but their relative abundance varied greatly across locations. Bacterial community structures were affected little by spatial distance, but structured more strongly by site, which was in accordance with the soil physicochemical compositions. At both the phylum and species levels, bacterial community structure was explained primarily by pH and water content, while certain earth elements and trace metals also played important roles in shaping community variation. The higher heterogeneity of the bacterial community structure found at this site indicates how soil bacterial communities have adapted to different compositions of edaphic variables under extreme environmental conditions. Taken together, these findings greatly advance our understanding of the adaption of soil bacterial populations to this harsh environment. PMID:25799273

SusG: A Unique Cell-Membrane-Associated [alpha]-Amylase from a Prominent Human Gut Symbiont Targets Complex Starch Molecules

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

Koropatkin, Nicole M.; Smith, Thomas J.

SusG is an {alpha}-amylase and part of a large protein complex on the outer surface of the bacterial cell and plays a major role in carbohydrate acquisition by the animal gut microbiota. Presented here, the atomic structure of SusG has an unusual extended, bilobed structure composed of amylase at one end and an unprecedented internal carbohydrate-binding motif at the other. Structural studies further demonstrate that the carbohydrate-binding motif binds maltooligosaccharide distal to, and on the opposite side of, the amylase catalytic site. SusG has an additional starch-binding site on the amylase domain immediately adjacent to the active cleft. Mutagenesis analysismore » demonstrates that these two additional starch-binding sites appear to play a role in catabolism of insoluble starch. However, elimination of these sites has only a limited effect, suggesting that they may have a more important role in product exchange with other Sus components.« less

G-quadruplex in animal development: Contribution to gene expression and genomic heterogeneity.

PubMed

Armas, Pablo; Calcaterra, Nora Beatriz

2018-05-18

During animal development, gene expression is orchestrated by specific and highly evolutionarily conserved mechanisms that take place accurately, both at spatial and temporal levels. The last decades have provided compelling evidence showing that chromatin state plays essential roles in orchestrating most of the stages of development. The DNA molecule can adopt alternative structures different from the helical duplex architecture. G-rich DNA sequences can fold as intrastrand quadruple helix structures called G-quadruplexes or G4-DNA. G4 can also be formed in RNA molecules, such as mRNA, lncRNA and pre-miRNA. Emerging evidences suggest that G4s have crucial roles in a variety of biological processes, including transcription, recombination, replication, translation and chromosome stability. In this review, we have collected recent information gathered by various laboratories showing the important role of G4 DNA and RNA structures in several steps of animal development. Copyright © 2018 Elsevier B.V. All rights reserved.

A Decade of Experience in Creating and Maintaining Data Elements for Structured Clinical Documentation in EHRs

PubMed Central

Zhou, Li; Collins, Sarah; Morgan, Stephen J.; Zafar, Neelam; Gesner, Emily J.; Fehrenbach, Martin; Rocha, Roberto A.

2016-01-01

Structured clinical documentation is an important component of electronic health records (EHRs) and plays an important role in clinical care, administrative functions, and research activities. Clinical data elements serve as basic building blocks for composing the templates used for generating clinical documents (such as notes and forms). We present our experience in creating and maintaining data elements for three different EHRs (one home-grown and two commercial systems) across different clinical settings, using flowsheet data elements as examples in our case studies. We identified basic but important challenges (including naming convention, links to standard terminologies, and versioning and change management) and possible solutions to address them. We also discussed more complicated challenges regarding governance, documentation vs. structured data capture, pre-coordination vs. post-coordination, reference information models, as well as monitoring, communication and training. PMID:28269927

Spatio-temporal reproducibility of the microbial food web structure associated with the change in temperature: Long-term observations in the Adriatic Sea

NASA Astrophysics Data System (ADS)

Šolić, Mladen; Grbec, Branka; Matić, Frano; Šantić, Danijela; Šestanović, Stefanija; Ninčević Gladan, Živana; Bojanić, Natalia; Ordulj, Marin; Jozić, Slaven; Vrdoljak, Ana

2018-02-01

Global and atmospheric climate change is altering the thermal conditions in the Adriatic Sea and, consequently, the marine ecosystem. Along the eastern Adriatic coast sea surface temperature (SST) increased by an average of 1.03 °C during the period from 1979 to 2015, while in the recent period, starting from 2008, a strong upward almost linear trend of 0.013 °C/month was noted. Being mainly oligotrophic, the middle Adriatic Sea is characterized by the important role played by the microbial food web in the production and transfer of biomass and energy towards higher trophic levels. It is very important to understand the effect of warming on microbial communities, since small temperature increases in surface seawater can greatly modify the microbial role in the global carbon cycle. In this study, the Self-Organizing Map (SOM) procedure was used to analyse the time series of a number of microbial parameters at two stations with different trophic status in the central Adriatic Sea. The results show that responses of the microbial food web (MFW) structure to temperature changes are reproducible in time. Furthermore, qualitatively similar changes in the structure of the MFW occurred regardless of the trophic status. The rise in temperature was associated with: (1) the increasing importance of microbial heterotrophic activities (increase bacterial growth and bacterial predator abundance, particularly heterotrophic nanoflagellates) and (2) the increasing importance of autotrophic picoplankton (APP) in the MFW.

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem.

PubMed

Zhou, Jizhong; Deng, Ye; Zhang, Ping; Xue, Kai; Liang, Yuting; Van Nostrand, Joy D; Yang, Yunfeng; He, Zhili; Wu, Liyou; Stahl, David A; Hazen, Terry C; Tiedje, James M; Arkin, Adam P

2014-03-04

Unraveling the drivers of community structure and succession in response to environmental change is a central goal in ecology. Although the mechanisms shaping community structure have been intensively examined, those controlling ecological succession remain elusive. To understand the relative importance of stochastic and deterministic processes in mediating microbial community succession, a unique framework composed of four different cases was developed for fluidic and nonfluidic ecosystems. The framework was then tested for one fluidic ecosystem: a groundwater system perturbed by adding emulsified vegetable oil (EVO) for uranium immobilization. Our results revealed that groundwater microbial community diverged substantially away from the initial community after EVO amendment and eventually converged to a new community state, which was closely clustered with its initial state. However, their composition and structure were significantly different from each other. Null model analysis indicated that both deterministic and stochastic processes played important roles in controlling the assembly and succession of the groundwater microbial community, but their relative importance was time dependent. Additionally, consistent with the proposed conceptual framework but contradictory to conventional wisdom, the community succession responding to EVO amendment was primarily controlled by stochastic rather than deterministic processes. During the middle phase of the succession, the roles of stochastic processes in controlling community composition increased substantially, ranging from 81.3% to 92.0%. Finally, there are limited successional studies available to support different cases in the conceptual framework, but further well-replicated explicit time-series experiments are needed to understand the relative importance of deterministic and stochastic processes in controlling community succession.

Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy.

PubMed

Lawrenz, Morgan; Wereszczynski, Jeff; Amaro, Rommie; Walker, Ross; Roitberg, Adrian; McCammon, J Andrew

2010-08-15

The highly pathogenic influenza strains H5N1 and H1N1 are currently treated with inhibitors of the viral surface protein neuraminidase (N1). Crystal structures of N1 indicate a conserved, high affinity calcium binding site located near the active site. The specific role of this calcium in the enzyme mechanism is unknown, though it has been shown to be important for enzymatic activity and thermostability. We report molecular dynamics (MD) simulations of calcium-bound and calcium-free N1 complexes with the inhibitor oseltamivir (marketed as the drug Tamiflu), independently using both the AMBER FF99SB and GROMOS96 force fields, to give structural insight into calcium stabilization of key framework residues. Y347, which demonstrates similar sampling patterns in the simulations of both force fields, is implicated as an important N1 residue that can "clamp" the ligand into a favorable binding pose. Free energy perturbation and thermodynamic integration calculations, using two different force fields, support the importance of Y347 and indicate a +3 to +5 kcal/mol change in the binding free energy of oseltamivir in the absence of calcium. With the important role of structure-based drug design for neuraminidase inhibitors and the growing literature on emerging strains and subtypes, inclusion of this calcium for active site stability is particularly crucial for computational efforts such as homology modeling, virtual screening, and free energy methods. 2010 Wiley-Liss, Inc.

Environmental Research At The Advanced Photon Source

EPA Science Inventory

Because of the importance of probing molecular-scale chemical and physical structure of environmental samples in their natural and often hydrated state, synchrotron radiation has been a powerful tool for environmental scientists for decades. Thus, the crucial role that a highly ...

How do glycerol and dimethyl sulphoxide affect local tetrahedral structure of water around a nonpolar solute at low temperature? Importance of preferential interaction.

PubMed

Daschakraborty, Snehasis

2018-04-07

Glycerol and dimethyl sulphoxide (DMSO) have vital roles in cryoprotection of living cells, tissues, etc. The above action has been directly linked with disruption of hydrogen (H-) bond structure and dynamics of water by these cosolvents at bulk region and around various complex units, such as peptide, amino acid, protein, and lipid membrane. However, the disruption of the local structure of the water solvent around a purely hydrophobic solute is still not studied extensively. The latter is also important in the context of stabilization of protein from cold denaturation. Through all-atom molecular dynamics simulation, we have investigated the comparative effect of glycerol and DMSO on the orientational order of water around a nonpolar solute at -5 °C. A steady reduction of the tetrahedral order of water is observed at bulk (>10 Å distance from the solute) and solute interface (<5.5 Å distance from the solute) with increasing the cosolvent concentration. Contrasting roles of glycerol and DMSO have been evidenced. While DMSO affects the H-bond structure of the interfacial water more than that of the bulk water, glycerol affects the water structure almost uniformly at all regions around the solute. Furthermore, while glycerol helps to retain water molecules at the interface, DMSO significantly reduces the water content in that region. We have put forward a plausible mechanism for these contrasting roles of these cosolvents. The solute-cosolvent hydrophobic-interaction-induced orientational alignment of an interfacial cosolvent molecule determines whether the involvement of the cosolvent molecules in H-bonding with solvent water in the interface is akin to the bulk region or not.

The Isoforms of the p53 Protein

PubMed Central

Khoury, Marie P.; Bourdon, Jean-Christophe

2010-01-01

p53 is a transcription factor with a key role in the maintenance of genetic stability and therefore preventing cancer formation. It belongs to a family of genes composed of p53, p63, and p73. The p63 and p73 genes have a dual gene structure with an internal promoter in intron-3 and together with alternative splicing, can express 6 and 29 mRNA variants, respectively. Such a complex expression pattern had not been previously described for the p53 gene, which was not consistent with our understanding of the evolution of the p53 gene family. Consequently, we revisited the human p53 gene structure and established that it encodes nine different p53 protein isoforms because of alternative splicing, alternative promoter usage, and alternative initiation sites of translation. Therefore, the human p53 gene family (p53, p63, and p73) has a dual gene structure. We determined that the dual gene structure is conserved in Drosophila and in zebrafish p53 genes. The conservation through evolution of the dual gene structure suggests that the p53 isoforms play an important role in p53 tumor-suppressor activity. We and others have established that the p53 isoforms can regulate cell-fate outcome in response to stress, by modulating p53 transcriptional activity in a promoter and stress-dependent manner. We have also shown that the p53 isoforms are abnormally expressed in several types of human cancers, suggesting that they play an important role in cancer formation. The determination of p53 isoforms' expression may help to link clinical outcome to p53 status and to improve cancer patient treatment. PMID:20300206

How do glycerol and dimethyl sulphoxide affect local tetrahedral structure of water around a nonpolar solute at low temperature? Importance of preferential interaction

NASA Astrophysics Data System (ADS)

Daschakraborty, Snehasis

2018-04-01

Glycerol and dimethyl sulphoxide (DMSO) have vital roles in cryoprotection of living cells, tissues, etc. The above action has been directly linked with disruption of hydrogen (H-) bond structure and dynamics of water by these cosolvents at bulk region and around various complex units, such as peptide, amino acid, protein, and lipid membrane. However, the disruption of the local structure of the water solvent around a purely hydrophobic solute is still not studied extensively. The latter is also important in the context of stabilization of protein from cold denaturation. Through all-atom molecular dynamics simulation, we have investigated the comparative effect of glycerol and DMSO on the orientational order of water around a nonpolar solute at -5 °C. A steady reduction of the tetrahedral order of water is observed at bulk (>10 Å distance from the solute) and solute interface (<5.5 Å distance from the solute) with increasing the cosolvent concentration. Contrasting roles of glycerol and DMSO have been evidenced. While DMSO affects the H-bond structure of the interfacial water more than that of the bulk water, glycerol affects the water structure almost uniformly at all regions around the solute. Furthermore, while glycerol helps to retain water molecules at the interface, DMSO significantly reduces the water content in that region. We have put forward a plausible mechanism for these contrasting roles of these cosolvents. The solute-cosolvent hydrophobic-interaction-induced orientational alignment of an interfacial cosolvent molecule determines whether the involvement of the cosolvent molecules in H-bonding with solvent water in the interface is akin to the bulk region or not.

A cloudiness transition in a marine boundary layer

NASA Technical Reports Server (NTRS)

Betts, Alan K.; Boers, Reinout

1990-01-01

Boundary layer cloudiness plays several important roles in the energy budget of the earth. Low level stratocumulus are highly reflective clouds which reduce the net incoming shortwave radiation at the earth's surface. Climatically, the transition to a small area fraction of scattered cumulus clouds occurs as the air flows over warmer water. Although these clouds reflect less sunlight, they still play an important role in the boundary layer equilibrium by transporting water vapor upwards, and enhancing the surface evaporation. The First ISCCP (International Satellite Cloud Climatology Project) Regional Experiment (FIRE) included a marine stratocumulus experiment off the southern California coast from June 29 to July 19, 1987. The objectives of this experiment were to study the controls on fractional cloudiness, and to assess the role of cloud-top entrainment instability (CTEI) and mesoscale structure in determining cloud type. The focus is one research day, July 7, 1987, when coordinated aircraft missions were flown by four research aircraft, centered on a LANDSAT scene at 1830 UTC. The remarkable feature of this LANDSAT scene is the transition from a clear sky in the west through broken cumulus to solid stratocumulus in the east. The dynamic and thermodynamic structure of this transition in cloudiness is analyzed using data from the NCAR Electra. By averaging the aircraft data, the internal structure of the different cloud regimes is documented, and it is shown that the transition between broken cumulus and stratocumulus is associated with a change in structure with respect to the CTEI condition. However, this results not from sea surface temperature changes, but mostly from a transition in the air above the inversion, and the breakup appears to be at a structure on the unstable side of the wet virtual adiabat.

Structural neural correlates of multitasking: A voxel-based morphometry study.

PubMed

Zhang, Rui-Ting; Yang, Tian-Xiao; Wang, Yi; Sui, Yuxiu; Yao, Jingjing; Zhang, Chen-Yuan; Cheung, Eric F C; Chan, Raymond C K

2016-12-01

Multitasking refers to the ability to organize assorted tasks efficiently in a short period of time, which plays an important role in daily life. However, the structural neural correlates of multitasking performance remain unclear. The present study aimed at exploring the brain regions associated with multitasking performance using global correlation analysis. Twenty-six healthy participants first underwent structural brain scans and then performed the modified Six Element Test, which required participants to attempt six subtasks in 10 min while obeying a specific rule. Voxel-based morphometry of the whole brain was used to detect the structural correlates of multitasking ability. Grey matter volume of the anterior cingulate cortex (ACC) was positively correlated with the overall performance and time monitoring in multitasking. In addition, white matter volume of the anterior thalamic radiation (ATR) was also positively correlated with time monitoring during multitasking. Other related brain regions associated with multitasking included the superior frontal gyrus, the inferior occipital gyrus, the lingual gyrus, and the inferior longitudinal fasciculus. No significant correlation was found between grey matter volume of the prefrontal cortex (Brodmann Area 10) and multitasking performance. Using a global correlation analysis to examine various aspects of multitasking performance, this study provided new insights into the structural neural correlates of multitasking ability. In particular, the ACC was identified as an important brain region that played both a general and a specific time-monitoring role in multitasking, extending the role of the ACC from lesioned populations to healthy populations. The present findings also support the view that the ATR may influence multitasking performance by affecting time-monitoring abilities. © 2016 The Institute of Psychology, Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

Rapid divergence of mussel populations despite incomplete barriers to dispersal.

PubMed

Maas, Diede L; Prost, Stefan; Bi, Ke; Smith, Lydia L; Armstrong, Ellie E; Aji, Ludi P; Toha, Abdul Hamid A; Gillespie, Rosemary G; Becking, Leontine E

2018-04-01

Striking genetic structure among marine populations at small spatial scales is becoming evident with extensive molecular studies. Such observations suggest isolation at small scales may play an important role in forming patterns of genetic diversity within species. Isolation-by-distance, isolation-by-environment and historical priority effects are umbrella terms for a suite of processes that underlie genetic structure, but their relative importance at different spatial and temporal scales remains elusive. Here, we use marine lakes in Indonesia to assess genetic structure and assess the relative roles of the processes in shaping genetic differentiation in populations of a bivalve mussel (Brachidontes sp.). Marine lakes are landlocked waterbodies of similar age (6,000-10,000 years), but with heterogeneous environments and varying degrees of connection to the sea. Using a population genomic approach (double-digest restriction-site-associated DNA sequencing), we show strong genetic structuring across populations (range F ST : 0.07-0.24) and find limited gene flow through admixture plots. At large spatial scales (>1,400 km), a clear isolation-by-distance pattern was detected. At smaller spatial scales (<200 km), this pattern is maintained, but accompanied by an association of genetic divergence with degree of connection. We hypothesize that (incomplete) dispersal barriers can cause initial isolation, allowing priority effects to give the numerical advantage necessary to initiate strong genetic structure. Priority effects may be strengthened by local adaptation, which the data may corroborate by showing a high correlation between mussel genotypes and temperature. Our study indicates an often-neglected role of (evolution-mediated) priority effects in shaping population divergence. © 2018 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.

As You Sow, So Shall You Reap: Gender-Role Attitudes and Late-Life Cognition.

PubMed

Bonsang, Eric; Skirbekk, Vegard; Staudinger, Ursula M

2017-09-01

Some studies have found that women outperform men in episodic memory after midlife. But is this finding universal, and what are the reasons? Gender differences in cognition are the result of biopsychosocial interactions throughout the life course. Social-cognitive theory of gender development posits that gender roles may play an important mediating role in these interactions. We analyzed country differences in the gender differential in cognition after midlife using data from individuals age 50 and above ( N = 226,661) from 27 countries. As expected, older women performed relatively better in countries characterized by more equal gender-role attitudes. This result was robust to cohort differences as well as reverse causality. The effect was partially mediated by education and labor-force participation. Cognition in later life thus cannot be fully understood without reference to the opportunity structures that sociocultural environments do (or do not) provide. Global population aging raises the importance of understanding that gender roles affect old-age cognition and productivity.

[Diet and civilization diseases--carbohydrate aspects].

PubMed

Haslbeck, M

1990-01-01

Carbohydrates are a major component of our food, they are important as body energy stores and they play an important role in cellular structures. In the present paper a classification of food carbohydrates, of dietary fibers and sweeteners is presented and the major physiological effects are discussed. Furthermore, the significance of carbohydrates for the etiology and the treatment of nutrition related diseases which are closely related to the development of arteriosclerosis is outlined. Carbohydrates are beside fat the major determinants of the daily caloric intake. This illustrates their impact on the development of obesity with its predominant role as a risk factor for the development of cardiovascular disease. Furthermore, the role of sugar consumption in the relation to dental caries is stressed. Also the central role of carbohydrate consumption for the treatment of diabetes mellitus is described. Problems of the diabetes diet, the role of the dietary fiber in the treatment of different diseases and the necessity of sweetness in nutrition are discussed in greater detail.

α,β-Unsaturated monoterpene acid glucose esters: structural diversity, bioactivities and functional roles.

PubMed

Goodger, Jason Q D; Woodrow, Ian E

2011-12-01

The glycosylation of lipophilic small molecules produces many important plant secondary metabolites. The majority of these are O-glycosides with relatively fewer occurring as glucose esters of aromatic or aliphatic acids. In particular, monoterpene acid glucose esters have much lower structural diversity and distribution compared to monoterpene glycosides. Nevertheless, there have been over 20 monoterpene acid glucose esters described from trees in the genus Eucalyptus (Myrtaceae) in recent years, all based on oleuropeic acid, menthiafolic acid or both. Here we review all of the glucose esters containing these monoterpenoids identified in plants to date. Many of the compounds contain phenolic aglycones and all contain at least one α,β-unsaturated carbonyl, affording a number of important potential therapeutic reactivities such as anti-tumor promotion, carcinogenesis suppression, and anti-oxidant and anti-inflammatory activities. Additional properties such as cytotoxicity, bitterness, and repellency are suggestive of a role in plant defence, but we also discuss their localization to the exterior of foliar secretory cavity lumina, and suggest they may also protect secretory cells from toxic terpenes housed within these structures. Finally we discuss how the use of a recently developed protocol to isolate secretory cavities in a functional state could be used in conjunction with systems biology approaches to help characterize their biosynthesis and roles in plants. Copyright © 2011 Elsevier Ltd. All rights reserved.

On the role of spatial phase and phase correlation in vision, illusion, and cognition

PubMed Central

Gladilin, Evgeny; Eils, Roland

2015-01-01

Numerous findings indicate that spatial phase bears an important cognitive information. Distortion of phase affects topology of edge structures and makes images unrecognizable. In turn, appropriately phase-structured patterns give rise to various illusions of virtual image content and apparent motion. Despite a large body of phenomenological evidence not much is known yet about the role of phase information in neural mechanisms of visual perception and cognition. Here, we are concerned with analysis of the role of spatial phase in computational and biological vision, emergence of visual illusions and pattern recognition. We hypothesize that fundamental importance of phase information for invariant retrieval of structural image features and motion detection promoted development of phase-based mechanisms of neural image processing in course of evolution of biological vision. Using an extension of Fourier phase correlation technique, we show that the core functions of visual system such as motion detection and pattern recognition can be facilitated by the same basic mechanism. Our analysis suggests that emergence of visual illusions can be attributed to presence of coherently phase-shifted repetitive patterns as well as the effects of acuity compensation by saccadic eye movements. We speculate that biological vision relies on perceptual mechanisms effectively similar to phase correlation, and predict neural features of visual pattern (dis)similarity that can be used for experimental validation of our hypothesis of “cognition by phase correlation.” PMID:25954190

On the role of spatial phase and phase correlation in vision, illusion, and cognition.

PubMed

Gladilin, Evgeny; Eils, Roland

2015-01-01

Numerous findings indicate that spatial phase bears an important cognitive information. Distortion of phase affects topology of edge structures and makes images unrecognizable. In turn, appropriately phase-structured patterns give rise to various illusions of virtual image content and apparent motion. Despite a large body of phenomenological evidence not much is known yet about the role of phase information in neural mechanisms of visual perception and cognition. Here, we are concerned with analysis of the role of spatial phase in computational and biological vision, emergence of visual illusions and pattern recognition. We hypothesize that fundamental importance of phase information for invariant retrieval of structural image features and motion detection promoted development of phase-based mechanisms of neural image processing in course of evolution of biological vision. Using an extension of Fourier phase correlation technique, we show that the core functions of visual system such as motion detection and pattern recognition can be facilitated by the same basic mechanism. Our analysis suggests that emergence of visual illusions can be attributed to presence of coherently phase-shifted repetitive patterns as well as the effects of acuity compensation by saccadic eye movements. We speculate that biological vision relies on perceptual mechanisms effectively similar to phase correlation, and predict neural features of visual pattern (dis)similarity that can be used for experimental validation of our hypothesis of "cognition by phase correlation."

The reticulons: Guardians of the structure and function of the endoplasmic reticulum

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

Di Sano, Federica; Bernardoni, Paolo; Piacentini, Mauro, E-mail: mauro.piacentini@uniroma2.it

2012-07-01

The endoplasmic reticulum (ER) consists of the nuclear envelope and a peripheral network of tubules and membrane sheets. The tubules are shaped by a specific class of curvature stabilizing proteins, the reticulons and DP1; however it is still unclear how the sheets are assembled. The ER is the cellular compartment responsible for secretory and membrane protein synthesis. The reducing conditions of ER lead to the intra/inter-chain formation of new disulphide bonds into polypeptides during protein folding assessed by enzymatic or spontaneous reactions. Moreover, ER represents the main intracellular calcium storage site and it plays an important role in calcium signalingmore » that impacts many cellular processes. Accordingly, the maintenance of ER function represents an essential condition for the cell, and ER morphology constitutes an important prerogative of it. Furthermore, it is well known that ER undergoes prominent shape transitions during events such as cell division and differentiation. Thus, maintaining the correct ER structure is an essential feature for cellular physiology. Now, it is known that proper ER-associated proteins play a fundamental role in ER tubules formation. Among these ER-shaping proteins are the reticulons (RTN), which are acquiring a relevant position. In fact, beyond the structural role of reticulons, in very recent years new and deeper functional implications of these proteins are emerging in relation to their involvement in several cellular processes.« less

Dzyaloshinskii-Moriya interaction and magnetic anisotropies in Uranium compounds

NASA Astrophysics Data System (ADS)

Sandratskii, L. M.

2018-05-01

We report on the first-principles study of complex noncollinear magnetic structures in Uranium compounds. We contrast two cases. The first is the periodic magnetic structure of U2Pd2In with exactly orthogonal atomic moments, the second is an incommensurate plane spiral structure of UPtGe where the angle between atomic moments of nearest neighbors is also close to 90°. We demonstrate that the hierarchy of magnetic interactions leading to the formation of the magnetic structure is opposite in the two cases. In U2Pd2In, the magnetic anisotropy plays the leading role, followed by the Dzyaloshinskii-Moriya interaction (DMI) interaction specifying the chirality of the structure. Here, the interatomic exchange interaction does not play important role. In UPtGe the hierarchy of the interactions is opposite. The leading interaction is the interatomic exchange interaction responsible for the formation of the incommensurate spiral structure followed by the DMI responsible for the selected chirality of the helix. The magnetic anisotropy is very weak that is a prerequisite for keeping the distortion of the helical structure weak.

Deciphering the role of the Gag-Pol ribosomal frameshift signal in HIV-1 RNA genome packaging.

PubMed

Nikolaitchik, Olga A; Hu, Wei-Shau

2014-04-01

A key step of retroviral replication is packaging of the viral RNA genome during virus assembly. Specific packaging is mediated by interactions between the viral protein Gag and elements in the viral RNA genome. In HIV-1, similar to most retroviruses, the packaging signal is located within the 5' untranslated region and extends into the gag-coding region. A recent study reported that a region including the Gag-Pol ribosomal frameshift signal plays an important role in HIV-1 RNA packaging; deletions or mutations that affect the RNA structure of this signal lead to drastic decreases (10- to 50-fold) in viral RNA packaging and virus titer. We examined here the role of the ribosomal frameshift signal in HIV-1 RNA packaging by studying the RNA packaging and virus titer in the context of proviruses. Three mutants with altered ribosomal frameshift signal, either through direct deletion of the signal, mutation of the 6U slippery sequence, or alterations of the secondary structure were examined. We found that RNAs from all three mutants were packaged efficiently, and they generate titers similar to that of a virus containing the wild-type ribosomal frameshift signal. We conclude that although the ribosomal frameshift signal plays an important role in regulating the replication cycle, this RNA element is not directly involved in regulating RNA encapsidation. To generate infectious viruses, HIV-1 must package viral RNA genome during virus assembly. The specific HIV-1 genome packaging is mediated by interactions between the structural protein Gag and elements near the 5' end of the viral RNA known as packaging signal. In this study, we examined whether the Gag-Pol ribosomal frameshift signal is important for HIV-1 RNA packaging as recently reported. Our results demonstrated that when Gag/Gag-Pol is supplied in trans, none of the tested ribosomal frameshift signal mutants has defects in RNA packaging or virus titer. These studies provide important information on how HIV-1 regulates its genome packaging and generate infectious viruses necessary for transmission to new hosts.

Modulation of a Pore in the Capsid of JC Polyomavirus Reduces Infectivity and Prevents Exposure of the Minor Capsid Proteins

PubMed Central

Nelson, Christian D. S.; Ströh, Luisa J.; Gee, Gretchen V.; O'Hara, Bethany A.; Stehle, Thilo

2015-01-01

ABSTRACT JC polyomavirus (JCPyV) infection of immunocompromised individuals results in the fatal demyelinating disease progressive multifocal leukoencephalopathy (PML). The viral capsid of JCPyV is composed primarily of the major capsid protein virus protein 1 (VP1), and pentameric arrangement of VP1 monomers results in the formation of a pore at the 5-fold axis of symmetry. While the presence of this pore is conserved among polyomaviruses, its functional role in infection or assembly is unknown. Here, we investigate the role of the 5-fold pore in assembly and infection of JCPyV by generating a panel of mutant viruses containing amino acid substitutions of the residues lining this pore. Multicycle growth assays demonstrated that the fitness of all mutants was reduced compared to that of the wild-type virus. Bacterial expression of VP1 pentamers containing substitutions to residues lining the 5-fold pore did not affect pentamer assembly or prevent association with the VP2 minor capsid protein. The X-ray crystal structures of selected pore mutants contained subtle changes to the 5-fold pore, and no other changes to VP1 were observed. Pore mutant pseudoviruses were not deficient in assembly, packaging of the minor capsid proteins, or binding to cells or in transport to the host cell endoplasmic reticulum. Instead, these mutant viruses were unable to expose VP2 upon arrival to the endoplasmic reticulum, a step that is critical for infection. This study demonstrated that the 5-fold pore is an important structural feature of JCPyV and that minor modifications to this structure have significant impacts on infectious entry. IMPORTANCE JCPyV is an important human pathogen that causes a severe neurological disease in immunocompromised individuals. While the high-resolution X-ray structure of the major capsid protein of JCPyV has been solved, the importance of a major structural feature of the capsid, the 5-fold pore, remains poorly understood. This pore is conserved across polyomaviruses and suggests either that these viruses have limited structural plasticity in this region or that this pore is important in infection or assembly. Using a structure-guided mutational approach, we showed that modulation of this pore severely inhibits JCPyV infection. These mutants do not appear deficient in assembly or early steps in infectious entry and are instead reduced in their ability to expose a minor capsid protein in the host cell endoplasmic reticulum. Our work demonstrates that the 5-fold pore is an important structural feature for JCPyV. PMID:25609820

Molecular modeling and docking studies of human 5-hydroxytryptamine 2A (5-HT2A) receptor for the identification of hotspots for ligand binding.

PubMed

Kanagarajadurai, Karuppiah; Malini, Manoharan; Bhattacharya, Aditi; Panicker, Mitradas M; Sowdhamini, Ramanathan

2009-12-01

The serotonergic system has been implicated in emotional and cognitive function. In particular, 5-HT(2A) (5-hydroxytrytamine receptor 2A) is attributed to a number of disorders like schizophrenia, depression, eating disorders and anxiety. 5-HT(2A), being a GPCR (G-protein coupled receptor), is important in the pharmaceutical industry as a proven target for these disorders. Despite their extensive clinical importance, the structural studies of this protein is lacking due to difficulties in determining its crystal structure. We have performed sequence analysis and molecular modeling of 5-HT(2A) that has revealed a set of conserved residues and motifs considered to play an important role in maintaining structural integrity and function of the receptor. The analysis also revealed a set of residues specific to the receptor which distinguishes them from other members of the subclass and their orthologs. Further, starting from the model structure of human 5-HT(2A) receptor, docking studies were attempted to envisage how it might interact with eight of its ligands (such as serotonin, dopamine, DOI, LSD, haloperidol, ketanserin, risperidone and clozapine). The binding studies of dopamine to 5-HT(2A) receptor can bring up better understanding in the etiology of a number of neurological disorders involving both these two receptors. Our sequence analysis and study of interactions of this receptor with other ligands reveal additional residue hotspots such as Asn 363 and Tyr 370. The function of these residues can be further analyzed by rational design of site-directed mutagenesis. Two distinct binding sites are identified which could play important roles in ligand binding and signaling.

The Fluid-Mosaic Model of Membrane Structure: still relevant to understanding the structure, function and dynamics of biological membranes after more than 40 years.

PubMed

Nicolson, Garth L

2014-06-01

In 1972 the Fluid-Mosaic Membrane Model of membrane structure was proposed based on thermodynamic principals of organization of membrane lipids and proteins and available evidence of asymmetry and lateral mobility within the membrane matrix [S. J. Singer and G. L. Nicolson, Science 175 (1972) 720-731]. After over 40years, this basic model of the cell membrane remains relevant for describing the basic nano-structures of a variety of intracellular and cellular membranes of plant and animal cells and lower forms of life. In the intervening years, however, new information has documented the importance and roles of specialized membrane domains, such as lipid rafts and protein/glycoprotein complexes, in describing the macrostructure, dynamics and functions of cellular membranes as well as the roles of membrane-associated cytoskeletal fences and extracellular matrix structures in limiting the lateral diffusion and range of motion of membrane components. These newer data build on the foundation of the original model and add new layers of complexity and hierarchy, but the concepts described in the original model are still applicable today. In updated versions of the model more emphasis has been placed on the mosaic nature of the macrostructure of cellular membranes where many protein and lipid components are limited in their rotational and lateral motilities in the membrane plane, especially in their natural states where lipid-lipid, protein-protein and lipid-protein interactions as well as cell-matrix, cell-cell and intracellular membrane-associated protein and cytoskeletal interactions are important in restraining the lateral motility and range of motion of particular membrane components. The formation of specialized membrane domains and the presence of tightly packed integral membrane protein complexes due to membrane-associated fences, fenceposts and other structures are considered very important in describing membrane dynamics and architecture. These structures along with membrane-associated cytoskeletal and extracellular structures maintain the long-range, non-random mosaic macro-organization of membranes, while smaller membrane nano- and submicro-sized domains, such as lipid rafts and protein complexes, are important in maintaining specialized membrane structures that are in cooperative dynamic flux in a crowded membrane plane. This Article is Part of a Special Issue Entitled: Membrane Structure and Function: Relevance in the Cell's Physiology, Pathology and Therapy. © 2013.

Structure of Zebrafish IRBP Reveals Fatty Acid Binding

PubMed Central

Ghosh, Debashis; Haswell, Karen M.; Sprada, Molly; Gonzalez-Fernandez, Federico

2015-01-01

Interphotoreceptor retinoid-binding protein (IRBP) has a remarkable role in targeting and protecting all-trans and 11-cis retinol, and 11-cis retinal during the rod and cone visual cycles. Little is known about how the correct retinoid is efficiently delivered and removed from the correct cell at the required time. It has been proposed that different fatty composition at that the outer-segments and retinal-pigmented epithelium could have an important role is regulating the delivery and uptake of the visual cycle retinoids at the cell-interphotoreceptor-matrix interface. Although this suggests intriguing mechanisms for the role of local fatty acids in visual-cycle retinoid trafficking, nothing is known about the structural basis of IRBP-fatty acid interactions. Such regulation may be mediated through IRBP’s unusual repeating homologous modules, each containing about 300 amino acids. We have been investigating structure-function relationships of Zebrafish IRBP (zIRBP), which has only two tandem modules (z1 and z2), as a model for the more complex four-module mammalian IRBP’s. Here we report the first X-ray crystal structure of a teleost IRBP, and the only structure with a bound ligand. The X-ray structure of z1, determined at 1.90Å resolution, reveals a two-domain organization of the module (domains A and B). A deep hydrophobic pocket was identified within the N-terminal domain A. In fluorescence titrations assays, oleic acid displaced all-trans retinol from zIRBP. Our study, which provides the first structure of an IRBP with bound ligand, supports a potential role for fatty acids in regulating retinoid binding. PMID:26344741

In silico characterization of a novel pathogenic deletion mutation identified in XPA gene in a Pakistani family with severe xeroderma pigmentosum.

PubMed

Nasir, Muhammad; Ahmad, Nafees; Sieber, Christian M K; Latif, Amir; Malik, Salman Akbar; Hameed, Abdul

2013-09-24

Xeroderma Pigmentosum (XP) is a rare skin disorder characterized by skin hypersensitivity to sunlight and abnormal pigmentation. The aim of this study was to investigate the genetic cause of a severe XP phenotype in a consanguineous Pakistani family and in silico characterization of any identified disease-associated mutation. The XP complementation group was assigned by genotyping of family for known XP loci. Genotyping data mapped the family to complementation group A locus, involving XPA gene. Mutation analysis of the candidate XP gene by DNA sequencing revealed a novel deletion mutation (c.654del A) in exon 5 of XPA gene. The c.654del A, causes frameshift, which pre-maturely terminates protein and result into a truncated product of 222 amino acid (aa) residues instead of 273 (p.Lys218AsnfsX5). In silico tools were applied to study the likelihood of changes in structural motifs and thus interaction of mutated protein with binding partners. In silico analysis of mutant protein sequence, predicted to affect the aa residue which attains coiled coil structure. The coiled coil structure has an important role in key cellular interactions, especially with DNA damage-binding protein 2 (DDB2), which has important role in DDB-mediated nucleotide excision repair (NER) system. Our findings support the fact of genetic and clinical heterogeneity in XP. The study also predicts the critical role of DDB2 binding region of XPA protein in NER pathway and opens an avenue for further research to study the functional role of the mutated protein domain.

Computational study of stability of an H-H-type pseudoknot motif.

PubMed

Wang, Jun; Zhao, Yunjie; Wang, Jian; Xiao, Yi

2015-12-01

Motifs in RNA tertiary structures are important to their structural organizations and biological functions. Here we consider an H-H-type pseudoknot (HHpk) motif that consists of two hairpins connected by a junction loop and with kissing interactions between the two hairpin loops. Such a tertiary structural motif is recurrently found in RNA tertiary structures, but is difficult to predict computationally. So it is important to understand the mechanism of its formation and stability. Here we investigate the stability of the HHpk tertiary structure by using an all-atom molecular dynamics simulation. The results indicate that the HHpk tertiary structure is stable. However, it is found that this stability is not due to the helix-helix packing, as is usually expected, but is maintained by the combined action of the kissing hairpin loops and junctions, although the former plays the main role. Stable HHpk motifs may form structural platforms for the molecules to realize their biological functions. These results are useful for understanding the construction principle of RNA tertiary structures and structure prediction.

The elusive structural role of ubiquitinated histones.

PubMed

Moore, Susan C; Jason, Laure; Ausió, Juan

2002-01-01

It is increasingly apparent that histone posttranslational modifications are important in chromatin structure and dynamics. However, histone ubiquitination has received little attention. Histones H1, H3, H2A, and H2B can be ubiquitinated in vivo, but the most prevalent are uH2A and uH2B. The size of this modification suggests some sort of structural impact. Physiological observations suggest that ubiquitinated histones may have multiple functions and structural effects. Ubiquitinated histones have been correlated with transcriptionally active DNA, implying that it may prevent chromatin folding or help maintain an open conformation. Also, in some organisms during spermiogenesis, a process involving extensive chromatin remodeling, uH2A levels increase just prior to histone replacement by protamines. Determination of chromatin's structural changes resulting from histone ubiquitination is therefore important. Recent work using reconstituted nucleosomes and chromatin fibers containing uH2A indicate that in the absence of linker histones, ubiquitination has little structural impact. DNase I digests and analytical ultracentrifugation of reconstituted ubiquitinated nucleosomes show no structural differences. Solubility assays using reconstituted chromatin fibers in the presence of divalent ions demonstrate that uH2A fibers are slightly more prone to aggregation than controls, and analytical ultracentrifugation results with different MgCl2 and NaCl concentrations determined that chromatin folding is not affected by this modification. Additional work to assess possible synergistic affects with histone acetylation also precludes any structural implications. Protamine displacement experiments concluded that the presence of uH2A does not significantly affect the ability of the protamines to displace histones. In addition, uH2A does not interfere with histone H1 binding to the nucleosome. While work with uH2B remains insufficient to come to any definitive conclusions about its structural impact, current work with uH-2A indicates that, contrary to predictions, this histone modification does not affect either nucleosome or chromatin structure. Consequently, the search for a structural role for ubiquitinated histones continues and their effect on and importance in chromatin dynamics remains elusive.

Impact of biogenic amine molecular weight and structure on surfactant adsorption at the air-water interface.

PubMed

Penfold, Jeffrey; Thomas, Robert K; Li, Peixun

2016-02-01

The oligoamines, such as ethylenediamine to pentaethylenetetramine, and the aliphatic biogenic amines, such as putrescine, spermidine and spermine, strongly interact with anionic surfactants, such as sodium dodecylsulfate, SDS. It has been shown that this results in pronounced surfactant adsorption at the air-water interface and the transition from monolayer to multilayer adsorption which depends upon solution pH and oligoamine structure. In the neutron reflectivity, NR, and surface tension, ST, results presented here the role of the oligoamine structure on the adsorption of SDS is investigated more fully using a range of different biogenic amines. The effect of the extent of the intra-molecular spacing between amine groups on the adsorption has been extended by comparing results for cadavarine with putrescine and ethylenediamine. The impact of more complex biogenic amine structures on the adsorption has been investigated with the aromatic phenethylamine, and the heterocyclic amines histamine and melamine. The results provide an important insight into how surfactant adsorption at interfaces can be manipulated by the addition of biogenic amines, and into the role of solution pH and oligoamine structure in modifying the interaction between the surfactant and oligoamine. The results impact greatly upon potential applications and in understanding some of the important biological functions of biogenic amines. Copyright © 2015 Elsevier Inc. All rights reserved.

Structural insights of ZIP4 extracellular domain critical for optimal zinc transport

NASA Astrophysics Data System (ADS)

Zhang, Tuo; Sui, Dexin; Hu, Jian

2016-06-01

The ZIP zinc transporter family is responsible for zinc uptake from the extracellular milieu or intracellular vesicles. The LIV-1 subfamily, containing nine out of the 14 human ZIP proteins, is featured with a large extracellular domain (ECD). The critical role of the ECD is manifested by disease-causing mutations on ZIP4, a representative LIV-1 protein. Here we report the first crystal structure of a mammalian ZIP4-ECD, which reveals two structurally independent subdomains and an unprecedented dimer centred at the signature PAL motif. Structure-guided mutagenesis, cell-based zinc uptake assays and mapping of the disease-causing mutations indicate that the two subdomains play pivotal but distinct roles and that the bridging region connecting them is particularly important for ZIP4 function. These findings lead to working hypotheses on how ZIP4-ECD exerts critical functions in zinc transport. The conserved dimeric architecture in ZIP4-ECD is also demonstrated to be a common structural feature among the LIV-1 proteins.

Defining the Pathophysiological Role of Tau in Experimental TBI

DTIC Science & Technology

2016-10-01

in AD. This pathway is a major source for excitatory innervation of hippocampus , a structure vital for memory formation. Damage to the EC or...hippocampal input pathway that is both preferentially vulnerable in early-stage AD and critically important for long-term memory . The model confines...structure and function of the hippocampus after single or repetitive mild TBI, and whether mild TBI exacerbates ongoing tauopathy to promote a chronic

Interaction of foot-and-mouth disease virus non-structural protein 3A with host protein DCTN3 is important for viral virulence in cattle

USDA-ARS?s Scientific Manuscript database

Non-structural protein 3A of foot-and-mouth disease virus (FMDV) is a partially conserved protein of 153 amino acids in most FMDVs examined to date. The role of 3A in virus growth and virulence within the natural host is not well understood. Using a yeast two-hybrid approach, we identified cellular ...

Ultrafast and Wide Range Analysis of DNA Molecules Using Rigid Network Structure of Solid Nanowires

PubMed Central

Rahong, Sakon; Yasui, Takao; Yanagida, Takeshi; Nagashima, Kazuki; Kanai, Masaki; Klamchuen, Annop; Meng, Gang; He, Yong; Zhuge, Fuwei; Kaji, Noritada; Kawai, Tomoji; Baba, Yoshinobu

2014-01-01

Analyzing sizes of DNA via electrophoresis using a gel has played an important role in the recent, rapid progress of biology and biotechnology. Although analyzing DNA over a wide range of sizes in a short time is desired, no existing electrophoresis methods have been able to fully satisfy these two requirements. Here we propose a novel method using a rigid 3D network structure composed of solid nanowires within a microchannel. This rigid network structure enables analysis of DNA under applied DC electric fields for a large DNA size range (100 bp–166 kbp) within 13 s, which are much wider and faster conditions than those of any existing methods. The network density is readily varied for the targeted DNA size range by tailoring the number of cycles of the nanowire growth only at the desired spatial position within the microchannel. The rigid dense 3D network structure with spatial density control plays an important role in determining the capability for analyzing DNA. Since the present method allows the spatial location and density of the nanostructure within the microchannels to be defined, this unique controllability offers a new strategy to develop an analytical method not only for DNA but also for other biological molecules. PMID:24918865

Molecular Structure and Regulation of P2X Receptors With a Special Emphasis on the Role of P2X2 in the Auditory System.

PubMed

Mittal, Rahul; Chan, Brandon; Grati, M'hamed; Mittal, Jeenu; Patel, Kunal; Debs, Luca H; Patel, Amit P; Yan, Denise; Chapagain, Prem; Liu, Xue Zhong

2016-08-01

The P2X purinergic receptors are cation-selective channels gated by extracellular adenosine 5'-triphosphate (ATP). These purinergic receptors are found in virtually all mammalian cell types and facilitate a number of important physiological processes. Within the past few years, the characterization of crystal structures of the zebrafish P2X4 receptor in its closed and open states has provided critical insights into the mechanisms of ligand binding and channel activation. Understanding of this gating mechanism has facilitated to design and interpret new modeling and structure-function experiments to better elucidate how different agonists and antagonists can affect the receptor with differing levels of potency. This review summarizes the current knowledge on the structure, activation, allosteric modulators, function, and location of the different P2X receptors. Moreover, an emphasis on the P2X2 receptors has been placed in respect to its role in the auditory system. In particular, the discovery of three missense mutations in P2X2 receptors could become important areas of study in the field of gene therapy to treat progressive and noise-induced hearing loss. J. Cell. Physiol. 231: 1656-1670, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

How is quantum information localized in gravity?

NASA Astrophysics Data System (ADS)

Donnelly, William; Giddings, Steven B.

2017-10-01

A notion of localization of information within quantum subsystems plays a key role in describing the physics of quantum systems, and in particular is a prerequisite for discussing important concepts such as entanglement and information transfer. While subsystems can be readily defined for finite quantum systems and in local quantum field theory, a corresponding definition for gravitational systems is significantly complicated by the apparent nonlocality arising due to gauge invariance, enforced by the constraints. A related question is whether "soft hair" encodes otherwise localized information, and the question of such localization also remains an important puzzle for proposals that gravity emerges from another structure such as a boundary field theory as in AdS/CFT. This paper describes different approaches to defining local subsystem structure, and shows that at least classically, perturbative gravity has localized subsystems based on a split structure, generalizing the split property of quantum field theory. This, and related arguments for QED, give simple explanations that in these theories there is localized information that is independent of fields outside a region, in particular so that there is no role for "soft hair" in encoding such information. Additional subtleties appear in quantum gravity. We argue that localized information exists in perturbative quantum gravity in the presence of global symmetries, but that nonperturbative dynamics is likely tied to a modification of such structure.

Ultrafast and Wide Range Analysis of DNA Molecules Using Rigid Network Structure of Solid Nanowires

NASA Astrophysics Data System (ADS)

Rahong, Sakon; Yasui, Takao; Yanagida, Takeshi; Nagashima, Kazuki; Kanai, Masaki; Klamchuen, Annop; Meng, Gang; He, Yong; Zhuge, Fuwei; Kaji, Noritada; Kawai, Tomoji; Baba, Yoshinobu

2014-06-01

Analyzing sizes of DNA via electrophoresis using a gel has played an important role in the recent, rapid progress of biology and biotechnology. Although analyzing DNA over a wide range of sizes in a short time is desired, no existing electrophoresis methods have been able to fully satisfy these two requirements. Here we propose a novel method using a rigid 3D network structure composed of solid nanowires within a microchannel. This rigid network structure enables analysis of DNA under applied DC electric fields for a large DNA size range (100 bp-166 kbp) within 13 s, which are much wider and faster conditions than those of any existing methods. The network density is readily varied for the targeted DNA size range by tailoring the number of cycles of the nanowire growth only at the desired spatial position within the microchannel. The rigid dense 3D network structure with spatial density control plays an important role in determining the capability for analyzing DNA. Since the present method allows the spatial location and density of the nanostructure within the microchannels to be defined, this unique controllability offers a new strategy to develop an analytical method not only for DNA but also for other biological molecules.

Structure-based characterization of multiprotein complexes.

PubMed

Wiederstein, Markus; Gruber, Markus; Frank, Karl; Melo, Francisco; Sippl, Manfred J

2014-07-08

Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Modes of therapeutic action.

PubMed

Jones, E E

1997-12-01

The dialectic in psychoanalysis between theories about the mutative effects of interpretation and psychological knowledge and those concerning the effects of interpersonal interaction constitutes an important tension for approaches to psychoanalytic technique. This essay briefly summarises the thinking around these alternative conceptualisations of therapeutic action, and introduces a new empirically derived model, that of 'repetitive interaction structure', which attempts to bridge therapeutic action by insight and by relationship. Interaction structure is a way of formulating those aspects of the analytic process that have come to be termed intersubjectivity, transference-countertransference enactments and role responsiveness. The concept operationalises important aspects of interpersonal interaction, and can help specify the two-person patterns that emerge in an analysis. Patient and analyst interact in repetitive ways; these patterns of interaction, which are slow to change, probably reflect the psychological structure of both patient and analyst, whether psychic structure is conceptualised in terms of object-representations or compromise formations and impulse-defence configurations. Therapeutic action is located in the experience, recognition and understanding by patient and analyst of these repetitive interactions. Interaction structures stress the importance of the intrapsychic as a basis for what becomes manifest in the interactive field. Clinical illustrations from a psychoanalysis are provided, and research on repetitive interaction structures is described.

Introducing New Peer Worker Roles into Mental Health Services in England: Comparative Case Study Research Across a Range of Organisational Contexts.

PubMed

Gillard, Steve; Holley, Jess; Gibson, Sarah; Larsen, John; Lucock, Mike; Oborn, Eivor; Rinaldi, Miles; Stamou, Elina

2015-11-01

A wide variety of peer worker roles is being introduced into mental health services internationally. Empirical insight into whether conditions supporting role introduction are common across organisational contexts is lacking. A qualitative, comparative case study compared the introduction of peer workers employed in the statutory sector, voluntary sector and in organisational partnerships. We found good practice across contexts in structural issues including recruitment and training, but differences in expectations of the peer worker role in different organisational cultures. Issues of professionalism and practice boundaries were important everywhere but could be understood very differently, sometimes eroding the distinctiveness of the role.

A Simplified Representation of the Chemical Nature and Reactions of Soil Humus.

ERIC Educational Resources Information Center

Stevenson, F. J.; Olsen, R. A.

1989-01-01

Presented is a comprehensible structural representation of humic substances. A number of important roles of soil organic matter, including contribution to the cation-exchange capacity, binding of pesticides, and formation of complexes with micronutrient cations, are illustrated. (Author/CW)

The physics of pollinator attraction.

PubMed

Moyroud, Edwige; Glover, Beverley J

2017-10-01

Contents 350 I. 350 II. 350 III. 352 IV. 353 V. 353 353 References 354 SUMMARY: This Tansley Insight focuses on recent advances in our understanding of how flowers manipulate physical forces to attract animal pollinators and ensure reproductive success. Research has traditionally explored the role of chemical pigments and volatile organic compounds as cues for pollinators, but recent reports have demonstrated the importance of physical and structural means of pollinator attraction. Here we explore the role of petal microstructure in influencing floral light capture and optics, analysing colour, gloss and polarization effects. We discuss the interaction between flower, pollinator and gravity, and how petal surface structure can influence that interaction. Finally, we consider the role of electrostatic forces in pollen transfer and pollinator attraction. We conclude that this new interdisciplinary field is evolving rapidly. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Gaming-simulation and health education an overview.

PubMed

Greenblat, C S

1977-01-01

Simulation entails abstraction and representation from a larger system in terms of process as well as structure. Central features are identified and simplified, less important elements are omitted from the model. In medical and health education, simulation enables learners to practice in an environment where mistakes are not costly, such as with simulated patients. Gaming-simulation incorporates role-playing into a defined system of interaction simulating a real world system and is characterized by the degree of structure of the roles and the focus on role interactions. Employment of gaming-simulation is embryonic in health education. Examples included in this Monograph concern problems of aging, hemophiliacs, and the dying; teaching interpersonal skills in psychiatric nursing; interactions of health care systems with their communities; and several other topics. Evaluation is discussed in a separate paper. A variety of health care gaming resources are described.

Brain aromatase: roles in reproduction and neuroprotection.

PubMed

Roselli, Charles F

2007-01-01

It is well established that aromatization constitutes an essential part of testosterone's signaling pathway in brain and that estrogen metabolites, often together with testosterone, organize and activate masculine neural circuits. This paper summarizes the current understanding regarding the distribution, regulation and function of brain aromatase in mammals. Data from our laboratory are presented that highlight the important function of aromatase in the regulation of androgen feedback sensitivity in non-human primates and the possible role that aromatase plays in determining the brain structure and sexual partner preferences of rams. In addition, new data is presented indicating that the capacity for aromatization in cortical astrocytes is associated with cell survival and may be important for neuroprotection. It is anticipated that a better appreciation of the physiological and pathophysiological functions of aromatase will lead to important clinical insights.

Changes at the KinA PAS-A Dimerization Interface Influence Histidine Kinase Function

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

Lee, James; Tomchick, Diana R.; Brautigam, Chad A.

2008-11-12

The Bacillus subtilis KinA protein is a histidine protein kinase that controls the commitment of this organism to sporulate in response to nutrient deprivation and several other conditions. Prior studies indicated that the N-terminal Per-ARNT-Sim domain (PAS-A) plays a critical role in the catalytic activity of this enzyme, as demonstrated by the significant decrease of the autophosphorylation rate of a KinA protein lacking this domain. On the basis of the environmental sensing role played by PAS domains in a wide range of proteins, including other bacterial sensor kinases, it has been suggested that the PAS-A domain plays an important regulatorymore » role in KinA function. We have investigated this potential by using a combination of biophysical and biochemical methods to examine PAS-A structure and function, both in isolation and within the intact protein. Here, we present the X-ray crystal structure of the KinA PAS-A domain, showing that it crystallizes as a homodimer using {beta}-sheet/{beta}-sheet packing interactions as observed for several other PAS domain complexes. Notably, we observed two dimers with tertiary and quaternary structure differences in the crystalline lattice, indicating significant structural flexibility in these domains. To confirm that KinA PAS-A also forms dimers in solution, we used a combination of NMR spectroscopy, gel filtration chromatography, and analytical ultracentrifugation, the results of which are all consistent with the crystallographic results. We experimentally tested the importance of several residues at the dimer interface using site-directed mutagenesis, finding changes in the PAS-A domain that significantly alter KinA enzymatic activity in vitro and in vivo. These results support the importance of PAS domains within KinA and other histidine kinases and suggest possible routes for natural or artificial regulation of kinase activity.« less

Sabellaria spinulosa (Polychaeta, Annelida) reefs in the Mediterranean Sea: Habitat mapping, dynamics and associated fauna for conservation management

NASA Astrophysics Data System (ADS)

Gravina, Maria Flavia; Cardone, Frine; Bonifazi, Andrea; Bertrandino, Marta Simona; Chimienti, Giovanni; Longo, Caterina; Marzano, Carlotta Nonnis; Moretti, Massimo; Lisco, Stefania; Moretti, Vincenzo; Corriero, Giuseppe; Giangrande, Adriana

2018-01-01

Bio-constructions by Sabellaria worms play a key functional role in the coastal ecosystems being an engineer organism and for this reason are the object of protection. The most widespread reef building species along Atlantic and Mediterranean coasts is S. alveolata (L.), while the aggregations of S. spinulosa are typically limited to the North Sea coasts. This paper constitutes the first detailed description of unusual large S. spinulosa reefs in the Mediterranean Sea. Defining current health status and evaluating the most important threats and impacts is essential to address conservation needs and design management plans for these large biogenic structures. Present knowledge on Mediterranean reefs of S. alveolata is fragmentary compared to Northeast Atlantic reefs, and concerning S. spinulosa, this paper represents a focal point in the knowledge on Mediterranean reefs of this species. A one-year study on temporal changes in reef structure and associated fauna is reported. The annual cycle of S. spinulosa reef shows a spawning event in winter-early spring, a period of growth and tubes aggregation from spring-early summer to autumn and a degeneration phase in winter. The variations exhibited in density of the worm aggregation and the changes in the reef elevation highlight a decline and regeneration of the structure over a year. The many ecological roles of the S. spinulosa reef were mainly in providing a diversity of microhabitats hosting hard and sandy bottom species, sheltering rare species, and producing biogenic structures able to provide coastal protection. The Mediterranean S. spinulosa reef does not shelter a distinctive associated fauna; however the richness in species composition underscores the importance of the reef as a biodiversity hot-spot. Finally, the roles of the biogenic formations and their important biotic and physical dynamics support the adoption of strategies for conservation of Mediterranean S.spinulosa reefs, according to the aims of the Habitat Directive.

Divergence of Mammalian Higher Order Chromatin Structure Is Associated with Developmental Loci

PubMed Central

Chambers, Emily V.; Bickmore, Wendy A.; Semple, Colin A.

2013-01-01

Several recent studies have examined different aspects of mammalian higher order chromatin structure – replication timing, lamina association and Hi-C inter-locus interactions — and have suggested that most of these features of genome organisation are conserved over evolution. However, the extent of evolutionary divergence in higher order structure has not been rigorously measured across the mammalian genome, and until now little has been known about the characteristics of any divergent loci present. Here, we generate a dataset combining multiple measurements of chromatin structure and organisation over many embryonic cell types for both human and mouse that, for the first time, allows a comprehensive assessment of the extent of structural divergence between mammalian genomes. Comparison of orthologous regions confirms that all measurable facets of higher order structure are conserved between human and mouse, across the vast majority of the detectably orthologous genome. This broad similarity is observed in spite of many loci possessing cell type specific structures. However, we also identify hundreds of regions (from 100 Kb to 2.7 Mb in size) showing consistent evidence of divergence between these species, constituting at least 10% of the orthologous mammalian genome and encompassing many hundreds of human and mouse genes. These regions show unusual shifts in human GC content, are unevenly distributed across both genomes, and are enriched in human subtelomeric regions. Divergent regions are also relatively enriched for genes showing divergent expression patterns between human and mouse ES cells, implying these regions cause divergent regulation. Particular divergent loci are strikingly enriched in genes implicated in vertebrate development, suggesting important roles for structural divergence in the evolution of mammalian developmental programmes. These data suggest that, though relatively rare in the mammalian genome, divergence in higher order chromatin structure has played important roles during evolution. PMID:23592965

Parametric computational study of sheaths in multicomponent Ar/O2 plasma

NASA Astrophysics Data System (ADS)

Hromadka, J.; Ibehej, T.; Hrach, R.

2018-02-01

Our study is devoted to sheath structures emerging in Ar/O2 plasma. By means of two dimensional PIC/MCC computer model two configurations were investigated - sheath structure in the vicinity of a cylindrical Langmuir probe for two different biases and changes of the sheath structure when a cylindrical probe passes into a semi-planar probe. It was shown that O+ ions play important role in shielding out negative bias of a solid immersed in Ar/O2 plasma and edge effects of a semi-planar probe on its sheath structure were evaluated.

Treating hypertension while protecting the vulnerable islet in the cardiometabolic syndrome

PubMed Central

Hayden, Melvin R.; Sowers, James R.

2008-01-01

Hypertension, a multifactorial-polygenic disease, interacts with multiple environmental stressors and results in functional and structural changes in numerous end organs, including the cardiovascular system. This can result in coronary heart disease, stroke, peripheral vascular disease, congestive heart failure, end-stage renal disease, insulin resistance, and damage to the pancreatic islet. Hypertension is the most important modifiable risk factor for major health problems encountered in clinical practice. Whereas hypertension was once thought to be a medical condition based on discrete blood pressure readings, a new concept has emerged defining hypertension as part of a complex and progressive metabolic and cardiovascular disease, an important part of a cardiometabolic syndrome. The central role of insulin resistance, oxidative stress, endothelial dysfunction, metabolic signaling defects within tissues, and the role of enhanced tissue renin-angiotensin-aldosterone system activity as it relates to hypertension and type 2 diabetes mellitus is emphasized. Additionally, this review focuses on the effect of hypertension on functional and structural changes associated with the vulnerable pancreatic islet. Various classes of antihypertensive drugs are reviewed, especially their roles in delaying or preventing damage to the vulnerable pancreatic islet, and thus delaying the development of type 2 diabetes mellitus. PMID:20409906

nextPARS: parallel probing of RNA structures in Illumina

PubMed Central

Saus, Ester; Willis, Jesse R.; Pryszcz, Leszek P.; Hafez, Ahmed; Llorens, Carlos; Himmelbauer, Heinz

2018-01-01

RNA molecules play important roles in virtually every cellular process. These functions are often mediated through the adoption of specific structures that enable RNAs to interact with other molecules. Thus, determining the secondary structures of RNAs is central to understanding their function and evolution. In recent years several sequencing-based approaches have been developed that allow probing structural features of thousands of RNA molecules present in a sample. Here, we describe nextPARS, a novel Illumina-based implementation of in vitro parallel probing of RNA structures. Our approach achieves comparable accuracy to previous implementations, while enabling higher throughput and sample multiplexing. PMID:29358234

Significance of Nanoparticles and the Role of Amino Acids in Structuring Them-A Review.

PubMed

Kulandaisamy, Arockia Jayalatha; Rayappan, John Bosco Balaguru

2018-08-01

Nanoparticles has occupied an eminent place in our tech-facilitated society. The processes involved in synthesizing nanoparticles are important not only to find their applications, but also to make them eco-friendly. Attempts are being made to replace the use of harmful surfactants/reagents by amino acids, in the due course of nanoparticle synthesis. Especially in synthesizing the multifunctional metal and metal oxide nanoparticles the use of amino acids as surfactant/as catalyst, helps to obtain required size and shape. Amino acids have the inherent property in directing and assembling the superstructures. They have the tendency to act as a capping agent and their presence during the synthesis processes alters the synthesized particles' morphology. Review has been made to study the role of amino acids like histidine, lysine, arginine in structuring ZnO, FeO, Au and Ag nanoparticles. The change in their morphology that resulted due to the addition of amino acids has been compared. It is important to understand the role of amino acids in synthesizing the nanoparticles, and so it is more important to understand the internal energy variation of the same. To achieve this, the interaction between the bio (amino acids) and non-bio (metal and metal oxide) nanoparticles are to be discussed both experimentally and theoretically. At times the theoretical characterization, especially at low dimensions, help us to understand inter-particle interaction and intra-particle interaction by determining their chemical potential and Lennard-Jones potential. This review has been concluded with a model to characterize the precursor solution (amino acids and inorganic materials) by considering the Equation of State for liquids, which could also be extended to determine the structure factor of nanoparticles.

Processes governing the temperature structure of the tropical tropopause layer (Invited)

NASA Astrophysics Data System (ADS)

Birner, T.

2013-12-01

The tropical tropopause layer (TTL) is among the most important but least understood regions of the global climate system. The TTL sets the boundary condition for atmospheric tracers entering the stratosphere. Specifically, TTL temperatures control stratospheric water vapor concentrations, which play a key role in the radiative budget of the entire stratosphere with implications for tropospheric and surface climate. The TTL shows a curious stratification structure: temperature continues to decrease beyond the level of main convective outflow (~200 hPa) up to the cold point tropopause (~100 hPa), but TTL lapse rates are smaller than in the upper troposphere. A cold point tropopause well separated from the level of main convective outflow requires TTL cooling which may be the result of: 1) the detailed radiative balance in the TTL, 2) large-scale upwelling (forced by extratropical or tropical waves), 3) the large-scale hydrostatic response aloft deep convective heating, 4) overshooting convection, 5) breaking gravity waves. All of these processes may act in isolation or combine to produce the observed TTL temperature structure. Here, a critical discussion of these processes / mechanisms and their role in lifting the cold point tropopause above the level of main convective outflow is presented. Results are based on idealized radiative-convective equilibrium model simulations, contrasting single-column with cloud-resolving simulations, as well on simulations with chemistry-climate models and reanalysis data. While all of the above processes are capable of producing a TTL-like region in isolation, their combination is found to produce important feedbacks. In particular, both water vapor and ozone are found to have strong radiative effects on TTL temperatures, highlighting important feedbacks between transport circulations setting temperatures and tracer structures and the resulting tracer structures in turn affecting temperatures.

Packaging of Mason-Pfizer monkey virus (MPMV) genomic RNA depends upon conserved long-range interactions (LRIs) between U5 and gag sequences.

PubMed

Kalloush, Rawan M; Vivet-Boudou, Valérie; Ali, Lizna M; Mustafa, Farah; Marquet, Roland; Rizvi, Tahir A

2016-06-01

MPMV has great potential for development as a vector for gene therapy. In this respect, precisely defining the sequences and structural motifs that are important for dimerization and packaging of its genomic RNA (gRNA) are of utmost importance. A distinguishing feature of the MPMV gRNA packaging signal is two phylogenetically conserved long-range interactions (LRIs) between U5 and gag complementary sequences, LRI-I and LRI-II. To test their biological significance in the MPMV life cycle, we introduced mutations into these structural motifs and tested their effects on MPMV gRNA packaging and propagation. Furthermore, we probed the structure of key mutants using SHAPE (selective 2'hydroxyl acylation analyzed by primer extension). Disrupting base-pairing of the LRIs affected gRNA packaging and propagation, demonstrating their significance to the MPMV life cycle. A double mutant restoring a heterologous LRI-I was fully functional, whereas a similar LRI-II mutant failed to restore gRNA packaging and propagation. These results demonstrate that while LRI-I acts at the structural level, maintaining base-pairing is not sufficient for LRI-II function. In addition, in vitro RNA dimerization assays indicated that the loss of RNA packaging in LRI mutants could not be attributed to the defects in dimerization. Our findings suggest that U5-gag LRIs play an important architectural role in maintaining the structure of the 5' region of the MPMV gRNA, expanding the crucial role of LRIs to the nonlentiviral group of retroviruses. © 2016 Kalloush et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

The role of family members and close persons in health-care treatment of incompetent patients: a Portuguese approach.

PubMed

André, Pereira

2011-12-01

This article analyses the role of family members and other close persons in the health-care decisions of incompetent patients. It will scrutinize the right to visit a patient in hospital and the importance of the beloved ones in that vulnerable stage of life. It notices a change in society recognized by law in two dimensions: the increasing autonomy of the patient, while nominating the persons who may visit at the hospital or who may participate in the decisions or even appointing a health care proxy; secondly the important role of close persons and friends. This signifies a changing family structure, whereby affections may take supremacy over traditional institutions. There will also be a reference to PVS cases and decisions concerning the collection of organs. Finally the importance of an advance directive that may be binding through procedural control is affirmed. Finally, these themes show the autonomy of medical law in several domains: sources of law, methodology and scope.

Exploring ischemia-induced vascular lesions and potential pharmacological intervention strategies.

PubMed

Aliev, G; Obrenovich, M E; Seyidova, D; de la Torre, J C

2005-01-01

Structural changes in vessels under the influence of ischemia play an important role in the pathogenesis of many diseases, most important of which are stroke and myocardial infarction or myocardial insult. Over the years, information has been gathered, which implicate a role for ischemic vascular changes in the pathogenesis of crush-syndrome, atherosclerosis and other vascular diseases. When blood vessels are damaged they become unresponsive to a stimulus, which normally elicits vasodilatation and can lead to intraluminal thrombosis and ischemic events. The aim of this review is to explore the structural changes seen in vessels affected by ischemia reperfusion injury. With ischemia, the development of observable changes to vascular structure is multifactorial. One key factor is reperfusion ischemic injury. Moreover, the duration of the ischemic event is an important factor when determining both the prognosis and the type of morphological change that is observable in affected vessel walls. In this regard, the deleterious progression of blood flow impairment and its severity depends on the specific organ involved and the type of tissue affected. Further, there are regional differences within affected tissues and the degree of microvascular injury is well correlated with differences in the nature and severity of the ischemic event. Any method aimed at preventing and treating ischemic reperfusion injuries in vessels, based on these investigations, should likewise be able to decrease the early signs of brain, cerebrovascular and heart injury and preserve normal cellular architecture.

Climate effects and feedback structure determining weed population dynamics in a long-term experiment.

PubMed

Lima, Mauricio; Navarrete, Luis; González-Andujar, José Luis

2012-01-01

Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years) on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors). Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements.

Climate Effects and Feedback Structure Determining Weed Population Dynamics in a Long-Term Experiment

PubMed Central

Lima, Mauricio; Navarrete, Luis; González-Andujar, José Luis

2012-01-01

Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years) on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors). Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements. PMID:22272362

Development of ship structure health monitoring system based on IOT technology

NASA Astrophysics Data System (ADS)

Yang, Sujun; Shi, Lei; Chen, Demin; Dong, Yuqing; Hu, Zhenyi

2017-06-01

It is very important to monitor the ship structure, because ships are affected by all kinds of wind wave and current environment factor. At the same time, internet of things (IOT) technology plays more and more important role of in the development of industrial process. In the paper, real-time online monitoring of the ship can be realized by means of IOT technology. Ship stress, vibration and dynamic parameters are measured. Meanwhile, data is transmitted to remote monitoring system through intelligent data gateway. Timely remote support can be realized for dangerous stage of ship. Safe navigation of ships is guaranteed through application of the system.

Spatial Guilds in the Serengeti Food Web Revealed by a Bayesian Group Model

PubMed Central

Baskerville, Edward B.; Dobson, Andy P.; Bedford, Trevor; Allesina, Stefano; Anderson, T. Michael; Pascual, Mercedes

2011-01-01

Food webs, networks of feeding relationships in an ecosystem, provide fundamental insights into mechanisms that determine ecosystem stability and persistence. A standard approach in food-web analysis, and network analysis in general, has been to identify compartments, or modules, defined by many links within compartments and few links between them. This approach can identify large habitat boundaries in the network but may fail to identify other important structures. Empirical analyses of food webs have been further limited by low-resolution data for primary producers. In this paper, we present a Bayesian computational method for identifying group structure using a flexible definition that can describe both functional trophic roles and standard compartments. We apply this method to a newly compiled plant-mammal food web from the Serengeti ecosystem that includes high taxonomic resolution at the plant level, allowing a simultaneous examination of the signature of both habitat and trophic roles in network structure. We find that groups at the plant level reflect habitat structure, coupled at higher trophic levels by groups of herbivores, which are in turn coupled by carnivore groups. Thus the group structure of the Serengeti web represents a mixture of trophic guild structure and spatial pattern, in contrast to the standard compartments typically identified. The network topology supports recent ideas on spatial coupling and energy channels in ecosystems that have been proposed as important for persistence. Furthermore, our Bayesian approach provides a powerful, flexible framework for the study of network structure, and we believe it will prove instrumental in a variety of biological contexts. PMID:22219719

OAPEC: Organization of Arab Petroleum Exporting Countries

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

Maachou, A.

1983-01-01

The organization of Arab Petroleum Exporting Countries plays an important role in furthering the aims of the New International Economic Order. Here, Abdelkader Maachou outlines its structure and its part in furthering the aims of its member countries. The study focuses on the newly created judicial branch and on the economic activities of this important Arab organization. Its contribution to the general intellectual climate of the area is also discussed.

X-ray and Neutron Scattering Study of the Formation of Core–Shell-Type Polyoxometalates

DOE PAGES

Yin, Panchao; Wu, Bin; Mamontov, Eugene; ...

2016-02-05

A typical type of core-shell polyoxometalates can be obtained through the Keggin-type polyoxometalate-templated growth of a layer of spherical shell structure of {Mo 72Fe 30}. Small angle X-ray scattering is used to study the structural features and stability of the core-shell structures in aqueous solutions. Time-resolved small angle X-ray scattering is applied to monitor the synthetic reactions and a three-stage formation mechanism is proposed to describe the synthesis of the core-shell polyoxometalates based on the monitoring results. Quasi-elastic and inelastic neutron scattering are used to probe the dynamics of water molecules in the core-shell structures and two different types ofmore » water molecules, the confined and structured water, are observed. These water molecules play an important role in bridging core and shell structures and stabilizing the cluster structures. A typical type of core shell polyoxometalates can be obtained through the Keggin-type polyoxometalate-templated growth of a layer of spherical shell structure of {Mo 72Fe 30}. Small-angle X-ray scattering is used to study the structural features and stability of the core shell structures in aqueous solutions. Time-resolved small-angle X-ray scattering is applied to monitor the synthetic reactions, and a three-stage formation mechanism is proposed to describe the synthesis of the core shell polyoxometalates based on the monitoring results. New protocols have been developed by fitting the X-ray data with custom physical models, which provide more convincing, objective, and completed data interpretation. Quasi-elastic and inelastic neutron scattering are used to probe the dynamics of water molecules in the core shell structures, and two different types of water molecules, the confined and structured water, are observed. These water molecules play an important role in bridging core and shell structures and stabilizing the cluster structures.« less

Mathematical methods for protein science

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

Hart, W.; Istrail, S.; Atkins, J.

1997-12-31

Understanding the structure and function of proteins is a fundamental endeavor in molecular biology. Currently, over 100,000 protein sequences have been determined by experimental methods. The three dimensional structure of the protein determines its function, but there are currently less than 4,000 structures known to atomic resolution. Accordingly, techniques to predict protein structure from sequence have an important role in aiding the understanding of the Genome and the effects of mutations in genetic disease. The authors describe current efforts at Sandia to better understand the structure of proteins through rigorous mathematical analyses of simple lattice models. The efforts have focusedmore » on two aspects of protein science: mathematical structure prediction, and inverse protein folding.« less

Structural, electronic and photocatalytic properties of atomic defective BiI3 monolayers

NASA Astrophysics Data System (ADS)

Yan, Huang; Ziyu, Hu; Xu, Gong; Xiaohong, Shao

2018-01-01

The structural, electronic and photocatalytic properties of five vacancy-containing 2D BiI3 monolayers are investigated by the first-principle calculations. The electronic structures show that the five structures are stable and have comparable binding energies to that of the pristine BiI3 monolayer, and the defects can tune the band gaps. Optical spectra indicate that the five structures retain high absorption capacity for visible light. The spin-orbit coupling (SOC) effect is found to play an important role in the band edge of defective structures, and the VBi and VBi-I3 defective BiI3 monolayers can make absolute band edges straddle water redox potentials more easily.

Origin of heat-induced structural changes in dissolved organic matter.

PubMed

Drastík, Martin; Novák, František; Kučerík, Jiří

2013-01-01

Humic substances play an important role in many environmental processes such as sequestration and transport of hydrophobic compounds. The supramolecular character of humic substances imparts high flexibility of the aggregates associated with their variable reactivity under different conditions. In this study, heat-induced transitions and character of the hydration shell of sodium salts of humic and fulvic acids originating from various sources were investigated using ultrasonic velocimetry in the temperature interval from 5 to 90 °C. Results clearly showed differences in stability and characteristics of the hydrated states at concentrations above and below 1 g L(-1) with the exception of Pahokee peat fulvic acids. It has been concluded that predominantly the relaxation part of the adiabatic compressibility plays an important role below 1 g L(-1) in contrast to both relaxation and intrinsic parts of the compressibility being important at higher concentrations. Dilution brought several temperature induced transitions which were investigated with respect to composition of all investigated humic substances. Correlation analysis revealed that the transition around 17 °C is associated with disruption of H-interactions whereas the transition around 42 °C depends on the aromaticity. Comparison of cooling and heating records revealed hysteresis in the structural relaxation resembling the behavior of physically stabilized hydrogels. Results indicated a difference in the conformation and therefore reactivity of dissolved humic substances in the dependence on temperature and thermal history. It has been hypothesized that this may play an important role in the transport and sequestration of hydrophobic pollutants by dissolved organic matter. Copyright © 2012 Elsevier Ltd. All rights reserved.

Effects of landscape and patch-level attributes on regional population persistence

EPA Science Inventory

Habitat patch size and isolation are often described as the key habitat variables influencing population dynamics. Yet habitat quality may also play an important role in influencing the regional persistence of spatially structured populations as the value or density of resources ...

Building on Florida's strength in space : a plan for action

DOT National Transportation Integrated Search

1999-12-01

The report is structured as follows: : 1) Section II provides background information on the role of the space sector : in Florida. It is presented to help the reader understand: : 2) Why space is important to the current and future economy of Florida...

NATURE OF CUMULATIVE IMPACTS ON BIOTIC DIVERSITY OF WETLAND VERTEBRATES

EPA Science Inventory

There is no longer any doubt that cumulative impacts have important effects on wetland vertebrates. he interactions of species diversity and community structure produce a complex pattern in which environmental impacts can play a highly significant role. ariety of examples shows h...

RIPARIAN FOREST INDICATORS OF POTENTIAL FUTURE STREAM CONDITION

EPA Science Inventory

Large wood in streams can play an extraordinarily important role in influencing the physical structure of streams and in providing habitat for aquatic organisms. Since wood is continually lost from streams, predicting the future input of wood to streams from riparian forests is c...

Population dynamics of HIV-1 inferred from gene sequences.

PubMed Central

Grassly, N C; Harvey, P H; Holmes, E C

1999-01-01

A method for the estimation of population dynamic history from sequence data is described and used to investigate the past population dynamics of HIV-1 subtypes A and B. Using both gag and env gene alignments the effective population size of each subtype is estimated and found to be surprisingly small. This may be a result of the selective sweep of mutations through the population, or may indicate an important role of genetic drift in the fixation of mutations. The implications of these results for the spread of drug-resistant mutations and transmission dynamics, and also the roles of selection and recombination in shaping HIV-1 genetic diversity, are discussed. A larger estimated effective population size for subtype A may be the result of differences in time of origin, transmission dynamics, and/or population structure. To investigate the importance of population structure a model of population subdivision was fitted to each subtype, although the improvement in likelihood was found to be nonsignificant. PMID:9927440

Hydrogen bonds and heat diffusion in α-helices: a computational study.

PubMed

Miño, German; Barriga, Raul; Gutierrez, Gonzalo

2014-08-28

Recent evidence has shown a correlation between the heat diffusion pathways and the known allosteric communication pathways in proteins. Allosteric communication in proteins is a central, yet unsolved, problem in biochemistry, and the study and characterization of the structural determinants that mediate energy transfer among different parts of proteins is of major importance. In this work, we characterized the role of hydrogen bonds in diffusivity of thermal energy for two sets of α-helices with different abilities to form hydrogen bonds. These hydrogen bonds can be a constitutive part of the α-helices or can arise from the lateral chains. In our in vacuo simulations, it was observed that α-helices with a higher possibility of forming hydrogen bonds also had higher rates of thermalization. Our simulations also revealed that heat readily flowed through atoms involved in hydrogen bonds. As a general conclusion, according to our simulations, hydrogen bonds fulfilled an important role in heat diffusion in structural patters of proteins.

Lipid Cell Biology: A Focus on Lipids in Cell Division.

PubMed

Storck, Elisabeth M; Özbalci, Cagakan; Eggert, Ulrike S

2018-06-20

Cells depend on hugely diverse lipidomes for many functions. The actions and structural integrity of the plasma membrane and most organelles also critically depend on membranes and their lipid components. Despite the biological importance of lipids, our understanding of lipid engagement, especially the roles of lipid hydrophobic alkyl side chains, in key cellular processes is still developing. Emerging research has begun to dissect the importance of lipids in intricate events such as cell division. This review discusses how these structurally diverse biomolecules are spatially and temporally regulated during cell division, with a focus on cytokinesis. We analyze how lipids facilitate changes in cellular morphology during division and how they participate in key signaling events. We identify which cytokinesis proteins are associated with membranes, suggesting lipid interactions. More broadly, we highlight key unaddressed questions in lipid cell biology and techniques, including mass spectrometry, advanced imaging, and chemical biology, which will help us gain insights into the functional roles of lipids.

Implications of the giant planets for the formation and evolution of planetary systems

NASA Technical Reports Server (NTRS)

Stevenson, David J.

1989-01-01

The giant planet region in the solar system appears to be bounded inside by the limit of water condensation, suggesting that the most abundant astrophysical condensate plays an important role in giant planet formation. Indeed, Jupiter and Saturn exhibit evidence for rock and/or ice cores or central concentrations that probably accumulated first, acting as nuclei for subsequent gas accumulation. This is a 'planetary' accumulation process, distinct from the stellar formation process, even though most of Jupiter has a similar composition to the primordial sun. Uranus and Neptune appear to exhibit evidence of an important role for giant impacts in their structure and evolution. No simple picture emerges for the temperature structure of the solar nebula from observations alone. However, it seems likely that Jupiter is the key to the planetary system, and a similar planet could be expected for other systems. The data and inferences from these data are summarized for the entire known solar system beyond the asteroid belt.

Trends in Asset Structure between Not-for-Profit and Investor Owned Hospitals

PubMed Central

Song, Paula H.; Reiter, Kristin L.

2010-01-01

The delivery of health care is a capital intensive industry and thus hospital investment strategy continues to be an important area of interest for both health policy and research. Much attention has been given to hospitals’ capital investment policies with relatively little attention to investments in financial assets, which serve an important role in NFP hospitals. This study describes and analyzes trends in aggregate asset structure between NFP and IO hospitals during the post-capital based PPS implementation period, providing the first documentation of long-term trends in hospital investment. We find hospitals’ aggregate asset structure differs significantly based on ownership, size, and profitability. For both NFP and IO hospitals, financial securities have remained consistent over time, while fixed asset representation has declined in IO hospitals. PMID:20519429

LncRNA Structural Characteristics in Epigenetic Regulation

PubMed Central

Wang, Chenguang; Wang, Lianzong; Ding, Yu; Lu, Xiaoyan; Zhang, Guosi; Yang, Jiaxin; Zheng, Hewei; Wang, Hong; Jiang, Yongshuai; Xu, Liangde

2017-01-01

The rapid development of new generation sequencing technology has deepened the understanding of genomes and functional products. RNA-sequencing studies in mammals show that approximately 85% of the DNA sequences have RNA products, for which the length greater than 200 nucleotides (nt) is called long non-coding RNAs (lncRNA). LncRNAs now have been shown to play important epigenetic regulatory roles in key molecular processes, such as gene expression, genetic imprinting, histone modification, chromatin dynamics, and other activities by forming specific structures and interacting with all kinds of molecules. This paper mainly discusses the correlation between the structure and function of lncRNAs with the recent progress in epigenetic regulation, which is important to the understanding of the mechanism of lncRNAs in physiological and pathological processes. PMID:29292750

Association of Membrane Rafts and Postsynaptic Density: Proteomics, Biochemical, and Ultrastructural Analyses

PubMed Central

Suzuki, Tatsuo; Zhang, Jingping; Miyazawa, Shoko; Liu, Qian; Farzan, Michael R.; Yao, Wei-Dong

2011-01-01

Postsynaptic membrane rafts are believed to play important roles in synaptic signaling, plasticity, and maintenance. However, their molecular identities remain elusive. Further, how they interact with the well-established signaling specialization, the postsynaptic density (PSD), is poorly understood. We previously detected a number of conventional PSD proteins in detergent-resistant membranes (DRMs). Here, we have performed LC-MS/MS (liquid chromatography coupled with tandem mass spectrometry) analyses on postsynaptic membrane rafts and PSDs. Our comparative analysis identified an extensive overlap of protein components in the two structures. This overlapping could be explained, at least partly, by a physical association of the two structures. Meanwhile, a significant number of proteins displayed biased distributions to either rafts or PSDs, suggesting distinct roles for the two postsynaptic specializations. Using biochemical and electron microscopic methods, we directly detected membrane raft-PSD complexes. In vitro reconstitution experiments indicated that the formation of raft-PSD complexes was not due to the artificial reconstruction of once-solubilized membrane components and PSD structures, supporting that these complexes occurred in vivo. Taking together, our results provide evidence that postsynaptic membrane rafts and PSDs may be physically associated. Such association could be important in postsynaptic signal integration, synaptic function, and maintenance. PMID:21797867

Variation in structure of proteins by adjusting reactive oxygen and nitrogen species generated from dielectric barrier discharge jet

NASA Astrophysics Data System (ADS)

Park, Ji Hoon; Kim, Minsup; Shiratani, Masaharu; Cho, Art. E.; Choi, Eun Ha; Attri, Pankaj

2016-10-01

Over the last few years, the variation in liquid chemistry due to the development of radicals generated by cold atmospheric plasma (CAP) has played an important role in plasma medicine. CAP direct treatment or CAP activated media treatment in cancer cells shows promising anticancer activity for both in vivo and in vitro studies. However, the anticancer activity or antimicrobial activity varies between plasma devices due to the different abilities among plasma devices to generate the reactive oxygen and nitrogen species (RONS) at different ratios and in different concentrations. While the generation of RONS depends on many factors, the feeding gas plays the most important role among the factors. Hence, in this study we used different compositions of feeding gas while fixing all other plasma characteristics. We used Ar, Ar-O2 (at different ratios), and Ar-N2 (at different ratios) as the working gases for CAP and investigated the structural changes in proteins (Hemoglobin (Hb) and Myoglobin (Mb)). We then analyzed the influence of RONS generated in liquid on the conformations of proteins. Additionally, to determine the influence of H2O2 on the Hb and Mb structures, we used molecular dynamic simulation.

The role of leukotrienes in airway inflammation.

PubMed

Ogawa, Yoshiko; Calhoun, William J

2006-10-01

Cysteinyl leukotrienes (cysLTs) are a class of closely structurally related lipid molecules, originally described as slow-reacting substance of anaphylaxis, with a myriad of biologic functions. These activities include producing smooth muscle contraction and mucus secretion, recruiting allergic inflammatory cells, modulating cytokine production, influencing neural transmission, and altering structural changes in the airway. Administration of cysLTs to animals and human subjects reproduces many features of allergic inflammation and asthma. Leukotriene (LT) blockers have independent efficacy in asthma and improve pulmonary function when added to inhaled steroids. Conversely, blockade of this pathway both in animals and in human subjects results in important reductions in inflammation and its consequences and might reduce structural changes of remodeling. These data collectively make a compelling case for an important role of cysLTs in airway inflammation and asthma. However, the magnitude of effect of anti-LTs is smaller than that of corticosteroids, and there is more variability in benefit of LT blockade than is seen with inhaled steroids. In addition, adding anti-LTs to inhaled steroids in asthmatic patients does not appear to produce added anti-inflammatory benefit. Genetic polymorphisms and environmental factors, such as tobacco smoke exposure, might underlie some of the heterogeneity of response to LT blockers.

[The evoked activity of the lateral hypothalamus during extinction and differential inhibition].

PubMed

Vanetsian, G L

1995-01-01

Character of interaction between symmetric points of the cat's auditory cortex (A1) and the lateral hypothalamus (HL) was determined by calculating Spearman correlation coefficients between averaged summed sound-evoked activity (AEP) of the structures before, during elaboration, extinction and restoration, as well as differentiation of food-procuring conditioned reflex and in the eating full. Close mutual co-tuning between the cortex and hypothalamus characteristic for stable conditioned reflex was found to disrupted during its extinction, elaboration of differentiation and fullness eat inhibition due to entire reduction of hypothalamic AEP and disappearance of correlated with negativity of HL AEP "doubling" of the first positive wave of A1 AEP. Hyperactivity stage, expressed at the beginning of extinction and at the end of differentiation, preceded inactivation of hypothalamic afferents during elaboration of conditioned inhibition. The stage of hyperactivity, initiated by the elevated emotional state of the animal, testifies to an important role of emotional brain structures in the process of internal inhibition. The stage of HL and A1 hyperactivity initiated by emotional stress of the animal and following HL inactivation during inhibition of the conditioned response point to an important role of emotional subcortical brain structures in the mechanisms of inhibitory conditioning.

Delinquency Among Members of Hong Kong Youth Street Gangs: The Role of the Organizational Structures of Gangs and Triad Affiliations.

PubMed

Chui, Wing Hong; Khiatani, Paul Vinod

2018-07-01

This study explores the importance of organizational structures and formal affiliations with the Hong Kong triads to delinquency among youth street gang members in Hong Kong. More specifically, this study examines the relative importance of the number of organizational structures and triad affiliation to patterns of delinquency in a sample of active members of youth street gangs ( N = 201). With the aid of outreach social workers, a convenience sampling method was used to recruit a gender-balanced sample of at-risk youths. Logistic regression analysis of the survey data that was gathered indicated that formal affiliation to Hong Kong triads and the presence of organizational structures significantly increased the odds of delinquency (independently of each other). Suggestions for future research on gang membership and delinquency, with particular reference to the Asian context, are provided.

Models of S/π interactions in protein structures: Comparison of the H2S–benzene complex with PDB data

PubMed Central

Ringer, Ashley L.; Senenko, Anastasia; Sherrill, C. David

2007-01-01

S/π interactions are prevalent in biochemistry and play an important role in protein folding and stabilization. Geometries of cysteine/aromatic interactions found in crystal structures from the Brookhaven Protein Data Bank (PDB) are analyzed and compared with the equilibrium configurations predicted by high-level quantum mechanical results for the H2S–benzene complex. A correlation is observed between the energetically favorable configurations on the quantum mechanical potential energy surface of the H2S–benzene model and the cysteine/aromatic configurations most frequently found in crystal structures of the PDB. In contrast to some previous PDB analyses, configurations with the sulfur over the aromatic ring are found to be the most important. Our results suggest that accurate quantum computations on models of noncovalent interactions may be helpful in understanding the structures of proteins and other complex systems. PMID:17766371

Revisiting place and temporal theories of pitch

PubMed Central

2014-01-01

The nature of pitch and its neural coding have been studied for over a century. A popular debate has revolved around the question of whether pitch is coded via “place” cues in the cochlea, or via timing cues in the auditory nerve. In the most recent incarnation of this debate, the role of temporal fine structure has been emphasized in conveying important pitch and speech information, particularly because the lack of temporal fine structure coding in cochlear implants might explain some of the difficulties faced by cochlear implant users in perceiving music and pitch contours in speech. In addition, some studies have postulated that hearing-impaired listeners may have a specific deficit related to processing temporal fine structure. This article reviews some of the recent literature surrounding the debate, and argues that much of the recent evidence suggesting the importance of temporal fine structure processing can also be accounted for using spectral (place) or temporal-envelope cues. PMID:25364292

Optimal multi-community network modularity for information diffusion

NASA Astrophysics Data System (ADS)

Wu, Jiaocan; Du, Ruping; Zheng, Yingying; Liu, Dong

2016-02-01

Studies demonstrate that community structure plays an important role in information spreading recently. In this paper, we investigate the impact of multi-community structure on information diffusion with linear threshold model. We utilize extended GN network that contains four communities and analyze dynamic behaviors of information that spreads on it. And we discover the optimal multi-community network modularity for information diffusion based on the social reinforcement. Results show that, within the appropriate range, multi-community structure will facilitate information diffusion instead of hindering it, which accords with the results derived from two-community network.

[Possible effect of E-selectine on structure and function of arterial vessels in patients with metabolic syndrome].

PubMed

Voloshyna, O O; Lyzohub, V H; Romanenko, I M

2007-01-01

Endothelial dysfunction and endothelial cells activation as it was shown in patients with ischemic heart disease play important role in atherosclerosis progression and the development of cardiovascular events. Relationship between E-selectine and functional/ structural changes of the arterial vessels in patients with metabolic syndrome was not explored. We revealed that both activation of the endothelial cells and structural/functional changes of the arterial wall mostly depend on obesity and dislipedemia and in less extent on carbohydrates metabolism disorders.

Reforming Science: Structural Reforms

PubMed Central

2012-01-01

Science has a critical role to play in addressing humanity's most important challenges in the twenty-first century. However, the contemporary scientific enterprise has developed in ways that prevent it from reaching maximum effectiveness and detract from the appeal of a research career. To be effective, the methodological and culture reforms discussed in the accompanying essay must be accompanied by fundamental structural reforms that include a renewed vigorous societal investment in science and scientists. PMID:22184420

Multiscale Space-Time Computational Methods for Fluid-Structure Interactions

DTIC Science & Technology

2015-09-13

prescribed fully or partially, is from an actual locust, extracted from high-speed, multi-camera video recordings of the locust in a wind tunnel . We use...With creative methods for coupling the fluid and structure, we can increase the scope and efficiency of the FSI modeling . Multiscale methods, which now...play an important role in computational mathematics, can also increase the accuracy and efficiency of the computer modeling techniques. The main

On the Role of Interchange Reconnection in the Generation of the Slow Solar Wind

NASA Astrophysics Data System (ADS)

Edmondson, J. K.

2012-11-01

The heating of the solar corona and therefore the generation of the solar wind, remain an active area of solar and heliophysics research. Several decades of in situ solar wind plasma observations have revealed a rich bimodal solar wind structure, well correlated with coronal magnetic field activity. Therefore, the reconnection processes associated with the large-scale dynamics of the corona likely play a major role in the generation of the slow solar wind flow regime. In order to elucidate the relationship between reconnection-driven coronal magnetic field structure and dynamics and the generation of the slow solar wind, this paper reviews the observations and phenomenology of the solar wind and coronal magnetic field structure. The geometry and topology of nested flux systems, and the (interchange) reconnection process, in the context of coronal physics is then explained. Once these foundations are laid out, the paper summarizes several fully dynamic, 3D MHD calculations of the global coronal system. Finally, the results of these calculations justify a number of important implications and conclusions on the role of reconnection in the structural dynamics of the coronal magnetic field and the generation of the solar wind.

Inhibition of projections from the basolateral amygdala to the entorhinal cortex disrupts the acquisition of contextual fear

PubMed Central

Sparta, Dennis R.; Smithuis, Jim; Stamatakis, Alice M.; Jennings, Joshua H.; Kantak, Pranish A.; Ung, Randall L.; Stuber, Garret D.

2014-01-01

The development of excessive fear and/or stress responses to environmental cues such as contexts associated with a traumatic event is a hallmark of post-traumatic stress disorder (PTSD). The basolateral amygdala (BLA) has been implicated as a key structure mediating contextual fear conditioning. In addition, the hippocampus has an integral role in the encoding and processing of contexts associated with strong, salient stimuli such as fear. Given that both the BLA and hippocampus play an important role in the regulation of contextual fear conditioning, examining the functional connectivity between these two structures may elucidate a role for this pathway in the development of PTSD. Here, we used optogenetic strategies to demonstrate that the BLA sends a strong glutamatergic projection to the hippocampal formation through the entorhinal cortex (EC). Next, we photoinhibited glutamatergic fibers from the BLA terminating in the EC during the acquisition or expression of contextual fear conditioning. In mice that received optical inhibition of the BLA-to-EC pathway during the acquisition session, we observed a significant decrease in freezing behavior in a context re-exposure session. In contrast, we observed no differences in freezing behavior in mice that were only photoinhibited during the context re-exposure session. These data demonstrate an important role for the BLA-to-EC glutamatergic pathway in the acquisition of contextual fear conditioning. PMID:24834031

Nanoscale Insight and Control of Structural and Electronic Properties of Organic Semiconductor / Metal Interfaces

NASA Astrophysics Data System (ADS)

Maughan, Bret

Organic semiconductor interfaces are promising materials for use in next-generation electronic and optoelectronic devices. Current models for metal-organic interfacial electronic structure and dynamics are inadequate for strongly hybridized systems. This work aims to address this issue by identifying the factors most important for understanding chemisorbed interfaces with an eye towards tuning the interfacial properties. Here, I present the results of my research on chemisorbed interfaces formed between thin-films of phthalocyanine molecules grown on monocrystalline Cu(110). Using atomically-resolved nanoscale imaging in combination with surface-sensitive photoemission techniques, I show that single-molecule level interactions control the structural and electronic properties of the interface. I then demonstrate that surface modifications aimed at controlling interfacial interactions are an effective way to tailor the physical and electronic structure of the interface. This dissertation details a systematic investigation of the effect of molecular and surface functionalization on interfacial interactions. To understand the role of molecular structure, two types of phthalocyanine (Pc) molecules are studied: non-planar, dipolar molecules (TiOPc), and planar, non-polar molecules (H2Pc and CuPc). Multiple adsorption configurations for TiOPc lead to configuration-dependent self-assembly, Kondo screening, and electronic energy-level alignment. To understand the role of surface structure, the Cu(110) surface is textured and passivated by oxygen chemisorption prior to molecular deposition, which gives control over thin-film growth and interfacial electronic structure in H2Pc and CuPc films. Overall, the work presented here demonstrates a method for understanding interfacial electronic structure of strongly hybridized interfaces, an important first step towards developing more robust models for metal-organic interfaces, and reliable, predictive tuning of interfacial properties.

The perspective of medical students regarding the roles and characteristics of a clinical role model

PubMed Central

Bahmanbijari, Bahareh; Beigzadeh, Amin; Etminan, Abbas; Najarkolai, Atena Rahmati; Khodaei, Marzieh; Askari, Seyed Mostafa Seyed

2017-01-01

Background As medical students spend most of their time with their clinical teachers and imitate their roles and characteristics during the school year, it is important to identify the roles and characteristics that they find essential in their role models. These traits play a part in their future professions as doctors. Objective The aim of this study was to determine the perspective of students, interns, and residents regarding the roles and characteristics of a clinical role model. Methods In an analytical cross-sectional study, a structured and self-developed questionnaire was completed by 185 medical students at educational hospitals of Kerman University of Medical Sciences during April and May 2015. Participants were selected using convenience sampling method. For data analysis, we used descriptive and inferential statistics. SPSS software version 16 was used as needed. Results In total, 90 medical students (48.7%), 65 interns (35.1%), and 30 residents (16.2%) participated in this study. Male respondents (n=75) comprised 40.5% and female respondents (n=110) 59.5% of the study sample. The three most important roles of a clinical teacher were organizer role (99.7), teacher role (101.7), and supporter role (109.5) for students, interns, and residents respectively. On the other hand, supporter role (85.4), communicator role (86.4) and organizer role (83.4) were ranked as the least important for students, interns, and residents respectively. There was no significant association among the three batches and the roles of a clinical teacher (p>0.05). Conversely, Females rated the roles of a clinical teacher significantly higher than males (p<0.05). Conclusions As teachers are frequently perceived by students as role models in medical schools, great attention should be given to their roles. Teachers must be aware that their roles have an impact on students’ professional development and performance. PMID:28607645

Algorithm to find distant repeats in a single protein sequence

PubMed Central

Banerjee, Nirjhar; Sarani, Rangarajan; Ranjani, Chellamuthu Vasuki; Sowmiya, Govindaraj; Michael, Daliah; Balakrishnan, Narayanasamy; Sekar, Kanagaraj

2008-01-01

Distant repeats in protein sequence play an important role in various aspects of protein analysis. A keen analysis of the distant repeats would enable to establish a firm relation of the repeats with respect to their function and three-dimensional structure during the evolutionary process. Further, it enlightens the diversity of duplication during the evolution. To this end, an algorithm has been developed to find all distant repeats in a protein sequence. The scores from Point Accepted Mutation (PAM) matrix has been deployed for the identification of amino acid substitutions while detecting the distant repeats. Due to the biological importance of distant repeats, the proposed algorithm will be of importance to structural biologists, molecular biologists, biochemists and researchers involved in phylogenetic and evolutionary studies. PMID:19052663

Chromatin Dynamics in Genome Stability: Roles in Suppressing Endogenous DNA Damage and Facilitating DNA Repair

PubMed Central

Nair, Nidhi; Shoaib, Muhammad

2017-01-01

Genomic DNA is compacted into chromatin through packaging with histone and non-histone proteins. Importantly, DNA accessibility is dynamically regulated to ensure genome stability. This is exemplified in the response to DNA damage where chromatin relaxation near genomic lesions serves to promote access of relevant enzymes to specific DNA regions for signaling and repair. Furthermore, recent data highlight genome maintenance roles of chromatin through the regulation of endogenous DNA-templated processes including transcription and replication. Here, we review research that shows the importance of chromatin structure regulation in maintaining genome integrity by multiple mechanisms including facilitating DNA repair and directly suppressing endogenous DNA damage. PMID:28698521

Carotenoids, versatile components of oxygenic photosynthesis.

PubMed

Domonkos, Ildikó; Kis, Mihály; Gombos, Zoltán; Ughy, Bettina

2013-10-01

Carotenoids (CARs) are a group of pigments that perform several important physiological functions in all kingdoms of living organisms. CARs serve as protective agents, which are essential structural components of photosynthetic complexes and membranes, and they play an important role in the light harvesting mechanism of photosynthesizing plants and cyanobacteria. The protection against reactive oxygen species, realized by quenching of singlet oxygen and the excited states of photosensitizing molecules, as well as by the scavenging of free radicals, is one of the main biological functions of CARs. X-ray crystallographic localization of CARs revealed that they are present at functionally and structurally important sites of both the PSI and PSII reaction centers. Characterization of a CAR-less cyanobacterial mutant revealed that while the absence of CARs prevents the formation of PSII complexes, it does not abolish the assembly and function of PSI. CAR molecules assist in the formation of protein subunits of the photosynthetic complexes by gluing together their protein components. In addition to their aforementioned indispensable functions, CARs have a substantial role in the formation and maintenance of proper cellular architecture, and potentially also in the protection of the translational machinery under stress conditions. Copyright © 2013 Elsevier Ltd. All rights reserved.

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

PubMed Central

Zhou, Jizhong; Deng, Ye; Zhang, Ping; Xue, Kai; Liang, Yuting; Van Nostrand, Joy D.; Yang, Yunfeng; He, Zhili; Wu, Liyou; Stahl, David A.; Hazen, Terry C.; Tiedje, James M.; Arkin, Adam P.

2014-01-01

Unraveling the drivers of community structure and succession in response to environmental change is a central goal in ecology. Although the mechanisms shaping community structure have been intensively examined, those controlling ecological succession remain elusive. To understand the relative importance of stochastic and deterministic processes in mediating microbial community succession, a unique framework composed of four different cases was developed for fluidic and nonfluidic ecosystems. The framework was then tested for one fluidic ecosystem: a groundwater system perturbed by adding emulsified vegetable oil (EVO) for uranium immobilization. Our results revealed that groundwater microbial community diverged substantially away from the initial community after EVO amendment and eventually converged to a new community state, which was closely clustered with its initial state. However, their composition and structure were significantly different from each other. Null model analysis indicated that both deterministic and stochastic processes played important roles in controlling the assembly and succession of the groundwater microbial community, but their relative importance was time dependent. Additionally, consistent with the proposed conceptual framework but contradictory to conventional wisdom, the community succession responding to EVO amendment was primarily controlled by stochastic rather than deterministic processes. During the middle phase of the succession, the roles of stochastic processes in controlling community composition increased substantially, ranging from 81.3% to 92.0%. Finally, there are limited successional studies available to support different cases in the conceptual framework, but further well-replicated explicit time-series experiments are needed to understand the relative importance of deterministic and stochastic processes in controlling community succession. PMID:24550501

Structure prediction of the second extracellular loop in G-protein-coupled receptors.

PubMed

Kmiecik, Sebastian; Jamroz, Michal; Kolinski, Michal

2014-06-03

G-protein-coupled receptors (GPCRs) play key roles in living organisms. Therefore, it is important to determine their functional structures. The second extracellular loop (ECL2) is a functionally important region of GPCRs, which poses significant challenge for computational structure prediction methods. In this work, we evaluated CABS, a well-established protein modeling tool for predicting ECL2 structure in 13 GPCRs. The ECL2s (with between 13 and 34 residues) are predicted in an environment of other extracellular loops being fully flexible and the transmembrane domain fixed in its x-ray conformation. The modeling procedure used theoretical predictions of ECL2 secondary structure and experimental constraints on disulfide bridges. Our approach yielded ensembles of low-energy conformers and the most populated conformers that contained models close to the available x-ray structures. The level of similarity between the predicted models and x-ray structures is comparable to that of other state-of-the-art computational methods. Our results extend other studies by including newly crystallized GPCRs. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Effect of gravity on the stability and structure of lean hydrogen-air flames

NASA Technical Reports Server (NTRS)

Patnaik, G.; Kailasanath, K.

1991-01-01

Detailed, time-dependent, 2D numerical simulations with full hydrogen-oxygen chemistry are used to investigate the effects of gravity on the stability and structure of laminar flames in lean, premixed hydrogen-air mixtures. The calculations show that the effects of gravity becomes more important as the lean flammability limit is approached. In a 12 percent hydrogen-air mixture, gravity plays only a secondary role in determining the multidimensional structure of the flame with the stability and structure of the flame controlled primarily by the thermo-diffusive instability mechanism. However, in leaner hydrogen-air mixtures gravity becomes more important. Upward-propagating flames are highly curved and evolve into a bubble rising upwards in the tube. Downward-propagating flames are flat or even oscillate between structures with concave and convex curvatures. The zero-gravity flame shows only cellular structures. Cellular structures which are present in zero gravity can be suppressed by the effect of buoyancy for mixtures leaner than 11 percent hydrogen. These observations are explained on the basis of an interaction between the processes leading to buoyancy-induced Rayleigh-Taylor instability and the thermo-diffusive instability.

Structural analysis of the intracellular domain of (pro)renin receptor fused to maltose-binding protein

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

Zhang, Yanfeng; Gao, Xiaoli; Michael Garavito, R., E-mail: garavito@msu.edu

2011-04-22

Highlights: {yields} Crystal structure of the intracellular domain of (pro)renin receptor (PRR-IC) as MBP fusion protein at 2.0 A (maltose-free) and 2.15 A (maltose-bound). {yields} MBP fusion protein is a dimer in crystals in the presence and absence of maltose. {yields} PRR-IC domain is responsible for the dimerization of the fusion protein. {yields} Residues in the PRR-IC domain, particularly two tyrosines, dominate the intermolecular interactions, suggesting a role for the PRR-IC domain in PRR dimerization. -- Abstract: The (pro)renin receptor (PRR) is an important component of the renin-angiotensin system (RAS), which regulates blood pressure and cardiovascular function. The integral membranemore » protein PRR contains a large extracellular domain ({approx}310 amino acids), a single transmembrane domain ({approx}20 amino acids) and an intracellular domain ({approx}19 amino acids). Although short, the intracellular (IC) domain of the PRR has functionally important roles in a number of signal transduction pathways activated by (pro)renin binding. Meanwhile, together with the transmembrane domain and a small portion of the extracellular domain ({approx}30 amino acids), the IC domain is also involved in assembly of V{sub 0} portion of the vacuolar proton-translocating ATPase (V-ATPase). To better understand structural and multifunctional roles of the PRR-IC, we report the crystal structure of the PRR-IC domain as maltose-binding protein (MBP) fusion proteins at 2.0 A (maltose-free) and 2.15 A (maltose-bound). In the two separate crystal forms having significantly different unit-cell dimensions and molecular packing, MBP-PRR-IC fusion protein was found to be a dimer, which is different with the natural monomer of native MBP. The PRR-IC domain appears as a relatively flexible loop and is responsible for the dimerization of MBP fusion protein. Residues in the PRR-IC domain, particularly two tyrosines, dominate the intermonomer interactions, suggesting a role for the PRR-IC domain in protein oligomerization.« less

Assessing the Role of Spirituality in Coping Among African Americans Diagnosed with Cancer

PubMed Central

Schulz, Emily; Caplan, Lee; Blake, Victor; Southward, Vivian L.; Buckner, Ayanna V.

2013-01-01

Spirituality plays an important role in cancer coping among African Americans. The purpose of this study was to report on the initial psychometric properties of instruments specific to the cancer context, assessing the role of spirituality in coping. Items were developed based on a theoretical model of spirituality and qualitative patient interviews. The instruments reflected connections to self, others, God, and the world. One hundred African American cancer survivors completed the instruments by telephone. The instruments showed adequate internal reliability, mixed convergent validity, discriminant validity, and interpretable factor structures. PMID:21246282

The role of the amygdala in the pathophysiology of panic disorder: evidence from neuroimaging studies

PubMed Central

2012-01-01

Although the neurobiological mechanisms underlying panic disorder (PD) are not yet clearly understood, increasing amount of evidence from animal and human studies suggests that the amygdala, which plays a pivotal role in neural network of fear and anxiety, has an important role in the pathogenesis of PD. This article aims to (1) review the findings of structural, chemical, and functional neuroimaging studies on PD, (2) relate the amygdala to panic attacks and PD development, (3) discuss the possible causes of amygdalar abnormalities in PD, (4) and suggest directions for future research. PMID:23168129

Non-encapsidation Activities of the Capsid Proteins of Positive-strand RNA Viruses

PubMed Central

Ni, Peng; Kao, C. Cheng

2013-01-01

Viral capsid proteins (CPs) are characterized by their role in forming protective shells around viral genomes. However, CPs have additional and important roles in the virus infection cycles and in the cellular response to infection. These activities involve CP binding to RNAs in both sequence-specific and nonspecific manners as well as association with other proteins. This review focuses on CPs of both plant and animal-infecting viruses with positive-strand RNA genomes. We summarize the structural features of CPs and describe their modulatory roles in viral translation, RNA-dependent RNA synthesis, and host defense responses. PMID:24074574

Hippocampal Structure Predicts Statistical Learning and Associative Inference Abilities during Development.

PubMed

Schlichting, Margaret L; Guarino, Katharine F; Schapiro, Anna C; Turk-Browne, Nicholas B; Preston, Alison R

2017-01-01

Despite the importance of learning and remembering across the lifespan, little is known about how the episodic memory system develops to support the extraction of associative structure from the environment. Here, we relate individual differences in volumes along the hippocampal long axis to performance on statistical learning and associative inference tasks-both of which require encoding associations that span multiple episodes-in a developmental sample ranging from ages 6 to 30 years. Relating age to volume, we found dissociable patterns across the hippocampal long axis, with opposite nonlinear volume changes in the head and body. These structural differences were paralleled by performance gains across the age range on both tasks, suggesting improvements in the cross-episode binding ability from childhood to adulthood. Controlling for age, we also found that smaller hippocampal heads were associated with superior behavioral performance on both tasks, consistent with this region's hypothesized role in forming generalized codes spanning events. Collectively, these results highlight the importance of examining hippocampal development as a function of position along the hippocampal axis and suggest that the hippocampal head is particularly important in encoding associative structure across development.

The role of inheritance in structuring hyperextended rift systems

NASA Astrophysics Data System (ADS)

Manatschal, Gianreto; Lavier, Luc; Chenin, Pauline

2015-04-01

A long-standing question in Earth Sciences is related to the importance of inheritance in controlling tectonic processes. In contrast to physical processes that are generally applicable, assessing the role of inheritance suffers from two major problems: firstly, it is difficult to appraise without having insights into the history of a geological system; and secondly all inherited features are not reactivated during subsequent deformation phases. Therefore, the aim of our presentation is to give some conceptual framework about how inheritance may control the architecture and evolution of hyperextended rift systems. We use the term inheritance to refer to the difference between an "ideal" layer-cake type lithosphere and a "real" lithosphere containing heterogeneities and we define 3 types of inheritance, namely structural, compositional and thermal inheritance. Moreover, we assume that the evolution of hyperextended rift systems reflects the interplay between their inheritance (innate/"genetic code") and the physical processes at play (acquired/external factors). Thus, by observing the architecture and evolution of hyperextended rift systems and integrating the physical processes, one my get hints on what may have been the original inheritance of a system. Using this approach, we focus on 3 well-studied rift systems that are the Alpine Tethys, Pyrenean-Bay of Biscay and Iberia-Newfoundland rift systems. For the studied examples we can show that: 1) strain localization on a local scale and during early stages of rifting is controlled by inherited structures and weaknesses 2) the architecture of the necking zone seems to be influenced by the distribution and importance of ductile layers during decoupled deformation and is consequently controlled by the thermal structure and/or the inherited composition of the curst 3) the location of breakup in the 3 examples is not significantly controlled by the inherited structures 4) inherited mantle composition and rift-related mantle processes may control the rheology of the mantle, the magmatic budget, the thermal structure and the localization of final rifting Conversely, the deformation in hyperextended domains is strongly controlled by weak hydrated minerals (e.g. clay, serpentinite) that result form the breakdown of feldspar and olivine due to fluid and reaction assisted deformation and is consequently not inherited but the result of rift induced processes. These key observations show that both inheritance and rift-induced processes play a significant role in the development of magma-poor rift systems and that the role of inheritance may change as the physical conditions vary during the evolving rifting and as rift-induced processes (serpentinization; magma) become more important. Thus, it is not only important to determine the "genetic code" of a rift system, but also to understand how it interacts and evolves during rifting. Understand how far these new ideas and concepts derived from the southern North Atlantic and Alpine Tethys can be translated to other less explored hyperextended rift systems will be one of the challenges of the future research in rifted margins.

Applying Psychology in Outer Space: Unfulfilled Promises Revisited.

ERIC Educational Resources Information Center

Helmreich, Robert L.

1983-01-01

Argues that research in personality and social psychology has an important role in the nation's spage program. Holds that psychologists' indifference and the structure of the National Aeronautics and Space Administration have led to underutilization of psychological data in space exploration. Presents suggestions for increasing psychology's role…

MORE THAN JUST BAIT: BURROWING SHRIMP AS ECOSYSTEM ENGINEERS IN OREGON ESTUARIES - SEPTEMBER 2006

EPA Science Inventory

Burrowing shrimp may be most widely known as excellent fishing bait, but they also play important roles in estuaries of the Pacific Northwest. These shrimps strongly affect carbon and nutrient cycling, phytoplankton abundance, food web structure and dynamics, sediment stability,...

A Chemist’s Perspective on the Role of Phosphorus at the Origins of Life

PubMed Central

Fernández-García, Christian; Coggins, Adam J.

2017-01-01

The central role that phosphates play in biological systems, suggests they also played an important role in the emergence of life on Earth. In recent years, numerous important advances have been made towards understanding the influence that phosphates may have had on prebiotic chemistry, and here, we highlight two important aspects of prebiotic phosphate chemistry. Firstly, we discuss prebiotic phosphorylation reactions; we specifically contrast aqueous electrophilic phosphorylation, and aqueous nucleophilic phosphorylation strategies, with dry-state phosphorylations that are mediated by dissociative phosphoryl-transfer. Secondly, we discuss the non-structural roles that phosphates can play in prebiotic chemistry. Here, we focus on the mechanisms by which phosphate has guided prebiotic reactivity through catalysis or buffering effects, to facilitating selective transformations in neutral water. Several prebiotic routes towards the synthesis of nucleotides, amino acids, and core metabolites, that have been facilitated or controlled by phosphate acting as a general acid–base catalyst, pH buffer, or a chemical buffer, are outlined. These facile and subtle mechanisms for incorporation and exploitation of phosphates to orchestrate selective, robust prebiotic chemistry, coupled with the central and universally conserved roles of phosphates in biochemistry, provide an increasingly clear message that understanding phosphate chemistry will be a key element in elucidating the origins of life on Earth. PMID:28703763

Role of Protein Flexibility in Ion Permeation: A Case Study in Gramicidin A

PubMed Central

Baştuğ, Turgut; Gray-Weale, Angus; Patra, Swarna M.; Kuyucak, Serdar

2006-01-01

Proteins have a flexible structure, and their atoms exhibit considerable fluctuations under normal operating conditions. However, apart from some enzyme reactions involving ligand binding, our understanding of the role of flexibility in protein function remains mostly incomplete. Here we investigate this question in the realm of membrane proteins that form ion channels. Specifically, we consider ion permeation in the gramicidin A channel, and study how the energetics of ion conduction changes as the channel structure is progressively changed from completely flexible to a fixed one. For each channel structure, the potential of mean force for a permeating potassium ion is determined from molecular dynamics (MD) simulations. Using the same molecular dynamics data for completely flexible gramicidin A, we also calculate the average densities and fluctuations of the peptide atoms and investigate the correlations between these fluctuations and the motion of a permeating ion. Our results show conclusively that peptide flexibility plays an important role in ion permeation in the gramicidin A channel, thus providing another reason—besides the well-known problem with the description of single file pore water—why this channel cannot be modeled using continuum electrostatics with a fixed structure. The new method developed here for studying the role of protein flexibility on its function clarifies the contributions of the fluctuations to energy and entropy, and places limits on the level of detail required in a coarse-grained model. PMID:16415054

Genetic diversity and population structure of bocachico Prochilodus magdalenae (Pisces, Prochilodontidae) in the Magdalena River basin and its tributaries, Colombia

PubMed Central

Berdugo, Gilberto Orozco; Narváez Barandica, Juan C.

2014-01-01

Prochilodus magdalenae is an endemic freshwater fish that occurs in the Magdalena, Sinú and Atrato hydrographic basins. It has an important economic role and is a food resource for the artisanal fishing communities. Its socioeconomic importance contrasts with the current status of its fisheries, where stocks are being depleted. Considering its importance and lack of information on its genetic structure, we used seven microsatellite markers to assess the genetic structure of wild populations of P. magdalenae. The genetic diversity was assessed and the population genetic structure was estimated through Fst, analysis of molecular variance and Bayesian analysis. A total of 290 alleles were found in all loci throughout all population. The high polymorphism contrasts with the levels of observed heterozygosity (Ho = 0.276), which are the lowest values recorded for the family. We found three populations of bocachico coexisting throughout the studied system, contradicting the hypothesis that freshwater migratory fish form panmictic populations. These results on the genetic structure of P. magdalenae constitute tools for a better understanding of the behavior and biology of this species, contributing to fish management and conservation programs. PMID:24688289

Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling.

PubMed

Jo, Sunhwan; Lee, Hui Sun; Skolnick, Jeffrey; Im, Wonpil

2013-01-01

Understanding glycan structure and dynamics is central to understanding protein-carbohydrate recognition and its role in protein-protein interactions. Given the difficulties in obtaining the glycan's crystal structure in glycoconjugates due to its flexibility and heterogeneity, computational modeling could play an important role in providing glycosylated protein structure models. To address if glycan structures available in the PDB can be used as templates or fragments for glycan modeling, we present a survey of the N-glycan structures of 35 different sequences in the PDB. Our statistical analysis shows that the N-glycan structures found on homologous glycoproteins are significantly conserved compared to the random background, suggesting that N-glycan chains can be confidently modeled with template glycan structures whose parent glycoproteins share sequence similarity. On the other hand, N-glycan structures found on non-homologous glycoproteins do not show significant global structural similarity. Nonetheless, the internal substructures of these N-glycans, particularly, the substructures that are closer to the protein, show significantly similar structures, suggesting that such substructures can be used as fragments in glycan modeling. Increased interactions with protein might be responsible for the restricted conformational space of N-glycan chains. Our results suggest that structure prediction/modeling of N-glycans of glycoconjugates using structure database could be effective and different modeling approaches would be needed depending on the availability of template structures.

Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling

PubMed Central

Jo, Sunhwan; Lee, Hui Sun; Skolnick, Jeffrey; Im, Wonpil

2013-01-01

Understanding glycan structure and dynamics is central to understanding protein-carbohydrate recognition and its role in protein-protein interactions. Given the difficulties in obtaining the glycan's crystal structure in glycoconjugates due to its flexibility and heterogeneity, computational modeling could play an important role in providing glycosylated protein structure models. To address if glycan structures available in the PDB can be used as templates or fragments for glycan modeling, we present a survey of the N-glycan structures of 35 different sequences in the PDB. Our statistical analysis shows that the N-glycan structures found on homologous glycoproteins are significantly conserved compared to the random background, suggesting that N-glycan chains can be confidently modeled with template glycan structures whose parent glycoproteins share sequence similarity. On the other hand, N-glycan structures found on non-homologous glycoproteins do not show significant global structural similarity. Nonetheless, the internal substructures of these N-glycans, particularly, the substructures that are closer to the protein, show significantly similar structures, suggesting that such substructures can be used as fragments in glycan modeling. Increased interactions with protein might be responsible for the restricted conformational space of N-glycan chains. Our results suggest that structure prediction/modeling of N-glycans of glycoconjugates using structure database could be effective and different modeling approaches would be needed depending on the availability of template structures. PMID:23516343

In silico characterization of a novel pathogenic deletion mutation identified in XPA gene in a Pakistani family with severe xeroderma pigmentosum

PubMed Central

2013-01-01

Background Xeroderma Pigmentosum (XP) is a rare skin disorder characterized by skin hypersensitivity to sunlight and abnormal pigmentation. The aim of this study was to investigate the genetic cause of a severe XP phenotype in a consanguineous Pakistani family and in silico characterization of any identified disease-associated mutation. Results The XP complementation group was assigned by genotyping of family for known XP loci. Genotyping data mapped the family to complementation group A locus, involving XPA gene. Mutation analysis of the candidate XP gene by DNA sequencing revealed a novel deletion mutation (c.654del A) in exon 5 of XPA gene. The c.654del A, causes frameshift, which pre-maturely terminates protein and result into a truncated product of 222 amino acid (aa) residues instead of 273 (p.Lys218AsnfsX5). In silico tools were applied to study the likelihood of changes in structural motifs and thus interaction of mutated protein with binding partners. In silico analysis of mutant protein sequence, predicted to affect the aa residue which attains coiled coil structure. The coiled coil structure has an important role in key cellular interactions, especially with DNA damage-binding protein 2 (DDB2), which has important role in DDB-mediated nucleotide excision repair (NER) system. Conclusions Our findings support the fact of genetic and clinical heterogeneity in XP. The study also predicts the critical role of DDB2 binding region of XPA protein in NER pathway and opens an avenue for further research to study the functional role of the mutated protein domain. PMID:24063568

The genomic structure: proof of the role of non-coding DNA.

PubMed

Bouaynaya, Nidhal; Schonfeld, Dan

2006-01-01

We prove that the introns play the role of a decoy in absorbing mutations in the same way hollow uninhabited structures are used by the military to protect important installations. Our approach is based on a probability of error analysis, where errors are mutations which occur in the exon sequences. We derive the optimal exon length distribution, which minimizes the probability of error in the genome. Furthermore, to understand how can Nature generate the optimal distribution, we propose a diffusive random walk model for exon generation throughout evolution. This model results in an alpha stable exon length distribution, which is asymptotically equivalent to the optimal distribution. Experimental results show that both distributions accurately fit the real data. Given that introns also drive biological evolution by increasing the rate of unequal crossover between genes, we conclude that the role of introns is to maintain a genius balance between stability and adaptability in eukaryotic genomes.

Recent structural and mechanistic insights into post-translational enzymatic glycosylation.

PubMed

Hurtado-Guerrero, Ramon; Davies, Gideon J

2012-12-01

Enzymatic glycosylation of proteins, a post-transitional modification of great significance, is carried out by diverse glycosyltransferases (GTs) that harness activated sugar donors, typically nucleotide or lipid-phosphate linked species. Recent work has seen a major increase in the study of the 3D structure and reaction mechanism of these enzymes. Key advances include the dissection of the classical O-glycosylating and N-glycosylating apparatus, revealing unusual folds and hitherto unconsidered chemical mechanisms for acceptor activation. There has been considerable success in the application of kinetic isotope effects and quantum simulations to address the controversial issue of the reaction mechanism of retaining GTs. New roles for old modifications, exemplified by potential epigenetic roles for glycosylation, have been discovered and there has also been a plethora of studies into important mammalian glycosylations that play key roles in cellular biology, opening up new targets for chemical intervention approaches. Copyright © 2012 Elsevier Ltd. All rights reserved.

Protein kinase M ζ and the maintenance of long-term memory.

PubMed

Zhang, Yang; Zong, Wei; Zhang, Lei; Ma, Yuanye; Wang, Jianhong

2016-10-01

Although various molecules have been found to mediate the processes of memory acquisition and consolidation, the molecular mechanism to maintain memory still remains elusive. In recent years, a molecular pathway focusing on protein kinase Mζ (PKMζ) has become of interest to researchers because of its potential role in long-term memory maintenance. PKMζ is an isoform of protein kinase C (PKC) and has a related structure that influences its function in maintaining memory. Considerable evidence has been gathered on PKMζ activity, including loss of function studies using PKMζ inhibitors, such as PKMζ inhibitory peptide (ZIP), suggesting PKMζ plays an important role in long-term memory maintenance. This review provides an overview of the role of PKMζ in long-term memory and outlines the molecular structure of PKMζ, the molecular mechanism of PKMζ in long-term memory maintenance and future directions of PKMζ research. Copyright © 2016 Elsevier Ltd. All rights reserved.

Interactions of Kraft lignin and wheat gluten during biomaterial processing: evidence for the role of phenolic groups.

PubMed

Kaewtatip, Kaewta; Menut, Paul; Auvergne, Remi; Tanrattanakul, Varaporn; Morel, Marie-Helene; Guilbert, Stephane

2010-04-14

The chemical interactions between Kraft lignin and wheat gluten under processing conditions were investigated by determining the extent of the protein network formation. To clarify the role of different chemical functions found in lignin, the effect of Kraft lignin was compared with that of an esterified lignin, in which hydroxyl groups had been suppressed by esterification, and with a series of simple aromatics and phenolic structures with different functionalities (conjugated double bonds, hydroxyl, carboxylic acid, and aldehyde). The protein solubility was determined by using the Kjeldahl method. The role of the hydroxyl function was assessed by the significantly lower effect of esterified lignin. The importance of the phenolic radical scavenging structure is evidenced by the effect of guaiacol, which results in a behavior similar to that of the Kraft lignin. In addition, the significant effect of conjugated double bonds on gluten reactivity, through nucleophilic addition, was demonstrated.

Structural insights into xenobiotic and inhibitor binding to human aldehyde oxidase.

PubMed

Coelho, Catarina; Foti, Alessandro; Hartmann, Tobias; Santos-Silva, Teresa; Leimkühler, Silke; Romão, Maria João

2015-10-01

Aldehyde oxidase (AOX) is a xanthine oxidase (XO)-related enzyme with emerging importance due to its role in the metabolism of drugs and xenobiotics. We report the first crystal structures of human AOX1, substrate free (2.6-Å resolution) and in complex with the substrate phthalazine and the inhibitor thioridazine (2.7-Å resolution). Analysis of the protein active site combined with steady-state kinetic studies highlight the unique features, including binding and substrate orientation at the active site, that characterize human AOX1 as an important drug-metabolizing enzyme. Structural analysis of the complex with the noncompetitive inhibitor thioridazine revealed a new, unexpected and fully occupied inhibitor-binding site that is structurally conserved among mammalian AOXs and XO. The new structural insights into the catalytic and inhibition mechanisms of human AOX that we now report will be of great value for the rational analysis of clinical drug interactions involving inhibition of AOX1 and for the prediction and design of AOX-stable putative drugs.

Structure of FGFR3 transmembrane domain dimer: implications for signaling and human pathologies.

PubMed

Bocharov, Eduard V; Lesovoy, Dmitry M; Goncharuk, Sergey A; Goncharuk, Marina V; Hristova, Kalina; Arseniev, Alexander S

2013-11-05

Fibroblast growth factor receptor 3 (FGFR3) transduces biochemical signals via lateral dimerization in the plasma membrane, and plays an important role in human development and disease. Eight different pathogenic mutations, implicated in cancers and growth disorders, have been identified in the FGFR3 transmembrane segment. Here, we describe the dimerization of the FGFR3 transmembrane domain in membrane-mimicking DPC/SDS (9/1) micelles. In the solved NMR structure, the two transmembrane helices pack into a symmetric left-handed dimer, with intermolecular stacking interactions occurring in the dimer central region. Some pathogenic mutations fall within the helix-helix interface, whereas others are located within a putative alternative interface. This implies that although the observed dimer structure is important for FGFR3 signaling, the mechanism of FGFR3-mediated transduction across the membrane is complex. We propose an FGFR3 signaling mechanism that is based on the solved structure, available structures of isolated soluble FGFR domains, and published biochemical and biophysical data. Copyright © 2013 Elsevier Ltd. All rights reserved.

Job characteristics, flow, and performance: the moderating role of conscientiousness.

PubMed

Demerouti, Evangelia

2006-07-01

The present article aims to show the importance of positive work-related experiences within occupational health psychology by examining the relationship between flow at work (i.e., absorption, work enjoyment, and intrinsic work motivation) and job performance. On the basis of the literature, it was hypothesized that (a) motivating job characteristics are positively related to flow at work and (b) conscientiousness moderates the relationship between flow and other ratings of (in-role and out-of-role) performance. The hypotheses were tested on a sample of 113 employees from several occupations. Results of moderated structural equation modeling analyses generally supported the hypotheses. Motivating job characteristics were predictive of flow, and flow predicted in-role and extra-role performance, for only conscientious employees.

Oligomerization of G protein-coupled receptors: computational methods.

PubMed

Selent, J; Kaczor, A A

2011-01-01

Recent research has unveiled the complexity of mechanisms involved in G protein-coupled receptor (GPCR) functioning in which receptor dimerization/oligomerization may play an important role. Although the first high-resolution X-ray structure for a likely functional chemokine receptor dimer has been deposited in the Protein Data Bank, the interactions and mechanisms of dimer formation are not yet fully understood. In this respect, computational methods play a key role for predicting accurate GPCR complexes. This review outlines computational approaches focusing on sequence- and structure-based methodologies as well as discusses their advantages and limitations. Sequence-based approaches that search for possible protein-protein interfaces in GPCR complexes have been applied with success in several studies, but did not yield always consistent results. Structure-based methodologies are a potent complement to sequence-based approaches. For instance, protein-protein docking is a valuable method especially when guided by experimental constraints. Some disadvantages like limited receptor flexibility and non-consideration of the membrane environment have to be taken into account. Molecular dynamics simulation can overcome these drawbacks giving a detailed description of conformational changes in a native-like membrane. Successful prediction of GPCR complexes using computational approaches combined with experimental efforts may help to understand the role of dimeric/oligomeric GPCR complexes for fine-tuning receptor signaling. Moreover, since such GPCR complexes have attracted interest as potential drug target for diverse diseases, unveiling molecular determinants of dimerization/oligomerization can provide important implications for drug discovery.

On the binding of indeno[1,2-c]isoquinolines in the DNA-topoisomerase I cleavage complex.

PubMed

Xiao, Xiangshu; Antony, Smitha; Pommier, Yves; Cushman, Mark

2005-05-05

An ab initio quantum mechanics calculation is reported which predicts the orientation of indenoisoquinoline 4 in the ternary cleavage complex formed from DNA and topoisomerase I (top1). The results of this calculation are consistent with the hypothetical structures previously proposed for the indenoisoquinoline-DNA-top1 ternary complexes based on molecular modeling, the crystal structure of a recently reported ternary complex, and the biological results obtained with a pair of diaminoalkyl-substituted indenoisoquinoline enantiomers. The results of these studies indicate that the pi-pi stacking interactions between the indenoisoquinolines and the neighboring DNA base pairs play a major role in determining binding orientation. The calculation of the electrostatic potential surface maps of the indenoisoquinolines and the adjacent DNA base pairs shows electrostatic complementarity in the observed binding orientation, leading to the conclusion that electrostatic attraction between the intercalators and the base pairs in the cleavage complex plays a major stabilizing role. On the other hand, the calculation of LUMO and HOMO energies of indenoisoquinoline 13b and neighboring DNA base pairs in conjunction with NBO analysis indicates that charge transfer complex formation plays a relatively minor role in stabilizing the ternary complexes derived from indenoisoquinolines, DNA, and top1. The results of these studies are important in understanding the existing structure-activity relationships for the indenoisoquinolines as top1 inhibitors and as anticancer agents, and they will be important in the future design of indenoisoquinoline-based top1 inhibitors.

Role models and professional development in dentistry: an important resource: The views of early career stage dentists at one academic health science centre in England.

PubMed

Mohamed Osama, O; Gallagher, J E

2018-02-01

The importance of role models, and their differing influence in early, mid- and late careers, has been identified in the process of professional development of medical doctors. There is a paucity of evidence within dentistry on role models and their attributes. To explore the views of early career dentists on positive and negative role models across key phases of professional development, together with role models' attributes and perceived influence. This is a phenomenological study collecting qualitative data through semi-structured interviews based on a topic guide. Dentists in junior (core training) hospital posts in one academic health science centre were all invited to participate. Interviews were recorded, transcribed verbatim and analysed using framework analysis. Twelve early career stage dentists, 10 of whom were female, reported having role models, mainly positive, in their undergraduate and early career phases. Participants defined role models' attributes in relation to three distinct domains: clinical attributes, personal qualities and teaching skills. Positive role models were described as "prioritising the patient's best interests", "delivering learner-centred teaching and training" and "exhibiting a positive personality", whilst negative role models demonstrated the converse. Early career dentists reported having largely positive dentist role models during- and post-dental school and report their impact on professional values and aspirations, learning outcomes and career choice. The findings suggest that these early career dentists in junior hospital posts have largely experienced and benefitted from positive role models, notably dentists, perceived as playing an important and creative influence promoting professionalism and shaping the career choices of early career stage dentists. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Collaboration and co-production of climate knowledge: lessons from a network on the front-line

NASA Astrophysics Data System (ADS)

Kettle, N.

2016-12-01

The science-practice gap is broadly considered a major barrier to the production and application of decision-relevant science. This study uses a social network analysis, based on 126 interviews, to analyze the roles and network ties among climate scientists, service providers, and decision makers in Alaska. Our research highlights the importance of key actors and significant differences in bonding and bridging ties across roles - structural characteristics that provide a basis for informing recommendations to build adaptive capacity and support the co-production of knowledge. Our findings also illustrate that some individuals in the network engage in multiple roles, suggesting that conceptualizing the science-practice interface as consisting of "producers" and "consumers" oversimplifies how individuals engage in climate science, services, and decision making. This research supports the notion that the development and use of climate information is a networked phenomenon. It also emphasizes the importance of centralized individuals who are capable of engaging in multiple roles for the transition of knowledge action.

Key vortical structure causing laminar-turbulent transition in a boundary layer disturbed by a short-duration jet

NASA Astrophysics Data System (ADS)

Yoshikawa, Joe; Nishio, Yu; Izawa, Seiichiro; Fukunishi, Yu

2018-01-01

Numerical simulations are carried out to discover the flow structure that plays an important role in the laminar-turbulent transition process of a boundary layer on a flat plate. The boundary layer is destabilized by ejecting a short-duration jet from a hole in the surface. When the jet velocity is set to 20% of the uniform-flow velocity, a laminar-turbulent transition takes place, whereas in the 18% case, the disturbances created by the jet decay downstream. It is found that in both cases, hairpin vortices are generated; however, these first-generation hairpins do not directly cause the transition. Only in the 20% case does a new hairpin vortex of a different shape with wider distance between the legs appear. The new hairpin grows with time and evokes the generation of vortical structures one after another around it, turning the flow turbulent. It is found that the difference between the two cases is whether or not one of the first-generation hairpin vortices gets connected with the nearby longitudinal vortices. Only when the connection is successful is the new hairpin vortex with wider distance between the legs created. For each of several cases tested with changing jet-ejecting conditions, no difference is found in the importance of the role of the hairpin structure. Therefore, we conclude that the hairpin vortex with widespread legs is a key structure in the transition to turbulence.

The Extracellular Environment of the CNS: Influence on Plasticity, Sprouting, and Axonal Regeneration after Spinal Cord Injury

PubMed Central

Forbes, Lindsey H.

2018-01-01

The extracellular environment of the central nervous system (CNS) becomes highly structured and organized as the nervous system matures. The extracellular space of the CNS along with its subdomains plays a crucial role in the function and stability of the CNS. In this review, we have focused on two components of the neuronal extracellular environment, which are important in regulating CNS plasticity including the extracellular matrix (ECM) and myelin. The ECM consists of chondroitin sulfate proteoglycans (CSPGs) and tenascins, which are organized into unique structures called perineuronal nets (PNNs). PNNs associate with the neuronal cell body and proximal dendrites of predominantly parvalbumin-positive interneurons, forming a robust lattice-like structure. These developmentally regulated structures are maintained in the adult CNS and enhance synaptic stability. After injury, however, CSPGs and tenascins contribute to the structure of the inhibitory glial scar, which actively prevents axonal regeneration. Myelin sheaths and mature adult oligodendrocytes, despite their important role in signal conduction in mature CNS axons, contribute to the inhibitory environment existing after injury. As such, unlike the peripheral nervous system, the CNS is unable to revert to a “developmental state” to aid neuronal repair. Modulation of these external factors, however, has been shown to promote growth, regeneration, and functional plasticity after injury. This review will highlight some of the factors that contribute to or prevent plasticity, sprouting, and axonal regeneration after spinal cord injury. PMID:29849554

Numerical simulations (2D) on the influence of pre-existing local structures and seismic source characteristics in earthquake-volcano interactions

NASA Astrophysics Data System (ADS)

Farías, Cristian; Galván, Boris; Miller, Stephen A.

2017-09-01

Earthquake triggering of hydrothermal and volcanic systems is ubiquitous, but the underlying processes driving these systems are not well-understood. We numerically investigate the influence of seismic wave interaction with volcanic systems simulated as a trapped, high-pressure fluid reservoir connected to a fluid-filled fault system in a 2-D poroelastic medium. Different orientations and earthquake magnitudes are studied to quantify dynamic and static stress, and pore pressure changes induced by a seismic event. Results show that although the response of the system is mainly dominated by characteristics of the radiated seismic waves, local structures can also play an important role on the system dynamics. The fluid reservoir affects the seismic wave front, distorts the static overpressure pattern induced by the earthquake, and concentrates the kinetic energy of the incoming wave on its boundaries. The static volumetric stress pattern inside the fault system is also affected by the local structures. Our results show that local faults play an important role in earthquake-volcanic systems dynamics by concentrating kinetic energy inside and acting as wave-guides that have a breakwater-like behavior. This generates sudden changes in pore pressure, volumetric expansion, and stress gradients. Local structures also influence the regional Coulomb yield function. Our results show that local structures affect the dynamics of volcanic and hydrothermal systems, and should be taken into account when investigating triggering of these systems from nearby or distant earthquakes.

From kinetic-structure analysis to engineering crystalline fiber networks in soft materials.

PubMed

Wang, Rong-Yao; Wang, Peng; Li, Jing-Liang; Yuan, Bing; Liu, Yu; Li, Li; Liu, Xiang-Yang

2013-03-07

Understanding the role of kinetics in fiber network microstructure formation is of considerable importance in engineering gel materials to achieve their optimized performances/functionalities. In this work, we present a new approach for kinetic-structure analysis for fibrous gel materials. In this method, kinetic data is acquired using a rheology technique and is analyzed in terms of an extended Dickinson model in which the scaling behaviors of dynamic rheological properties in the gelation process are taken into account. It enables us to extract the structural parameter, i.e. the fractal dimension, of a fibrous gel from the dynamic rheological measurement of the gelation process, and to establish the kinetic-structure relationship suitable for both dilute and concentrated gelling systems. In comparison to the fractal analysis method reported in a previous study, our method is advantageous due to its general validity for a wide range of fractal structures of fibrous gels, from a highly compact network of the spherulitic domains to an open fibrous network structure. With such a kinetic-structure analysis, we can gain a quantitative understanding of the role of kinetic control in engineering the microstructure of the fiber network in gel materials.

Functional and Structural Characterization of a Receptor-Like Kinase Involved in Germination and Cell Expansion in Arabidopsis.

PubMed

Wu, Zhen; Liang, Shan; Song, Wen; Lin, Guangzhong; Wang, Weiguang; Zhang, Heqiao; Han, Zhifu; Chai, Jijie

2017-01-01

Leucine-rich repeat receptor-like kinases (LRR-RLKs) are widespread in different plant species and play important roles in growth and development. Germination inhibition is vital for the completion of seed maturation and cell expansion is a fundamental cellular process driving plant growth. Here, we report genetic and structural characterizations of a functionally uncharacterized LRR-RLK, named GRACE (Germination Repression and Cell Expansion receptor-like kinase). Overexpression of GRACE in Arabidopsis exhibited delayed germination, enlarged cotyledons, rosette leaves and stubbier petioles. Conversely, these phenotypes were reversed in the T-DNA insertion knock-down mutant grace-1 plants. A crystal structure of the extracellular domain of GRACE (GRACE-LRR) determined at the resolution of 3.0 Å revealed that GRACE-LRR assumed a right-handed super-helical structure with an island domain (ID). Structural comparison showed that structure of the ID in GRACE-LRR is strikingly different from those observed in other LRR-RLKs. This structural observation implies that GRACE might perceive a new ligand for signaling. Collectively, our data support roles of GRACE in repressing seed germination and promoting cell expansion of Arabidopsis , presumably by perception of unknown ligand(s).

Functional and Structural Characterization of a Receptor-Like Kinase Involved in Germination and Cell Expansion in Arabidopsis

PubMed Central

Wu, Zhen; Liang, Shan; Song, Wen; Lin, Guangzhong; Wang, Weiguang; Zhang, Heqiao; Han, Zhifu; Chai, Jijie

2017-01-01

Leucine-rich repeat receptor-like kinases (LRR-RLKs) are widespread in different plant species and play important roles in growth and development. Germination inhibition is vital for the completion of seed maturation and cell expansion is a fundamental cellular process driving plant growth. Here, we report genetic and structural characterizations of a functionally uncharacterized LRR-RLK, named GRACE (Germination Repression and Cell Expansion receptor-like kinase). Overexpression of GRACE in Arabidopsis exhibited delayed germination, enlarged cotyledons, rosette leaves and stubbier petioles. Conversely, these phenotypes were reversed in the T-DNA insertion knock-down mutant grace-1 plants. A crystal structure of the extracellular domain of GRACE (GRACE-LRR) determined at the resolution of 3.0 Å revealed that GRACE-LRR assumed a right-handed super-helical structure with an island domain (ID). Structural comparison showed that structure of the ID in GRACE-LRR is strikingly different from those observed in other LRR-RLKs. This structural observation implies that GRACE might perceive a new ligand for signaling. Collectively, our data support roles of GRACE in repressing seed germination and promoting cell expansion of Arabidopsis, presumably by perception of unknown ligand(s). PMID:29213277

Using Social Network Analysis to Examine the Effect of Care Management Structure on Chronic Disease Management Communication Within Primary Care.

PubMed

Holtrop, Jodi Summers; Ruland, Sandra; Diaz, Stephanie; Morrato, Elaine H; Jones, Eric

2018-05-01

Care management and care managers are becoming increasingly prevalent in primary care medical practice as a means of improving population health and reducing unnecessary care. Care managers are often involved in chronic disease management and associated transitional care. In this study, we examined the communication regarding chronic disease care within 24 primary care practices in Michigan and Colorado. We sought to answer the following questions: Do care managers play a key role in chronic disease management in the practice? Does the prominence of the care manager's connectivity within the practice's communication network vary by the type of care management structure implemented? Individual written surveys were given to all practice members in the participating practices. Survey questions assessed demographics as well as practice culture, quality improvement, care management activities, and communication regarding chronic disease care. Using social network analysis and other statistical methods, we analyzed the communication dynamics related to chronic disease care for each practice. The structure of chronic disease communication varies greatly from practice to practice. Care managers who were embedded in the practice or co-located were more likely to be in the core of the communication network than were off-site care managers. These care managers also had higher in-degree centrality, indicating that they acted as a hub for communication with team members in many other roles. Social network analysis provided a useful means of examining chronic disease communication in practice, and highlighted the central role of care managers in this communication when their role structure supported such communication. Structuring care managers as embedded team members within the practice has important implications for their role in chronic disease communication within primary care.

Description of strong M1 transitions between 4^+ states at N=52 within the sdg-IBM-2

NASA Astrophysics Data System (ADS)

Casperson, R. J.; Werner, V.; Heinze, S.

2009-10-01

The interplay between collective and single-particle degrees of freedom for nuclei near the N=50 shell closure have recently been under investigation. In Molybdenum and Ruthenium nuclei, collective symmetric and mixed-symmetric structures have been identified, while in Zirconium, underlying shell-structure plays an enhanced role. The one-phonon 2^+ mixed-symmetry state was identified from its strong M1 transition to the 2^+1 state. Similar transitions were observed between 4^+ states in ^94Mo and ^92Zr, and shell model calculations indicate that hexadecapole excitations play a role. These phenomena will be investigated within the sdg-Interacting Boson Model-2 in order to gain a better understanding about the structure of the states involved, and to which extent the hexadecapole degree of freedom is important at relatively low energies. First calculations within this model, using an F-spin conserving Hamiltonian to disentangle symmetric and mixed- symmetric structures, will be presented and compared to data.

Simultaneous cryo X-ray ptychographic and fluorescence microscopy of green algae

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

Deng, Junjing; Vine, David J.; Chen, Si

Trace metals play important roles in normal and in disease-causing biological functions. X-ray fluorescence microscopy reveals trace elements with no dependence on binding affinities (unlike with visible light fluorophores) and with improved sensitivity relative to electron probes. However, X-ray fluorescence is not very sensitive for showing the light elements that comprise the majority of cellular material. Here we show that X-ray ptychography can be combined with fluorescence to image both cellular structure and trace element distribution in frozen-hydrated cells at cryogenic temperatures, with high structural and chemical fidelity. Ptychographic reconstruction algorithms deliver phase and absorption contrast images at a resolutionmore » beyond that of the illuminating lens or beam size. Using 5.2-keV X-rays, we have obtained sub-30-nm resolution structural images and ~90-nm-resolution fluorescence images of several elements in frozen-hydrated green algae. Finally, this combined approach offers a way to study the role of trace elements in their structural context.« less

Simultaneous cryo X-ray ptychographic and fluorescence microscopy of green algae

DOE PAGES

Deng, Junjing; Vine, David J.; Chen, Si; ...

2015-02-24

Trace metals play important roles in normal and in disease-causing biological functions. X-ray fluorescence microscopy reveals trace elements with no dependence on binding affinities (unlike with visible light fluorophores) and with improved sensitivity relative to electron probes. However, X-ray fluorescence is not very sensitive for showing the light elements that comprise the majority of cellular material. Here we show that X-ray ptychography can be combined with fluorescence to image both cellular structure and trace element distribution in frozen-hydrated cells at cryogenic temperatures, with high structural and chemical fidelity. Ptychographic reconstruction algorithms deliver phase and absorption contrast images at a resolutionmore » beyond that of the illuminating lens or beam size. Using 5.2-keV X-rays, we have obtained sub-30-nm resolution structural images and ~90-nm-resolution fluorescence images of several elements in frozen-hydrated green algae. Finally, this combined approach offers a way to study the role of trace elements in their structural context.« less

Simultaneous cryo X-ray ptychographic and fluorescence microscopy of green algae

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

Deng, Junjing; Vine, David J.; Chen, Si

Trace metals play important roles in normal and in disease-causing biological functions. X-ray fluorescence microscopy reveals trace elements with no dependence on binding affinities (unlike with visible light fluorophores) and with improved sensitivity relative to electron probes. However, X-ray fluorescence is not very sensitive for showing the light elements that comprise the majority of cellular material. Here we show that X-ray ptychography can be combined with fluorescence to image both cellular structure and trace element distribution in frozen-hydrated cells at cryogenic temperatures, with high structural and chemical fidelity. Ptychographic reconstruction algorithms deliver phase and absorption contrast images at a resolutionmore » beyond that of the illuminating lens or beam size. Using 5.2-keV X-rays, we have obtained sub-30-nm resolution structural images and similar to 90-nm-resolution fluorescence images of several elements in frozen-hydrated green algae. This combined approach offers a way to study the role of trace elements in their structural context.« less

Emerging concepts in smooth muscle contributions to airway structure and function: implications for health and disease

PubMed Central

2016-01-01

Airway structure and function are key aspects of normal lung development, growth, and aging, as well as of lung responses to the environment and the pathophysiology of important diseases such as asthma, chronic obstructive pulmonary disease, and fibrosis. In this regard, the contributions of airway smooth muscle (ASM) are both functional, in the context of airway contractility and relaxation, as well as synthetic, involving production and modulation of extracellular components, modulation of the local immune environment, cellular contribution to airway structure, and, finally, interactions with other airway cell types such as epithelium, fibroblasts, and nerves. These ASM contributions are now found to be critical in airway hyperresponsiveness and remodeling that occur in lung diseases. This review emphasizes established and recent discoveries that underline the central role of ASM and sets the stage for future research toward understanding how ASM plays a central role by being both upstream and downstream in the many interactive processes that determine airway structure and function in health and disease. PMID:27742732

Effect of structural phase transformation in FeGaO{sub 3} on its magnetic and ferroelectric properties

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

Lone, A. G., E-mail: agl221986@gmail.com; Bhowmik, R. N.

2015-06-24

We investigate the structural phase transformation from orthorhombic to rhombohedral structure in FeGaO{sub 3} by adopting a combined effect of mechanical alloying/milling and solid state sintering techniques. The structural phase formation of the FeGaO{sub 3} compound has been characterized by X-ray diffraction pattern. Mechanical milling played a significant role on the stabilization of rhombohedral phase in FeGaO{sub 3}, where as high temperature sintering stabilized the system in orthorhombic phase. A considerable difference has been observed in magnetic and ferroelectric properties of the system in two phases. The system in rhombohedral (R-3c) phase exhibited better ferromagnetic and of ferroelectric properties atmore » room temperature in comparison to orthorhombic (Pc2{sub 1}n) phase. The rhombohedral phase appears to be good for developing metal doped hematite system for spintronics applications and in that process mechanical milling played an important role.« less

Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain

PubMed Central

2012-01-01

Background Post-transcriptional control of gene expression is mostly conducted by specific elements in untranslated regions (UTRs) of mRNAs, in collaboration with specific binding proteins and RNAs. In several well characterized cases, these RNA elements are known to form stable secondary structures. RNA secondary structures also may have major functional implications for long noncoding RNAs (lncRNAs). Recent transcriptional data has indicated the importance of lncRNAs in brain development and function. However, no methodical efforts to investigate this have been undertaken. Here, we aim to systematically analyze the potential for RNA structure in brain-expressed transcripts. Results By comprehensive spatial expression analysis of the adult mouse in situ hybridization data of the Allen Mouse Brain Atlas, we show that transcripts (coding as well as non-coding) associated with in silico predicted structured probes are highly and significantly enriched in almost all analyzed brain regions. Functional implications of these RNA structures and their role in the brain are discussed in detail along with specific examples. We observe that mRNAs with a structure prediction in their UTRs are enriched for binding, transport and localization gene ontology categories. In addition, after manual examination we observe agreement between RNA binding protein interaction sites near the 3’ UTR structures and correlated expression patterns. Conclusions Our results show a potential use for RNA structures in expressed coding as well as noncoding transcripts in the adult mouse brain, and describe the role of structured RNAs in the context of intracellular signaling pathways and regulatory networks. Based on this data we hypothesize that RNA structure is widely involved in transcriptional and translational regulatory mechanisms in the brain and ultimately plays a role in brain function. PMID:22651826

Evidence for Model-based Computations in the Human Amygdala during Pavlovian Conditioning

PubMed Central

Prévost, Charlotte; McNamee, Daniel; Jessup, Ryan K.; Bossaerts, Peter; O'Doherty, John P.

2013-01-01

Contemporary computational accounts of instrumental conditioning have emphasized a role for a model-based system in which values are computed with reference to a rich model of the structure of the world, and a model-free system in which values are updated without encoding such structure. Much less studied is the possibility of a similar distinction operating at the level of Pavlovian conditioning. In the present study, we scanned human participants while they participated in a Pavlovian conditioning task with a simple structure while measuring activity in the human amygdala using a high-resolution fMRI protocol. After fitting a model-based algorithm and a variety of model-free algorithms to the fMRI data, we found evidence for the superiority of a model-based algorithm in accounting for activity in the amygdala compared to the model-free counterparts. These findings support an important role for model-based algorithms in describing the processes underpinning Pavlovian conditioning, as well as providing evidence of a role for the human amygdala in model-based inference. PMID:23436990

"Making a good time": the role of friendship in living successfully with aphasia.

PubMed

Brown, Kyla; Davidson, Bronwyn; Worrall, Linda E; Howe, Tami

2013-04-01

Loss of friendship post-onset of aphasia is well documented, with reduced social network size and social isolation commonly reported. Because friendship has strong links to psychological well-being and health, increased knowledge about friendships of individuals with aphasia will have important clinical implications. This study aimed to explore the perspectives of 25 community dwelling individuals with chronic aphasia on the role of friendship in living successfully with aphasia. Thematic analysis of transcripts from semi-structured in-depth interviews revealed three over-arching themes relating to the role of friendship in participants' experience of life with aphasia: living with changes in friendships, good times together and support from friends, and the importance of stroke and aphasia friends. Overall, findings highlighted the valued role of friendship in living successfully with aphasia, while also providing evidence of how friendships change and evolve in both negative and positive ways following onset of aphasia. Clinicians are challenged to work creatively to address the role of friendship in life post-stroke in partnership with individuals with aphasia, their families, and friends.

The role of modifier cation field strength, oxygen speciation and network cation interaction in pressure-induced structural changes of silicate melts and glasses: 27Al, and 11B MAS NMR studies

NASA Astrophysics Data System (ADS)

Bista, S.; Stebbins, J. F.

2017-12-01

In aluminosilicate melts and glasses, both non-bridging oxygen content (NBO) and modifier cation field strength (Mg>Ca>Na>K) are known to facilitate network cation (e.g. Al, B) coordination increase with pressure. However, the role of these two compositional parameters in pressure-induced structural changes is derived from data for a limited set of compositions, where effects of the interaction between these parameters is less understood. For example, the effects of NBO are largely based on studies of Na and K aluminosilicate glasses, but effects of geologically important, higher field strength modifier cations such as Mg2+ and Fe2+ could well be significantly different. In this study, we look at a wide compositional range of Na, Ca and Mg aluminosilicate glasses (quenched from high pressure melts near to the glass transition temperature) to understand the roles of NBO and modifier cation field strength that can extend our view of processes important for silicate melts common in nature. Our results show that the role of NBO in pressure-induced structural changes varies systematically with increasing field strength of the modifier cation. In Na aluminosilicate glasses recovered from 1.5 to 3 GPa, large increases in average aluminum coordination are observed in glasses with high NBO content, while no detectable increases are seen for low nominal NBO (jadeite). In contrast, Mg aluminosilicate glasses with both high and low NBO show similar, large increases in average aluminum coordination with increasing pressure. The behaviors of Ca aluminosilicates fall between those of Na and Mg-rich glasses. We have also looked at interactions between different network forming cations in pressure-induced structural changes in low NBO Ca-aluminoborosilicate glasses with varying B/Si. Both aluminum and boron increase dramatically in coordination in these compositions 1.5 to 3 GPa. Increases in both average aluminum coordination and densification are larger in compositions containing higher boron concentrations, suggesting an interaction between boron and aluminum network cations in pressure-induced structural changes.

Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology

PubMed Central

Lezon, Timothy R.; Bahar, Ivet

2010-01-01

Comparison of elastic network model predictions with experimental data has provided important insights on the dominant role of the network of inter-residue contacts in defining the global dynamics of proteins. Most of these studies have focused on interpreting the mean-square fluctuations of residues, or deriving the most collective, or softest, modes of motions that are known to be insensitive to structural and energetic details. However, with increasing structural data, we are in a position to perform a more critical assessment of the structure-dynamics relations in proteins, and gain a deeper understanding of the major determinants of not only the mean-square fluctuations and lowest frequency modes, but the covariance or the cross-correlations between residue fluctuations and the shapes of higher modes. A systematic study of a large set of NMR-determined proteins is analyzed using a novel method based on entropy maximization to demonstrate that the next level of refinement in the elastic network model description of proteins ought to take into consideration properties such as contact order (or sequential separation between contacting residues) and the secondary structure types of the interacting residues, whereas the types of amino acids do not play a critical role. Most importantly, an optimal description of observed cross-correlations requires the inclusion of destabilizing, as opposed to exclusively stabilizing, interactions, stipulating the functional significance of local frustration in imparting native-like dynamics. This study provides us with a deeper understanding of the structural basis of experimentally observed behavior, and opens the way to the development of more accurate models for exploring protein dynamics. PMID:20585542

Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology.

PubMed

Lezon, Timothy R; Bahar, Ivet

2010-06-17

Comparison of elastic network model predictions with experimental data has provided important insights on the dominant role of the network of inter-residue contacts in defining the global dynamics of proteins. Most of these studies have focused on interpreting the mean-square fluctuations of residues, or deriving the most collective, or softest, modes of motions that are known to be insensitive to structural and energetic details. However, with increasing structural data, we are in a position to perform a more critical assessment of the structure-dynamics relations in proteins, and gain a deeper understanding of the major determinants of not only the mean-square fluctuations and lowest frequency modes, but the covariance or the cross-correlations between residue fluctuations and the shapes of higher modes. A systematic study of a large set of NMR-determined proteins is analyzed using a novel method based on entropy maximization to demonstrate that the next level of refinement in the elastic network model description of proteins ought to take into consideration properties such as contact order (or sequential separation between contacting residues) and the secondary structure types of the interacting residues, whereas the types of amino acids do not play a critical role. Most importantly, an optimal description of observed cross-correlations requires the inclusion of destabilizing, as opposed to exclusively stabilizing, interactions, stipulating the functional significance of local frustration in imparting native-like dynamics. This study provides us with a deeper understanding of the structural basis of experimentally observed behavior, and opens the way to the development of more accurate models for exploring protein dynamics.

Hierarchy of low-energy models of the electronic structure of cuprate HTSCs: The role of long-range spin-correlated hops

NASA Astrophysics Data System (ADS)

Val'kov, V. V.; Mitskan, V. A.; Dzebisashvili, D. M.; Barabanov, A. F.

2018-02-01

It is shown that for the three-band Emery p-d-model that reflects the real structure of the CuO2-plane of high-temperature superconductors in the regime of strong electron correlations, it is possible to carry out a sequence of reductions to the effective models reproducing low-energy features of elementary excitation spectrum and revealing the spin-polaron nature of the Fermi quasiparticles. The first reduction leads to the spin-fermion model in which the subsystem of spin moments, coupled by the exchange interaction and localized on copper ions, strongly interacts with oxygen holes. The second reduction deals with the transformation from the spin-fermion model to the φ-d-exchange model. An important feature of this transformation is the large energy of the φ-d-exchange coupling, which leads to the formation of spin polarons. The use of this fact allows us to carry out the third reduction, resulting in the t ˜-J˜ *-I -model. Its distinctive feature is the importance of spin-correlated hops as compared to the role of such processes in the commonly used t-J*-model derived from the Hubbard model. Based on the comparative analysis of the spectrum of Fermi excitations calculated for the obtained effective models of the CuO2-plane of high-temperature superconductors, the important role of the usually ignored long-range spin-correlated hops is determined.

NMR studies of protein-nucleic acid interactions.

PubMed

Varani, Gabriele; Chen, Yu; Leeper, Thomas C

2004-01-01

Protein-DNA and protein-RNA complexes play key functional roles in every living organism. Therefore, the elucidation of their structure and dynamics is an important goal of structural and molecular biology. Nuclear magnetic resonance (NMR) studies of protein and nucleic acid complexes have common features with studies of protein-protein complexes: the interaction surfaces between the molecules must be carefully delineated, the relative orientation of the two species needs to be accurately and precisely determined, and close intermolecular contacts defined by nuclear Overhauser effects (NOEs) must be obtained. However, differences in NMR properties (e.g., chemical shifts) and biosynthetic pathways for sample productions generate important differences. Chemical shift differences between the protein and nucleic acid resonances can aid the NMR structure determination process; however, the relatively limited dispersion of the RNA ribose resonances makes the process of assigning intermolecular NOEs more difficult. The analysis of the resulting structures requires computational tools unique to nucleic acid interactions. This chapter summarizes the most important elements of the structure determination by NMR of protein-nucleic acid complexes and their analysis. The main emphasis is on recent developments (e.g., residual dipolar couplings and new Web-based analysis tools) that have facilitated NMR studies of these complexes and expanded the type of biological problems to which NMR techniques of structural elucidation can now be applied.

Effect of polarization on the stability of a helix dimer

NASA Astrophysics Data System (ADS)

Wang, Xing Y.; Zhang, John Z. H.

2011-01-01

Molecular dynamics (MD) simulations have been carried out to study helix-helix interaction using both standard AMBER and polarized force fields. Comparison of the two simulations shows that electrostatic polarization of intra-protein hydrogen bonds plays a significant role in stabilizing the structure of helix dimer. This stabilizing effect is clearly demonstrated by examining the monomer structure, helix crossing angle and stability of backbone hydrogen bonds under AMBER and PPC. Since reliable prediction of protein-protein structure is a significant challenge, the current study should help shed light on the importance of electrostatic polarization of protein in helix-helix interaction and helix bundle structures.

Structural dynamics of the mitochondrial compartment.

PubMed

Thorsness, P E

1992-09-01

The metabolic activities of mitochondria have been extensively characterized. However, there is much less known about the morphogenic changes of the mitochondrial compartment during growth, development and aging of the cell and the consequences of those structural changes on cellular metabolism. There is a growing body of evidence for interactions of mitochondria with cytoskeletal components and changes of mitochondrial structure during development and in response to changing environmental conditions. Segregation and recombination of mitochondrial genomes are also processes dependent upon the dynamic nature of the mitochondrial compartment. These regulatory and structural aspects of mitochondrial compartment dynamics will play an important role in the analysis of mitochondrial function and pathology.

Ionizing gas breakdown waves in strong electric fields.

NASA Technical Reports Server (NTRS)

Klingbeil, R.; Tidman, D. A.; Fernsler, R. F.

1972-01-01

A previous analysis by Albright and Tidman (1972) of the structure of an ionizing potential wave driven through a dense gas by a strong electric field is extended to include atomic structure details of the background atoms and radiative effects, especially, photoionization. It is found that photoionization plays an important role in avalanche propagation. Velocities, electron densities, and temperatures are presented as a function of electric field for both negative and positive breakdown waves in nitrogen.

Are Eyewall Replacement Cycles Governed Largely by Axisymmetric Balance Dynamics?

DTIC Science & Technology

2015-01-01

this viewpoint, the inward contraction of an eyewall is a mechanism driven by differential diabatic heating, and friction plays an un- important role...shows the azimuthally averaged kinematic and thermodynamical structure of the RAMS simulation, along with the corresponding averaged diabatic heating rate...structure of the storm, with the 360-K isotherm sloping upward from 9 to 13.5km between the center of the storm and 150-km radius. The mean diabatic heating

The structure of ethnic attitudes: the effects of target group, region, gender, and national identity.

PubMed

Verkuyten, M

1997-08-01

The present study was an assessment of attitudes of 410 ethnically Dutch adolescents toward three ethnic minority groups living in the Netherlands. Stereotypes, symbolic beliefs, affective associations, and the evaluation of possible interactions were used to predict the global evaluation of ethnic outgroups and accounted for much of the variance in ethnic attitudes. The relative importance of the four predictors varied by target group and location. Gender differences were found in the structure of attitudes; symbolic beliefs played a greater role in the attitudes of boys, whereas emotions played a more central role in the attitudes of girls. The evaluation of Dutch identity was related to the favorability of ethnic attitudes and also to the underlying structure. Respondents with a positive national identity had less favorable ethnic attitudes, and emotions were more predictive of their attitudes, whereas symbolic beliefs were most predictive among respondents with a less positive national identity.

Clusterin promotes amyloid plaque formation and is critical for neuritic toxicity in a mouse model of Alzheimer's disease

PubMed Central

DeMattos, Ronald B.; O'dell, Mark A.; Parsadanian, Maia; Taylor, Jennie W.; Harmony, Judith A. K.; Bales, Kelly R.; Paul, Steven M.; Aronow, Bruce J.; Holtzman, David M.

2002-01-01

Studies have shown that clusterin (also called apolipoprotein J) can influence the structure and toxicity of amyloid-β (Aβ) in vitro. To determine whether endogenous clusterin plays a role in influencing Aβ deposition, structure, and toxicity in vivo, we bred PDAPP mice, a transgenic mouse model of Alzheimer's disease, to clusterin−/− mice. By 12 months of age, PDAPP, clusterin−/− mice had similar levels of brain Aβ deposition as did PDAPP, clusterin+/+ mice. Although Aβ deposition was similar, PDAPP, clusterin−/− mice had significantly fewer fibrillar Aβ (amyloid) deposits than PDAPP mice expressing clusterin. In the absence of clusterin, neuritic dystrophy associated with the deposited amyloid was markedly reduced, resulting in a dissociation between fibrillar amyloid formation and neuritic dystrophy. These findings demonstrate that clusterin markedly influences Aβ structure and neuritic toxicity in vivo and is likely to play an important role in Alzheimer's disease pathogenesis. PMID:12145324

Thermoelectric band engineering: The role of carrier scattering

NASA Astrophysics Data System (ADS)

Witkoske, Evan; Wang, Xufeng; Lundstrom, Mark; Askarpour, Vahid; Maassen, Jesse

2017-11-01

Complex electronic band structures, with multiple valleys or bands at the same or similar energies, can be beneficial for thermoelectric performance, but the advantages can be offset by inter-valley and inter-band scattering. In this paper, we demonstrate how first-principles band structures coupled with recently developed techniques for rigorous simulation of electron-phonon scattering provide the capabilities to realistically assess the benefits and trade-offs associated with these materials. We illustrate the approach using n-type silicon as a model material and show that intervalley scattering is strong. This example shows that the convergence of valleys and bands can improve thermoelectric performance, but the magnitude of the improvement depends sensitively on the relative strengths of intra- and inter-valley electron scattering. Because anisotropy of the band structure also plays an important role, a measure of the benefit of band anisotropy in the presence of strong intervalley scattering is presented.

Role of structural barriers in the in vitro bioaccessibility of anthocyanins in comparison with carotenoids.

PubMed

Carrillo, Celia; Buvé, Carolien; Panozzo, Agnese; Grauwet, Tara; Hendrickx, Marc

2017-07-15

Although natural structural barriers are factors limiting nutrient bioaccessibility, their specific role in anthocyanin bioaccessibility is still unknown. To better understand how natural barriers govern bioactive compound bioaccessibility, an experimental approach comparing anthocyanins and carotenoids was designed, using a single plant matrix. Initial results revealed increased anthocyanin bioaccessibility in masticated black carrot. To explain this observation, samples with increasing levels of bioencapsulation (free-compound, homogenized-puree, puree) were examined. While carotenoid bioaccessibility was inversely proportional to the level of bioencapsulation, barrier disruption did not increase anthocyanin bioaccessibility. This means that mechanical processing is of particular importance in the case of carotenoid bioaccessibility. While micelle incorporation is the limiting factor for carotenoid bioaccessibility, anthocyanin degradation under alkaline conditions in the gastrointestinal tract dominates. In the absence of structural barriers, anthocyanin bioaccessibility is greater than that of carotenoids. Copyright © 2017 Elsevier Ltd. All rights reserved.

Patellofemoral anatomy and biomechanics: current concepts

PubMed Central

ZAFFAGNINI, STEFANO; DEJOUR, DAVID; GRASSI, ALBERTO; BONANZINGA, TOMMASO; MUCCIOLI, GIULIO MARIA MARCHEGGIANI; COLLE, FRANCESCA; RAGGI, FEDERICO; BENZI, ANDREA; MARCACCI, MAURILIO

2013-01-01

The patellofemoral joint, due to its particular bone anatomy and the numerous capsuloligamentous structures and muscles that act dynamically on the patella, is considered one of the most complex joints in the human body from the biomechanical point of view. The medial patellofemoral ligament (MPFL) has been demonstrated to contribute 60% of the force that opposes lateral displacement of the patella, and MPFL injury results in an approximately 50% reduction in the force needed to dislocate the patella laterally with the knee extended. For this reason, recent years have seen a growing interest in the study of this important anatomical structure, whose aponeurotic nature has thus been demonstrated. The MPFL acts as a restraint during motion, playing an active role under conditions of laterally applied stress, but an only marginal role during natural knee flexion. However, it remains extremely difficult to clearly define the anatomy of the MPFL and its relationships with other anatomical structures. PMID:25606512

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

Moczydlowski, Edward G.

Ion channel proteins regulate complex patterns of cellular electrical activity and ionic signaling. Certain K+ channels play an important role in immunological biodefense mechanisms of adaptive and innate immunity. Most ion channel proteins are oligomeric complexes with the conductive pore located at the central subunit interface. The long-term activity of many K+ channel proteins is dependent on the concentration of extracellular K+; however, the mechanism is unclear. Thus, this project focused on mechanisms underlying structural stability of tetrameric K+ channels. Using KcsA of Streptomyces lividans as a model K+ channel of known structure, the molecular basis of tetramer stability wasmore » investigated by: 1. Bioinformatic analysis of the tetramer interface. 2. Effect of two local anesthetics (lidocaine, tetracaine) on tetramer stability. 3. Molecular simulation of drug docking to the ion conduction pore. The results provide new insights regarding the structural stability of K+ channels and its possible role in cell physiology.« less

Structural and Dynamical Details of Biotin

NASA Astrophysics Data System (ADS)

Korter, Timothy; Dunmire, David; Romero, Danilo; Middleton, Chris; Jenkins, Tim; Hudson, Bruce; Hight Walker, Angela

2003-03-01

Biotin, one of the B vitamins, is a key cofactor of enzymes that transfer units of CO2. Chemically linked to a lysine residue via its carboxylic acid side chain, biotin exhibits incredible flexibility when performing its intraprotein transport role. Not only does Biotin play a critical role in gluconeogenesis, it also is commonly used throughout biotechnology research due to its strong binding affinity for attachment, tethering and labeling chemistries. Therefore, a detailed probe of the structure and dynamics of biotin is important both metabolically and to aid further research. Here, we used several vibrational techniques, THz, IR, Raman and Inelastic Neutron Scattering, to gain a comprehensive understanding of biotin's structure, flexibility and dynamics. Specifically our interests are in hydrogen bonding interactions, torsional vibrations, and conformational changes with varying environments, which frequently lie in the far-infrared region of the spectrum below 200 cm-1. Interpretation and comparison of our multi-technique data are guided by high-level ab initio calculations.

Structure and inhibition analysis of the mouse SAD-B C-terminal fragment.

PubMed

Ma, Hui; Wu, Jing-Xiang; Wang, Jue; Wang, Zhi-Xin; Wu, Jia-Wei

2016-10-01

The SAD (synapses of amphids defective) kinases, including SAD-A and SAD-B, play important roles in the regulation of neuronal development, cell cycle, and energy metabolism. Our recent study of mouse SAD-A identified a unique autoinhibitory sequence (AIS), which binds at the junction of the kinase domain (KD) and the ubiquitin-associated (UBA) domain and exerts autoregulation in cooperation with UBA. Here, we report the crystal structure of the mouse SAD-B C-terminal fragment including the AIS and the kinase-associated domain 1 (KA1) at 2.8 Å resolution. The KA1 domain is structurally conserved, while the isolated AIS sequence is highly flexible and solvent-accessible. Our biochemical studies indicated that the SAD-B AIS exerts the same autoinhibitory role as that in SAD-A. We believe that the flexible isolated AIS sequence is readily available for interaction with KD-UBA and thus inhibits SAD-B activity.

Structural Studies of Cinnamoyl-CoA Reductase and Cinnamyl-Alcohol Dehydrogenase, Key Enzymes of Monolignol Biosynthesis[C][W

PubMed Central

Pan, Haiyun; Zhou, Rui; Louie, Gordon V.; Mühlemann, Joëlle K.; Bomati, Erin K.; Bowman, Marianne E.; Dudareva, Natalia; Dixon, Richard A.; Noel, Joseph P.; Wang, Xiaoqiang

2014-01-01

The enzymes cinnamoyl-CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD) catalyze the two key reduction reactions in the conversion of cinnamic acid derivatives into monolignol building blocks for lignin polymers in plant cell walls. Here, we describe detailed functional and structural analyses of CCRs from Medicago truncatula and Petunia hybrida and of an atypical CAD (CAD2) from M. truncatula. These enzymes are closely related members of the short-chain dehydrogenase/reductase (SDR) superfamily. Our structural studies support a reaction mechanism involving a canonical SDR catalytic triad in both CCR and CAD2 and an important role for an auxiliary cysteine unique to CCR. Site-directed mutants of CAD2 (Phe226Ala and Tyr136Phe) that enlarge the phenolic binding site result in a 4- to 10-fold increase in activity with sinapaldehyde, which in comparison to the smaller coumaraldehyde and coniferaldehyde substrates is disfavored by wild-type CAD2. This finding demonstrates the potential exploitation of rationally engineered forms of CCR and CAD2 for the targeted modification of monolignol composition in transgenic plants. Thermal denaturation measurements and structural comparisons of various liganded and unliganded forms of CCR and CAD2 highlight substantial conformational flexibility of these SDR enzymes, which plays an important role in the establishment of catalytically productive complexes of the enzymes with their NADPH and phenolic substrates. PMID:25217505

BAYESIAN PROTEIN STRUCTURE ALIGNMENT.

PubMed

Rodriguez, Abel; Schmidler, Scott C

The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identification and evaluation of structural similarity between proteins; such analysis can aid in understanding the role of newly discovered proteins and help elucidate evolutionary relationships between organisms. Computational biologists have developed many clever algorithmic techniques for comparing protein structures, however, all are based on heuristic optimization criteria, making statistical interpretation somewhat difficult. Here we present a fully probabilistic framework for pairwise structural alignment of proteins. Our approach has several advantages, including the ability to capture alignment uncertainty and to estimate key "gap" parameters which critically affect the quality of the alignment. We show that several existing alignment methods arise as maximum a posteriori estimates under specific choices of prior distributions and error models. Our probabilistic framework is also easily extended to incorporate additional information, which we demonstrate by including primary sequence information to generate simultaneous sequence-structure alignments that can resolve ambiguities obtained using structure alone. This combined model also provides a natural approach for the difficult task of estimating evolutionary distance based on structural alignments. The model is illustrated by comparison with well-established methods on several challenging protein alignment examples.

Old moms with new tricks: modeling the effects of age-specific spawning behaviors in Pacific Ocean perch

EPA Science Inventory

In commercially exploited, long-lived fish species, age structure plays an important role in determining population stability and resilience to human and environmental impacts. The often observed increase in energy allocation per offspring by older females can improve larval surv...

Phonetics and Phonology of Thematic Contrast in German

ERIC Educational Resources Information Center

Braun, Bettina

2006-01-01

It is acknowledged that contrast plays an important role in understanding discourse and information structure. While it is commonly assumed that contrast can be marked by intonation only, our understanding of the intonational realization of contrast is limited. For German there is mainly introspective evidence that the rising theme accent (or…

Antimicrobial and cold plasma treatments for inactivation of listeria monocytogenes on whole apple surface

USDA-ARS?s Scientific Manuscript database

Introduction: Produce and bacterial cell surface structure play an important role as to where and how bacteria attach to produce surfaces. The efficacy of a novel antimicrobial solution developed in our laboratory was investigated in combination with cold plasma treatments for inactivation of Liste...

Metaphor in Professional Counseling

ERIC Educational Resources Information Center

Wagener, Alwin E.

2017-01-01

Metaphors are linked to how individuals process information and emotions, and they are important to understand and utilize in counseling. A description of the structure of metaphors and metaphor theory is provided. The role of metaphors in emotional processing is explained, and the process of counseling is tied to the therapeutic usage of…

Value Orientations of Future Teachers-Researchers

ERIC Educational Resources Information Center

Botalova, Olga B.; Osipova, Seraphima V.; Asenova, Nazymgul S.; Kenenbaeva, Marzhan A.; Kuderina, Aizhan Y.; Zholtaeva, Gulnar; Boribekova, Farzana; Zhanatbekova, Nazym; Vedilina, Elena A.; Azanbekova, Gulnaz

2016-01-01

Values are keystones of society; they can vary depending on the professional activity. Teacher's values play an important role, since they directly affect the formation of knowledge of students. The paper presents the characteristics of one of the structural components of future teachers' active scientific position--pedagogic values such as…

Building Path Diagrams for Multilevel Models

ERIC Educational Resources Information Center

Curran, Patrick J.; Bauer, Daniel J.

2007-01-01

Multilevel models have come to play an increasingly important role in many areas of social science research. However, in contrast to other modeling strategies, there is currently no widely used approach for graphically diagramming multilevel models. Ideally, such diagrams would serve two functions: to provide a formal structure for deriving the…

It's Music!

ERIC Educational Resources Information Center

Ramsey, Marjorie E., Ed.

Learning related to music is considered a developmental process in this collection of five articles on music education for young learners. The first article considers music in terms of the educational process and the nature of art. The importance of musical concepts and structures to understanding music is emphasized, as is the role of music in…

Department Networks and Distributed Leadership in Schools

ERIC Educational Resources Information Center

de Lima, Jorge Avila

2008-01-01

Many schools are organised into departments which function as contexts that frame teachers' professional experiences in important ways. Some educational systems have adopted distributed forms of leadership within schools that rely strongly on the departmental structure and on the role of the department coordinator as teacher leader. This paper…

Affect Regulation as a Mediator of Attachment and Deliberate Self-Harm

ERIC Educational Resources Information Center

Kimball, Joan S.; Diddams, Margaret

2007-01-01

The authors used structural equation modeling to test the mediational role of affect regulation on attachment and deliberate self-harm in 216 undergraduates. Results suggest that affect regulation mediates the relationship between attachment and deliberate self-harm, providing support for the theoretical importance of attachment and affect…

Are Grade Expectations Rational? A Classroom Experiment

ERIC Educational Resources Information Center

Hossain, Belayet; Tsigaris, Panagiotis

2015-01-01

This study examines students' expectations about their final grade. An attempt is made to determine whether students form expectations rationally. Expectations in economics, rational or otherwise, carry valuable information and have important implications in terms of both teaching effectiveness and the role of grades as an incentive structure for…

Motivations of Faculty Engagement in Internationalization: A Survey in China

ERIC Educational Resources Information Center

Li, Bihong; Tu, Yangjun

2016-01-01

Faculty plays a critical role in the growing trend of internationalization in higher education. Thus, it is important to understand the factors that drive faculty members to get involved in internationalization. Employing structural equation model with data gathered from questionnaire, this study attempts to explore how faculty engagement in…

Final Conversations, Phase 2: Children and Everyday Communication

ERIC Educational Resources Information Center

Keeley, Maureen; Baldwin, Paula

2012-01-01

This qualitative study examined messages of everyday communication (small talk and routine interactions). The importance of these messages was highlighted in light of their role in creating structure, safety, and meaning making in the family at the end of life. In addition, family rituals that developed from children's everyday communication were…

Composition of fungal communities in soil and endophytic in raspberry production systems

USDA-ARS?s Scientific Manuscript database

Fungi play important roles as decomposers, plant symbionts and pathogens in soil. While endophytes are microorganisms that dwell within plant tissues and have a symbiotic association with the host. The structures of fungal communities in the soil and in endophytic association are dependent up comple...

The Trust Imperative in the School Principalship: The Canadian Perspective

ERIC Educational Resources Information Center

Kutsyuruba, Benjamin; Walker, Keith; Noonan, Brian

2016-01-01

As a fundamental concept in human interactions, trust is important for understanding and mediating the social structures in schools. The instrumental work of cultivating, brokering, and maintaining trust in schools lies within the role of the school administrator. Our exploratory study examined the Canadian school principals' perceptions of their…

Modeling Protein Self Assembly

ERIC Educational Resources Information Center

Baker, William P.; Jones, Carleton Buck; Hull, Elizabeth

2004-01-01

Understanding the structure and function of proteins is an important part of the standards-based science curriculum. Proteins serve vital roles within the cell and malfunctions in protein self assembly are implicated in degenerative diseases. Experience indicates that this topic is a difficult one for many students. We have found that the concept…

Enteral leucine and protein synthesis in skeletal and cardiac muscle

USDA-ARS?s Scientific Manuscript database

There are three members of the Branch Chain Amino Acids: leucine, isoleucine, and valine. As essential amino acids, these amino acids have important functions which include a primary role in protein structure and metabolism. It is intriguing that the requirement for BCAA in humans comprise about 40–...

Ecohydrological Responses of Dense Canopies to Environmental Variability Part 2: Role of Acclimation Under Elevated CO2

USDA-ARS?s Scientific Manuscript database

The ability to accurately predict land-atmosphere exchange of mass, energy, and momentum over the coming century requires the consideration of plant biochemical, ecophysiological and structural acclimation to modifications of the ambient environment. Amongst the most important environmental changes ...

[Research advances in the role of sphingolipids in HCV and HBV life cycles].

PubMed

Zhang, J Y; Duan, Z P; Zhang, J L; Zheng, S J

2016-12-20

Sphingolipids and their metabolites are not only important structural molecules of the cell membrane, but also involved in all phases of viral life cycle, including cell adhesion, membrane fusion, viral replication, viral assembly, intracellular transport, protein sorting, and exocytosis. In recent years, sphingolipids have become one of the focuses of lipid research. This article reviews the role of sphingolipids in the life cycles of hepatitis C virus and hepatitis B virus with reference to recent research achievements in China and foreign countries.

Life is three-dimensional, and it begins with molecules.

PubMed

Bourne, Philip E

2017-03-01

The iconic image of the DNA double helix embodies the central role that three-dimensional structures play in understanding biological processes, which, in turn, impact health and well-being. Here, that role is explored through the eyes of one scientist, who has been lucky enough to have over 150 talented people pass through his laboratory. Each contributed to that understanding. What follows is a small fraction of their story, with an emphasis on basic research outcomes of importance to society at large.

The small heat shock protein Hsp27: Present understanding and future prospects.

PubMed

Singh, Manish Kumar; Sharma, Bechan; Tiwari, Pramod K

2017-10-01

Heat shock proteins are important for maintaining protein homeostasis and cell survival. Among different classes of highly conserved Hsps, low molecular weight Hsps (sHsps) have significant place, particularly Hsp27, whose role has been demonstrated in wide range of biological processes, including development, immunity, diseases and therapy. In this review, the structure and functions of Hsp27 and related genes, their role in different cellular processes as well as in stress tolerance, is highlighted. Copyright © 2017 Elsevier Ltd. All rights reserved.

The role of actin networks in cellular mechanosensing

NASA Astrophysics Data System (ADS)

Azatov, Mikheil

Physical processes play an important role in many biological phenomena, such as wound healing, organ development, and tumor metastasis. During these processes, cells constantly interact with and adapt to their environment by exerting forces to mechanically probe the features of their surroundings and generating appropriate biochemical responses. The mechanisms underlying how cells sense the physical properties of their environment are not well understood. In this thesis, I present my studies to investigate cellular responses to the stiffness and topography of the environment. In order to sense the physical properties of their environment, cells dynamically reorganize the structure of their actin cytoskeleton, a dynamic network of biopolymers, altering the shape and spatial distribution of protein assemblies. Several observations suggest that proteins that crosslink actin filaments may play an important role in cellular mechanosensitivity. Palladin is an actin-crosslinking protein that is found in the lamellar actin network, stress fibers and focal adhesions, cellular structures that are critical for mechanosensing of the physical environment. By virtue of its close interactions with these structures in the cell, palladin may play an important role in cell mechanics. However, the role of actin crosslinkers in general, and palladin in particular, in cellular force generation and mechanosensing is not well known. I have investigated the role of palladin in regulating the plasticity of the actin cytoskeleton and cellular force generation in response to alterations in substrate stiffness. I have shown that the expression levels of palladin modulate the forces exerted by cells and their ability to sense substrate stiffness. Perturbation experiments also suggest that palladin levels in cells altered myosin motor activity. These results suggest that the actin crosslinkers, such as palladin, and myosin motors coordinate for optimal cell function and to prevent aberrant behavior as in cancer metastasis. In addition to stiffness, the local geometry or topography of the surface has been shown to modulate the movement, morphology, and cytoskeletal organization of cells. However, the effect of topography on fluctuations of intracellular structures, which arise from motor driven activity on a viscoelastic actin network are not known. I have used nanofabricated substrates with parallel ridges to show that the cell shape, the actin cytoskeleton and focal adhesions all align along the direction of the ridges, exhibiting a biphasic dependence on the spacing between ridges. I further demonstrated that palladin bands along actin stress fibers undergo a complex diffusive motion with velocities aligned along the direction of ridges. These results provide insight into the mechanisms of cellular mechanosensing of the environment, suggesting a complex interplay between the actin cytoskeleton and cellular adhesions in coordinating cellular response to surface topography. Overall, this work has advanced our understanding of mechanisms that govern cellular responses to their physical environment.

P21 activated kinases: structure, regulation, and functions.

PubMed

Rane, Chetan K; Minden, Audrey

2014-01-01

The p21 activated kinases (Paks) are well known effector proteins for the Rho GTPases Cdc42 and Rac. The Paks contain 6 members, which fall into 2 families of proteins. The first family consists of Paks 1, 2, and 3, and the second consists of Paks 4, 5, and 6. While some of the Paks are ubiquitously expressed, others have more restrictive tissue specificity. All of them are found in the nervous system. Studies using cell culture, transgenic mice, and knockout mice, have revealed important roles for the Paks in cytoskeletal organization and in many aspects of cell growth and development. This review discusses the basic structures of the Paks, and their roles in cell growth, development, and in cancer.

Centrioles in flies: the exception to the rule?

PubMed

Gogendeau, Delphine; Basto, Renata

2010-04-01

Centrioles and basal bodies are MT based structures that present a highly conserved ninefold symmetry. Centrioles can be found at the core of the centrosome where they participate in PCM recruitment and organization, contributing to cytoplasmic MT nucleation. Basal bodies are normally located closely to the plasma membrane where they are responsible for axoneme assembly to form structures such as cilia or flagella. While it is well accepted that these organelles have important roles in cell and tissue organization, their contribution to certain phases of animal development is still not entirely established. Here we review the role of centrosomes and cilia in Drosophila melanogaster and briefly discuss the implications of these findings to other model organisms. Copyright 2009 Elsevier Ltd. All rights reserved.

A systemic approach to occupational and environmental health.

PubMed

Spitzer, Skip

2005-01-01

As the corporate role in occupational and public health receives increased scrutiny, it is essential to recognize that it is not sufficient to identify specific acts of malfeasance or influence, or even to campaign to address them. A more comprehensive and systemic framework for understanding the role of corporations requires consideration of corporate power and its effects as endemic features of national socioeconomic systems and the rapidly integrating global order. The underlying social structures that produce social and environmental problems, and undermine reform, make systemic change necessary. Identifying this "structure of harm" provides important implications for researchers, policymakers, activists, and others trying to address environmental and social problems, particularly with regard to integrating efforts to address immediate impacts with those for longer-term, systemic change.

On the role of weak interface in crack blunting process in nanoscale layered composites

NASA Astrophysics Data System (ADS)

Li, Yi; Zhou, Qing; Zhang, Shuang; Huang, Ping; Xu, Kewei; Wang, Fei; Lu, Tianjian

2018-03-01

Heterointerface in a nanoscale metallic layered composite could improve its crack resistance. However, the influence of metallic interface structures on crack propagation has not been well understood at atomic scale. By using the method of molecular dynamics (MD) simulation, the crack propagation behavior in Cu-Nb bilayer is compared with that in Cu-Ni bilayer. We find that the weak Cu-Nb interface plays an important role in hindering crack propagation in two ways: (i) dislocation nucleation at the interface releases stress concentration for the crack to propagate; (ii) the easily sheared weak incoherent interface blunts the crack tip. The results are helpful for understanding the interface structure dependent crack resistance of nanoscale bicrystal interfaces.

Keeping time: could quantum beating in microtubules be the basis for the neural synchrony related to consciousness?

PubMed

Craddock, Travis J A; Priel, Avner; Tuszynski, Jack A

2014-06-01

This paper discusses the possibility of quantum coherent oscillations playing a role in neuronal signaling. Consciousness correlates strongly with coherent neural oscillations, however the mechanisms by which neurons synchronize are not fully elucidated. Recent experimental evidence of quantum beats in light-harvesting complexes of plants (LHCII) and bacteria provided a stimulus for seeking similar effects in important structures found in animal cells, especially in neurons. We argue that microtubules (MTs), which play critical roles in all eukaryotic cells, possess structural and functional characteristics that are consistent with quantum coherent excitations in the aromatic groups of their tryptophan residues. Furthermore we outline the consequences of these findings on neuronal processes including the emergence of consciousness.

Thermal buckling optimisation of composite plates using firefly algorithm

NASA Astrophysics Data System (ADS)

Kamarian, S.; Shakeri, M.; Yas, M. H.

2017-07-01

Composite plates play a very important role in engineering applications, especially in aerospace industry. Thermal buckling of such components is of great importance and must be known to achieve an appropriate design. This paper deals with stacking sequence optimisation of laminated composite plates for maximising the critical buckling temperature using a powerful meta-heuristic algorithm called firefly algorithm (FA) which is based on the flashing behaviour of fireflies. The main objective of present work was to show the ability of FA in optimisation of composite structures. The performance of FA is compared with the results reported in the previous published works using other algorithms which shows the efficiency of FA in stacking sequence optimisation of laminated composite structures.

Aurora Kinase B, a novel regulator of TERF1 binding and telomeric integrity

PubMed Central

Chan, Foong Lyn; Vinod, Benjamin; Novy, Karel; Schittenhelm, Ralf B.; Huang, Cheng; Udugama, Maheshi; Nunez-Iglesias, Juan; Lin, Jane I.; Hii, Linda; Chan, Julie; Pickett, Hilda A.; Daly, Roger J.

2017-01-01

Abstract AURKB (Aurora Kinase B) is a serine/threonine kinase better known for its role at the mitotic kinetochore during chromosome segregation. Here, we demonstrate that AURKB localizes to the telomeres in mouse embryonic stem cells, where it interacts with the essential telomere protein TERF1. Loss of AURKB function affects TERF1 telomere binding and results in aberrant telomere structure. In vitro kinase experiments successfully identified Serine 404 on TERF1 as a putative AURKB target site. Importantly, in vivo overexpression of S404-TERF1 mutants results in fragile telomere formation. These findings demonstrate that AURKB is an important regulator of telomere structural integrity. PMID:29040668

The Structural Changes of Tropical Cyclones Upon Interaction with Vertical Wind Shear

NASA Technical Reports Server (NTRS)

Ritchie, Elizabeth A.

2003-01-01

The Fourth Convection and Moisture Experiment (CAMEX-4) provided a unique opportunity to observe the distributions and document the roles of important atmospheric factors that impact the development of the core asymmetries and core structural changes of tropical cyclones embedded in vertical wind shear. The state-of-the-art instruments flown on the NASA DC-8 and ER-2, in addition to those on the NOAA aircraft, provided a unique set of observations that documented the core structure throughout the depth of the tropical cyclone. These data have been used to conduct a combined observational and modeling study using a state-of-the-art, high- resolution mesoscale model to examine the role of the environmental vertical wind shear in producing tropical cyclone core asymmetries, and the effects on the structure and intensity of tropical cyclones.The scientific objectives of this study were to obtain in situ measurements that would allow documentation of the physical mechanisms that influence the development of the asymmetric convection and its effect on the core structure of the tropical cyclone.

Crystal Structure of the GRAS Domain of SCARECROW-LIKE7 in Oryza sativa

PubMed Central

Li, Shengping; Zhao, Yanhe; Zhao, Zheng; Wu, Xiuling; Sun, Lifang; Liu, Qingsong; Wu, Yunkun

2016-01-01

GRAS proteins belong to a plant-specific protein family with many members and play essential roles in plant growth and development, functioning primarily in transcriptional regulation. Proteins in the family are minimally defined as containing the conserved GRAS domain. Here, we determined the structure of the GRAS domain of Os-SCL7 from rice (Oryza sativa) to 1.82 Å. The structure includes cap and core subdomains and elucidates the features of the conserved GRAS LRI, VHIID, LRII, PFYRE, and SAW motifs. The structure is a dimer, with a clear groove to accommodate double-stranded DNA. Docking a DNA segment into the groove to generate an Os-SCL7/DNA complex provides insight into the DNA binding mechanism of GRAS proteins. Furthermore, the in vitro DNA binding property of Os-SCL7 and model-defined recognition residues are assessed by electrophoretic mobility shift analysis and mutagenesis assays. These studies reveal the structure and preliminary DNA interaction mechanisms of GRAS proteins and open the door to in-depth investigation and understanding of the individual pathways in which they play important roles. PMID:27081181

Rational redesign of inhibitors of furin/kexin processing proteases by electrostatic mutations.

PubMed

Cai, Xiao-hui; Zhang, Qing; Ding, Da-fu

2004-12-01

To model the three-dimensional structure and investigate the interaction mechanism of the proprotein convertase furin/kexin and their inhibitors (eglin c mutants). The three-dimensional complex structures of furin/kexin with its inhibitors, eglin c mutants, were generated by modeller program using the newly published X-ray crystallographical structures of mouse furin and yeast kexin as templates. The electrostatic interaction energy of each complex was calculated and the results were compared with the experimentally determined inhibition constants to find the correlation between them. High quality models of furin/kexin-eglin c mutants were obtained and used for calculation of the electrostatic interaction energies between the proteases and their inhibitors. The calculated electrostatic energies of interaction showed a linear correlation to the experimental inhibition constants. The modeled structures give good explanations of the specificity of eglin c mutants to furin/kexin. The electrostatic interactions play important roles in inhibitory activity of eglin c mutants to furin/kexin. The results presented here provided quantitative structural and functional information concerning the role of the charge-charge interactions in the binding of furin/kexin and their inhibitors.

How does morality work in the brain? A functional and structural perspective of moral behavior

PubMed Central

Pascual, Leo; Rodrigues, Paulo; Gallardo-Pujol, David

2013-01-01

Neural underpinnings of morality are not yet well understood. Researchers in moral neuroscience have tried to find specific structures and processes that shed light on how morality works. Here, we review the main brain areas that have been associated with morality at both structural and functional levels and speculate about how it can be studied. Orbital and ventromedial prefrontal cortices are implicated in emotionally-driven moral decisions, while dorsolateral prefrontal cortex appears to moderate its response. These competing processes may be mediated by the anterior cingulate cortex. Parietal and temporal structures play important roles in the attribution of others' beliefs and intentions. The insular cortex is engaged during empathic processes. Other regions seem to play a more complementary role in morality. Morality is supported not by a single brain circuitry or structure, but by several circuits overlapping with other complex processes. The identification of the core features of morality and moral-related processes is needed. Neuroscience can provide meaningful insights in order to delineate the boundaries of morality in conjunction with moral psychology. PMID:24062650

Specific cytoarchitectureal changes in hippocampal subareas in daDREAM mice.

PubMed

Mellström, Britt; Kastanauskaite, Asta; Knafo, Shira; Gonzalez, Paz; Dopazo, Xose M; Ruiz-Nuño, Ana; Jefferys, John G R; Zhuo, Min; Bliss, Tim V P; Naranjo, Jose R; DeFelipe, Javier

2016-02-29

Transcriptional repressor DREAM (downstream regulatory element antagonist modulator) is a Ca(2+)-binding protein that regulates Ca(2+) homeostasis through gene regulation and protein-protein interactions. It has been shown that a dominant active form (daDREAM) is implicated in learning-related synaptic plasticity such as LTP and LTD in the hippocampus. Neuronal spines are reported to play important roles in plasticity and memory. However, the possible role of DREAM in spine plasticity has not been reported. Here we show that potentiating DREAM activity, by overexpressing daDREAM, reduced dendritic basal arborization and spine density in CA1 pyramidal neurons and increased spine density in dendrites in dentate gyrus granule cells. These microanatomical changes are accompanied by significant modifications in the expression of specific genes encoding the cytoskeletal proteins Arc, Formin 1 and Gelsolin in daDREAM hippocampus. Our results strongly suggest that DREAM plays an important role in structural plasticity in the hippocampus.

The Role of School Principals in Shaping Children's Values.

PubMed

Berson, Yair; Oreg, Shaul

2016-12-01

Instilling values in children is among the cornerstones of every society. There is wide agreement that beyond academic teaching, schools play an important role in shaping schoolchildren's character, imparting in them values such as curiosity, achievement, benevolence, and citizenship. Despite the importance of this topic, we know very little about whether and how schools affect children's values. In this large-scale longitudinal study, we examined school principals' roles in the development of children's values. We hypothesized that relationships exist between principals' values and changes in children's values through the mediating effect of the school climate. To test our predictions, we collected data from 252 school principals, 3,658 teachers, and 49,401 schoolchildren. A multilevel structural-equation-modeling analysis yielded overall support for our hypotheses. These findings contribute to understanding the development of children's values and the far-reaching impact of leaders' values. They also demonstrate effects of schools on children beyond those on academic achievement.

Structure of Escherichia coli Arginyl-tRNA Synthetase in Complex with tRNAArg: Pivotal Role of the D-loop.

PubMed

Stephen, Preyesh; Ye, Sheng; Zhou, Ming; Song, Jian; Zhang, Rongguang; Wang, En-Duo; Giegé, Richard; Lin, Sheng-Xiang

2018-05-25

Aminoacyl-tRNA synthetases are essential components in protein biosynthesis. Arginyl-tRNA synthetase (ArgRS) belongs to the small group of aminoacyl-tRNA synthetases requiring cognate tRNA for amino acid activation. The crystal structure of Escherichia coli (Eco) ArgRS has been solved in complex with tRNA Arg at 3.0-Å resolution. With this first bacterial tRNA complex, we are attempting to bridge the gap existing in structure-function understanding in prokaryotic tRNA Arg recognition. The structure shows a tight binding of tRNA on the synthetase through the identity determinant A20 from the D-loop, a tRNA recognition snapshot never elucidated structurally. This interaction of A20 involves 5 amino acids from the synthetase. Additional contacts via U20a and U16 from the D-loop reinforce the interaction. The importance of D-loop recognition in EcoArgRS functioning is supported by a mutagenesis analysis of critical amino acids that anchor tRNA Arg on the synthetase; in particular, mutations at amino acids interacting with A20 affect binding affinity to the tRNA and specificity of arginylation. Altogether the structural and functional data indicate that the unprecedented ArgRS crystal structure represents a snapshot during functioning and suggest that the recognition of the D-loop by ArgRS is an important trigger that anchors tRNA Arg on the synthetase. In this process, A20 plays a major role, together with prominent conformational changes in several ArgRS domains that may eventually lead to the mature ArgRS:tRNA complex and the arginine activation. Functional implications that could be idiosyncratic to the arginine identity of bacterial ArgRSs are discussed. Copyright © 2018 Elsevier Ltd. All rights reserved.

Organizational culture, intersectoral collaboration and mental health care.

PubMed

Mitchell, Penelope Fay; Pattison, Philippa Eleanor

2012-01-01

This study aims to investigate whether and how organizational culture moderates the influence of other organizational capacities on the uptake of new mental health care roles by non-medical primary health and social care services. Using a cross-sectional survey design, data were collected in 2004 from providers in 41 services in Victoria, Australia, recruited using purposeful sampling. Respondents within each service worked as a group to complete a structured interview that collected quantitative and qualitative data simultaneously. Five domains of organizational capacity were analyzed: leadership, moral support and participation; organizational culture; shared concepts, policies, processes and structures; access to resource support; and social model of health. A principal components analysis explored the structure of data about roles and capacities, and multiple regression analysis examined relationships between them. The unit of analysis was the service (n = 41). Organizational culture was directly associated with involvement in two types of mental health care roles and moderated the influence of factors in the inter-organizational environment on role involvement. Congruence between the values embodied in organizational culture, communicated in messages from the environment, and underlying particular mental health care activities may play a critical role in shaping the emergence of intersectoral working and the uptake of new roles. This study is the first to demonstrate the importance of organizational culture to intersectoral collaboration in health care, and one of very few to examine organizational culture as a predictor of performance, compared with other organizational-level factors, in a multivariate analysis. Theory is developed to explain the findings.

Hierarchical structures of correlations networks among Turkey’s exports and imports by currencies

NASA Astrophysics Data System (ADS)

Kocakaplan, Yusuf; Deviren, Bayram; Keskin, Mustafa

2012-12-01

We have examined the hierarchical structures of correlations networks among Turkey’s exports and imports by currencies for the 1996-2010 periods, using the concept of a minimal spanning tree (MST) and hierarchical tree (HT) which depend on the concept of ultrametricity. These trees are useful tools for understanding and detecting the global structure, taxonomy and hierarchy in financial markets. We derived a hierarchical organization and build the MSTs and HTs during the 1996-2001 and 2002-2010 periods. The reason for studying two different sub-periods, namely 1996-2001 and 2002-2010, is that the Euro (EUR) came into use in 2001, and some countries have made their exports and imports with Turkey via the EUR since 2002, and in order to test various time-windows and observe temporal evolution. We have carried out bootstrap analysis to associate a value of the statistical reliability to the links of the MSTs and HTs. We have also used the average linkage cluster analysis (ALCA) to observe the cluster structure more clearly. Moreover, we have obtained the bidimensional minimal spanning tree (BMST) due to economic trade being a bidimensional problem. From the structural topologies of these trees, we have identified different clusters of currencies according to their proximity and economic ties. Our results show that some currencies are more important within the network, due to a tighter connection with other currencies. We have also found that the obtained currencies play a key role for Turkey’s exports and imports and have important implications for the design of portfolio and investment strategies.

Trends in asset structure between not-for-profit and investor-owned hospitals.

PubMed

Song, Paula H; Reiter, Kristin L

2010-12-01

The delivery of health care is a capital-intensive industry, and thus, hospital investment strategy continues to be an important area of interest for both health policy and research. Much attention has been given to hospitals' capital investment policies with relatively little attention to investments in financial assets, which serve an important role in not-for-profit (NFP) hospitals. This study describes and analyzes trends in aggregate asset structure between NFP and investor-owned (IO) hospitals during the post-capital-based prospective payment system implementation period, providing the first documentation of long-term trends in hospital investment. The authors find hospitals' aggregate asset structure differs significantly based on ownership, size, and profitability. For both NFP and IO hospitals, financial securities have remained consistent over time, while fixed asset representation has declined in IO hospitals.

Vibration characteristics and damage detection in a suspension bridge

NASA Astrophysics Data System (ADS)

Wickramasinghe, Wasanthi R.; Thambiratnam, David P.; Chan, Tommy H. T.; Nguyen, Theanh

2016-08-01

Suspension bridges are flexible and vibration sensitive structures that exhibit complex and multi-modal vibration. Due to this, the usual vibration based methods could face a challenge when used for damage detection in these structures. This paper develops and applies a mode shape component specific damage index (DI) to detect and locate damage in a suspension bridge with pre-tensioned cables. This is important as suspension bridges are large structures and damage in them during their long service lives could easily go un-noticed. The capability of the proposed vibration based DI is demonstrated through its application to detect and locate single and multiple damages with varied locations and severity in the cables of the suspension bridge. The outcome of this research will enhance the safety and performance of these bridges which play an important role in the transport network.

A Versatile Strategy for the Semisynthetic Production of Ser65 Phosphorylated Ubiquitin and Its Biochemical and Structural Characterisation

PubMed Central

Han, Cong; Pao, Kuan-Chuan; Kazlauskaite, Agne; Muqit, Miratul M K; Virdee, Satpal

2015-01-01

Ubiquitin phosphorylation is emerging as an important regulatory layer in the ubiquitin system. This is exemplified by the phosphorylation of ubiquitin on Ser65 by the Parkinson's disease-associated kinase PINK1, which mediates the activation of the E3 ligase Parkin. Additional phosphorylation sites on ubiquitin might also have important cellular roles. Here we report a versatile strategy for preparing phosphorylated ubiquitin. We biochemically and structurally characterise semisynthetic phospho-Ser65-ubiquitin. Unexpectedly, we observed disulfide bond formation between ubiquitin molecules, and hence a novel crystal form. The method outlined provides a direct approach to study the combinatorial effects of phosphorylation on ubiquitin function. Our analysis also suggests that disulfide engineering of ubiquitin could be a useful strategy for obtaining alternative crystal forms of ubiquitin species thereby facilitating structural validation. PMID:26010437

Workflows and the Role of Images for Virtual 3d Reconstruction of no Longer Extant Historic Objects

NASA Astrophysics Data System (ADS)

Münster, S.

2013-07-01

3D reconstruction technologies have gained importance as tools for the research and visualization of no longer extant historic objects during the last decade. Within such reconstruction processes, visual media assumes several important roles: as the most important sources especially for a reconstruction of no longer extant objects, as a tool for communication and cooperation within the production process, as well as for a communication and visualization of results. While there are many discourses about theoretical issues of depiction as sources and as visualization outcomes of such projects, there is no systematic research about the importance of depiction during a 3D reconstruction process and based on empirical findings. Moreover, from a methodological perspective, it would be necessary to understand which role visual media plays during the production process and how it is affected by disciplinary boundaries and challenges specific to historic topics. Research includes an analysis of published work and case studies investigating reconstruction projects. This study uses methods taken from social sciences to gain a grounded view of how production processes would take place in practice and which functions and roles images would play within them. For the investigation of these topics, a content analysis of 452 conference proceedings and journal articles related to 3D reconstruction modeling in the field of humanities has been completed. Most of the projects described in those publications dealt with data acquisition and model building for existing objects. Only a small number of projects focused on structures that no longer or never existed physically. Especially that type of project seems to be interesting for a study of the importance of pictures as sources and as tools for interdisciplinary cooperation during the production process. In the course of the examination the authors of this paper applied a qualitative content analysis for a sample of 26 previously published project reports to depict strategies and types and three case studies of 3D reconstruction projects to evaluate evolutionary processes during such projects. The research showed that reconstructions of no longer existing historic structures are most commonly used for presentation or research purposes of large buildings or city models. Additionally, they are often realized by interdisciplinary workgroups using images as the most important source for reconstruction as far as important media for communication and quality control during the reconstruction process.

Extracellular domains play different roles in gap junction formation and docking compatibility.

PubMed

Bai, Donglin; Wang, Ao Hong

2014-02-15

GJ (gap junction) channels mediate direct intercellular communication and play an important role in many physiological processes. Six connexins oligomerize to form a hemichannel and two hemichannels dock together end-to-end to form a GJ channel. Connexin extracellular domains (E1 and E2) have been shown to be important for the docking, but the molecular mechanisms behind the docking and formation of GJ channels are not clear. Recent developments in atomic GJ structure and functional studies on a series of connexin mutants revealed that E1 and E2 are likely to play different roles in the docking. Non-covalent interactions at the docking interface, including hydrogen bonds, are predicted to form between interdocked extracellular domains. Protein sequence alignment analysis on the docking compatible/incompatible connexins indicate that the E1 domain is important for the formation of the GJ channel and the E2 domain is important in the docking compatibility in heterotypic channels. Interestingly, the hydrogen-bond forming or equivalent residues in both E1 and E2 domains are mutational hot spots for connexin-linked human diseases. Understanding the molecular mechanisms of GJ docking can assist us to develop novel strategies in rescuing the disease-linked connexin mutants.

Quaternary tectonics from seismic interpretation and its potential relation with deep geothermal fluids in the Marche (Central Italy).

NASA Astrophysics Data System (ADS)

Chicco, Jessica; Invernizzi, Chiara; Pierantoni, Pietro Paolo; Costa, Mario

2017-04-01

Knowledge of the structural features is fundamental in evaluating geothermal exchange potential and in modelling geothermal systems. In particular, faults and fractures play an important role for the circulation of fluids in the crust, and structural setting can influence groundwater flow, its regime, chemistry and electrical conductivity. In this context, data coming from accurate studies of groundwater physical properties in the Marche region (Central Italy), concerning electrical conductivity above all, revealed some anomalies in several localities that could be ascribed to a strong structural control. Data acquisition and interpretation of some SW-NE seismic reflection profiles crossing the Apennine chain to the Adriatic sea and kindly provided by ENI S.p.A, highlight important deep Plio-Quaternary structures connected with minor surface ones and to hydrogeological conditions. Seismic profiles interpretation allowed to reconstruct the structural setting and to identify the recent evolution of the Apennine Marche sector in more detail with respect to what is already known. In fact, some high angle structures affecting the whole sedimentary sequence and routing at high depth were labelled. These are NW-SE sub-parallel transpressive structures bounded by SW and NE-dipping high-angle reverse faults reaching > 10 km depth (positive flower structures), and probably involving the upper crust basement. Three main alignments were identified from W to the coast line. In some cases, flower nucleation gives rise to the lifting and counter-clockwise rotation of the Pre-Pliocene substratum blocks, with the upwelling and outcropping of Upper Miocene (Messinian) evaporite deposits along the axial zone of the transpressive structural highs. Noting the analyses of groundwater properties coming from wells placed in proximity of these structures or located along the analysed seismic profiles, anomalies in electrical conductivity are relevant. The activity of the deep rooting structures observed in the seismic profiles and the high degree of fracturing that accompanies these complex and recent fault systems can facilitate the exchange between deep and superficial fluids. In other cases, like in coastal structural high, it can have a role in preventing the sea water ingression. This significant consideration can be supported also by the direct relation of electrical conductivity with the amount of rainfall revealed from studied piezometers along the carbonate Marche ridge. It should be explained through a specific behaviour (typical of carbonate aquifers, known as the "piston-flow phase") which implies an increase of groundwater mineralization as a result of transmission of the hydraulic pressure from the saturated zone, through fractures as important way for fluids circulation. Ultimately, we suggest that the structural control could be an important factor in influencing both the surface and the groundwater flow behaviours, and then convective component of the heat transport in the studied area.

Compartments in a marine food web associated with phylogeny, body mass, and habitat structure.

PubMed

Rezende, Enrico L; Albert, Eva M; Fortuna, Miguel A; Bascompte, Jordi

2009-08-01

A long-standing question in community ecology is whether food webs are organized in compartments, where species within the same compartment interact frequently among themselves, but show fewer interactions with species from other compartments. Finding evidence for this community organization is important since compartmentalization may strongly affect food web robustness to perturbation. However, few studies have found unequivocal evidence of compartments, and none has quantified the suite of mechanisms generating such a structure. Here, we combine computational tools from the physics of complex networks with phylogenetic statistical methods to show that a large marine food web is organized in compartments, and that body size, phylogeny, and spatial structure are jointly associated with such a compartmentalized structure. Sharks account for the majority of predatory interactions within their compartments. Phylogenetically closely related shark species tend to occupy different compartments and have divergent trophic levels, suggesting that competition may play an important role structuring some of these compartments. Current overfishing of sharks has the potential to change the structural properties, which might eventually affect the stability of the food web.

Protein modeling and molecular dynamics simulation of SlWRKY4 protein cloned from drought tolerant tomato (Solanum habrochaites) line EC520061.

PubMed

Karkute, Suhas G; Easwaran, Murugesh; Gujjar, Ranjit Singh; Piramanayagam, Shanmughavel; Singh, Major

2015-10-01

WRKY genes are members of one of the largest families of plant transcription factors and play an important role in response to biotic and abiotic stresses, and overall growth and development. Understanding the interaction of WRKY proteins with other proteins/ligands in plant cells is of utmost importance to develop plants having tolerance to biotic and abiotic stresses. The SlWRKY4 gene was cloned from a drought tolerant wild species of tomato (Solanum habrochaites) and the secondary structure and 3D modeling of this protein were predicted using Schrödinger Suite-Prime. Predicted structures were also subjected to plot against Ramachandran's conformation, and the modeled structure was minimized using Macromodel. Finally, the minimized structure was simulated in the water environment to check the protein stability. The behavior of the modeled structure was well-simulated and analyzed through RMSD and RMSF of the protein. The present work provides the modeled 3D structure of SlWRKY4 that will help in understanding the mechanism of gene regulation by further in silico interaction studies.

The structural damages of lens crystallins induced by peroxynitrite and methylglyoxal, two causative players in diabetic complications and preventive role of lens antioxidant components.

PubMed

Moghadam, Sogand Sasan; Oryan, Ahmad; Kurganov, Boris I; Tamaddon, Ali-Mohammad; Alavianehr, Mohammad Mehdi; Moosavi-Movahedi, Ali Akbar; Yousefi, Reza

2017-10-01

Peroxynitrite (PON) and methylglyoxal (MGO), two diabetes-associated compounds, are believed to be important causative players in development of diabetic cataracts. In the current study, different spectroscopic methods, gel electrophoresis, lens culture and microscopic assessments were applied to examine the impact of individual, subsequent or simultaneous modification of lens crystallins with MGO and PON on their structure, oligomerization and aggregation. The protein modifications were confirmed with detection of the significantly increased quantity of carbonyl groups and decreased levels of sulfhydryl, tyrosine and tryptophan. Also, lens proteins modification with these chemical agents was accompanied with important structural alteration, oligomerization, disulfide/chromophore mediated protein crosslinking and important proteolytic instability. All these structural damages were more pronounced when the lens proteins were modified in the presence of both mentioned chemical agents, either in sequential or simultaneous manner. Ascorbic acid and glutathione, as the main components of lens antioxidant defense mechanism, were also capable to markedly prevent the damaging effects of PON and MGO on lens crystallins, as indicated by gel electrophoresis. The results of this study may highlight the importance of lens antioxidant defense system in protection of crystallins against the structural insults induced by PON and MGO during chronic hyperglycemia in the diabetic patients. Copyright © 2017 Elsevier B.V. All rights reserved.

Tongxinluo ameliorates renal structure and function by regulating miR-21-induced epithelial-to-mesenchymal transition in diabetic nephropathy.

PubMed

Wang, Jin-yang; Gao, Yan-bin; Zhang, Na; Zou, Da-wei; Xu, Li-ping; Zhu, Zhi-yao; Li, Jiao-yang; Zhou, Sheng-nan; Cui, Fang-qiang; Zeng, Xiang-jun; Geng, Jian-guo; Yang, Jin-kui

2014-03-01

Diabetic nephropathy (DN) is one of the most important diabetic microangiopathies. The epithelial-to-mesenchymal transition (EMT) plays an important role in DN. The physiological role of microRNA-21 (miR-21) was closely linked to EMT. However, it remained elusive whether tongxinluo (TXL) ameliorated renal structure and function by regulating miR-21-induced EMT in DN. This study aimed to determine the effect of TXL on miR-21-induced renal tubular EMT and to explore the relationship between miR-21 and TGF-β1/smads signals. Real-time RT-PCR, cell transfection, in situ hybridization (ISH), and laser confocal microscopy were used, respectively. Here, we revealed that TXL dose dependently lowered miR-21 expression in tissue, serum, and cells. Overexpression of miR-21 can enhance α-smooth muscle actin (SMA) expression and decrease E-cadherin expression by upregulating smad3/p-smad3 expression and downregulating smad7 expression. Interestingly, TXL also increased E-cadherin expression and decreased α-SMA expression by regulating miR-21 expression. More importantly, TXL decreased collagen IV, fibronectin, glomerular basement membrane, glomerular area, and the albumin/creatinine ratio, whereas it increased the creatinine clearance ratio. The results demonstrated that TXL ameliorated renal structure and function by regulating miR-21-induced EMT, which was one of the mechanisms to protect against DN, and that miR-21 may be one of the therapeutic targets for TXL in DN.

MOTHER-CHILD AND FATHER-CHILD PLAY INTERACTION: THE IMPORTANCE OF PARENTAL PLAYFULNESS AS A MODERATOR OF THE LINKS BETWEEN PARENTAL BEHAVIOR AND CHILD NEGATIVITY.

PubMed

Menashe-Grinberg, Atara; Atzaba-Poria, Naama

2017-11-01

Based on the premise that father-child play is an important context for children's development and that fathers "specialize" in play, similarities and differences in the role of playfulness in the father-child and mother-child relationship were examined. Participants in this study included 111 families (children's age: 1-3 years). Father-child and mother-child play interactions were videotaped and coded for parental playfulness, sensitivity, structuring, and nonintrusiveness as well as child negativity. Results indicated that mothers and fathers did not differ in playfulness and that mothers and fathers who were higher in playfulness had children with lower levels of negativity. However, playfulness differently moderated the links between parents' and children's behaviors for mothers and fathers. A double-risk pattern was found for mothers, such that the links between child negativity and maternal sensitivity, structuring, and nonintrusiveness were significant only for the subgroup of mothers with low levels of playfulness. When mothers had high levels of playfulness, these effects were negligible. For fathers, a double-buffer pattern was revealed, indicating that the links between child negativity and paternal sensitivity and structuring were significant only for fathers with high levels of playfulness. When fathers had low levels of playfulness, these effects were negligible. These findings demonstrate the important role that parental playfulness has on parent-child interaction as well as the need to examine moderation patterns separately for fathers and mothers. © 2017 Michigan Association for Infant Mental Health.

Processes of Equatorial Thermal Structure: An Analysis of Galileo Temperature Profile with 3-D Model

NASA Technical Reports Server (NTRS)

Majeed, T.; Waite, J. H., Jr.; Bougher, S. W.; Gladstone, G. R.

2005-01-01

The Jupiter Thermosphere General Circulation Model (JTGCM) calculates the global dynamical structure of Jupiter's thermosphere self-consistently with its global thermal structure and composition. The main heat source that drives the thermospheric flow is high-latitude Joule heating. A secondary source of heating is the auroral process of particle precipitation. Global simulations of Jovian thermospheric dynamics indicate strong neutral outflows from the auroral ovals with velocities up to approximately 2 kilometers per second and subsequent convergence and downwelling at the Jovian equator. Such circulation is shown to be an important process for transporting significant amounts of auroral energy to equatorial latitudes and for regulating the global heat budget in a manner consistent with the high thermospheric temperatures observed by the Galileo probe. Adiabatic compression of the neutral atmosphere resulting from downward motion is an important source of equatorial heating (less than 0.06 microbar). The adiabatic heating continues to dominate between 0.06 and 0.2 microbar, but with an addition of comparable heating due to horizontal advection induced by the meridional flow. Thermal conduction plays an important role in transporting heat down to lower altitudes (greater than 0.2microbar) where it is balanced by the cooling associated with the wind transport processes. Interestingly, we find that radiative cooling caused by H3(+), CH4, and C2H2 emissions does not play a significant role in interpreting the Galileo temperature profile.

Influence of the membrane lipophilic environment on the structure and on the substrate access/egress routes of the human aromatase enzyme. A computational study.

PubMed

Sgrignani, Jacopo; Magistrato, Alessandra

2012-06-25

Human aromatase (HA), an enzyme located on the membrane of the endoplasmatic reticulum, is of crucial biological importance in the biosynthesis of estrogens. High levels of estrogens are related with important pathologies, conferring to HA a key role as a pharmacological target. In this study we provide, for the first time, an atomistic model of HA embedded on a membrane model to understand the influence of the membrane lipophilic environment on the structural and dynamical properties of HA and on the access/egress pathways of the substrate (androstenedione, ASD) and of the oxygen molecule (involved in the enzymatic process) into/from the HA active site. To this end we used several computational techniques such as force field-based molecular dynamics (MD) simulations, Random Expulsion MD, Steered MD, and Implicit Ligand Sampling. Our results show that the membrane anchoring does not markedly affect the structural properties and the flexibility of the protein, but they clearly point out that the membrane has a marked effect on the access/egress routes of the reactants, stabilizing the formation of different channels for both ASD and O(2) with respect to those observed in pure water solution. Due to the importance of HA in medicine and since access/egress channels may influence its substrate selectivity, a detailed understanding of the role of the membrane in shaping these channels may be of valuable help in drug design.

Commonalities in the central nervous system's involvement with complementary medical therapies: limbic morphinergic processes.

PubMed

Esch, Tobias; Guarna, Massimo; Bianchi, Enrica; Zhu, Wei; Stefano, George B

2004-06-01

Currently, complementary and alternative medicine (CAM) are experiencing growing popularity, especially in former industrialized countries. However, most of the underlying physiological and molecular mechanisms as well as participating biological structures are still speculative. Specific and non-specific effects may play a role in CAM. Moreover, trust, belief, and expectation may be of importance, pointing towards common central nervous system (CNS) pathways involved in CAM. Four CAM approaches (acupuncture, meditation, music therapy, and massage therapy) were examined with regard to the CNS activity pattern involved. CNS commonalities between different approaches were investigated. Frontal/prefrontal and limbic brain structures play a role in CAM. Particularly, left-anterior regions of the brain and reward or motivation circuitry constituents are involved, indicating positive affect and emotion-related memory processing--accompanied by endocrinologic and autonomic functions--as crucial components of CAM effects. Thus, trust and belief in a therapist or positive therapy expectations seem to be important. However, besides common non-specific or subjective effects, specific (objective) physiological components also exist. Non-specific CNS commonalities are involved in various CAM therapies. Different therapeutic approaches physiologically overlap in the brain. However, molecular correspondents of the detected CNS analogies still have to be specified. In particular, fast acting autoregulatory signaling molecules presumably play a role. These may also be involved in the placebo response.

On the structural context and identification of enzyme catalytic residues.

PubMed

Chien, Yu-Tung; Huang, Shao-Wei

2013-01-01

Enzymes play important roles in most of the biological processes. Although only a small fraction of residues are directly involved in catalytic reactions, these catalytic residues are the most crucial parts in enzymes. The study of the fundamental and unique features of catalytic residues benefits the understanding of enzyme functions and catalytic mechanisms. In this work, we analyze the structural context of catalytic residues based on theoretical and experimental structure flexibility. The results show that catalytic residues have distinct structural features and context. Their neighboring residues, whether sequence or structure neighbors within specific range, are usually structurally more rigid than those of noncatalytic residues. The structural context feature is combined with support vector machine to identify catalytic residues from enzyme structure. The prediction results are better or comparable to those of recent structure-based prediction methods.

Cholesterol-Induced Formation of Liquid Ordered Phase-Like Structures in Non-Phospholipid Systems.

PubMed

Konno, Yoshikazu; Yoshimura, Akio; Naito, Noboru; Aramaki, Kenji

2018-01-01

The formation of liquid ordered (L o ) phase-like structures in stearyltrimethylammonium chloride/cholesterol/1,3-butanediol/water and hepta(oxyethylen) octadecyl ether/cholesterol/1,3-butanediol/water systems was investigated. Differential scanning calorimetry and X-ray scattering measurements confirmed that L o phase-like structures were formed in both surfactant/cholesterol systems, similar to the lysophospholipid/cholesterol system. It was revealed that the concentration of cholesterol at which only L o phase-like structures are formed increases in the order stearyltrimethylammonium chloride < lysophospholipid < hepta(oxyethylen) octadecyl ether. In addition, for both surfactants, the interlayer spacing, d, was larger for L o phase-like structures than for α-gel structures. These results suggest that the ionicity and structure of the hydrophilic group of each surfactant play important roles.

Modulation of inherent dynamical tendencies of the bisabolyl cation via preorganization in epi-isozizaene synthase.

PubMed

Pemberton, Ryan P; Ho, Krystina C; Tantillo, Dean J

2015-04-01

The relative importance of preorganization, selective transition state stabilization and inherent reactivity are assessed through quantum chemical and docking calculations for a sesquiterpene synthase ( epi -isozizaene synthase, EIZS). Inherent reactivity of the bisabolyl cation, both static and dynamic, appears to determine the pathway to product, although preorganization and selective binding of the final transition state structure in the multi-step carbocation cascade that forms epi -isozizaene appear to play important roles.

Accelerating Exploitation of Low-grade Intelligence through Semantic Text Processing of Social Media

DTIC Science & Technology

2013-06-01

importance as an information source. The brevity of social media content (e.g., 140 characters per tweet) combined with the increasing usage of mobile...platform imports unstructured text from a variety of sources and then maps the text to an existing ontology of frames (FrameNet, https...framenet.icsi.berkeley.edu/fndrupal/) during a process of Semantic Role Labeling ( SRL ). FrameNet is a structured language model grounded in the theory of Frame

Shape of the growing front of biofilms

NASA Astrophysics Data System (ADS)

Wang, Xin; Stone, Howard A.; Golestanian, Ramin

2017-12-01

The spatial organization of bacteria in dense biofilms is key to their collective behaviour, and understanding it will be important for medical and technological applications. Here we study the morphology of a compact biofilm that undergoes unidirectional growth, and determine the condition for the stability of the growing interface as a function of the nutrient concentration and mechanical tension. Our study suggests that transient behaviour may play an important role in shaping the structure of a biofilm.

Denaturation of collagen structures and their transformation under the physical and chemical effects

NASA Astrophysics Data System (ADS)

Ivankin, A.; Boldirev, V.; Fadeev, G.; Baburina, M.; Kulikovskii, A.; Vostrikova, N.

2017-11-01

The process of denaturation of collagen structures under the influence of physical and chemical factors play an important role in the manufacture of food technology and the production of drugs for medicine and cosmetology. The paper discussed the problem of the combined effects of heat treatment, mechanical dispersion and ultrasonic action on the structural changes of the animal collagen in the presence of weak protonated organic acids. Algorithm combined effects of physical and chemical factors as a result of the formation of the technological properties of products containing collagen has been shown.

The Human Placenta Project: Placental Structure, Development, and Function in Real Time

PubMed Central

Guttmacher, Alan E.; Maddox, Yvonne T.; Spong, Catherine Y.

2014-01-01

Despite its crucial role in the health of both the fetus and the pregnant woman, the placenta is the least understood human organ. Since a growing body of evidence also underscores the importance of placental development in the lifelong health of both mother and offspring, this lack of knowledge about placental structure and function is particularly concerning. Given modern approaches and technologies and the ability to develop new methods, we propose a coordinated “Human Placenta Project,” with the ultimate goal of understanding human placental structure, development, and function in real time. PMID:24661567

Key diffusion mechanisms involved in regulating bidirectional water permeation across E. coli outer membrane lectin

PubMed Central

Sachdeva, Shivangi; Kolimi, Narendar; Nair, Sanjana Anilkumar; Rathinavelan, Thenmalarchelvi

2016-01-01

Capsular polysaccharides (CPSs) are major bacterial virulent determinants that facilitate host immune evasion. E. coli group1 K30CPS is noncovalently attached to bacterial surface by Wzi, a lectin. Intriguingly, structure based phylogenetic analysis indicates that Wzi falls into porin superfamily. Molecular dynamics (MD) simulations further shed light on dual role of Wzi as it also functions as a bidirectional passive water specific porin. Such a functional role of Wzi was not realized earlier, due to the occluded pore. While five water specific entry points distributed across extracellular & periplasmic faces regulate the water diffusion involving different mechanisms, a luminal hydrophobic plug governs water permeation across the channel. Coincidently, MD observed open state structure of “YQF” triad is seen in sugar-binding site of sodium-galactose cotransporters, implicating its involvement in K30CPS surface anchorage. Importance of Loop 5 (L5) in membrane insertion is yet another highlight. Change in water diffusion pattern of periplasmic substitution mutants suggests Wzi’s role in osmoregulation by aiding in K30CPS hydration, corroborating earlier functional studies. Water molecules located inside β-barrel of Wzi crystal structure further strengthens the role of Wzi in osmoregulation. Thus, interrupting water diffusion or L5 insertion may reduce bacterial virulence. PMID:27320406

Structural and energetic study of cation-π-cation interactions in proteins.

PubMed

Pinheiro, Silvana; Soteras, Ignacio; Gelpí, Josep Lluis; Dehez, François; Chipot, Christophe; Luque, F Javier; Curutchet, Carles

2017-04-12

Cation-π interactions of aromatic rings and positively charged groups are among the most important interactions in structural biology. The role and energetic characteristics of these interactions are well established. However, the occurrence of cation-π-cation interactions is an unexpected motif, which raises intriguing questions about its functional role in proteins. We present a statistical analysis of the occurrence, composition and geometrical preferences of cation-π-cation interactions identified in a set of non-redundant protein structures taken from the Protein Data Bank. Our results demonstrate that this structural motif is observed at a small, albeit non-negligible frequency in proteins, and suggest a preference to establish cation-π-cation motifs with Trp, followed by Tyr and Phe. Furthermore, we have found that cation-π-cation interactions tend to be highly conserved, which supports their structural or functional role. Finally, we have performed an energetic analysis of a representative subset of cation-π-cation complexes combining quantum-chemical and continuum solvation calculations. Our results point out that the protein environment can strongly screen the cation-cation repulsion, leading to an attractive interaction in 64% of the complexes analyzed. Together with the high degree of conservation observed, these results suggest a potential stabilizing role in the protein fold, as demonstrated recently for a miniature protein (Craven et al., J. Am. Chem. Soc. 2016, 138, 1543). From a computational point of view, the significant contribution of non-additive three-body terms challenges the suitability of standard additive force fields for describing cation-π-cation motifs in molecular simulations.

Genetic architecture, epigenetic influence and environment exposure in the pathogenesis of Autism.

PubMed

Yu, Li; Wu, YiMing; Wu, Bai-Lin

2015-10-01

Autism spectrum disorder (ASD) is a spectral neurodevelopment disorder affecting approximately 1% of the population. ASD is characterized by impairments in reciprocal social interaction, communication deficits and restricted patterns of behavior. Multiple factors, including genetic/genomic, epigenetic/epigenomic and environmental, are thought to be necessary for autism development. Recent reviews have provided further insight into the genetic/genomic basis of ASD. It has long been suspected that epigenetic mechanisms, including DNA methylation, chromatin structures and long non-coding RNAs may play important roles in the pathology of ASD. In addition to genetic/genomic alterations and epigenetic/epigenomic influences, environmental exposures have been widely accepted as an important role in autism etiology, among which immune dysregulation and gastrointestinal microbiota are two prominent ones.

Direct DNA binding by Brca1.

PubMed

Paull, T T; Cortez, D; Bowers, B; Elledge, S J; Gellert, M

2001-05-22

The tumor suppressor Brca1 plays an important role in protecting mammalian cells against genomic instability, but little is known about its modes of action. In this work we demonstrate that recombinant human Brca1 protein binds strongly to DNA, an activity conferred by a domain in the center of the Brca1 polypeptide. As a result of this binding, Brca1 inhibits the nucleolytic activities of the Mre11/Rad50/Nbs1 complex, an enzyme implicated in numerous aspects of double-strand break repair. Brca1 displays a preference for branched DNA structures and forms protein-DNA complexes cooperatively between multiple DNA strands, but without DNA sequence specificity. This fundamental property of Brca1 may be an important part of its role in DNA repair and transcription.

Laser contrast and other key parameters enhancing the laser conversion efficiency in ion acceleration regime

NASA Astrophysics Data System (ADS)

Torrisi, Lorenzo

2018-01-01

Measurements of ion acceleration in plasma produced by fs lasers at intensity of the order of 1018 W/cm2 have been performed in different European laboratories. The forward emission in target-normal-sheath-acceleration (TNSA) regime indicated that the maximum energy is a function of the laser parameters, of the irradiation conditions and of the target properties.In particular the laser intensity and contrast play an important role to maximize the ion acceleration enhancing the conversion efficiency. Also the use of suitable prepulses, focal distances and polarized laser light has important roles. Finally the target composition, surface, geometry and multilayered structure, permit to enhance the electric field driving the forward ion acceleration.Experimental measurements will be reported and discussed.

Structure of the large FK506-binding protein FKBP51, an Hsp90-binding protein and a component of steroid receptor complexes

PubMed Central

Sinars, Cindy R.; Cheung-Flynn, Joyce; Rimerman, Ronald A.; Scammell, Jonathan G.; Smith, David F.; Clardy, Jon

2003-01-01

The ability to bind immunosuppressive drugs such as cyclosporin and FK506 defines the immunophilin family of proteins, and the FK506-binding proteins form the FKBP subfamily of immunophilins. Some FKBPs, notably FKBP12 (the 12-kDa FK506-binding protein), have defined roles in regulating ion channels or cell signaling, and well established structures. Other FKBPs, especially the larger ones, participate in important biological processes, but their exact roles and the structural bases for these roles are poorly defined. FKBP51 (the 51-kDa FKBP) associates with heat shock protein 90 (Hsp90) and appears in functionally mature steroid receptor complexes. In New World monkeys, FKBP51 has been implicated in cortisol resistance. We report here the x-ray structures of human FKBP51, to 2.7 Å, and squirrel monkey FKBP51, to 2.8 Å, by using multiwavelength anomalous dispersion phasing. FKBP51 is composed of three domains: two consecutive FKBP domains and a three-unit repeat of the TPR (tetratricopeptide repeat) domain. This structure of a multi-FKBP domain protein clarifies the arrangement of these domains and their possible interactions with other proteins. The two FKBP domains differ by an insertion in the second that affects the formation of the progesterone receptor complex. PMID:12538866

Back to the Origin

PubMed Central

Evertts, Adam G.

2012-01-01

In bacteria, replication is a carefully orchestrated event that unfolds the same way for each bacterium and each cell division. The process of DNA replication in bacteria optimizes cell growth and coordinates high levels of simultaneous replication and transcription. In metazoans, the organization of replication is more enigmatic. The lack of a specific sequence that defines origins of replication has, until recently, severely limited our ability to define the organizing principles of DNA replication. This question is of particular importance as emerging data suggest that replication stress is an important contributor to inherited genetic damage and the genomic instability in tumors. We consider here the replication program in several different organisms including recent genome-wide analyses of replication origins in humans. We review recent studies on the role of cytosine methylation in replication origins, the role of transcriptional looping and gene gating in DNA replication, and the role of chromatin’s 3-dimensional structure in DNA replication. We use these new findings to consider several questions surrounding DNA replication in metazoans: How are origins selected? What is the relationship between replication and transcription? How do checkpoints inhibit origin firing? Why are there early and late firing origins? We then discuss whether oncogenes promote cancer through a role in DNA replication and whether errors in DNA replication are important contributors to the genomic alterations and gene fusion events observed in cancer. We conclude with some important areas for future experimentation. PMID:23634256

Determinants of community structure of zooplankton in heavily polluted river ecosystems

NASA Astrophysics Data System (ADS)

Xiong, Wei; Li, Jie; Chen, Yiyong; Shan, Baoqing; Wang, Weimin; Zhan, Aibin

2016-02-01

River ecosystems are among the most affected habitats globally by human activities, such as the release of chemical pollutants. However, it remains largely unknown how and to what extent many communities such as zooplankton are affected by these environmental stressors in river ecosystems. Here, we aim to determine major factors responsible for shaping community structure of zooplankton in heavily polluted river ecosystems. Specially, we use rotifers in the Haihe River Basin (HRB) in North China as a case study to test the hypothesis that species sorting (i.e. species are “filtered” by environmental factors and occur at environmental suitable sites) plays a key role in determining community structure at the basin level. Based on an analysis of 94 sites across the plain region of HRB, we found evidence that both local and regional factors could affect rotifer community structure. Interestingly, further analyses indicated that local factors played a more important role in determining community structure. Thus, our results support the species sorting hypothesis in highly polluted rivers, suggesting that local environmental constraints, such as environmental pollution caused by human activities, can be stronger than dispersal limitation caused by regional factors to shape local community structure of zooplankton at the basin level.

The inverse niche model for food webs with parasites

USGS Publications Warehouse

Warren, Christopher P.; Pascual, Mercedes; Lafferty, Kevin D.; Kuris, Armand M.

2010-01-01

Although parasites represent an important component of ecosystems, few field and theoretical studies have addressed the structure of parasites in food webs. We evaluate the structure of parasitic links in an extensive salt marsh food web, with a new model distinguishing parasitic links from non-parasitic links among free-living species. The proposed model is an extension of the niche model for food web structure, motivated by the potential role of size (and related metabolic rates) in structuring food webs. The proposed extension captures several properties observed in the data, including patterns of clustering and nestedness, better than does a random model. By relaxing specific assumptions, we demonstrate that two essential elements of the proposed model are the similarity of a parasite's hosts and the increasing degree of parasite specialization, along a one-dimensional niche axis. Thus, inverting one of the basic rules of the original model, the one determining consumers' generality appears critical. Our results support the role of size as one of the organizing principles underlying niche space and food web topology. They also strengthen the evidence for the non-random structure of parasitic links in food webs and open the door to addressing questions concerning the consequences and origins of this structure.