bluuebunny/crossref_metadata_2025 huggingface dataset:
Zebrafish early cardiac connexin, Cx36.7/Ecx, regulates myofibril orientation and heart morphogenesis by establishing
Nkx2.5
expression
Authors: Sultana Naznin , Nag Kakon , Hoshijima Kazuyuki , Laird Dale W. , Kawakami Atsushi , Hirose Shigehisa
Published: March 2008

Heart development is a precisely coordinated process of cellular proliferation, migration, differentiation, and integrated morphogenetic interactions, and therefore it is highly susceptible to developmental anomalies such as the congenital heart disease (CHD). One of the major causes of CHD has been shown to be the mutations in key cardiac transcription factors, including
nkx2.5
. Here, we report the analysis of zebrafish mutant
ftk
that showed a progressive heart malformation in the later stages of heart morphogenesis. Our analyses revealed that the cardiac muscle maturation and heart morphogenesis in
ftk
mutants were impaired because of the disorganization of myofibrils. Notably, we found that the expression of
nkx2.5
was down-regulated in the
ftk
heart despite the normal expression of
gata4
and
tbx5
, suggesting a common mechanism for the occurrence of
ftk
phenotype and CHD. We identified
ftk
to be a loss-of-function mutation in a connexin gene,
cx36.7
/
early cardiac connexin
(
ecx
), expressed during early heart development. We further showed by a rescue experiment that Nkx2.5 is the downstream mediator of Ecx-mediated signaling. From these results, we propose that the cardiac connexin Ecx and its downstream signaling are crucial for establishing
nkx2.5
expression, which in turn promotes unidirectional, parallel alignment of myofibrils and the subsequent proper heart morphogenesis.
Rapid chemotactic response enables marine bacteria to exploit ephemeral microscale nutrient patches
Authors: Stocker Roman , Seymour Justin R. , Samadani Azadeh , Hunt Dana E. , Polz Martin F.
Published: March 2008

Because ocean water is typically resource-poor, bacteria may gain significant growth advantages if they can exploit the ephemeral nutrient patches originating from numerous, small sources. Although this interaction has been proposed to enhance biogeochemical transformation rates in the ocean, it remains questionable whether bacteria are able to efficiently use patches before physical mechanisms dissipate them. Here we show that the rapid chemotactic response of the marine bacterium
Pseudoalteromonas haloplanktis
substantially enhances its ability to exploit nutrient patches before they dissipate. We investigated two types of patches important in the ocean: nutrient pulses and nutrient plumes, generated for example from lysed algae and sinking organic particles, respectively. We used microfluidic devices to create patches with environmentally realistic dimensions and dynamics. The accumulation of
P. haloplanktis
in response to a nutrient pulse led to formation of bacterial hot spots within tens of seconds, resulting in a 10-fold higher nutrient exposure for the fastest 20% of the population compared with nonmotile cells. Moreover, the chemotactic response of
P. haloplanktis
was >10 times faster than the classic chemotaxis model
Escherichia coli
, leading to twice the nutrient exposure. We demonstrate that such rapid response allows
P. haloplanktis
to colonize nutrient plumes for realistic particle sinking speeds, with up to a 4-fold nutrient exposure compared with nonmotile cells. These results suggest that chemotactic swimming strategies of marine bacteria in patchy nutrient seascapes exert strong influence on carbon turnover rates by triggering the formation of microscale hot spots of bacterial productivity.
Bystander B cells rapidly acquire antigen receptors from activated B cells by membrane transfer
Authors: Quah Ben J. C. , Barlow Vaughan P. , McPhun Virginia , Matthaei Klaus I. , Hulett Mark D. , Parish Christopher R.
Published: March 2008

The B cell antigen receptor (BCR) efficiently facilitates the capture and processing of a specific antigen for presentation on MHC class II molecules to antigen-specific CD4+T cells (1). Despite this, the majority of B cells are thought to play only a limited role in CD4+T cell activation because BCRs are clonotypically expressed. Here, we show, however, that activated B cells can, bothin vitroandin vivo, rapidly donate their BCR to bystander B cells, a process that is mediated by direct membrane transfer between adjacent B cells and is amplified by the interaction of the BCR with a specific antigen. This results in a dramatic expansion in the number of antigen-binding B cellsin vivo, with the transferred BCR endowing recipient B cells with the ability to present a specific antigen to antigen-specific CD4+T cells.
Insulin signaling is involved in the regulation of worker division of labor in honey bee colonies
Authors: Ament Seth A. , Corona Miguel , Pollock Henry S. , Robinson Gene E.
Published: March 2008

It has been proposed that one route of behavioral evolution involves novel regulation of conserved genes. Age-related division of labor in honey bee colonies, a highly derived behavioral system, involves the performance of different feeding-related tasks by different groups of individuals. Older bees acquire the colony's food by foraging for nectar and pollen, and the younger “nurse” bees feed larvae processed foods. The transition from hive work to foraging has been shown to be socially regulated and associated both with decreases in abdominal lipid stores and with increases in brain expression of genes implicated in feeding behavior in
Drosophila melanogaster
. Here we show that division of labor is influenced by a canonical regulator of food intake and energy balance in solitary species, the insulin/insulin-like growth factor signaling (IIS) pathway. Foragers had higher levels of IIS gene expression in the brain and abdomen than did nurses, despite their low lipid stores. These differences are likely nutritionally mediated because manipulations that induced low lipid stores in young bees also up-regulated these genes. Changes in IIS also causally influenced the timing of behavioral maturation: inhibition of the insulin-related target of rapamycin pathway delayed the onset of foraging in a seasonally dependent manner. In addition, pathway analyses of microarray data revealed that nurses and foragers differ in brain energy metabolism gene expression, but the differences are opposite predictions based on their insulin-signaling status. These results suggest that changes in the regulation of the IIS pathway are associated with social behavior.
Holes and maps of Euclidean domains
Authors: Väisälä Jussi
Published: March 2008

We study the behavior of the quasiconvexity and bounded turning of holes of domains under quasisymmetric and bilipschitz maps.
Retracted: Lectin-deficient Calreticulin Retains Full Functionality as a Chaperone for Class I Histocompatibility Molecules
Authors: Ireland Breanna S. , Brockmeier Ulf , Howe Christopher M. , Elliott Tim , Williams David B.
Published: March 2008

Calreticulin is a molecular chaperone of the endoplasmic reticulum that uses both a lectin site specific for Glc1Man5-9GlcNAc2oligosaccharides and a polypeptide binding site to interact with nascent glycoproteins. The latter mode of substrate recognition is controversial. To examine the relevance of polypeptide binding to protein folding in living cells, we prepared lectin-deficient mutants of calreticulin and examined their abilities to support the assembly and quality control of mouse class I histocompatibility molecules. In cells lacking calreticulin, class I molecules exhibit inefficient loading of peptide ligands, reduced cell surface expression and aberrantly rapid export from the endoplasmic reticulum. Remarkably, expression of calreticulin mutants that are completely devoid of lectin function fully complemented all of the class I biosynthetic defects. We conclude that calreticulin can use nonlectin-based modes of substrate interaction to effect its chaperone and quality control functions on class I molecules in living cells. Furthermore, pulse-chase coimmunoisolation experiments revealed that lectin-deficient calreticulin bound to a similar spectrum of client proteins as wild-type calreticulin and dissociated with similar kinetics, suggesting that lectin-independent interactions are commonplace in cells and that they seem to be regulated during client protein maturation.
Functional Redundancy of the B9 Proteins and Nephrocystins inCaenorhabditis elegansCiliogenesis
Authors: Williams Corey L. , Winkelbauer Marlene E. , Schafer Jenny C. , Michaud Edward J. , Yoder Bradley K.
Published: March 2008

Meckel-Gruber syndrome (MKS), nephronophthisis (NPHP), and Joubert syndrome (JBTS) are a group of heterogeneous cystic kidney disorders with partially overlapping loci. Many of the proteins associated with these diseases interact and localize to cilia and/or basal bodies. One of these proteins is MKS1, which is disrupted in some MKS patients and contains a B9 motif of unknown function that is found in two other mammalian proteins, B9D2 and B9D1. Caenorhabditis elegans also has three B9 proteins: XBX-7 (MKS1), TZA-1 (B9D2), and TZA-2 (B9D1). Herein, we report that the C. elegans B9 proteins form a complex that localizes to the base of cilia. Mutations in the B9 genes do not overtly affect cilia formation unless they are in combination with a mutation in nph-1 or nph-4, the homologues of human genes (NPHP1 and NPHP4, respectively) that are mutated in some NPHP patients. Our data indicate that the B9 proteins function redundantly with the nephrocystins to regulate the formation and/or maintenance of cilia and dendrites in the amphid and phasmid ciliated sensory neurons. Together, these data suggest that the human homologues of the novel B9 genes B9D2 and B9D1 will be strong candidate loci for pathologies in human MKS, NPHP, and JBTS.
Alg13p, the Catalytic Subunit of the Endoplasmic Reticulum UDP-GlcNAc Glycosyltransferase, Is a Target for Proteasomal Degradation
Authors: Averbeck Nicole , Gao Xiao-Dong , Nishimura Shin-Ichiro , Dean Neta
Published: March 2008

The second step of dolichol-linked oligosaccharide synthesis in the N-linked glycosylation pathway at the endoplasmic reticulum (ER) membrane is catalyzed by an unusual hetero-oligomeric UDP-N-acetylglucosamine transferase that in most eukaryotes is comprised of at least two subunits, Alg13p and Alg14p. Alg13p is the cytosolic and catalytic subunit that is recruited to the ER by the membrane protein Alg14p. We show that in Saccharomyces cerevisiae, cytosolic Alg13p is very short-lived, whereas membrane-associated Alg13 is relatively stable. Cytosolic Alg13p is a target for proteasomal degradation, and the failure to degrade excess Alg13p leads to glycosylation defects. Alg13p degradation does not require ubiquitin but instead, requires a C-terminal domain whose deletion results in Alg13p stability. Conversely, appending this sequence onto normally long-lived β-galactosidase causes it to undergo rapid degradation, demonstrating that this C-terminal domain represents a novel and autonomous degradation motif. These data lead to the model that proteasomal degradation of excess unassembled Alg13p is an important quality control mechanism that ensures proper protein complex assembly and correct N-linked glycosylation.
Constitutive Activation of Chaperone-mediated Autophagy in Cells with Impaired Macroautophagy
Authors: Kaushik Susmita , Massey Ashish C. , Mizushima Noboru , Cuervo Ana Maria
Published: March 2008

Three different types of autophagy—macroautophagy, microautophagy, and chaperone-mediated autophagy (CMA)—contribute to degradation of intracellular components in lysosomes in mammalian cells. Although some level of basal macroautophagy and CMA activities has been described in different cell types and tissues, these two pathways are maximally activated under stress conditions. Activation of these two pathways is often sequential, suggesting the existence of some level of cross-talk between both stress-related autophagic pathways. In this work, we analyze the consequences of blockage of macroautophagy on CMA activity. Using mouse embryonic fibroblasts deficient in Atg5, an autophagy-related protein required for autophagosome formation, we have found that blockage of macroautophagy leads to up-regulation of CMA, even under basal conditions. Interestingly, different mechanisms contribute to the observed changes in CMA-related proteins and the consequent activation of CMA during basal and stress conditions in these macroautophagy-deficient cells. This work supports a direct cross-talk between these two forms of autophagy, and it identifies changes in the lysosomal compartment that underlie the basis for the communication between both autophagic pathways.
A Novel Protein Phosphatase is a Binding Partner for the Protein Kinase Domains of UNC-89 (Obscurin) inCaenorhabditis elegans
Authors: Qadota Hiroshi , McGaha Lee Anne , Mercer Kristina B. , Stark Thomas J. , Ferrara Tracey M. , Benian Guy M.
Published: March 2008

Mutation of the Caenorhabditis elegans gene unc-89 results in disorganization of muscle A-bands. unc-89 encodes a giant polypeptide (900 kDa) containing two protein kinase domains, PK1 and PK2. Yeast two-hybrid screening using a portion of UNC-89 including PK2, yielded SCPL-1 (small CTD phosphatase-like-1), which contains a C terminal domain (CTD) phosphatase type domain. In addition to the PK2 domain, interaction with SCPL-1 required the putative autoinhibitory sequence, and immunoglobulin (Ig) and fibronectin type 3 (Fn3) domains lying N-terminal of the kinase domain. SCPL-1 also interacts with PK1, and it similarly requires the kinase domain and upstream Fn3 and Ig domains. Analogous regions from the two other giant kinases of C. elegans, twitchin and TTN-1, failed to interact with SCPL-1. The interaction between SCPL-1 and either Ig-Fn3-PK2 or Fn3-Ig-PK1 was confirmed by biochemical methods. The scpl-1b promoter is expressed in the same set of muscles as unc-89. Antibodies to SCPL-1 localize to the M-line and a portion of the I-band. Bacterially expressed SCPL-1 proteins have phosphatase activity in vitro with properties similar to previously characterized members of the CTD phosphatase family. RNA interference knockdown results in a defect in the function of egg-laying muscles. These studies suggest a new role for the CTD phosphatase family, that is, in muscle giant kinase signaling.
The Taverna Interaction Service: enabling manual interaction in workflows
Authors: Lanzén Anders , Oinn Tom
Published: March 2008

Summary: Taverna is an application that eases the integration of tools and databases for life science research by the construction of workflows. The Taverna Interaction Service extends the functionality of Taverna by defining human interaction within a workflow and acting as a mediation layer between the automated workflow engine and one or more users.

Availability: Taverna, the Interaction Service plug-in and web application are available as open source and can be downloaded from http://taverna.sourceforge.net/

Contact:  taverna-users@lists.sourceforge.net
PlasmoGF: an integrated system for comparative genomics and phylogenetic analysis of Plasmodium gene families
Authors: Xu Xiang , Wu Jinyu , Xiao Jian , Tan Yi , Bao Qiyu , Zhao Fangqing , Li Xiaokun
Published: March 2008

Summary: Malaria, one of the world's most common diseases, is caused by the intracellular protozoan parasite known as Plasmodium. Recently, with the arrival of several malaria parasite genomes, we established an integrated system named PlasmoGF for comparative genomics and phylogenetic analysis of Plasmodium gene families. Gene families were clustered using the Markov Cluster algorithm implemented in TribeMCL program and could be searched using keywords, gene-family information, domain composition, Gene Ontology and BLAST. Moreover, a number of useful bioinformatics tools were implemented to facilitate the analysis of these putative Plasmodium gene families, including gene retrieval, annotation, sequence alignment, phylogeny construction and visualization. In the current version, PlasmoGF contained 8980 sets of gene families derived from six malaria parasite genomes: Plasmodium. falciparum, P. berghei, P. knowlesi, P. chabaudi, P. vivax and P. yoelii. The availability of such a highly integrated system would be of great interest for the community of researchers working on malaria parasite phylogenomics.

Availability: PlasmoGF is freely available at http://bioinformatics.zj.cn/pgf/

Contact:  xiaokunli@163.net; baoqy@genomics.org.cn; fuz3@psu.edu
A nearest neighbor approach for automated transporter prediction and categorization from protein sequences
Authors: Li Haiquan , Dai Xinbin , Zhao Xuechun
Published: March 2008

Motivation: Membrane transport proteins play a crucial role in the import and export of ions, small molecules or macromolecules across biological membranes. Currently, there are a limited number of published computational tools which enable the systematic discovery and categorization of transporters prior to costly experimental validation. To approach this problem, we utilized a nearest neighbor method which seamlessly integrates homologous search and topological analysis into a machine-learning framework.

Results: Our approach satisfactorily distinguished 484 transporter families in the Transporter Classification Database, a curated and representative database for transporters. A five-fold cross-validation on the database achieved a positive classification rate of 72.3% on average. Furthermore, this method successfully detected transporters in seven model and four non-model organisms, ranging from archaean to mammalian species. A preliminary literature-based validation has cross-validated 65.8% of our predictions on the 11 organisms, including 55.9% of our predictions overlapping with 83.6% of the predicted transporters in TransportDB.

Availability and Supplementary information:  http://bioinfo.noble.org/manuscript-support/transporter/

Contact:  pzhao@noble.org
Furtive foes: algal viruses as potential invaders
Authors: Lawrence Janice E.
Published: March 2008

Lawrence, J. E. 2008. Furtive foes: algal viruses as potential invaders. – ICES Journal of Marine Science, 65: 716–722. Viruses are abundant in the world's oceans, existing through parasitic relationships with their various hosts. Algal viruses infect representatives of all major algal taxa, influencing phytoplankton population dynamics, marine foodweb interactions, and global biogeochemical cycling. Although the transportation, spread, and persistence of specific viruses remain to be explored fully, the potential for algal virus introductions and invasions is clearly evident. An estimated 3 × 1022 viruses are transported globally in ballast water alone, destined for ports where few physiological or physical barriers inhibit their invasive success. This fact, coupled with recent findings that viruses are not homogeneously distributed throughout the world's oceans, suggests that virus invasions pose a potential threat to marine ecosystems.
Simple learning rules to cope with changing environments
Authors: Groß Roderich , Houston Alasdair I , Collins Edmund J , McNamara John M , Dechaume-Moncharmont François-Xavier , Franks Nigel R
Published: March 2008

We consider an agent that must choose repeatedly among several actions. Each action has a certain probability of giving the agent an energy reward, and costs may be associated with switching between actions. The agent does not know which action has the highest reward probability, and the probabilities change randomly over time. We study two learning rules that have been widely used to model decision-making processes in animals—one deterministic and the other stochastic. In particular, we examine the influence of the rules' ‘learning rate’ on the agent's energy gain. We compare the performance of each rule with the best performance attainable when the agent has either full knowledge or no knowledge of the environment. Over relatively short periods of time, both rules are successful in enabling agents to exploit their environment. Moreover, under a range of effective learning rates, both rules are equivalent, and can be expressed by a third rule that requires the agent to select the action for which the current run of unsuccessful trials is shortest. However, the performance of both rules is relatively poor over longer periods of time, and under most circumstances no better than the performance an agent could achieve without knowledge of the environment. We propose a simple extension to the original rules that enables agents to learn about and effectively exploit a changing environment for an unlimited period of time.
Tsunami: a history of the term and of scientific understanding of the phenomenon in Japanese and Western culture
Authors: Cartwright Julyan H.E , Nakamura Hisami
Published: March 2008

In the past few years we have unfortunately had several reminders of the ability of a particular type of ocean wave—a tsunami—to devastate coastal areas. The Indian Ocean tsunami of 2004, in particular, was one of the largest natural disasters of past decades in terms of the number of people killed. The name of this phenomenon,
tsunami
, is possibly the only term that has entered the physics lexicon from Japanese. We use Japanese and Western sources to document historical tsunami in Europe and Japan, the birth of the scientific understanding of tsunami, and how the Japanese term came to be adopted in English.
Determination ofB-cation chemical short-range order in perovskites from the total pair-distribution function
Authors: Krayzman Victor , Levin Igor
Published: March 2008

Short-rangeB-cation order affects the functional properties of many complex perovskites. However, current ability to measure the characteristics of such chemical short-range order (SRO) in perovskite-structured ceramics is limited. In the present study, two distinct methods are compared for the determination of theB-cation SRO parameters from the total scattering pair-distribution function (PDF). Both methods rely on reverse Monte Carlo refinements of the structural models but differ in the procedures used to extract the SRO characteristics. The accuracy of these methods was tested using synthetic PDF data generated for models of prototype Ca(Zr,Ti)O3solid solutions. One of the approaches developed in the present study, which proved to yield the most accurate results, was used to analyze the SRO of Ti and Zr in powder samples of Ca(Zr,Ti)O3.
Mercury CSD 2.0– new features for the visualization and investigation of crystal structures
Authors: Macrae Clare F. , Bruno Ian J. , Chisholm James A. , Edgington Paul R. , McCabe Patrick , Pidcock Elna , Rodriguez-Monge Lucia , Taylor Robin , van de Streek Jacco , Wood Peter A.
Published: March 2008

The programMercury, developed by the Cambridge Crystallographic Data Centre, is designed primarily as a crystal structure visualization tool. A new module of functionality has been produced, called theMaterials Module, which allows highly customizable searching of structural databases for intermolecular interaction motifs and packing patterns. This new module also includes the ability to perform packing similarity calculations between structures containing the same compound. In addition to theMaterials Module, a range of further enhancements toMercuryhas been added in this latest release, including void visualization and links toConQuest,MogulandIsoStar.
High-resolution X-ray diffractionin situstudy of very small complexes: the case of hydrogenated dilute nitrides
Authors: Bisognin G. , De Salvador D. , Napolitani E. , Berti M. , Polimeni A. , Capizzi M. , Rubini S. , Martelli F. , Franciosi A.
Published: March 2008

In this work it is demonstrated howin situhigh-resolution X-ray diffraction (HRXRD), performed during thermal annealing and employing a conventional laboratory source, can be used to obtain information on the evolution kinetics of very small complexes formed in an epitaxial layer. HRXRD allows the measurement of changes in the lattice parameter of the layer (i.e.the layer strain) with different annealing strategies (by linear temperature ramp or isothermal annealing). On the basis of these data and using an appropriate model, the dissolution energy values of the complexes can be extracted. The underlying idea is that every type of complex present in the layer gives a specific lattice strain which varies under annealing, allowing their evolution to be traced accurately. As an example, this methodology is applied to the study of N–H complexes formed in hydrogen-irradiated GaAs1−xNx/GaAs layers.
A cyberenvironment for crystallography and materials science and an integrated user interface to the Crystallography Open Database and Predicted Crystallography Open Database
Authors: Fennick Jacob R. , Keith J. Brandon , Leonard Robert H. , Truong Thanh N. , Lewis James P.
Published: March 2008

With the advent and subsequent evolution of the Internet the ways in which computational crystallographic research is conducted have dramatically changed. Consequently, secure, robust and efficient means of accessing remote data and computational resources have become a necessity. At present scientists in computational crystallography access remote data and resourcesviaseparate technologies, namely SSH and Web services. Computational Science and Engineering Online (CSE-Online) combines these two methods into a single seamless environment while simultaneously addressing issues such as stability with regard to Internet interruption. Presently CSE-Online contains several applications which are useful to crystallographers; however, continued development of new tools is necessary. Toward this end a Java application capable of running in CSE-Online, namely the Crystallography Open Database User Interface (CODUI), has been developed, which allows users to search for crystal structures stored in the Crystallography Open Database and Predicted Crystallography Open Database, to export structural data for visualization, or to input structural data in other CSE-Online applications.
Incorporation of a new design of backing seat and anvil in a Merrill–Bassett diamond anvil cell
Authors: Moggach Stephen A. , Allan David R. , Parsons Simon , Warren John E.
Published: March 2008

A modification to the Merrill–Bassett miniature diamond anvil cell is reported here, with the inclusion of tungsten carbide backing seats with Boehler–Almax-cut diamonds to replace the previously used beryllium seats and (typically) modified brilliant-cut anvils. This has led to the removal of troublesome beryllium powder lines from diffraction images, while maintaining the pressure range and opening angle of the original design.
DiXP: a Python-based GUI for controlling a powder diffractometerviathe Internet
Authors: Izaola Zunbeltz , Madariaga Gotzon
Published: March 2008

DiXPis a multi-platform data collection program decoupled from low-level basic hardware management and based on the idea of client/server remote control. The main function ofDiXPis the sequential coordination of those basic operations, allowing different strategies for the collection, archiving and graphical representation of measured data.DiXPand the control software reside, in general, on different computers and communicate with one anotherviathe Internet using TCP sockets. The disconnection between low-level handling and the measurement process makesDiXPof general use for controlling a two-circle diffractometer, and this approach can be easily extended to more complex goniometers.
Simulating X-ray diffraction of textured films
Authors: Breiby Dag W. , Bunk Oliver , Andreasen Jens W. , Lemke Henrik T. , Nielsen Martin M.
Published: March 2008

Computationally efficient simulations of grazing-incidence X-ray diffraction (GIXD) are discussed, with particular attention given to textured thin polycrystalline films on supporting substrates. A computer program has been developed for simulating scattering from thin films exhibiting varying degrees of preferred orientation. One emphasized common case is that of a `fibre' symmetry axis perpendicular to the sample plane, resulting from crystallites having one well defined crystal facet towards the substrate, but no preferred in-plane orientation. Peak splitting caused by additional scattering from the totally substrate-reflected beam (two-beam approximation) and refraction effects are also included in the program, together with the geometrical intensity corrections associated with GIXD measurements. To achieve `user friendliness' for scientists less familiar with diffraction, the mathematically simplest possible descriptions are sought whenever feasible. The practical use of the program is demonstrated for a selected thin-film example, perylene, which is of relevance for organic electronics.
Polystyrene-b-polyisoprene thin films with hexagonally perforated layer structure: quantitative grazing-incidence X-ray scattering analysis
Authors: Heo Kyuyoung , Yoon Jinhwan , Jin Sangwoo , Kim Jehan , Kim Kwang-Woo , Shin Tae Joo , Chung Bonghoon , Chang Taihyun , Ree Moonhor
Published: March 2008

Grazing-incidence X-ray scattering (GIXS) formulas for hexagonally perforated layer (HPL) structures withABCandABstacking sequences were derived, and used in the quantitative analysis of the two-dimensional GIXS patterns of polystyrene-b-polyisoprene (PS-b-PI) diblock copolymer thin films supported on silicon substrates. This quantitative analysis provided detailed information (shape, size and size distribution, packing order, layer packing sequence, and orientation) about the HPL structure of the diblock copolymer films that cannot be easily obtained with conventional X-ray and neutron scattering techniques or with conventional microscopic methods.
Optimal side-chain packing in proteins and crystallographic refinement
Authors: Gore Swanand , Blundell Tom
Published: March 2008

Amino acid side chains often adopt one of a few distinct, physicochemically favourable conformational states called rotamers. Rotameric preferences and compact packing are sufficient to estimate the conformations of most side chains, as demonstrated by approaches such asSCWRLin homology modelling, but such algorithms have not yet been applied to protein crystallographic refinement.SCWRL's combinatorial optimization algorithm was adapted for assigning side-chain rotameric states that maximize the electron density map occupation while minimizing steric clashes. Our program (OPSAX) was tested on five proteins by introducing error in main chains and comparing the subsequentCNS-only andCNS/OPSAXrefinements. The latter refinement was also extended to multiconformer models. A sequence-assignment exercise examined whetherCNS/OPSAXrefinement can discriminate between correct and incorrect assignments at various artificially lowered resolutions. The compositeCNS/OPSAXrefinement yielded better R_{\rm free} values thanCNS-only refinement. A further drop in R_{\rm free} was observed with multiconformer refinement. For complete main chains, the correct sequence could be discriminated efficiently in most cases even for a low observation-to-parameter ratio of 4, indicating that theOPSAXapproach should find useful applications in protein X-ray refinement.
X-ray diffraction contrast tomography: a novel technique for three-dimensional grain mapping of polycrystals. I. Direct beam case
Authors: Ludwig Wolfgang , Schmidt Søeren , Lauridsen Erik Mejdal , Poulsen Henning Friis
Published: March 2008

The principles of a novel technique for nondestructive and simultaneous mapping of the three-dimensional grain and the absorption microstructure of a material are explained. The technique is termed X-ray diffraction contrast tomography, underlining its similarity to conventional X-ray absorption contrast tomography with which it shares a common experimental setup. The grains are imaged using the occasionally occurring diffraction contribution to the X-ray attenuation coefficient each time a grain fulfils the diffraction condition. The three-dimensional grain shapes are reconstructed from a limited number of projections using an algebraic reconstruction technique. An algorithm based on scanning orientation space and aiming at determining the corresponding crystallographic grain orientations is proposed. The potential and limitations of a first approach, based on the acquisition of the direct beam projection images only, are discussed in this first part of the paper. An extension is presented in the second part of the paper [Johnson, King, Honnicke, Marrow & Ludwig (2008).J. Appl. Cryst.41, 310–318], addressing the case of combined direct and diffracted beam acquisition.
X-ray diffraction contrast tomography: a novel technique for three-dimensional grain mapping of polycrystals. II. The combined case
Authors: Johnson Greg , King Andrew , Honnicke Marcelo Goncalves , Marrow J. , Ludwig Wolfgang
Published: March 2008

By simultaneous acquisition of the transmitted and the diffracted beams, the applicability of the previously introduced diffraction contrast tomography technique [Ludwig, Schmidt, Lauridsen & Poulsen (2008).J. Appl. Cryst.41, 302–309] can be extended to the case of undeformed polycrystalline samples containing more than 100 grains per cross section. The grains are still imaged using the occasionally occurring diffraction contribution to the X-ray attenuation coefficient, which can be observed as a reduction in the intensity of the transmitted beam when a grain fulfils the diffraction condition. Automating the segmentation of the extinction spot images is possible with the additional diffracted beam information, even in the presence of significant spot overlap. By pairing the corresponding direct (`extinction') and diffracted beam spots a robust sorting and indexing approach has been implemented. The analysis procedure is illustrated on a real data set and the result is validated by comparison with a two-dimensional grain map obtained by electron backscatter diffraction.
ProgramCRYC3Dfor geometric computing in crystallography
Authors: Urzhumtseva Ludmila , Urzhumtsev Alexandre
Published: March 2008

The computer programCRYC3Dworks with three-dimensional crystallographic geometric objects or groups of them and calculates their basic geometric characteristics by a simple click in the menu. In particular, this includes vector operations in both direct and reciprocal spaces and cell transformations. Collecting basic crystallographic operations in a single and simple program helps crystallographers to avoid looking for `fast-and-dirty' scripts or using large and unwieldy packages and may be useful in everyday work. When running the program in its principal mode, macro-operations are accompanied by a list of elementary geometric operations. This feature, together with the presence of a single-command mode and online help, may be useful also as a teaching tool.
Structural characterization of the clay mineral illite-1M
Authors: Gualtieri Alessandro F. , Ferrari Simone , Leoni Matteo , Grathoff Georg , Hugo Richard , Shatnawi Mouath , Paglia Gianluca , Billinge Simon
Published: March 2008

This work reports the structural characterization of illite-1M from northern Hungary, with the first attempt to refine the structure model and locate the interlayer water molecule. Structural characterization was accomplished using state-of-the-art analytical methods available for clays. The results illustrate the status of techniques for clay structure determination, as well as providing a structural model for illite. The chemical formula for the illite-1M under investigation can be written as K0.78Ca0.02Na0.02(Mg0.34Al1.69FeIII0.02)[Si3.35Al0.65]O10(OH)2·nH2O. Structure simulations withWILDFIREyielded a model with 30% ofcis-vacant layers and an expandability percentage of 10%. The value of the percentage of expandability was confirmed withNEWMOD, with which the best simulation was obtained with 90% of di-octahedral mica with K (80% site population) in the interlayer region and 10% of expandable layers. The best structure simulation obtained withDIFFaXwas also obtained with a population of K atoms of 80%, six cells alongc(in agreement with the results of a transmission electron microscopy study) and an average dimension of the particles in theabplane of 300 nm. Besides the determination of the basic structure unit (the results are consistent with those obtained with the local information provided by a fit of the pair distribution function data) and the model of disorder, refinement withDIFFaX+allowed the calculation of a possible position for the interlayer water molecule. Although physically sound, both the observed tetrahedral layer corrugation and the location of the water molecule need further experimental evidence, because the final fit of the observed pattern is still imperfect. The reasons for this misfit are discussed.
Optimization and evaluation of data quality for charge density studies
Authors: Zhurov Vladimir V. , Zhurova Elizabeth A. , Pinkerton A. Alan
Published: March 2008

Criteria for the evaluation of hardware and software for the collection of charge density diffraction data are presented with examples. Evaluation of charge density studies using area detectors (based on 61 data sets) indicates that, although it is possible to obtain excellent data using such detectors, there are significant shortcomings which need to be addressed.
Non-ambient X-ray diffraction residual stress analysis of thin films: tracing nanosize-related effects on thermoelastic constants and identifying sources of residual stresses
Authors: Kuru Yener , Wohlschlögel Markus , Welzel Udo , Mittemeijer Eric J.
Published: March 2008

The stress evolutions at non-ambient temperatures in Ni and Pd layers (the thickness of each metal layer was 50 nm) were investigated employingin-situX-ray diffraction measurements in a temperature range between 173 and 523 K. Stress determinations were performed by analysing the X-ray diffraction data according to the sin2ψmethod on the basis of the crystallite group variant. The stress evolution in the Ni layer was correlated with the change of its coherently diffracting domain size and its microstrain with temperature. The advantage of measurements at temperatures below ambient to distinguish the thermal stresses from the effects of stress relaxation and emerging secondary stresses, arising from thermally activated processes (such as grain growth), is highlighted in this work for the first time. The possibility of using thein-situX-ray diffraction stress measurement to obtain coefficients of thermal expansion and thermoelastic slopes of thin films (with nanosized grains) is discussed in detail.
Distorted f.c.c. arrangement of gold nanoclusters: a model of spherical particles with microstrains and stacking faults
Authors: Longo Alessandro , Martorana Antonino
Published: March 2008

The structures of two samples of gold nanoclusters supported on silica were studied by X-ray powder diffraction (XRD) and X-ray absorption spectroscopy. The data relative to both techniques were analysed by an approach involving simulation based on structural models and fitting. The XRD model concerned a distorted f.c.c. (face-centred cubic) arrangement, with microstrains and parallel stacking faults in approximately spherical particles; as an alternative possibility, a linear combination of ordered f.c.c. and noncrystalline (decahedral and icosahedral) particles was also taken into account. Both approaches gave calculated patterns closely resembling the experimental data. X-ray absorption spectra were fitted on the basis of f.c.c. and noncrystalline arrangements. The best results were obtained by the f.c.c. motif, while a simulation consisting in the superposition of f.c.c. and noncrystalline components in the relative amounts determined by XRD analysis gave a poor agreement with the experimental data. It was concluded that the good XRD fitting obtained by linear combination of lognormal size-distributed f.c.c. cuboctahedral, decahedral and icosahedral contributions was a result of the flexibility of the basis set of functions, but that the complementary analysis of X-ray absorption data did not confirm the presence of a noteworthy fraction of noncrystalline particles.
Simultaneous estimation of the form factor and structure factor for globular particles in small-angle scattering
Authors: Hansen Steen
Published: March 2008

Small-angle scattering data from non-dilute solutions of particles are often analysed by indirect Fourier transformation using a specific model structure factor to obtain an estimate of the distance distribution function that is free from concentration effects. A new approach is suggested here, whereby the concentration effects are expressed solely through real space functions without the use of an explicit structure factor. This is done by dividing the total distance distribution function for the scattering into three different contributions, as suggested by Kruglov [(2005).J. Appl. Cryst.38, 716–720]: (i) the single particle distribution which is due to intraparticle effects, (ii) the excluded volume distribution from excluded volume effects which is only dependent upon the geometry of the particles, and (iii) a structure distribution which is due to the remaining interaction between the particles. Only the single particle distribution and the structure distribution are allowed to vary freely (within the restrictions of a smoothness constraint). These two distributions may be separated mainly because they differ in their regions of support in real space. From the estimated distributions the structure factor can be calculated. For deviations of particles from spherical symmetry, the excluded volume distribution may be approximated by that of an ellipsoid of revolution. Excluded volume distributions have been calculated for ellipsoids of revolution of axial ratios between 0.1 and 10 and implemented in the programIFTc, which is described in the appendix. The validity of the approach is demonstrated for globular particles.
Scale and density dependent relationships among roots, mycorrhizal fungi and collembola in grassland and forest
Authors: Steinaker Diego F. , Wilson Scott D.
Published: March 2008

Belowground foodwebs, which dominate energy flow in temperate systems, may yield insights into general foodweb function: do consumers drive resource levels or simply respond to them? Controversy exists about the relationships among fine roots, mycorrhizal fungi and invertebrate grazers because of the difficulty of studying belowground processes. We used contrasting temporal scales to examine relationships among roots, fungi and collembola in the top 90 cm of soil in native grassland and forest over three years, with data collected from minirhizotrons. Root production was generally similar between habitats, but fungal production and collembola density were mostly significantly greater in forest than grassland. All variables decreased significantly with increasing depth, except for forest mycorrhizal fungi. This exception suggests that forest mycorrhizae are especially important for nutrient uptake at greater soil depths. Relationships among roots, mycorrhizal fungi and collembola varied with the temporal scale considered. Over the entire growing season, collembola were significantly positively correlated with root production in forest, and with both fungal and root production in grassland, reflecting the broad positive associations between these groups. In contrast, over the shortest sampling interval (i.e. two weeks), strong negative relationships suggested that collembola grazing decreased fungal and root production. Data from all dates and depths considered together revealed that both fungal and root production were significantly higher at intermediate collembola density than at low or very high density. In summary, belowground consumers appear to drive resource levels at short time scales, but respond to broad variation in resource availability at annual time scales.
Energy metabolism and animal personality
Authors: Careau V. , Thomas D. , Humphries M. M. , Réale D.
Published: March 2008

In this paper we show how animal personality could explain some of the large inter‐individual variation in resting metabolic rate (MR) and explore methodological and functional linkages between personality and energetics. Personality will introduce variability in resting MR measures because individuals consistently differ in their stress response, exploration or activity levels, all of which influence MR measurements made with respirometry and the doubly‐labelled water technique. Physiologists try to exclude these behavioural influences from resting MR measurements, but animal personality research indicates that these attempts are unlikely to be successful. For example, because reactive animals “freeze” when submitted to a stress, their MR could be classified as “resting” because of immobility when in fact they are highly stressed with an elevated MR. More importantly, recent research demonstrating that behavioural responses to novel and highly artificial stimuli are correlated with both behaviour and fitness under more natural circumstances calls into question the wisdom of excluding these behavioural influences on MR measurements. The reason that intra‐specific variation in resting MR are so weakly correlated with daily energy expenditure (DEE) and fitness, may be that the latter two measures fully incorporate personality while the former partially excludes its influence. Because activity, exploration, boldness and aggressiveness are energetically costly, personality and metabolism should be correlated and physiological constraints may underlie behavioural syndromes. We show how physiological ecologists can better examine behavioural linkages between personality and metabolism, as required to better understand the physiological correlates of personality and the evolutionary consequences of metabolic variability.
Coping skills training and contingency management treatments for marijuana dependence: exploring mechanisms of behavior change
Authors: Litt Mark D. , Kadden Ronald M. , Kabela‐Cormier Elise , Petry Nancy M.
Published: March 2008

Aims  Achieving abstinence in the treatment of marijuana dependence has been difficult. To date the most successful treatments have included combinations of motivation enhancement treatment (MET) plus cognitive–behavioral coping skills training (CBT) and/or contingency management (ContM) approaches. Although these treatment approaches are theoretically based, their mechanisms of action have not been explored fully. The purpose of the present study was to explore mechanisms of behavior change from a marijuana treatment trial in which CBT and ContM were evaluated separately and in combination.

Design  A dismantling design was used in the context of a randomized clinical trial.

Setting  The setting was an out‐patient treatment research facility located in a university medical center.

Participants  Participants were 240 adult marijuana smokers, meeting criteria for cannabis dependence.

Interventions  Participants were assigned to one of four 9‐week treatment conditions: a case management control condition, MET/CBT coping skills training, ContM and MET/CBT + ContM.

Measurements  Outcome measures were total 90‐day abstinence, recorded every 90 days for 12 months post‐treatment.

Findings  Regardless of treatment condition, abstinence in near‐term follow‐ups was predicted most clearly by abstinence during treatment, but long‐term abstinence was predicted by use of coping skills and especially by post‐treatment self‐efficacy for abstinence.

Conclusions  It was concluded that the most efficacious treatments for marijuana dependence are likely to be those that increase self‐efficacy.