bluuebunny/crossref_metadata_2025 huggingface dataset:
The impact of generalized and institutional trust on donating to activist, leisure, and interest organizations: individual and contextual effects
Authors: Evers Anouk , Gesthuizen Maurice
Published: November 2011

In this paper, we answer the question as to what extent donating to activist, interest, and leisure organizations is affected by both individual and national levels of generalized and institutional trust. We use the European Social Survey 2002 to estimate multilevel random intercept models, based on more than 33 000 individuals living in 19 European countries and the USA. Our results show very consistent positive impacts of both individual generalized trust and institutional trust on donating to all types of organizations. The effects are strongest for donating to activist organizations and absent only for the relation between institutional trust and donating to interest organizations. At the national level, generalized trust positively affects donations to activist and leisure organizations, but not to interest organizations. Institutional trust at the national level is negatively related to donations to all types of organizations. This latter finding suggests that when institutions are perceived to function well, individuals estimate that their philanthropic donations are less needed. Copyright © 2011 John Wiley & Sons, Ltd.
Effect of additives on liquid phase epitaxy growth of non‐polar GaN single crystals using Na flux method
Authors: Masumoto K. , Someno T. , Murakami K. , Imabayashi H. , Takazawa H. , Kitamoto A. , Miyoshi N. , Maruyama M. , Imade M. , Yoshimura M. , Kitaoka Y. , Sasaki T. , Mori Y.
Published: November 2011

Non‐polar GaN substrates have attracted attention because they can improve the performance of GaN devices. Growth of high‐quality non‐polar GaN single crystals, however, has not been realized. Here, we attempted to grow m‐plane GaN crystals using the Na flux method and investigated the effect of additives such as Ca and Li in Na flux on transparency, surface roughness, and crystallinity. We found that the addition of Ca and Li improved the transparency and the surface roughness of the crystals. Moreover, high‐temperature growth improved crystallinity and decreased impurities such as Ca, Li, and O in GaN crystals. We also found that the crystallinity did not depend on the concentrations of impurities in GaN crystals. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Significance of initial stages on the epitaxial growth of AlN using high temperature halide chemical vapor deposition
Authors: Balaji Manavaimaran , Claudel Arnaud , Fellmann Vincent , Gélard Isabelle , Blanquet Elisabeth , Boichot Raphaël , Coindeau Stéphane , Roussel Hervé , Pique Didier , Baskar Krishnan , Pons Michel
Published: November 2011

AlN epilayers were grown on c‐plane Sapphire substrates using High Temperature Halide Chemical Vapor Deposition (HTCVD). Introduction of low temperature nucleation layers (NLs) prior to the high temperature AlN (HT‐AlN) layers was investigated. It was found that NLs stabilizes the epitaxial growth. NL deposition conditions were optimized to improve the quality of AlN epilayers. Increasing nucleation layer deposition temperature from 650 to 850 °C as well as the growth temperature of AlN epilayers from 1200 to 1400 °C improves the structural quality and surface morphology. X‐ray diffraction of θ/2θ scan confirms that AlN layers deposited on NLs are (0002) oriented and X‐ray rocking curve measurement shows FWHM values as low as 864 arcsec for (0002) plane. Surface steps and specular morphology were observed for such AlN epilayers (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
INTERNATIONALISATION AND CONSTITUTIONAL BORROWING IN DRAFTING BILLS OF RIGHTS
Authors: Smith Anne
Published: November 2011

This article looks at the recent phenomena of internationalisation and constitutional borrowing in drafting Bills of Rights. Using South Africa, Canada and Northern Ireland as its focus, this article posits key lessons to be considered in any society hoping to use these two strategies to best effect in designing indigenous Bills of Rights. This contribution makes the case that while these are viable strategies in equality and other rights provision drafting, before embarking on such trajectories, the local context must be considered. In short, effective and sensitive interaction between the ‘local and the global’ can result in a more rewarding project when those involved in formulating an indigenous Bill of Rights simultaneously reflect best international practice. The article is supported in its conclusions by a series of semi-structured interviews with key players involved in the drafting process in Northern Ireland and Canada.
The inseparability of cognition and emotion in second language learning
Authors: Swain Merrill
Published: November 2011

The scholarly literature about the process of second language (L2) learning has focused to a considerable extent on cognitive processes. Left aside are questions about how emotions fit into an understanding of L2 learning. One goal of this plenary is to demonstrate that we have limited our understanding of L2 learning by failing to take into account the roles played by emotions. A perspective which brings together cognition and emotion is that of Vygotsky's sociocultural theory (SCT) of mind. Vygotsky saw the two as being inextricably interconnected. However, many in the Western world who have taken up Vygotsky's ideas, myself included, have focused on the cognitive side of learning and development. The second goal of this plenary is therefore to redress this imbalance.
Shifting the stage
Authors: KAMEYAMA YUKIYOSHI , KISELYOV OLEG , SHAN CHUNG-CHIEH
Published: November 2011

It is often hard to write programs that are efficient yet reusable. For example, an efficient implementation of Gaussian elimination should be specialized to the structure and known static properties of the input matrix. The most profitable optimizations, such as choosing the best pivoting or memoization, cannot be expected of even an advanced compiler because they are specific to the domain, but expressing these optimizations directly makes for ungainly source code. Instead, a promising and popular way to reconcile efficiency with reusability is for a domain expert to write code generators.

Two pillars of this approach are types and effects. Typed multilevel languages such as MetaOCaml ensuresafetyand early error reporting: a well-typed code generator neither goes wrong nor generates code that goes wrong. Side effects such as state and control easecorrectnessandexpressivity: An effectful generator can resemble the textbook presentation of an algorithm, as is familiar to domain experts, yet insertletfor memoization andiffor bounds checking, as is necessary for efficiency. Together, types and effects enable structuring code generators as compositions of modules with well-defined interfaces, and hence scaling to large programs. However, blindly adding effects renders multilevel types unsound.

We introduce the first multilevel calculus with control effects and a sound type system. We give small-step operational semantics as well as a one-pass continuation-passing-style translation. For soundness, our calculus restricts the code generator's effects to the scope of generated binders. Even with this restriction, we can finally write efficient code generators for dynamic programming and numerical methods in direct style, like in algorithm textbooks, rather than in continuation-passing or monadic style.
Response and resilience of soil biocrust bacterial communities to chronic physical disturbance in arid shrublands
Authors: Kuske Cheryl R , Yeager Chris M , Johnson Shannon , Ticknor Lawrence O , Belnap Jayne
Published: November 2011

The impact of 10 years of annual foot trampling on soil biocrusts was examined in replicated field experiments at three cold desert sites of the Colorado Plateau, USA. Trampling detrimentally impacted lichens and mosses, and the keystone cyanobacterium, Microcoleus vaginatus, resulting in increased soil erosion and reduced C and N concentrations in surface soils. Trampled biocrusts contained approximately half as much extractable DNA and 20–52% less chlorophyll a when compared with intact biocrusts at each site. Two of the three sites also showed a decline in scytonemin-containing, diazotrophic cyanobacteria in trampled biocrusts. 16S rRNA gene sequence and terminal restriction fragment length polymorphism (T-RFLP) analyses of soil bacteria from untrampled and trampled biocrusts demonstrated a reduced proportion (23–65% reduction) of M. vaginatus and other Cyanobacteria in trampled plots. In parallel, other soil bacterial species that are natural residents of biocrusts, specifically members of the Actinobacteria, Chloroflexi and Bacteroidetes, became more readily detected in trampled than in untrampled biocrusts. Replicate 16S rRNA T-RFLP profiles from trampled biocrusts at all three sites contained significantly more fragments (n=17) than those of untrampled biocrusts (n⩽6) and exhibited much higher variability among field replicates, indicating transition to an unstable disturbed state. Despite the dramatic negative impacts of trampling on biocrust physical structure and composition, M. vaginatus could still be detected in surface soils after 10 years of annual trampling, suggesting the potential for biocrust re-formation over time. Physical damage of biocrusts, in concert with changing temperature and precipitation patterns, has potential to alter performance of dryland ecosystems for decades.
Body-Based Perceptual Rescaling Revealed through the Size — Weight Illusion
Authors: Linkenauger Sally A , Mohler Betty J , Proffitt Dennis R
Published: November 2011

An embodied approach to the perception of spatial layout contends that the body is used as a ‘perceptual ruler’ with which individuals scale the perceived environmental layout. In support of this notion, previous research has shown that the perceived size of objects can be influenced by changes in the apparent size of hand. The size – weight illusion is a well known phenomenon, which occurs when people lift two objects of equal weight but differing sizes and perceive that the larger object feels lighter. Therefore, if apparent hand size influences perceived object size, it should also influence the object's perceived weight. In this study, we investigated this possibility by using perceived weight as a measure and found that changes in the apparent size of the hand influence objects' perceived weight.
Paradoxical effects of kisspeptin: it enhances oocyte in vitro maturation but has an adverse impact on hatched blastocysts during in vitro culture
Authors: Saadeldin Islam M. , Koo Ok Jae , Kang Jung Taek , Kwon Dae Kee , Park Sol Ji , Kim Su Jin , Moon Joon Ho , Oh Hyun Ju , Jang Goo , Lee Byeong Chun
Published: November 2011

Kisspeptin (Kp) is best known as a multifunctional peptide with roles in reproduction, the cardiovascular system and cancer. In the present study the expression of kisspeptin hierarchy elements (KISS1, GNRH1 and LHB) and their receptors (KISS1R, GNRHR and LHCGR, respectively) in porcine ovary and in cumulus–oocyte complexes (COCs) were investigated, as were its effects on the in vitro maturation (IVM) of oocytes and their subsequent ability to sustain preimplantation embryo competence after parthenogenetic electrical activation. Kp system elements were expressed and affected IVM of oocytes when maturation medium was supplemented with 10–6 M Kp. Oocyte maturation, maternal gene expression (MOS, GDF9 and BMP15), blastocyst formation rate, blastocyst hatching and blastocyst total cell count were all significantly increased when oocytes were matured in medium containing Kp compared with the control group (without Kp). A Kp antagonist (p234) at 4 × 10–6 M interfered with this hierarchy but did not influence the threshold effect of gonadotrophins on oocyte maturation. FSH was critical and permissive to Kp action on COCs by increasing the relative expression of KISS1R. In contrast, Kp significantly increased apoptosis, the expression of pro-apoptotic gene, BAK1, and suppressed trophoblast outgrowths from hatched blastocysts cultured on feeder cells. The present study provides the first functional evidence of the Kp hierarchy in porcine COCs and its role in enhancing oocyte maturation and subsequent developmental competence in an autocrine–paracrine manner. However, Kp supplementation may have a harmful impact on cultured hatched blastocysts reflecting systemic or local regulation during the critical early period of embryonic development.
Eisosome proteins assemble into a membrane scaffold
Authors: Karotki Lena , Huiskonen Juha T. , Stefan Christopher J. , Ziółkowska Natasza E. , Roth Robyn , Surma Michal A. , Krogan Nevan J. , Emr Scott D. , Heuser John , Grünewald Kay , Walther Tobias C.
Published: November 2011

Spatial organization of membranes into domains of distinct protein and lipid composition is a fundamental feature of biological systems. The plasma membrane is organized in such domains to efficiently orchestrate the many reactions occurring there simultaneously. Despite the almost universal presence of membrane domains, mechanisms of their formation are often unclear. Yeast cells feature prominent plasma membrane domain organization, which is at least partially mediated by eisosomes. Eisosomes are large protein complexes that are primarily composed of many subunits of two Bin–Amphiphysin–Rvs domain–containing proteins, Pil1 and Lsp1. In this paper, we show that these proteins self-assemble into higher-order structures and bind preferentially to phosphoinositide-containing membranes. Using a combination of electron microscopy approaches, we generate structural models of Pil1 and Lsp1 assemblies, which resemble eisosomes in cells. Our data suggest that the mechanism of membrane organization by eisosomes is mediated by self-assembly of its core components into a membrane-bound protein scaffold with lipid-binding specificity.
SEPT9 occupies the terminal positions in septin octamers and mediates polymerization-dependent functions in abscission
Authors: Kim Moshe S. , Froese Carol D. , Estey Mathew P. , Trimble William S.
Published: November 2011

Septins are filamentous guanosine triphosphatase–binding proteins that are required for cytokinesis in a wide range of organisms from yeast to man. Several septins, including SEPT9, have been found to be altered in cancers, but their roles in malignancy and cytokinesis remain unclear. It is known that they assemble into rod-shaped oligomeric complexes that join end-on-end to form filaments, but whether SEPT9 incorporates into these complexes and how it does so are unanswered questions. We used tandem affinity purification of mammalian septin complexes to show that SEPT9 occupies a terminal position in an octameric septin complex. A mutant SEPT9, which cannot self-associate, disrupted septin filament formation and resulted in late abscission defects during cytokinesis but did not affect septin-dependent steps earlier in mitosis. These data suggest that mammalian SEPT9 holds a terminal position in the septin octamers, mediating abscission-specific polymerization during cytokinesis.
Determination of particle-induced structural disorder depth profile in crystals using the grazing-angle incidence hard x-ray backscattering diffraction technique*
Authors: Bezirganyan Hakob (Jacob) P , Bezirganyan Siranush E , Bezirganyan Petros H , Bezirganyan Hayk H
Published: November 2011

In this theoretical paper, we propose an x-ray imaging method for determination of particle-induced structural disorder depth profile in the crystalline materials based on the extremely sensitive, high-resolution, and non-destructive grazing-angle incidence hard x-ray backscattering diffraction technique. A peculiar value of the Bragg angle is discovered within the specular beam suppression angular region for which the curve of x-ray reflectivity is very close to the profile of the corresponding structural disorder. The coincidence presents a unique opportunity for the direct registration of the structural disorder depth profile in particle-irradiated crystals.
Collection efficiency of submicrometre particles using single and double DBD in a wire-to-square tube ESP
Authors: Gouri R , Zouzou N , Tilmatine A , Moreau E , Dascalescu L
Published: November 2011

The aim of this work is to study the collection of submicrometre particles charged by a dielectric barrier discharge (DBD) in two types of wire-to-square glass tube electrostatic precipitators (ESPs). They are, respectively, designated as single DBD-ESP and double DBD-ESP, depending on the absence or presence of a dielectric layer around the high-voltage wire electrode. The experiments are performed with incense smoke particles having a mean size of about 0.32 µm. An aerosol spectrometer is employed for characterizing the size distribution of these particles at the outlet of the ESPs. The collection efficiency is estimated for various applied voltages and frequencies (ranges: 8–28 kV, 0.3–1000 Hz) at a fixed air flow rate (5.1 L min−1). The electrical measurements show that in the case of the single DBD-ESP, the discharge mode is rather homogeneous. In contrast, the discharge has a filamentary behaviour in the case of the double DBD-ESP. Results show that the particle collection efficiency of both ESPs is higher at high applied voltages and within a certain frequency range. However, corroborating the collection efficiency results with the power consumption measurements reveals that the double DBD-ESP offers better performances for a larger frequency range.
Mechanism of femtosecond laser inducing inverted microstructures by employing different types of objective lens
Authors: Song Juan , Luo Fangfang , Hu Xiao , Zhao Quanzhong , Qiu Jianrong , Xu Zhizhan
Published: November 2011

In this paper, an interesting inverted structure, fabricated by focusing femtosecond laser pulses through two different objective lenses (an oil-immersion objective lens and a dry objective lens), is reviewed. According to the interface spherical aberration theory, reasonable models are built and the simulated laser fluence in the focal region is given. The distribution of laser fluence agrees with the structural characteristics of the experimentally obtained void array. We propose that the monotonic tendency that the aberration function changes with the azimuth angle determines the final ‘growth’ direction of the void array.
PLCζ causes Ca2+oscillations in mouse eggs by targeting intracellular and not plasma membrane PI(4,5)P2
Authors: Yu Yuansong , Nomikos Michail , Theodoridou Maria , Nounesis George , Lai F. Anthony , Swann Karl
Published: November 2011

Sperm-specific phospholipase C ζ (PLCζ) activates embryo development by triggering intracellular Ca2+oscillations in mammalian eggs indistinguishable from those at fertilization. Somatic PLC isozymes generate inositol 1,4,5-trisphophate–mediated Ca2+release by hydrolyzing phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) in the plasma membrane. Here we examine the subcellular source of PI(4,5)P2targeted by sperm PLCζ in mouse eggs. By monitoring egg plasma membrane PI(4,5)P2with a green fluorescent protein–tagged PH domain, we show that PLCζ effects minimal loss of PI(4,5)P2from the oolemma in contrast to control PLCδ1, despite the much higher potency of PLCζ in eliciting Ca2+oscillations. Specific depletion of this PI(4,5)P2pool by plasma membrane targeting of an inositol polyphosphate-5-phosphatase (Inp54p) blocked PLCδ1-mediated Ca2+oscillations but not those stimulated by PLCζ or sperm. Immunolocalization of PI(4,5)P2, PLCζ, and catalytically inactive PLCζ (ciPLCζ) revealed their colocalization to distinct vesicular structures inside the egg cortex. These vesicles displayed decreased PI(4,5)P2after PLCζ injection. Targeted depletion of vesicular PI(4,5)P2by expression of ciPLCζ-fused Inp54p inhibited the Ca2+oscillations triggered by PLCζ or sperm but failed to affect those mediated by PLCδ1. In contrast to somatic PLCs, our data indicate that sperm PLCζ induces Ca2+mobilization by hydrolyzing internal PI(4,5)P2stores, suggesting that the mechanism of mammalian fertilization comprises a novel phosphoinositide signaling pathway.
Effect of Allium fistulosum Extract on Ralstonia solanacearum Populations and Tomato Bacterial Wilt
Authors: Deberdt Péninna , Perrin Benjamin , Coranson-Beaudu Régine , Duyck Pierre-François , Wicker Emmanuel
Published: November 2011

To control bacterial wilt (Ralstonia solanacearum, phylotype IIB/4NPB), the antimicrobial effect of Allium fistulosum aqueous extract was assessed as a preplant soil treatment. Three concentrations of extract (100, 50, and 25%, 1:1 [wt/vol]) were evaluated by in vitro inhibition assay and in vivo experiments in a growth chamber. In vitro, A. fistulosum (100 and 50%) suppressed growth of R. solanacearum. Preplant treatment of the soil with A. fistulosum extract significantly reduced the R. solanacearum populations. No pathogen was detected in the soil after treatment with 100% concentrated extract from the third day after application until the end of the experiment. A. fistulosum also significantly reduced the incidence of tomato bacterial wilt. In the untreated control, the disease affected 61% of the plants whereas, with 100 and 50% extracts, only 6 and 14% of the plants, respectively, were affected. These results suggest that A. fistulosum extracts could be used in biocontrol-based management strategies for bacterial wilt of tomato.
Distributed inference in wireless sensor networks
Authors: Veeravalli Venugopal V. , Varshney Pramod K.
Published: November 2011

Statistical inference is a mature research area, but distributed inference problems that arise in the context of modern wireless sensor networks (WSNs) have new and unique features that have revitalized research in this area in recent years. The goal of this paper is to introduce the readers to these novel features and to summarize recent research developments in this area. In particular, results on distributed detection, parameter estimation and tracking in WSNs will be discussed, with a special emphasis on solutions to these inference problems that take into account the communication network connecting the sensors and the resource constraints at the sensors.
Rubella virus-like replicon particles: analysis of encapsidation determinants and non-structural roles of capsid protein in early post-entry replication
Authors: Claus Claudia , Tzeng Wen-Pin , Liebert U. G , Frey Teryl K.
Published: November 2011

Rubella virus (RUBV) contains a plus-strand RNA genome with two ORFs, one encoding the non-structural replicase proteins (NS-ORF) and the second encoding the virion structural proteins (SP-ORF). This study describes development and use of a trans-encapsidation system for the assembly of infectious RUBV-like replicon particles (VRPs) containing RUBV replicons (self replicating genomes with the SP-ORF replaced with a reporter gene). First, this system was used to map signals within the RUBV genome that mediate packaging of viral RNA. Mutations within a proposed packaging signal did not significantly affect relative packaging efficiency. The insertion of various fragments derived from the RUBV genome into Sindbis virus replicons revealed that there are several regions within the RUBV genome capable of enhancing encapsidation of heterologous replicon RNAs. Secondly, the trans-encapsidation system was used to analyse the effect of alterations within the capsid protein (CP) on release of VRPs and subsequent initiation of replication in newly infected cells. Deletion of the N-terminal eight amino acids of the CP reduced VRP titre significantly, which could be partially complemented by native CP provided in trans, indicating that this mutation affected an entry or post-entry event in the replication cycle. To test this hypothesis, the trans-encapsidation system was used to demonstrate the rescue of a lethal deletion within P150, one of the virus replicase proteins, by CP contained within the virus particle. This novel finding substantiated the functional role of CP in early post-entry replication.
The 1.7 Å resolution structure of At2g44920, a pentapeptide-repeat protein in the thylakoid lumen ofArabidopsis thaliana
Authors: Ni Shuisong , McGookey Michael E. , Tinch Stuart L. , Jones Alisha N. , Jayaraman Seetharaman , Tong Liang , Kennedy Michael A.
Published: November 2011

At2g44920 belongs to a diverse family (Pfam PF00805) of pentapeptide-repeat proteins (PRPs) that are present in all known organisms except yeast. PRPs contain at least eight tandem-repeating sequences of five amino acids with an approximate consensus sequence (STAV)(D/N)(L/F)(S/T/R)(X). Recent crystal structures show that PRPs adopt a highly regular four-sided right-handed β-helical structure consisting mainly of type II and type IV β-turns, sometimes referred to as a repeated five-residue (or Rfr) fold. Among sequenced genomes, PRP genes are most abundant in cyanobacteria, leading to speculation that PRPs play an important role in the unique lifestyle of photosynthetic cyanobacteria. Despite the recent structural characterization of several cyanobacterial PRPs, most of their functions remain unknown. Plants, whose chloroplasts are of cyanobacterial origin, have only four PRP genes in their genomes. At2g44920 is one of three PRPs located in the thylakoid lumen. Here, the crystal structure of a double methionine mutant of residues 81–224 of At2g44920, the naturally processed fragment of one of its full-length isoforms, is reported at 1.7 Å resolution. The structure of At2g44920 consists of the characteristic Rfr fold with five uninterrupted coils made up of 25 pentapeptide repeats and α-helical elements capping both termini. A disulfide bridge links the two α-helices with a conserved loop between the helical elements at its C-terminus. This structure represents the first structure of a PRP protein whose subcellular location has been experimentally confirmed to be the thylakoid lumen in a plant species.
Cloning, expression, purification and crystallization of dihydrodipicolinate synthase from the grapevine Vitis vinifera
Authors: Atkinson Sarah C. , Dogovski Con , Newman Janet , Dobson Renwick C. J. , Perugini Matthew A.
Published: November 2011

Dihydrodipicolinate synthase (DHDPS) catalyses the first committed step of the lysine-biosynthesis pathway in bacteria, plants and some fungi. This study describes the cloning, expression, purification and crystallization of DHDPS from the grapevine Vitis vinifera (Vv-DHDPS). Following in-drop cleavage of the hexahistidine tag, cocrystals of Vv-DHDPS with the substrate pyruvate were grown in 0.1 M Bis-Tris propane pH 8.2, 0.2 M sodium bromide, 20%(w/v) PEG 3350. X-ray diffraction data in space group P1 at a resolution of 2.2 Å are presented. Preliminary diffraction data analysis indicated the presence of eight molecules per asymmetric unit (V
M = 2.55 Å3 Da−1, 52% solvent content). The pending crystal structure of Vv-DHDPS will provide insight into the molecular evolution in quaternary structure of DHDPS enzymes.
Crystallization and preliminary X-ray analysis of crinumin, a chymotrypsin-like glycosylated serine protease with thrombolytic and antiplatelet activity
Authors: Singh Kunwar Awaneesh , Jagannadham M. V. , Rao G. R. K. , Celie Patrick H. N.
Published: November 2011

Crinumin, a novel glycosylated serine protease with chymotrypsin-like catalytic specificity, was purified from the medicinally important plant Crinum asiaticum. Crinumin is a 67.7 kDa protease with an extraordinary stability and activity over a wide range of pH and temperature and is functional in aqueous, organic and chaotropic solutions. The purified protease has thrombolytic and antiplatelet activity. The use of C. asiaticum extracts has also been reported for the treatment of a variety of disorders such as injury, joint inflammation and arthritis. In order to understand its structure–function relationship, the enzyme was purified from the plant latex and crystallized by the hanging-drop vapour-diffusion method. X-ray diffraction data were collected from a single crystal and processed to 2.8 Å resolution. The crystal belonged to the monoclinic space group C2, with unit-cell parameters a = 121.61, b = 95.00, c = 72.10 Å, α = γ = 90, β = 114.19°. The Matthews coefficient was 2.81 Å3 Da−1, corresponding to a solvent content of 56%, assuming one molecule in the asymmetric unit. Structure determination of the enzyme is in progress.
Engineered tryptophan in the adenine-binding pocket of catalytic subunit A of A-ATP synthase demonstrates the importance of aromatic residues in adenine binding, forming a tool for steady-state and time-resolved fluorescence spectroscopy
Authors: Tadwal Vikeramjeet Singh , Manimekalai Malathy Sony Subramanian , Grüber Gerhard
Published: November 2011

A reporter tryptophan residue was individually introduced by site-directed mutagenesis into the adenine-binding pocket of the catalytic subunit A (F427W and F508W mutants) of the motor protein A1AO ATP synthase from Pyrococcus horikoshii OT3. The crystal structures of the F427W and F508W mutant proteins were determined to 2.5 and 2.6 Å resolution, respectively. The tryptophan substitution caused the fluorescence signal to increase by 28% (F427W) and 33% (F508W), with a shift from 333 nm in the wild-type protein to 339 nm in the mutant proteins. Tryptophan emission spectra showed binding of Mg-ATP to the F427W mutant with a K
d of 8.5 µM. In contrast, no significant binding of nucleotide could be observed for the F508W mutant. A closer inspection of the crystal structure of the F427W mutant showed that the adenine-binding pocket had widened by 0.7 Å (to 8.70 Å) in comparison to the wild-type subunit A (8.07 Å) owing to tryptophan substitution, as a result of which it was able to bind ATP. In contrast, the adenine-binding pocket had narrowed in the F508W mutant. The two mutants presented demonstrate that the exact volume of the adenine ribose binding pocket is essential for nucleotide binding and even minor narrowing makes it unfit for nucleotide binding. In addition, structural and fluorescence data confirmed the viability of the fluorescently active mutant F427W, which had ideal tryptophan spectra for future structure-based time-resolved dynamic measurements of the catalytic subunit A of the ATP-synthesizing enzyme A-ATP synthase.
Therapeutic target-site variability in α1-antitrypsin characterized at high resolution
Authors: Patschull Anathe O. M. , Segu Lakshmi , Nyon Mun Peak , Lomas David A. , Nobeli Irene , Barrett Tracey E. , Gooptu Bibek
Published: November 2011

The intrinsic propensity of α1-antitrypsin to undergo conformational transitions from its metastable native state to hyperstable forms provides a motive force for its antiprotease function. However, aberrant conformational change can also occur via an intermolecular linkage that results in polymerization. This has both loss-of-function and gain-of-function effects that lead to deficiency of the protein in human circulation, emphysema and hepatic cirrhosis. One of the most promising therapeutic strategies being developed to treat this disease targets small molecules to an allosteric site in the α1-antitrypsin molecule. Partial filling of this site impedes polymerization without abolishing function. Drug development can be improved by optimizing data on the structure and dynamics of this site. A new 1.8 Å resolution structure of α1-antitrypsin demonstrates structural variability within this site, with associated fluctuations in its upper and lower entrance grooves and ligand-binding characteristics around the innermost stable enclosed hydrophobic recess. These data will allow a broader selection of chemotypes and derivatives to be tested in silico and in vitro when screening and developing compounds to modulate conformational change to block the pathological mechanism while preserving function.
Overexpression, purification, crystallization and preliminary crystallographic studies of a hyperthermophilic adenylosuccinate synthetase fromPyrococcus horikoshiiOT3
Authors: Wang Xiaoying , Akasaka Ryogo , Takemoto Chie , Morita Satoshi , Yamaguchi Machiko , Terada Takaho , Shirozu Mikako , Yokoyama Shigeyuki , Chen Shilin , Si Shuyi , Xie Yong
Published: November 2011

Adenylosuccinate synthetase (AdSS) is a ubiquitous enzyme that catalyzes the first committed step in the conversion of inosine monophosphate (IMP) to adenosine monophosphate (AMP) in the purine-biosynthetic pathway. Although AdSS from the vast majority of organisms is 430–457 amino acids in length, AdSS sequences isolated from thermophilic archaea are 90–120 amino acids shorter. In this study, crystallographic studies of a short AdSS sequence fromPyrococcus horikoshiiOT3 (PhAdSS) were performed in order to reveal the unusual structure of AdSS from thermophilic archaea. Crystals of PhAdSS were obtained by the microbatch-under-oil method and X-ray diffraction data were collected to 2.50 Å resolution. The crystal belonged to the trigonal space groupP3212, with unit-cell parametersa=b= 57.2,c= 107.9 Å. There was one molecule per asymmetric unit, giving a Matthews coefficient of 2.17 Å3 Da−1and an approximate solvent content of 43%. In contrast, the results of native polyacrylamide gel electrophoresis and analytical ultracentrifugation showed that the recombinant PhAdSS formed a dimer in solution.
Comprehensive taxon sampling reveals unaccounted diversity and morphological plasticity in a group of dimitic polypores (Polyporales, Basidiomycota)
Authors: Miettinen Otto , Larsson Ellen , Sjökvist Elisabet , Larsson Karl‐Henrik
Published: November 2011

The phylogeny of the poroid and hydnoid genera Antrodiella, Junghuhnia, and Steccherinum (Polyporales, Basidiomycota) was studied utilizing sequences of the gene regions ITS, nLSU, mtSSU, atp6, rpb2, and tef1. Altogether 148 taxa, represented by 549 sequences, were included in analyses. Results show that most species of these genera form a well supported clade in the Polyporales, called Steccherinaceae, along with 12 other hydnoid and poroid genera. Within the Steccherinaceae, generic concepts need to be revised: no fewer than 15 new genera are needed to accommodate existing and new species. At least 16 transitions have taken place between poroid and hydnoid hymenophore types within the Steccherinaceae, and similar plasticity can be seen in microscopic characters. Nevertheless, natural genera revealed in the analysis can mostly be characterized morphologically and, with few exceptions, poroid and hydnoid species belong to separate genera. The genus Steccherinum is shown to contain both hydnoid and poroid species. Species of the former Antrodiella belong to at least 10 genera within the Steccherinaceae.

© The Willi Hennig Society 2011.
Chronic fatigue syndrome: acute infection and history of physical activity affect resting levels and response to exercise of plasma oxidant/antioxidant status and heat shock proteins
Authors: Jammes Y. , Steinberg J. G. , Delliaux S.
Published: November 2011

Abstract.  Jammes Y, Steinberg JG, Delliaux S (Aix‐Marseille University, Marseille, France). Chronic fatigue syndrome: acute infection and history of physical activity affect resting levels and response to exercise of plasma oxidant/antioxidant status and heat shock proteins. J Intern Med 2012; 272: 74–84.

Objectives.  A history of high‐level physical activity and/or acute infection might constitute stress factors affecting the plasma oxidant–antioxidant status and levels of heat shock proteins (HSPs) in patients with chronic fatigue syndrome (CFS).

Design.  This case–control study compared data from 43 CFS patients to results from a matched control group of 23 healthy sedentary subjects.

Setting and subjects.  Five patients had no relevant previous history (group I). Eighteen had practised high‐level sport (group II), and severe acute infection had been diagnosed in nine patients (group III). A combination of sport practice and infection was noted in 11 patients (group IV).

Interventions.  After examination at rest, all subjects performed a maximal cycling exercise test. Plasma levels of two markers of oxidative stress [thiobarbituric acid reactive substances (TBARS) and reduced ascorbic acid (RAA)] and both HSP27 and HSP70 were measured.

Results.  At rest, compared with the control group, the TBARS level was higher in groups II, III and IV patients, and the RAA level was lower in groups III and IV. In addition, HSP70 levels were significantly lower in all CFS groups, compared with controls, but negative correlations were found between resting HSP27 and HSP70 levels and the history of physical activity. After exercise, the peak level of TBARS significantly increased in groups II, III and IV, and the variations in HSP27 and HSP70 were attenuated or suppressed, with the greatest effects in groups III and IV.

Conclusion.  The presence of stress factors in the history of CFS patients is associated with severe oxidative stress and the suppression of protective HSP27 and HSP70 responses to exercise.
QTL linkage mapping of wing length in zebra finch using genome‐wide single nucleotide polymorphisms markers
Authors: SCHIELZETH HOLGER , FORSTMEIER WOLFGANG , KEMPENAERS BART , ELLEGREN HANS
Published: November 2011

Avian wing length is an important trait that covaries with the ecology and migratory behaviour of a species and tends to change rapidly when the conditions are altered. Long‐distance migrants typically have longer wings than short‐distance migrants and sedentary species, and long‐winged species also tend to be more dispersive. Although the substantial heritability of avian wing length is well established, the identification of causal genes has remained elusive. Based on large‐scale genotyping of 1404 informative single nucleotide polymorphisms (SNP) in a captive population of 1067 zebra finches, we here show that the within‐population variation of relative wing length (h2 = 0.74 ± 0.05) is associated with standing genetic variation in at least six genomic regions (one genome‐wide significant and five suggestive). The variance explained by these six quantitative trait loci (QTL) sums to 36.8% of the phenotypic variance (half of the additive genetic variance), although this likely is an overestimate attributable to the Beavis effect. As avian wing length is primarily determined by the length of the primary feathers, we then searched for candidate genes that are related to feather growth. Interestingly, all of the QTL signals co‐locate withWntgrowth factors and closely interacting genes (Wnt3a,Wnt5a,Wnt6,Wnt7a,Wnt9a,RhoUandRhoV). Our findings therefore suggest that standing genetic variation in theWntgenes might be linked to avian wing morphology, although there are many other genes that also fall within the confidence regions.
Interaction between FliI ATPase and a flagellar chaperone FliT during bacterial flagellar protein export
Authors: Minamino Tohru , Kinoshita Miki , Imada Katsumi , Namba Keiichi
Published: November 2011

FliT is a flagellar type III export chaperone specific for the filament‐capping protein FliD. The FliT/FliD complex binds to the FliI ATPase of the flagellar export apparatus. The C‐terminal α4 helix of FliT controls its interaction with FliI but it remains unknown how it does so. Here, we analysed the FliI–FliT interaction by pull‐down assays using GST affinity chromatography. FliT94, missing the C‐terminal α4 helix, bound to the extreme N‐terminal region of FliI (FliIEN) with high affinity and to the C‐terminal ATPase domain (FliICAT) with low affinity. The C‐terminal α4 helix of FliT suppressed the interaction with FliIEN. FliH and FliT94 bound to a common binding site on FliIEN and hence FliH induced the release of FliI from FliT94 in an ATP‐independent manner. FliD increased the binding affinity of FliICAT for FliT. These results raise a possible hypothesis that the FliH/FliI complex binds to the FliT/FliD complex through FliICAT to escort it from the cytoplasm to the export gate made up of six integral membrane proteins and that, upon dissociation of FliD from FliT, FliT94 may bind to FliIEN and then FliI may transfer from FliT94 to FliH by the direct competition of FliT94 and FliH for FliIEN.
Effect of kidney transplantation on heart conduction disturbances in children treated with chronic hemodialysis – A pilot study
Authors: Polak‐Jonkisz Dorota , Laszki‐Szcząchor Krystyna , Sobieszczańska Małgorzata , Makulska Irena , Pilecki Witold , Rusiecki Lesław , Zwolińska Danuta
Published: November 2011

Polak‐Jonkisz D, Laszki‐Szcząchor K, Sobieszczańska M, Makulska I, Pilecki W, Rusiecki L, Zwolińska D. Effect of kidney transplantation on heart conduction disturbances in children treated with chronic hemodialysis – A pilot study.  Pediatr Transplantation 2011: 15: 835–843. © 2011 John Wiley & Sons A/S.

Abstract:  Aim of the study was to assess the effect of KT on heart conduction in HD children. Non‐invasive electrocardiographic method of BSPM was used. Isochrone maps, presenting a VAT distribution, were taken from eight HD patients and 26 normal subjects. Patients were divided into two groups: I – three children were HD <12 months prior to KT; II – five children were HD >12 months prior to KT. After KT, the groups were marked as IP and IIP. Serum iPTH and phosphate levels were significantly higher in both HD groups than in controls, with a considerable normalization after transplantation. HD patients demonstrated neither conduction abnormalities on ECG nor left ventricular hypertrophy. Group‐mean VAT maps revealed: I and II – similar patterns of complete LBBB; IP – partial normalization to a pattern of anterior fascicle block; IIP – preserved pattern of LBBB. Intraventricular conduction disturbances found in HD children using BSPM were alleviated by KT. Short HD therapy increases a chance of conduction disturbances regression after KT, contrary to the longer HD treatment. BSPM is more sensitive than standard ECG in detecting heart conduction impairments in the HD patients.
Chronic malnutrition favours smaller critical size for metamorphosis initiation in Drosophila melanogaster
Authors: VIJENDRAVARMA R. K. , NARASIMHA S. , KAWECKI T. J.
Published: November 2011

Critical size at which metamorphosis is initiated represents an important checkpoint in insect development. Here, we use experimental evolution in Drosophila melanogaster to test the long‐standing hypothesis that larval malnutrition should favour a smaller critical size. We report that six fly populations subject to 112 generations of laboratory natural selection on an extremely poor larval food evolved an 18% smaller critical size (compared to six unselected control populations). Thus, even though critical size is not plastic with respect to nutrition, smaller critical size can evolve as an adaptation to nutritional stress. We also demonstrate that this reduction in critical size (rather than differences in growth rate) mediates a trade‐off in body weight that the selected populations experience on standard food, on which they show a 15–17% smaller adult body weight. This illustrates how developmental mechanisms that control life history may shape constraints and trade‐offs in life history evolution.
Discovery of curcumin, a component of golden spice, and its miraculous biological activities
Authors: Gupta Subash C , Patchva Sridevi , Koh Wonil , Aggarwal Bharat B
Published: November 2011

1. Curcumin is the active ingredient of the dietary spice turmeric and has been consumed for medicinal purposes for thousands of years. Modern science has shown that curcumin modulates various signalling molecules, including inflammatory molecules, transcription factors, enzymes, protein kinases, protein reductases, carrier proteins, cell survival proteins, drug resistance proteins, adhesion molecules, growth factors, receptors, cell cycle regulatory proteins, chemokines, DNA, RNA and metal ions.

2. Because of this polyphenol’s potential to modulate multiple signalling molecules, it has been reported to possess pleiotropic activities. First demonstrated to have antibacterial activity in 1949, curcumin has since been shown to have anti‐inflammatory, anti‐oxidant, pro‐apoptotic, chemopreventive, chemotherapeutic, antiproliferative, wound healing, antinociceptive, antiparasitic and antimalarial properties as well. Animal studies have suggested that curcumin may be active against a wide range of human diseases, including diabetes, obesity, neurological and psychiatric disorders and cancer, as well as chronic illnesses affecting the eyes, lungs, liver, kidneys and gastrointestinal and cardiovascular systems.

3. Although many clinical trials evaluating the safety and efficacy of curcumin against human ailments have already been completed, others are still ongoing. Moreover, curcumin is used as a supplement in several countries, including India, Japan, the US, Thailand, China, Korea, Turkey, South Africa, Nepal and Pakistan. Although inexpensive, apparently well tolerated and potentially active, curcumin has not been approved for the treatment of any human disease.

4. In the present article, we discuss the discovery and key biological activities of curcumin, with a particular emphasis on its activities at the molecular and cellular levels, as well as in animals and humans.
Characteristics of the short children referred to an academic paediatric endocrine clinic in Greece
Authors: Papadimitriou Anastasios , Douros Konstantinos , Papadimitriou Dimitrios T , Kleanthous Kleanthis , Karapanou Olga , Fretzayas Andreas
Published: November 2011

Aim:  To describe the characteristics of short children in relation to gender and the various diagnoses.

Methods:  All new patients of Greek origin that were referred to our institution in the years 2007 and 2008 for evaluation of short stature were included in the study. Children were categorized according to the severity of their short stature in those with height standard deviation score (HSDS) ≤−3 and HSDS >−3.

Results:  Two hundred ninety‐five children (162 boys and 133 girls, ratio 1.2) were referred. HSDS of boys was −2.3 (0.6) and of girls −2.1 (0.5), P= 0.004. Girls had shorter parents, and the predicted adult HSDS was also shorter for girls −1.7 (0.8) than for boys −1.35 (0.76), P= 0.003. Seventy per cent of the children of both sexes had familial short stature (FSS), constitutional delay of growth or a combination of the two conditions. About 10% presented the auxological and biochemical criteria for growth hormone deficiency (GHD). In addition, 11.8% had a HSDS ≤−3, the most common diagnosis being GHD (36.1%); the less severely short children most commonly presented FSS (41.2%).

Conclusions:  There is no gender bias in referrals for short stature in Greece. About 70% of children of both sexes presented FSS or constitutional delay of growth or a combination of the two conditions, whereas GHD was diagnosed in about 10% of the children. Normal variants of growth were present in about 80% of children with HSDS >−3, but in only 40% when HSDS was ≤−3.