bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhanced Raman scattering from vertical silicon nanowires array
Authors: Huang Jian-An , Zhao Ying-Qi , Zhang Xue-Jin , Luo Lin-Bao , Liu Yan-Kuan , Zapien Juan Antonio , Surya Charles , Lee Shuit-Tong
Published: May 2011

We fabricated ordered hexagonal-packed vertical silicon nanowire (SiNW) arrays with varying diameters of 450–900 nm and varying lengths of 0.54–7.3 μm, and studied their Raman enhancement properties. We found the Raman enhancement per unit volume (REV) increased with decreasing wire diameters and oscillated with wire length, and the REV of seven 450-nm-diameter, 3-μm-long SiNWs was about twice that of a single SiNW having the same size. The differences were attributed to the vertical finite-length cylinder structures of the SiNW array, as supported by finite-difference-time-domain simulation results based on the helical resonant surface wave model.
Atomic scale characterization of GaInN/GaN multiple quantum wells in V-shaped pits
Authors: Tomiya Shigetaka , Kanitani Yuya , Tanaka Shinji , Ohkubo Tadakatsu , Hono Kazuhiro
Published: May 2011

High-angle annular dark field scanning transmission electron microscopy and atom probe tomography of the V-shaped pits in GaInN/GaN multiple quantum wells have revealed that a quantum well structure exists at the slope region of the V-shaped pits. Their thickness and In concentrations were found to be much lower compared to those of the flat region. This suggests that threading dislocations in the V-shaped pits act as energy barriers for the lateral transport of charge carries and that the pit center may not work properly for vertical transport because of the collapse of well-defined quantum well structures.
Carrier recombination processes in Mg-doped N-polar InN films
Authors: Imai Daichi , Ishitani Yoshihiro , Fujiwara Masayuki , Kusakabe Kazuhide , Wang Xinqian , Yoshikawa Akihiko
Published: May 2011

We investigate the nonradiative carrier recombination (NR) process in Mg-doped p-InN films having lower photoluminescence (PL) intensity than n-InN films. The NR activation energy in the p-type films is found to be in a range of 9–15 meV, which is smaller than that in n-InN films (40–65 meV). We also investigate the effect of the greater mean free path of minority carriers in p-InN. At room temperature the collision rate of minority carriers with NR centers within the radiative lifetime in p-InN is found to be three orders of magnitude greater than that in n-InN.
Depth localization of positive charge trapped in silicon oxynitride field effect transistors after positive and negative gate bias temperature stress
Authors: Toledano-Luque M. , Kaczer B. , Roussel Ph. J. , Franco J. , Ragnarsson L. Å. , Grasser T. , Groeseneken G.
Published: May 2011

Positive charge trapped in the SiO(N) gate dielectric of deeply-scaled p-channel metal-oxide-semiconductor field-effect transistors is observed after both negative and positive gate bias temperature stress. Emission of elementary trapped charges is demonstrated and analyzed through the quantized threshold voltage transients observed after stress. The magnitude distribution of the threshold voltage steps is used to estimate the depth of the traps in the gate dielectric to be about 0.5 nm from the injecting silicon-dielectric interface in both cases.
Structural and dynamic properties of linker histone H1 binding to DNA
Authors: Dootz Rolf , Toma Adriana C. , Pfohl Thomas
Published: May 2011

Found in all eukaryotic cells, linker histones H1 are known to bind to and rearrange nucleosomal linker DNA. In vitro, the fundamental nature of H1/DNA interactions has attracted wide interest among research communities—from biologists to physicists. Hence, H1/DNA binding processes and structural and dynamical information about these self-assemblies are of broad importance. Targeting a quantitative understanding of H1 induced DNA compaction mechanisms, our strategy is based on using small-angle x-ray microdiffraction in combination with microfluidics. The usage of microfluidic hydrodynamic focusing devices facilitates a microscale control of these self-assembly processes, which cannot be achieved using conventional bulk setups. In addition, the method enables time-resolved access to structure formation in situ, in particular, to transient intermediate states. The observed time dependent structure evolution shows that the H1/DNA interaction can be described as a two-step process: an initial unspecific binding of H1 to DNA is followed by a rearrangement of molecules within the formed assemblies. The second step is most likely induced by interactions between the DNA and the H1’s charged side chains. This leads to an increase in lattice spacing within the DNA/protein assembly and induces a decrease in the correlation length of the mesophases, probably due to a local bending of the DNA.
In-depth resolved Raman scattering analysis for the identification of secondary phases: Characterization of Cu2ZnSnS4 layers for solar cell applications
Authors: Fontané X. , Calvo-Barrio L. , Izquierdo-Roca V. , Saucedo E. , Pérez-Rodriguez A. , Morante J. R. , Berg D. M. , Dale P. J. , Siebentritt S.
Published: May 2011

This work reports the in-depth resolved Raman scattering analysis with different excitation wavelengths of Cu2ZnSnS4 layers. Secondary phases constitute a central problem in this material, particularly since they cannot be distinguished by x-ray diffraction. Raman spectra measured with 325 nm excitation light after sputtering the layers to different depths show peaks that are not detectable by excitation in the visible. These are identified with Cu3SnS4 modes at the surface region while spectra measured close to the back region show peaks from ZnS and MoS2. Observation of ZnS is enhanced by resonant excitation conditions achieved when working with UV excitation.
Erratum to: Relationship between litter birthweight and litter size in five goat genotypes
Authors: Mellado Miguel , Meza-Herrera Cesar A. , Arévalo José R. , De Santiago-Miramontes Maria A. , Rodríguez Alvaro , Luna-Orozco Juan R. , Veliz-Deras Francisco G.
Published: May 2011

The aim of the present study was to use a non-linear regression approach to investigate the relationship between litter birthweight and litter size of five breeds of goat under intensive conditions in a hot arid environment. Litter-size and litter-weight data on 20�117 kids from 13�685 litters representing five breeds, namely Saanen, Toggenburg, French Alpine, Anglo-Nubian and Granadina, were compared to evaluate this relationship. Regardless of breed, birthweight for kids born as twins, triplets and quadruplets was, on average, 92%, 87% and 83%, respectively, of that of singleton kids; litter size accounted for 81% of the variation in litter weight. The coefficient of the power regression differed (P < 0.01) among breeds, with similar slopes for French Alpine, Toggenburg and Saanen goats and a smaller litter-weight increase for every additional fetus in Anglo-Nubian and Granadina goats than in other breeds of goat. These results support the hypothesis that, regardless of parity, litter weight in dairy and Granadina goats increases at a reduced rate with increases in litter size, although the rate of change with the increasing number of fetuses was moderate, as indicated by a power regression of the form y = axb between these variables across age categories and breeds of goat.
Gene silencing in bovine zygotes: siRNA transfection versus microinjection
Authors: O'Meara Ciara M. , Murray James D. , Mamo Solomon , Gallagher Emma , Roche James , Lonergan Patrick
Published: May 2011

The aim of this study was to compare gene silencing in bovine zygotes when small interfering RNAs (siRNAs) were introduced into bovine zygotes by microinjection or lipid-based transfection. In Experiment 1, E-cadherin siRNA was injected at 100 or 375 µM and compared with PBS-injected and non-injected controls. Embryos were then cultured in vitro for 7 days and periodically assessed for development. For transfection, zona-free zygotes were incubated in transfection medium with siRNA for 1 h at 39°C and then cultured to Day 7. Injection of PBS or 375 µM E-cadherin siRNA resulted in a decrease in the number of embryos reaching the 8-cell stage (51.5% and 45.5%) or the blastocyst stage (39.0 and 32.5%) compared with non-injected controls (62.9 and 45.0%, respectively; P < 0.05). Messenger RNA abundance was suppressed by 36 and 46% when siRNA targeting E-cadherin was injected at 100 and 375 µM, respectively, compared with controls (P < 0.05). Transfection with 100 nM E-cadherin siRNA decreased development to the 8-cell stage (20.3 versus 53.0%) and blastocyst stage (7.2 versus 18.2%) compared with controls (P < 0.05). Messenger RNA relative abundance was not different between controls (non-transfected or transfected with GAPDH or scrambled siRNA). However, transfection of zygotes with 100 and 200 nM E-cadherin siRNA led to a 72 and 38% reduction, respectively, in E-cadherin mRNA relative abundance in Day 7 blastocysts compared with controls (P < 0.05).
Simulating landscape-scale effects of fuels treatments in the Sierra Nevada, California, USA
Authors: Syphard Alexandra D. , Scheller Robert M. , Ward Brendan C. , Spencer Wayne D. , Strittholt James R.
Published: May 2011

In many coniferous forests of the western United States, wildland fuel accumulation and projected climate conditions increase the likelihood that fires will become larger and more intense. Fuels treatments and prescribed fire are widely recommended, but there is uncertainty regarding their ability to reduce the severity of subsequent fires at a landscape scale. Our objective was to investigate the interactions among landscape-scale fire regimes, fuels treatments and fire weather in the southern Sierra Nevada, California. We used a spatially dynamic model of wildfire, succession and fuels management to simulate long-term (50 years), broad-scale (across 2.2 × 106 ha) effects of fuels treatments. We simulated thin-from-below treatments followed by prescribed fire under current weather conditions and under more severe weather. Simulated fuels management minimised the mortality of large, old trees, maintained total landscape plant biomass and extended fire rotation, but effects varied based on elevation, type of treatment and fire regime. The simulated area treated had a greater effect than treatment intensity, and effects were strongest where more fires intersected treatments and when simulated weather conditions were more severe. In conclusion, fuels treatments in conifer forests potentially minimise the ecological effects of high-severity fire at a landscape scale provided that 8% of the landscape is treated every 5 years, especially if future fire weather conditions are more severe than those in recent years.
Cysteine-rich intestinal protein 2
(
CRIP2
) acts as a repressor of NF-κB–mediated proangiogenic cytokine transcription to suppress tumorigenesis and angiogenesis
Authors: Cheung Arthur Kwok Leung , Ko Josephine M. Y. , Lung Hong Lok , Chan Kwok Wah , Stanbridge Eric J. , Zabarovsky Eugene , Tokino Takashi , Kashima Lisa , Suzuki Toshiharu , Kwong Dora Lai-Wan , Chua Daniel , Tsao Sai Wah , Lung Maria Li
Published: May 2011

Chromosome 14 was transferred into tumorigenic nasopharyngeal carcinoma and esophageal carcinoma cell lines by a microcell-mediated chromosome transfer approach. Functional complementation of defects present in the cancer cells suppressed tumor formation. A candidate tumor-suppressor gene,
cysteine-rich intestinal protein 2
(
CRIP2
), located in the hot spot for chromosomal loss at 14q32.3, was identified as an important candidate gene capable of functionally suppressing tumor formation. Previous studies have shown that
CRIP2
is associated with development. To date, no report has provided functional evidence supporting a role for
CRIP2
in tumor development. The present study provides unequivocal evidence that
CRIP2
can functionally suppress tumorigenesis.
CRIP2
is significantly down-regulated in nasopharyngeal carcinoma cell lines and tumors.
CRIP2
reexpression functionally suppresses in vivo tumorigenesis and angiogenesis; these effects are induced by its transcription-repressor capability. It interacts with the NF-κB/p65 to inhibit its DNA-binding ability to the promoter regions of the major proangiogenesis cytokines critical for tumor progression, including IL6, IL8, and VEGF. In conclusion, we provide compelling evidence that
CRIP2
acts as a transcription repressor of the NF-κB–mediated proangiogenic cytokine expression and thus functionally inhibits tumor formation and angiogenesis.
It’s Not Me, It’s You: How Gift Giving Creates Giver Identity Threat as a Function of Social Closeness
Authors: Ward Morgan K. , Broniarczyk Susan M.
Published: May 2011

Prior research has established that consumers are motivated to purchase identity-consistent products. We extend consumer identity research into an important consumer context, gift giving, in which individuals may make product choices that run counter to their own identities in order to fulfill the desires of the intended recipient. We find that purchasing an identity-contrary gift for a close (vs. distant) friend who is an integral part of the self can itself cause an identity threat to the giver. Four experiments in a gift registry context show that after making an identity-contrary gift choice for a close (vs. distant) friend, givers subsequently engage in behaviors that reestablish their identity such as indicating greater identity affiliation with the threatened identity and greater likelihood to purchase identity-expressive products. This research highlights the opposing forces that product purchase may exert on consumer identity as both a potential threat and means of self-verification.
Poly(ethylene oxide) : succinonitrile—a polymeric matrix for fast-ion conducting redox-couple solid electrolytes
Authors: Gupta Ravindra Kumar , Kim Hyun-Min , Rhee Hee-Woo
Published: May 2011

A blend of poly(ethylene oxide), PEO, and succinonitrile, SN, was investigated for the first time for applying it as a polymeric matrix of low-cost and thermally stable fast-ion conducting redox-couple solid polymer electrolytes. The PEO–SN blend in equal weight fraction showed room temperature ionic conductivity of 1 × 10−8 S cm−1 with nearly two orders of magnitude higher than that of PEO due to reduced crystallinity. The blend resulted in a solid electrolyte with improved ionic conductivity of ∼7 × 10−4 S cm−1 at 25 °C. The blend and its electrolyte showed thermal stability up to 100 °C, which is essential for outdoor application of dye-sensitized solar cells.
Improved differential Ka band dielectrometer based on the wave propagation in a quartz cylinder surrounded by high loss liquid under test
Authors: Skresanov Valery N , Eremenko Zoya E , Glamazdin Vladimir V , Shubnyi Alexander I
Published: May 2011

The differential dielectrometer was designed to measure small differences in complex permittivity (CP) of two high loss liquids at frequency 32.82 GHz. The measurements are fully computer-aided with the exception of liquids filling and draining in the measurement cells. The time of one measurement cycle does not exceed 3 min. The dielectrometer is easy-to-work and can be used under the conditions of scientific and industrial physical–chemical laboratories. The sensitivity of the difference in the phase coefficients of the electromagnetic waves propagated in the measurement cells is better than 0.05% and that of the attenuation coefficient is of the order of 0.2%. The dielectrometer contains two measurement cells that are dielectric quartz cylinders surrounded by high loss liquids. We developed the CP calculation algorithm using the known CP of the reference liquid and the difference coefficients of complex wave propagation in the cells. The origins of the measurement errors are studied in detail and recommendations were made to avoid some of them. The dielectrometer can be used to express the identification of wine and must authenticity by means of their CP values. The CP measurement results for solutions of some substances that make wine and must composition are obtained. The possibility of using the dielectrometer for the detection of added water in wines or musts is shown.
The dynamin-related GTPase Opa1 is required for glucose-stimulated ATP production in pancreatic beta cells
Authors: Zhang Zhongyan , Wakabayashi Nobunao , Wakabayashi Junko , Tamura Yasushi , Song Woo-Jin , Sereda Sam , Clerc Pascaline , Polster Brian M. , Aja Susan M. , Pletnikov Mikhail V. , Kensler Thomas W. , Shirihai Orian S. , Iijima Miho , Hussain Mehboob A. , Sesaki Hiromi
Published: May 2011

Previous studies using in vitro cell culture systems have shown the role of the dynamin-related GTPase Opa1 in apoptosis prevention and mitochondrial DNA (mtDNA) maintenance. However, it remains to be tested whether these functions of Opa1 are physiologically important in vivo in mammals. Here, using the Cre-loxP system, we deleted mouse Opa1 in pancreatic beta cells, in which glucose-stimulated ATP production in mitochondria plays a key role in insulin secretion. Beta cells lacking Opa1 maintained normal copy numbers of mtDNA; however, the amount and activity of electron transport chain complex IV were significantly decreased, leading to impaired glucose-stimulated ATP production and insulin secretion. In addition, in Opa1-null beta cells, cell proliferation was impaired, whereas apoptosis was not promoted. Consequently, mice lacking Opa1 in beta cells develop hyperglycemia. The data suggest that the function of Opa1 in the maintenance of the electron transport chain is physiologically relevant in beta cells.
Regulation of Greatwall kinase during Xenopus oocyte maturation
Authors: Yamamoto Tomomi M. , Blake-Hodek Kristina , Williams Byron C. , Lewellyn Andrea L. , Goldberg Michael L. , Maller James L.
Published: May 2011

Greatwall kinase has been identified as a key element in M phase initiation and maintenance in Drosophila, Xenopus oocytes/eggs, and mammalian cells. In M phase, Greatwall phosphorylates endosulfine and related proteins that bind to and inhibit protein phosphatase 2A/B55, the principal phosphatase for Cdk-phosphorylated substrates. We show that Greatwall binds active PP2A/B55 in G2 phase oocytes but dissociates from it when progesterone-treated oocytes reach M phase. This dissociation does not require Greatwall kinase activity or phosphorylation at T748 in the presumptive T loop of the kinase. A mutant K71M Greatwall, also known as Scant in Drosophila, induces M phase in the absence of progesterone when expressed in oocytes, despite its reduced stability and elevated degradation by the proteasome. M phase induction by Scant Greatwall requires protein synthesis but is not associated with altered binding or release of PP2A/B55 as compared to wild-type Greatwall. However, in vitro studies with Greatwall proteins purified from interphase cells indicate that Scant, but not wild-type Greatwall, has low but detectable activity against endosulfine. These results demonstrate progesterone-dependent regulation of the PP2A/B55–Greatwall interaction during oocyte maturation and suggest that the cognate Scant Greatwall mutation has sufficient constitutive kinase activity to promote M phase in Xenopus oocytes.
Invasion by Invitation: Rhizobial Infection in Legumes
Authors: Murray Jeremy D.
Published: May 2011

Nodulation of legume roots typically begins with rhizobia attaching to the tip of a growing root-hair cell. The attached rhizobia secrete Nod factors (NF), which are perceived by the plant. This initiates a series of preinfection events that include cytoskeletal rearrangements, curling at the root-hair tip, and formation of radially aligned cytoplasmic bridges called preinfection threads (PIT) in outer cortical cells. Within the root-hair curl, an infection pocket filled with bacteria forms, from which originates a tubular invagination of cell wall and membrane called an infection thread (IT). IT formation is coordinated with nodule development in the underlying root cortex tissues. The IT extends from the infection pocket down through the root hair and into the root cortex, where it passes through PIT and eventually reaches the nascent nodule. As the IT grows, it is colonized by rhizobia that are eventually released into cells within the nodule, where they fix nitrogen. NF can also induce cortical root hairs that appear to originate from PIT and can become infected like normal root hairs. Several genes involved in NF signaling and some of the downstream transcription factors required for infection have been characterized. More recently, several genes with direct roles in infection have been identified, some with roles in actin rearrangement and others with possible roles in protein turnover and secretion. This article provides an overview of the infection process, including the roles of NF signaling, actin, and calcium and the influence of the hormones ethylene and cytokinin.
Use of a Secretion Trap Screen in Pepper FollowingPhytophthora capsiciInfection Reveals Novel Functions of Secreted Plant Proteins in Modulating Cell Death
Authors: Yeom Seon-In , Baek Hyang-Ku , Oh Sang-Keun , Kang Won-Hee , Lee Sang Jik , Lee Je Min , Seo Eunyoung , Rose Jocelyn K. C. , Kim Byung-Dong , Choi Doil
Published: May 2011

In plants, the primary defense against pathogens is mostly inducible and associated with cell wall modification and defense-related gene expression, including many secreted proteins. To study the role of secreted proteins, a yeast-based signal-sequence trap screening was conducted with the RNA from Phytophthora capsici-inoculated root of Capsicum annuum ‘Criollo de Morelos 334’ (CM334). In total, 101 Capsicum annuum secretome (CaS) clones were isolated and identified, of which 92 were predicted to have a secretory signal sequence at their N-terminus. To identify differences in expressed CaS genes between resistant and susceptible cultivars of pepper, reverse Northern blots and real-time reverse-transcription polymerase chain reaction were performed with RNA samples isolated at different time points following P. capsici inoculation. In an attempt to assign biological functions to CaS genes, we performed in planta knock-down assays using the Tobacco rattle virus-based gene-silencing method. Silencing of eight CaS genes in pepper resulted in suppression of the cell death induced by the non-host bacterial pathogen (Pseudomonas syringae pv. tomato T1). Three CaS genes induced phenotypic abnormalities in silenced plants and one, CaS259 (PR4-l), caused both cell death suppression and perturbed phenotypes. These results provide evidence that the CaS genes may play important roles in pathogen defense as well as developmental processes.
Approximation of potential-driven flow dynamics in large-scale self-similar tree networks
Authors: Mayes Jason , Sen Mihir
Published: May 2011

Dynamic analysis of large-scale flow networks is made difficult by the large system of differential-algebraic equations resulting from its modelling. To simplify analysis, the mathematical model must be sufficiently reduced in complexity. For self-similar tree networks, this reduction can be made using the network’s structure in way that can allow simple, analytical solutions. For very large, but finite, networks, analytical solutions are more difficult to obtain. In the infinite limit, however, analysis is sometimes greatly simplified. It is shown that approximating large finite networks as infinite not only simplifies the analysis, but also provides an excellent approximate solution.
The First Stars: clues from quasar absorption systems
Authors: Pettini Max
Published: May 2011

Astronomers now have at their disposal telescopes and instruments that allow them to look back in time over most of the history of the Universe, from the present epoch to less than a billion years after the Big Bang, when the Universe was still in its infancy. Using quasars (the bright nuclei of distant galaxies) as background sources of light, we can follow the evolution of galaxies and of the matter between them from the First Stars to the rich diversity of the Universe today. In this article, I focus on recent developments in the study of the most metal-poor gas seen in the spectra of quasars, whose properties can be used to infer the nature of the First Stars and, in some cases, even determine the universal fraction of baryons.
Comparative genomics of citric-acid-producingAspergillus nigerATCC 1015 versus enzyme-producing CBS 513.88
Authors: Andersen Mikael R. , Salazar Margarita P. , Schaap Peter J. , van de Vondervoort Peter J.I. , Culley David , Thykaer Jette , Frisvad Jens C. , Nielsen Kristian F. , Albang Richard , Albermann Kaj , Berka Randy M. , Braus Gerhard H. , Braus-Stromeyer Susanna A. , Corrochano Luis M. , Dai Ziyu , van Dijck Piet W.M. , Hofmann Gerald , Lasure Linda L. , Magnuson Jon K. , Menke Hildegard , Meijer Martin , Meijer Susan L. , Nielsen Jakob B. , Nielsen Michael L. , van Ooyen Albert J.J. , Pel Herman J. , Poulsen Lars , Samson Rob A. , Stam Hein , Tsang Adrian , van den Brink Johannes M. , Atkins Alex , Aerts Andrea , Shapiro Harris , Pangilinan Jasmyn , Salamov Asaf , Lou Yigong , Lindquist Erika , Lucas Susan , Grimwood Jane , Grigoriev Igor V. , Kubicek Christian P. , Martinez Diego , van Peij Noël N.M.E. , Roubos Johannes A. , Nielsen Jens , Baker Scott E.
Published: May 2011

The filamentous fungusAspergillus nigerexhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producingA. nigerstrain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook whole-genome sequencing of the acidogenicA. nigerwild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi.
A Hormonal Regulatory Module That Provides Flexibility to Tropic Responses
Authors: Gallego-Bartolomé Javier , Kami Chitose , Fankhauser Christian , Alabadí David , Blázquez Miguel A.
Published: May 2011

Plants orient their growth depending on directional stimuli such as light and gravity, in a process known as tropic response. Tropisms result from asymmetrical accumulation of auxin across the responding organ relative to the direction of the stimulus, which causes differential growth rates on both sides of the organ. Here, we show that gibberellins (GAs) attenuate the gravitropic reorientation of stimulated hypocotyls of dark-grown Arabidopsis (Arabidopsis thaliana) seedlings. We show that the modulation occurs through induction of the expression of the negative regulator of auxin signaling INDOLE-3-ACETIC ACID INDUCIBLE19/MASSUGU2. The biological significance of this regulatory mechanism involving GAs and auxin seems to be the maintenance of a high degree of flexibility in tropic responses. This notion is further supported by observations that GA-deficient seedlings showed a much lower variance in the response to gravity compared to wild-type seedlings and that the attenuation of gravitropism by GAs resulted in an increased phototropic response. This suggests that the interplay between auxin and GAs may be particularly important for plant orientation under competing tropic stimuli.
Extending SILAC to Proteomics of Plant Cell Lines
Authors: Schütz Wolfgang , Hausmann Niklas , Krug Karsten , Hampp Rüdiger , Macek Boris
Published: May 2011

Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) is a widespread method for metabolic labeling of cells and tissues in quantitative proteomics; however, incomplete incorporation of the label has so far restricted its wider use in plants. Here, we argue that differential labeling by two different versions of the labeled amino acids renders SILAC fully applicable to dark-grown plant cell lines. By comparing Arabidopsis thaliana cell cultures labeled with two versions of heavy Lys (Lys-4 and Lys-8), we show that this simple modification of the SILAC protocol enables similar quantitation accuracy, precision, and reproducibility as conventional SILAC in animal cells.
Treatment of hydrogen background in bulk and nanocrystalline neutron total scattering experiments
Authors: Page Katharine , White Claire E. , Estell Eben G. , Neder Reinhard B. , Llobet Anna , Proffen Thomas
Published: May 2011

Nuclear incoherent neutron scattering contributions present a challenge in the structural characterization of many classes of materials. This article introduces methods for the correction of nanoparticle, bulk crystalline and amorphous powder neutron scattering data with significant incoherent contributions from hydrogen, and describes the effects the corrections have on the resulting atomic pair distribution function data sets. The approach is presented in the context of thePDFgetNdata-reduction program [Peterson, Gutmann, Proffen & Billinge (2000).J. Appl. Cryst.33, 1192].
Structure of PEP–PEO block copolymer micelles: exploiting the complementarity of small-angle X-ray scattering and static light scattering
Authors: Jensen Grethe Vestergaard , Shi Qing , Hernansanz María J. , Oliveira Cristiano L. P. , Deen G. Roshan , Almdal Kristoffer , Pedersen Jan Skov
Published: May 2011

The structure of large block copolymer micelles is traditionally determined by small-angle neutron scattering (SANS), covering a large range of scattering vectors and employing contrast variation to determine the overall micelle morphology as well as the internal structure on shorter length scales. The present work shows that the same information can be obtained by combining static light scattering (SLS) and small-angle X-ray scattering (SAXS), which provide information on, respectively, large and short length scales. Micelles of a series of block copolymers of poly(ethylene propylene)-b-poly(ethylene oxide) (PEP–PEO) in a 70% ethanol solution are investigated. The polymers have identical PEP blocks of 5.0 kDa and varying PEO blocks of 2.8–49 kDa. The SLS contrasts of PEP and PEO are similar, providing a homogeneous contrast, making SLS ideal for determining the overall micelle morphology. The SAXS contrasts of the two components are very different, allowing for resolution of the internal micelle structure. A core–shell model with a PEP core and PEO corona is fitted simultaneously to the SAXS and SLS data using the different contrasts of the two blocks for each technique. With increasing PEO molecular weight, a transition from cylindrical to spherical micelles is observed. This transition cannot be identified from the SAXS data alone, but only from the SLS data.
Migration ecology of juvenile temperate seabass Lateolabrax japonicus: a carbon stable‐isotope approach
Authors: Fuji T. , Kasai A. , Suzuki K. W. , Ueno M. , Yamashita Y.
Published: May 2011

The migration pattern of juvenile temperate seabass Lateolabrax japonicus in the stratified estuary of the Yura River was examined using carbon stable‐isotope ratios (δ13C). δ13C values of mysids, which are the most important prey items for this species, were consistently enriched in the lower estuary and surf zone (LES), while depleted in the freshwater zone (FW). δ13C values of juveniles in LES were enriched, while those in FW were depleted, consistent with the δ13C difference in prey items. The results of δ13C showed that many juveniles migrated upstream from April to June and most of them stayed in FW until at least July. Juveniles that stayed in FW and LES for a relatively longer period (> c. 20 days) showed higher condition factors than those that stayed in FW for a short period (several days). This indicates that residence in FW enabled juveniles to achieve as good a body condition as residence in LES.
Impaired immune function in children with Fanconi anaemia
Authors: Myers Kasiani C. , Bleesing Jack J. , Davies Stella M. , Zhang Xue , Martin Lisa J. , Mueller Robin , Harris Richard E. , Filipovich Alexandra H. , Kovacic Melinda B. , Wells Susanne I. , Mehta Parinda A.
Published: May 2011

Fanconi anaemia is an autosomal recessive or X‐linked disease characterized by progressive bone marrow failure, variable congenital abnormalities and a predisposition to malignancy. Reports of immune function in this population are limited, and include only specific areas of immune performance, showing variable defects. We report a cross‐sectional immunological assessment in 10 children with FA. Absolute numbers of B cells and natural killer (NK) cells were reduced compared to controls (P = 0·048 and P = 0·0002, respectively), while absolute number of T cells were within normal range. Perforin and granzyme content of NK cells was reduced (P < 0·00001 and P = 0·0057, respectively) along with the NK cell cytotoxicity (P < 0·001). Antigen proliferation in response to tetanus was decreased (P = 0·008) while responses to candida and phytohaemagglutinin were not. Cytotoxic T cell function was also reduced (P < 0·0001). Immunoglobulin G levels were normal in those evaluated. Our series represents the first attempt at a comprehensive quantitative and functional evaluation of immune function in this rare group of patients and demonstrates a significant deficit in the NK cell compartment, a novel quantitative B cell defect, along with abnormal cytotoxic function. These findings may be especially relevant in this patient population with known predisposition to DNA damage and malignancy.
Habitual physical activity in Dutch children and adolescents with haemophilia
Authors: GROEN W. G. , TAKKEN T. , VAN DER NET J. , HELDERS P. J. M. , FISCHER K.
Published: May 2011

Summary.  For patients with haemophilia, a physically active lifestyle is important to maintain musculoskeletal health and to prevent chronic diseases, such as cardiovascular disease. Therefore, we studied physical activity levels, in Dutch children and adolescents with haemophilia as well as its association with aerobic fitness and joint health. Forty‐seven boys with haemophilia (aged 8–18) participated. Physical activity was measured using the Modifiable Activity Questionnaire (MAQ) and was compared with the general population. Aerobic fitness was determined using peak oxygen uptake (VO2peak). Joint health was measured using the Haemophilia Joint Health Score (HJHS). Associations between physical activity, joint health and aerobic fitness were evaluated by correlation analysis. Subjects were 12.5 (SD 2.9) years old, had a Body Mass Index (BMI) of 19.5 (SD 3.1; z‐score 0.5) and a median HJHS score of 0 (range 0–6). Cycling, physical education and swimming were most frequently reported (86%, 69% and 50% respectively). Children with severe haemophilia participated significantly less in competitive soccer and more in swimming than children with non‐severe haemophilia. Physical activity levels were similar across haemophilia severities and comparable to the general population. VO2peak kg−1 was slightly lower than healthy boys (42.9 ± 8.6 vs. 46.9 ± 1.9 mL kg−1 min−1; P = 0.03). Joint health, aerobic fitness and physical activity showed no correlation. Dutch children with haemophilia engaged in a wide range of activities of different intensities and showed comparable levels of physical activity to the general population. Aerobic fitness was well preserved and showed no associations with physical activity levels or joint health.
Spanish nurses’ attitudes towards research and perceived barriers and facilitators of research utilisation: a comparative survey of nurses with and without experience as principal investigators
Authors: Moreno‐Casbas Teresa , Fuentelsaz‐Gallego Carmen , de Miguel Ángel Gil , González‐María Esther , Clarke Sean P
Published: May 2011

Aims and objective.  To examine attitudes towards research and perceived barriers and facilitators of research utilisation in clinical practice in a broad cross‐section of Spanish nurses.

Background.  Nurses’ attitudes towards research are critical in determining whether study findings are used to improve practice.

Design.  Cross‐sectional comparative survey in Hospitals, Primary Care Centres and University‐affiliated schools of nursing.

Methods.  Surveys were completed by 917 nurses: 69 who received funding from the Spanish national agency (1998–2004) and a nationally representative sample of 848 nurses who did not have the same research experience (the Comparison group). Two instruments (BARRIERS and Attitudes towards nursing research) were translated and culturally adapted for use in Spain. A descriptive analysis of demographic and practice characteristics was performed. Total scale scores, as well as subscale scores, were computed and compared across the two groups using one‐way analysis of variance (anova) and multivariate analysis of variance (manova) with post hoc tests. Pearson product‐moment correlation coefficients were computed between the total tool scores and subscales measuring barriers and attitudes in both groups.

Results.  The investigators differed from other nurses on several demographic and work characteristics (more males, older age and more likely to work a fixed day shift schedule). On the whole, investigators showed more favourable attitudes but perceived several elements as posing greater barriers to research utilisation than the Comparison groups. Across all respondents, issues related to the quality of research were rated as the greatest barriers to research utilisation, followed by organisational barriers, barriers involving the communication of findings and finally, those related to nurses’ values, awareness and skills.

Conclusions.  Very similar profiles of perceptions and attitudes regarding research were found in these samples of Spanish nurses relative to those from other countries in earlier reports. Nurses who had experience conducting research demonstrated more favourable research‐related attitudes and perceived barriers differently than those without such experience.

Relevance to clinical practice.  Understanding different organisational and experience perspectives is important to identify challenges and opportunities to ensure research utilisation in clinical practice.
Examining the relationship between risk assessment and risk management in mental health
Authors: GILBERT E. , ADAMS A. , BUCKINGHAM C. D.
Published: May 2011

Accessible summary

Risk assessment is crucial for developing risk management plans to prevent or minimize mental health patients' risks that will impede their recovery.

Risk assessments and risk management plans should be closely linked. Their content and the extent to which they are linked within one Trust is explored.

There is a great deal of variability in the amount and detail of risk information collected by nurses and how this is used to develop risk management plans.

Keeping risk assessment information in one place rather than scattered throughout patient records is important for ensuring it can be accessed easily and linked properly to risk management plans.

Strengthening the link between risk assessment and management will help ensure interventions and care is tailored to the specific needs of individual patients, thus promoting their safety and well‐being.

Thorough risk assessment helps in developing risk management plans that minimize risks that can impede mental health patients' recovery. Department of Health policy states that risk assessments and risk management plans should be inextricably linked. This paper examines their content and linkage within one Trust. Four inpatient wards for working age adults (18–65 years) in a large mental health Trust in England were included in the study. Completed risk assessment forms, for all patients in each inpatient ward were examined (n= 43), followed by an examination of notes for the same patients. Semi‐structured interviews took place with ward nurses (n= 17). Findings show much variability in the amount and detail of risk information collected by nurses, which may be distributed in several places. Gaps in the risk assessment and risk management process are evident, and a disassociation between risk information and risk management plans is often present. Risk information should have a single location so that it can be easily found and updated. Overall, a more integrated approach to risk assessment and management is required, to help patients receive timely and appropriate interventions that can reduce risks such as suicide or harm to others.
A central metabolic circuit controlled by QseC in pathogenic Escherichia coli
Authors: Hadjifrangiskou Maria , Kostakioti Maria , Chen Swaine L. , Henderson Jeffrey P. , Greene Sarah E. , Hultgren Scott J.
Published: May 2011

The QseC sensor kinase regulates virulence in multiple Gram‐negative pathogens, by controlling the activity of the QseB response regulator. We have previously shown that qseC deletion interferes with dephosphorylation of QseB thus unleashing what appears to be an uncontrolled positive feedback loop stimulating increased QseB levels. Deletion of QseC downregulates virulence gene expression and attenuates enterohaemorrhagic and uropathogenic Escherichia coli (EHEC and UPEC), Salmonella typhimurium, and Francisella tularensis. Given that these pathogens employ different infection strategies and virulence factors, we used genome‐wide approaches to better understand the role of the QseBC interplay in pathogenesis. We found that deletion of qseC results in misregulation of nucleotide, amino acid, and carbon metabolism. Comparable metabolic changes are seen in EHEC ΔqseC, suggesting that deletion of qseC confers similar pleiotropic effects in these two different pathogens. Disruption of representative metabolic enzymes phenocopied UPEC ΔqseC in vivo and resulted in virulence factor downregulation. We thus propose that in the absence of QseC, the constitutively active QseB leads to pleiotropic effects, impairing bacterial metabolism, and thereby attenuating virulence. These findings provide a basis for the development of antimicrobials targeting the phosphatase activity of QseC, as a means to attenuate a wide range of QseC‐bearing pathogens.
Distribution of killer cell immunoglobulin‐like receptor genes and combinations with HLA‐C ligands in an isolated Han population in southwest China
Authors: Shi L. , Shi L. , Tao Y. , Lin K. , Liu S. , Yu L. , Yang Z. , Yi W. , Huang X. , Sun H. , Chu J. , Yao Y.
Published: May 2011

Human natural killer cells express killer cell immunoglobulin‐like receptors (KIRs), which interact with human leukocyte antigen (HLA) class I molecules. KIR/HLA combinations play an important role in innate and adaptive immunity. In the current study, 16 KIR genes were analyzed in an isolated Han group living in the Fengyandong (FYDH) region in the Yunnan province of southwest China. The framework KIR genes 3DL2, 3DL3, 3DP1, and 2DL4 were found in all individuals. A total of 22 distinct KIR genotypes were observed, four of which were unknown previously. Genotype 1 (N = 52, 55.9%) was the predominant genotype. Analysis of inhibitory and activating KIR and HLA‐C ligands showed that all individuals displayed at least one inhibitory or activating KIR/HLA‐C pair. One KIR/HLA‐C pair was the most frequent (67/93), followed by two pairs (21/93), and three pairs (6/93). The comparison of KIR and HLA frequencies between FYDH and a local Han population showed that the two populations showed similar frequencies for the KIR genes. In contrast, the distribution of HLA alleles and haplotypes showed significant differences between them.
Heritability of short‐scale natal dispersal in a large‐scale foraging bird, the wandering albatross
Authors: CHARMANTIER A. , BUORO M. , GIMENEZ O. , WEIMERSKIRCH H.
Published: May 2011

Natal dispersal is a key life history trait for the evolution and adaptation of wild populations. Although its evolution has repeatedly been related to the social and environmental context faced by individuals, parent–offspring regressions have also highlighted a possible heritable component. In this study, we explore heritability of natal dispersal, at the scale of the sub‐Antarctic Possession Island, for a large‐scale foraging seabird, the Wandering albatrossDiomedea exulans, exploiting a pedigree spanning over four decades and a maximum of four generations. The comparison of three different methods shows that heritability on the liability scale can vary drastically depending on the type of model (heritability from 6% to 86%), with a notable underestimation by restricted maximum likelihood animal models (6%) compared to Bayesian animal models (36%). In all cases, however, our results point to significant additive genetic variance in the individual propensity to disperse, after controlling for substantial effects of sex and natal colony. These results reveal promising evolutionary potential for short‐scale natal dispersal, which could play a critical role for the long‐term persistence of this species on the long run.
Influence of pollinator grooming on pollen‐mediated gene dispersal in Mimulus ringens (Phrymaceae)
Authors: HOLMQUIST KARSTEN G. , MITCHELL RANDALL J. , KARRON JEFFREY D.
Published: May 2011

Pollinator foraging patterns and the dynamics of pollen transport influence the quality and diversity of flowering plant mating opportunities. For species pollinated by grooming pollinators, such as bees, the amount of pollen carried between a donor flower and potential recipient flowers depends on how grooming influences pollen transfer. To investigate the relationship between grooming and pollen‐mediated gene dispersal, we studied bumblebee (Bombus fervidus) foraging behavior and resulting gene dispersal in linear arrays of Mimulus ringens. Each of the 14 plants in an array had a unique multilocus genotype, facilitating unambiguous assignment of paternity to 1050 progeny. Each plant was trimmed to a single flower so that pollinator movements could be linked directly to resulting gene dispersal patterns. Pollen‐mediated gene dispersal was very limited. More than 95% of the seeds sired by a donor flower were distributed over the first three recipient flowers in the visitation sequence. However, seeds were occasionally sired on flowers visited later in the pollinator's floral visitation sequence. Intensive grooming immediately following pollen removal from a donor flower significantly increased the decay rate of the donor flower's gene dispersal curve. These results suggest that the frequency and relative intensity of grooming can have significant effects on patterns of pollen‐mediated gene dispersal from individual pollen donors.