bluuebunny/crossref_metadata_2025 huggingface dataset:
Dissociation of gaseous zwitterion glycine-betaine by slow electrons
Authors: Kopyra J. , Abdoul-Carime H.
Published: June 2010

In this work, we investigate dissociation processes induced by low-energy electrons to gas phase N,N,N-trimethylglycine [glycine-betaine, (CH3)3N+CH2COO−] molecules. Glycine-betaine represents a model system for zwitterions. All negative fragments are observed to be produced only at subelectronic excitation energies (<4 eV). With the exception of the loss of a neutral H atom that could arise from any CH bond breaking, we tentatively suggest that the zwitterion dissociates exclusively from the fragmentation of the cation site of the molecule, subsequent to the attachment of the excess electron. Within the context of radiation induced damage to biological systems, the present findings contribute to a more complete description of the fragmentation mechanism occurring to amino acids, peptides, and proteins since they adopt usually a zwitterion structure.
Ion-ion coincidence studies on multiple ionizations of N2 and O2 molecules irradiated by extreme ultraviolet free-electron laser pulses
Authors: Yamada A. , Fukuzawa H. , Motomura K. , Liu X.-J. , Foucar L. , Kurka M. , Okunishi M. , Ueda K. , Saito N. , Iwayama H. , Nagaya K. , Sugishima A. , Murakami H. , Yao M. , Rudenko A. , Kühnel K. U. , Ullrich J. , Feifel R. , Czasch A. , Dörner R. , Nagasono M. , Higashiya A. , Yabashi M. , Ishikawa T. , Ohashi H. , Kimura H. , Togashi T.
Published: June 2010

We have investigated multiple ionization of N2 and O2 molecules by 52 nm extreme-ultraviolet light pulses at the free-electron laser facility SCSS in Japan. Coulomb break-up of parent ions with charge states up to 5+ is found by the ion-ion coincidence technique. The charge-state dependence of kinetic energy release distributions suggests that the electrons are emitted sequentially in competition with the elongation of the bond length.
Two dimensional electrostatic shock waves in relativistic electron positron ion plasmas
Authors: Masood W. , Rizvi H.
Published: June 2010

Ion-acoustic shock waves (IASWs) are studied in an unmagnetized plasma consisting of electrons, positrons and hot ions. In this regard, Kadomtsev–Petviashvili–Burgers (KPB) equation is derived using the small amplitude perturbation expansion method. The dependence of the IASWs on various plasma parameters is numerically investigated. It is observed that ratio of ion to electron temperature, kinematic viscosity, positron concentration, and the relativistic ion streaming velocity affect the structure of the IASW. Limiting case of the KPB equation is also discussed. Stability of KPB equation is also presented. The present investigation may have relevance in the study of electrostatic shock waves in relativistic electron-positron-ion plasmas.
Improved stability of free-standing lipid bilayers based on nanoporous alumina films
Authors: Hirano-Iwata Ayumi , Taira Tasuku , Oshima Azusa , Kimura Yasuo , Niwano Michio
Published: June 2010

In this study, we propose a method for improving the stability of free-standing bilayer lipid membranes (BLMs) by preparing BLMs across nanoporous alumina films. The use of porous alumina reduced individual membrane size to improve the BLM stability. The BLMs were stable under an applied voltage of ±1 V. The lifetime of the BLMs was 16–30 h with and without incorporated gramicidin channels. Electric properties of the BLMs as a platform for channel-current recordings are also discussed. Since the total area of the BLMs is still large to facilitate protein incorporation, our approach is useful for designing highly sensitive biosensors based on channel proteins.
Addition of aluminum to solution processed conductive indium tin oxide thin film for an oxide thin film transistor
Authors: Jeon J. H. , Hwang Y. H. , Bae B. S. , Kwon H. L. , Kang H. J.
Published: June 2010

Aluminum was added to a solution-processed conductive indium tin oxide thin film to be optimized as a channel layer for a thin film transistor (TFT). The conductive crystalline thin film becomes an amorphous semiconductor as the band gap enlarges with increasing Al content. Also, systematic variation in TFT characteristics was observed clearly, displaying transformation to a semiconductor. At the final composition of (Al2O3)0.3(In2O3)0.6(SnO2)0.1, the film channel layer exhibits a high mobility of 13.3 cm2 V−1 s−1, a high on-to-off ratio of 107 and a low subthreshold swing of 1.01 V/dec.
Optical identification of atomically thin dichalcogenide crystals
Authors: Castellanos-Gomez A , Agraït N , Rubio-Bollinger G
Published: June 2010

We present a systematic study of the optical contrast of niobium diselenide and molybdenum disulfide flakes deposited onto silicon wafers with a thermally grown silicon oxide layer. We measure the optical contrast of flakes whose thickness, which is obtained by atomic force microscopy, ranges from 200 layers down to a monolayer using different illumination wavelengths in the visible spectrum. The refractive index of these thin crystals has been obtained from the optical contrast using Fresnel law. In this way the optical microscopy data can be quantitatively analyzed to determine the thickness of the flakes in a fast and nondestructive way.
Experimental observation of the trapped rainbow
Authors: Smolyaninova Vera N. , Smolyaninov Igor I. , Kildishev Alexander V. , Shalaev Vladimir M.
Published: June 2010

We report on the experimental demonstration of the broadband “trapped rainbow” in the visible frequency range using an adiabatically tapered optical nano waveguide. Being a distinct case of the slow light phenomenon, the trapped rainbow effect could be applied to optical computing and signal processing, such as spectroscopy on a chip, and to providing enhanced light-matter interactions.
Production of highly ionized species in high-current pulsed cathodic arcs
Authors: Sanginés R. , Israel A. M. , Falconer I. S. , McKenzie D. R. , Bilek M. M. M.
Published: June 2010

Time resolved optical diagnostic techniques were used to study the production of highly ionized species in aluminum plasma produced by a centered-triggered high-current pulsed cathodic arc. Controlling the spacing between cathode spots enabled a correlation between a reduction in the mean charge state and an increase in the spacing of cathode spots to be observed. As the cathode current was increased, the distances between spots were reduced and these charge states were produced for longer times. Strong cathode spot coupling is proposed as a mechanism for the production of high charge states.
Enhanced conductivity of tunnel junctions employing semimetallic nanoparticles through variation in growth temperature and deposition
Authors: Nair Hari P. , Crook Adam M. , Bank Seth R.
Published: June 2010

We report ErAs nanoparticle-enhanced tunnel junctions grown on GaAs with low specific resistances (<2×10−4 Ω cm−2), approximately tenfold lower than previous reports. A reduction in specific resistance was achieved by modifying the ErAs nanoparticle morphology through the molecular beam epitaxial growth conditions, particularly lower growth temperatures. A further investigation of the variation in tunnel junction resistance with the amount of ErAs deposited and growth temperature shows that nanoparticle surface coverage may not be the only factor determining tunnel junction resistance.
Radiative and nonradiative recombination in an ultraviolet GaN/AlGaN multiple-quantum-well laser diode
Authors: Yoshida Harumasa , Kuwabara Masakazu , Yamashita Yoji , Uchiyama Kazuya , Kan Hirofumi
Published: June 2010

We have experimentally investigated the radiative and nonradiative recombination in a GaN/AlGaN multiple-quantum-well laser diode. The each carrier lifetime has been evaluated based on a rate equation analysis of light output-current characteristics of the laser diode. The estimated nonradiative carrier lifetime is 830 ps, and the Auger recombination is negligibly small at room temperature. At a threshold current density of 8 kA cm−2, the carrier density and the internal quantum efficiency are estimated to be 2.6×1019 cm−3 and 34%, respectively. These results are responsible for experimental and theoretical analysis of optical and electrical properties in AlGaN-based laser diodes.
Doubly, triply, and multiply excited states from a constrained optimized effective potential method
Authors: Glushkov V. N. , Assfeld X.
Published: June 2010

This article further develops and applies a constrained optimized effective potential (COEP) approach for the practical calculations of doubly and multiply excited states of atoms and molecules. The COEP method uses the time-independent theory of pure excited states and implements a simple asymptotic projection method to take orthogonality constraints into account. We show that, in contrast with the common time-dependent density functional method, the COEP methodology is capable of treating doubly, triply, and multiply excited states and can be easily applied to both atoms and molecules. In particular, doubly excited energies of each state are calculated through a constrained minimization procedure including constraints that make its Slater determinantal functions orthogonal to those of the ground and all lower-lying doubly excited states. The performance of the proposed method is examined by calculations of doubly excited state energies for the He atom and H2 molecule at exchange-only and exchange-correlation level of approximation.
Megalasers to pulse in several new EU countries
Authors: Feder Toni
Published: June 2010

As the world celebrates 50 years since the invention of the laser, a European facility approaching exawatt power is expected to stimulate new research areas and communities.
DOE begins rationing helium-3
Authors: Kramer David
Published: June 2010

As the extent of the shortage becomes clear, an interagency task force is giving scientific users priority, but some say the material is not available at any price.
James Franck: Science and conscience
Authors: Hippel Frank von
Published: June 2010

In World War I, Franck helped his native Germany develop gas-warfare defenses. Three decades later he urged the US, his adopted country, to tread carefully with an even more terrible weapon.
Walking on water
Authors: Bush John W. M. , Hu David L.
Published: June 2010

The ingenious methods employed by insects and spiders to move across a water surface rely on microphysics that is of little use to larger water walkers but of considerable interest to the microfluidics community.
Genotype by environment interactions of lucerne (Medicago sativa L.) in a cool temperate climate
Authors: Pembleton K. G. , Smith R. S. , Rawnsley R. P. , Donaghy D. J. , Humphries A. W.
Published: June 2010

Genotype by environmental interactions in lucerne (Medicago sativa L.) present considerable challenges when selecting an appropriate cultivar for a particular location and farming system. Data on the yield and persistence of a range of lucerne cultivars and experimental lines grown in two Tasmanian environments, Forth (41.20°S, 146.27°E, Red Ferrosol soil, under cutting with high fertiliser inputs, i.e. a high yield potential environment) and Cranbook (42.00°S, 148.03°E, Red Ferrosol soil, under grazing with low fertiliser inputs, i.e. a low yield potential environment) were examined using winter activity class as the experimental factor. At Forth, winter-dormant lucernes were the lowest yielding genotypes. In contrast, at Cranbrook, highly winter-active genotypes had lower plant persistence and dry matter yield than winter-dormant genotypes. Modified joint linear regression analysis showed that in a cool temperate climate, winter-dormant genotypes are more suited to a low yield potential environment, whereas highly winter-active genotypes are adapted to a high yield potential environment. Both the semi-winter-dormant and the winter-active genotypes were adapted to all environments. The dry matter yield of winter-dormant and highly winter-active genotypes was most sensitive to environmental conditions in winter and spring, while performance of all cultivars and experimental lines was most stable over summer.
Trigenomic hybrids from interspecific crosses between Brassica napus and B. nigra
Authors: Pradhan Aneeta , Plummer Julie A. , Nelson Matthew N. , Cowling Wallace A. , Yan Guijun
Published: June 2010

Interspecific hybridisation was carried out between five cultivars of Brassica napus and five accessions of B. nigra in all possible cross combinations including reciprocals. Crossing success was higher when B. napus genotypes were used as female parents. Pollination of 799 B. napus flowers with B. nigra pollen resulted in 433 pods set and 2063 putative hybrid seeds. In the reciprocal direction, pollination of 877 B. nigra flowers with B. napus pollen resulted in 281 pods set and 113 putative hybrid seeds. Pod and seed set varied with genotype and only 19 out of 25 combinations of B. napus × B. nigra and 14 out of 25 combinations of B. nigra × B. napus yielded seeds. Hybridity of 2176 putative hybrid seeds (2063 from B. napus × B. nigra and 113 from B. nigra × B. napus) was tested. Microsatellite markers with known locations for the A, B and C genomes indicated that six plants were true hybrids and one more plant remained unconfirmed for hybrid status. All other plants from putative hybrid seeds had the same DNA banding patterns and similar morphological characters as the female parent. However, the true hybrids had DNA bands from both parents and an intermediate morphology for colour and hairiness of leaf, stem and petiole. Anthers were shrunken and thin with a very limited number of sterile pollen grains. Cytological examination confirmed the triploid status of the hybrid with 27 chromosomes. The unconfirmed hybrid had 9% pollen viability and chromosome count was 27 as with the true hybrid; however, there was no clear B-genome marker from B. nigra.
Genetic main effect and genotype×environment interaction for cooking quality traits in a diallel set of Indica rice (Oryza sativa L.) varieties
Authors: Sharifi Peyman , Dehghani Hamid , Moumeni Ali , Moghaddam Mohammad
Published: June 2010

Genetic main effects and genotype × environment (GE) interactions were determined for cooking quality traits of rice (Oryza sativa L.) using a complete diallel cross of seven. The field experiments were carried out over 2 years as a randomised complete block design with two replications. Amylose content (AC), gel consistency (GC) and gelatinisation temperature (GT) were affected by both genetic effects and GE interaction. Grain elongation (GEL) was found to be controlled by genetic main effects and general combining ability (GCA) × environment interaction. The high magnitude of GCA variances for all traits indicated that additive effects were more prominent in the determination of these characteristics. Narrow-sense heritabilities for AC, GT, GC and GEL were 61.21, 60.83, 29.98 and 52.29%, respectively. Among the genetic and GE interaction effects, GCA and GCA × environment were the main components for all traits. Relatively large narrow-sense heritabilities for AC, GT and GEL indicated that selection for these traits could be possible. However, due to the significance of genotype × year effects for AC, GT, and GEL genetic materials should be evaluated over several years in breeding programs.
Early hominin diet included diverse terrestrial and aquatic animals 1.95 Ma in East Turkana, Kenya
Authors: Braun David R. , Harris John W. K. , Levin Naomi E. , McCoy Jack T. , Herries Andy I. R. , Bamford Marion K. , Bishop Laura C. , Richmond Brian G. , Kibunjia Mzalendo
Published: June 2010

The manufacture of stone tools and their use to access animal tissues by Pliocene hominins marks the origin of a key adaptation in human evolutionary history. Here we report an in situ archaeological assemblage from the Koobi Fora Formation in northern Kenya that provides a unique combination of faunal remains, some with direct evidence of butchery, and Oldowan artifacts, which are well dated to 1.95 Ma. This site provides the oldest in situ evidence that hominins, predatingHomo erectus, enjoyed access to carcasses of terrestrial and aquatic animals that they butchered in a well-watered habitat. It also provides the earliest definitive evidence of the incorporation into the hominin diet of various aquatic animals including turtles, crocodiles, and fish, which are rich sources of specific nutrients needed in human brain growth. The evidence here shows that these critical brain-growth compounds were part of the diets of hominins before the appearance ofHomo ergaster/erectusand could have played an important role in the evolution of larger brains in the early history of our lineage.
Antigen persistence and the control of local T cell memory by migrant respiratory dendritic cells after acute virus infection
Authors: Kim Taeg S. , Hufford Matthew M. , Sun Jie , Fu Yang-Xin , Braciale Thomas J.
Published: June 2010

Acute viral infections induce robust adaptive immune responses resulting in virus clearance. Recent evidence suggests that there may be depots of viral antigen that persist in draining lymph nodes (DLNs) after virus clearance and could, therefore, affect the adaptive immune response and memory T cell formation. The nature of these residual antigen depots, the mechanism of antigen persistence, and the impact of the persistent antigen on memory T cells remain ill defined. Using a mouse model of influenza virus infection of the respiratory tract, we identified respiratory dendritic cells (RDCs) as essential for both sampling and presenting residual viral antigen. RDCs in the previously infected lung capture residual viral antigen deposited in an irradiation-resistant cell type. RDCs then transport the viral antigen to the LNs draining the site of infection, where they present the antigen to T cells. Lastly, we document preferential localization of memory T cells to the DLNs after virus clearance as a consequence of presentation of residual viral antigen by the migrant RDC.
The miR-144/451 locus is required for erythroid homeostasis
Authors: Rasmussen Kasper D. , Simmini Salvatore , Abreu-Goodger Cei , Bartonicek Nenad , Di Giacomo Monica , Bilbao-Cortes Daniel , Horos Rastislav , Von Lindern Marieke , Enright Anton J. , O’Carroll Dónal
Published: June 2010

The process of erythropoiesis must be efficient and robust to supply the organism with red bloods cells both under condition of homeostasis and stress. The microRNA (miRNA) pathway was recently shown to regulate erythroid development. Here, we show that expression of the locus encoding miR-144 and miR-451 is strictly dependent on Argonaute 2 and is required for erythroid homeostasis. Mice deficient for the miR-144/451 cluster display a cell autonomous impairment of late erythroblast maturation, resulting in erythroid hyperplasia, splenomegaly, and a mild anemia. Analysis of gene expression profiles from wild-type and miR-144/451–deficient erythroblasts revealed that the miR-144/451 cluster acts as a “tuner” of gene expression, influencing the expression of many genes. MiR-451 imparts a greater impact on target gene expression than miR-144. Accordingly, mice deficient in miR-451 alone exhibited a phenotype indistinguishable from miR-144/451–deficient mice. Thus, the miR-144/451 cluster tunes gene expression to impart a robustness to erythropoiesis that is critical under conditions of stress.
Nonparametric Estimation of Mean Willingness to Pay from Discrete Response Valuation Data
Authors: Watanabe Masahide
Published: June 2010

This article develops a nonparametric method to consistently estimate mean willingness to pay (WTP) in various discrete response valuation methods. The advantage of this method is that it can consistently estimate unconditional mean WTP with astonishing ease under some assumptions of the bid distribution. In addition, we develop a method for estimating the best linear predictor for conditional mean WTP using a linear projection. This method is applicable to single‐bounded and double‐bounded contingent valuation, and some forms of choice experiment.
Gap5—editing the billion fragment sequence assembly
Authors: Bonfield James K. , Whitwham Andrew
Published: June 2010

Motivation: Existing sequence assembly editors struggle with the volumes of data now readily available from the latest generation of DNA sequencing instruments.

Results: We describe the Gap5 software along with the data structures and algorithms used that allow it to be scalable. We demonstrate this with an assembly of 1.1 billion sequence fragments and compare the performance with several other programs. We analyse the memory, CPU, I/O usage and file sizes used by Gap5.

Availability and Implementation: Gap5 is part of the Staden Package and is available under an Open Source licence from http://staden.sourceforge.net. It is implemented in C and Tcl/Tk. Currently it works on Unix systems only.

Contact:  jkb@sanger.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
SLIMS—a user-friendly sample operations and inventory management system for genotyping labs
Authors: Van Rossum Thea , Tripp Ben , Daley Denise
Published: June 2010

Summary: We present the Sample-based Laboratory Information Management System (SLIMS), a powerful and user-friendly open source web application that provides all members of a laboratory with an interface to view, edit and create sample information. SLIMS aims to simplify common laboratory tasks with tools such as a user-friendly shopping cart for subjects, samples and containers that easily generates reports, shareable lists and plate designs for genotyping. Further key features include customizable data views, database change-logging and dynamically filled pre-formatted reports. Along with being feature-rich, SLIMS' power comes from being able to handle longitudinal data from multiple time-points and biological sources. This type of data is increasingly common from studies searching for susceptibility genes for common complex diseases that collect thousands of samples generating millions of genotypes and overwhelming amounts of data. LIMSs provide an efficient way to deal with this data while increasing accessibility and reducing laboratory errors; however, professional LIMS are often too costly to be practical. SLIMS gives labs a feasible alternative that is easily accessible, user-centrically designed and feature-rich. To facilitate system customization, and utilization for other groups, manuals have been written for users and developers.

Availability: Documentation, source code and manuals are available at http://genapha.icapture.ubc.ca/SLIMS/index.jsp. SLIMS was developed using Java 1.6.0, JSPs, Hibernate 3.3.1.GA, DB2 and mySQL, Apache Tomcat 6.0.18, NetBeans IDE 6.5, Jasper Reports 3.5.1 and JasperSoft's iReport 3.5.1.

Contact:  denise.daley@hli.ubc.ca
FastMEDUSA: a parallelized tool to infer gene regulatory networks
Authors: Bozdag Serdar , Li Aiguo , Wuchty Stefan , Fine Howard A.
Published: June 2010

Motivation: In order to construct gene regulatory networks of higher organisms from gene expression and promoter sequence data efficiently, we developed FastMEDUSA. In this parallelized version of the regulatory network-modeling tool MEDUSA, expression and sequence data are shared among a user-defined number of processors on a single multi-core machine or cluster. Our results show that FastMEDUSA allows a more efficient utilization of computational resources. While the determination of a regulatory network of brain tumor in Homo sapiens takes 12 days with MEDUSA, FastMEDUSA obtained the same results in 6 h by utilizing 100 processors.

Availability: Source code and documentation of FastMEDUSA are available at https://wiki.nci.nih.gov/display/NOBbioinf/FastMEDUSA

Contact:  hfine@mail.nih.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
Mechanisms of HDA6-mediated rRNA gene silencing: suppression of intergenic Pol II transcription and differential effects on maintenance versus siRNA-directed cytosine methylation
Authors: Earley Keith W. , Pontvianne Frédéric , Wierzbicki Andrzej T. , Blevins Todd , Tucker Sarah , Costa-Nunes Pedro , Pontes Olga , Pikaard Craig S.
Published: June 2010

The Arabidopsis histone deacetylase HDA6 is required to silence transgenes, transposons, and ribosomal RNA (rRNA) genes subjected to nucleolar dominance in genetic hybrids. In nonhybrid Arabidopsis thaliana, we show that a class of 45S rRNA gene variants that is normally inactivated during development fails to be silenced in hda6 mutants. In these mutants, symmetric cytosine methylation at CG and CHG motifs is reduced, and spurious RNA polymerase II (Pol II) transcription occurs throughout the intergenic spacers. The resulting sense and antisense spacer transcripts facilitate a massive overproduction of siRNAs that, in turn, direct de novo cytosine methylation of corresponding gene sequences. However, the resulting de novo DNA methylation fails to suppress Pol I or Pol II transcription in the absence of HDA6 activity; instead, euchromatic histone modifications typical of active genes accumulate. Collectively, the data reveal a futile cycle of unregulated transcription, siRNA production, and siRNA-directed DNA methylation in the absence of HDA6-mediated histone deacetylation. We propose that spurious Pol II transcription throughout the intergenic spacers in hda6 mutants, combined with losses of histone deacetylase activity and/or maintenance DNA methylation, eliminates repressive chromatin modifications needed for developmental rRNA gene dosage control.
Dynamic SpoIIIE assembly mediates septal membrane fission during Bacillus subtilis sporulation
Authors: Fleming Tinya C. , Shin Jae Yen , Lee Sang-Hyuk , Becker Eric , Huang Kerwyn Casey , Bustamante Carlos , Pogliano Kit
Published: June 2010

SpoIIIE is an FtsK-related protein that transports the forespore chromosome across the Bacillus subtilis sporulation septum. We use membrane photobleaching and protoplast assays to demonstrate that SpoIIIE is required for septal membrane fission in the presence of trapped DNA, and that DNA is transported across separate daughter cell membranes, suggesting that SpoIIIE forms a channel that partitions the daughter cell membranes. Our results reveal a close correlation between septal membrane fission and the assembly of a stable SpoIIIE translocation complex at the septal midpoint. Time-lapse epifluorescence, total internal reflection fluorescence (TIRF) microscopy, and live-cell photoactivation localization microscopy (PALM) demonstrate that the SpoIIIE transmembrane domain mediates dynamic localization to active division sites, whereas the assembly of a stable focus also requires the cytoplasmic domain. The transmembrane domain fails to completely separate the membrane, and it assembles unstable foci. TIRF microscopy and biophysical modeling of fluorescence recovery after photobleaching (FRAP) data suggest that this unstable protein transitions between disassembled and assembled oligomeric states. We propose a new model for the role of SpoIIIE assembly in septal membrane fission that has strong implications for how the chromosome terminus crosses the septum.
Distinct Sonic Hedgehog signaling dynamics specify floor plate and ventral neuronal progenitors in the vertebrate neural tube
Authors: Ribes Vanessa , Balaskas Nikolaos , Sasai Noriaki , Cruz Catarina , Dessaud Eric , Cayuso Jordi , Tozer Samuel , Yang Lin Lin , Novitch Ben , Marti Elisa , Briscoe James
Published: June 2010

The secreted ligand Sonic Hedgehog (Shh) organizes the pattern of cellular differentiation in the ventral neural tube. For the five neuronal subtypes, increasing levels and durations of Shh signaling direct progenitors to progressively more ventral identities. Here we demonstrate that this mode of action is not applicable to the generation of the most ventral cell type, the nonneuronal floor plate (FP). In chick and mouse embryos, FP specification involves a biphasic response to Shh signaling that controls the dynamic expression of key transcription factors. During gastrulation and early somitogenesis, FP induction depends on high levels of Shh signaling. Subsequently, however, prospective FP cells become refractory to Shh signaling, and this is a prerequisite for the elaboration of their identity. This prompts a revision to the model of graded Shh signaling in the neural tube, and provides insight into how the dynamics of morphogen signaling are deployed to extend the patterning capacity of a single ligand. In addition, we provide evidence supporting a common scheme for FP specification by Shh signaling that reconciles mechanisms of FP development in teleosts and amniotes.
Regulation of ribonucleotide reductase by Spd1 involves multiple mechanisms
Authors: Nestoras Konstantinos , Mohammed Asma Hadi , Schreurs Ann-Sofie , Fleck Oliver , Watson Adam T. , Poitelea Marius , O'Shea Charlotte , Chahwan Charly , Holmberg Christian , Kragelund Birthe B. , Nielsen Olaf , Osborne Mark , Carr Antony M. , Liu Cong
Published: June 2010

The correct levels of deoxyribonucleotide triphosphates and their relative abundance are important to maintain genomic integrity. Ribonucleotide reductase (RNR) regulation is complex and multifaceted. RNR is regulated allosterically by two nucleotide-binding sites, by transcriptional control, and by small inhibitory proteins that associate with the R1 catalytic subunit. In addition, the subcellular localization of the R2 subunit is regulated through the cell cycle and in response to DNA damage. We show that the fission yeast small RNR inhibitor Spd1 is intrinsically disordered and regulates R2 nuclear import, as predicted by its relationship to Saccharomyces cerevisiae Dif1. We demonstrate that Spd1 can interact with both R1 and R2, and show that the major restraint of RNR in vivo by Spd1 is unrelated to R2 subcellular localization. Finally, we identify a new behavior for RNR complexes that potentially provides yet another mechanism to regulate dNTP synthesis via modulation of RNR complex architecture.
Treatment of Surfaces with Poly-L-Lysine for Drosophila Cell Cultivation
Authors: Cherbas Lucy , Cherbas Peter
Published: June 2010

INTRODUCTION

Most commonly used Drosophila cell lines adhere only loosely to the substrate. For some purposes (e.g., time-lapse photography and cytological examination of living cells), it is desirable to fix the growing cells more firmly to the substrate. As described in this protocol, this can be accomplished by treating the substrate with poly-L-lysine, with no obvious detrimental effect on the growth of the cells.
Preparation of Cytoplasmic and Nuclear RNA from Tissue Culture Cells
Authors: Rio Donald C. , Ares Manuel , Hannon Gregory J. , Nilsen Timothy W.
Published: June 2010

INTRODUCTION

It often is desirable to “prefractionate” RNA before analysis. Ordinarily, this can only be done with tissue culture cells, although it is possible to isolate nuclei and cytoplasm from certain “soft” tissues such as liver and white blood cells. This protocol describes a method for separating nuclei from the cytoplasm that can be used for many tissue culture types. This procedure also is useful for cells grown in suspension or for adherent cells. The procedure relies on swelling in hypotonic buffer, subsequent gentle homogenization, and centrifugation. This method is not appropriate for material (e.g., bacteria, yeast) that has high intrinsic RNase activity, or tissues that are difficult to solubilize, such as muscle tissue or plant material.
Determining the Yield and Quality of Purified RNA
Authors: Rio Donald C. , Ares Manuel , Hannon Gregory J. , Nilsen Timothy W.
Published: June 2010

INTRODUCTION

After any RNA purification by any method, it is necessary to ascertain both the amount (yield) and the integrity (quality) of the RNA obtained. This is essential for any subsequent analysis and critical for any comparative analyses. This article discusses several methods for RNA quantitation and provides tips for each.
‘Stew Without Bread or Bread Without Stew’: Children’s Understandings of Poverty in Ethiopia
Authors: Camfield Laura
Published: June 2010

This paper explores children’s understandings of poverty, ill‐being and well‐being in Ethiopia using data collected through group exercises with children aged 5–6 and 11–13 participating in Young Lives, an international study of childhood poverty. In some respects the characteristics of poverty reported by children resemble those reported by adults participating in similar exercises. However, the children’s addition of appearance and clothing, and their explanations of the reasoning behind the importance of these indicators of well‐being reflect growing inequalities in Ethiopia, where experiences of relative poverty and social exclusion are increasingly common. This evidence argues for broadening the focus of child poverty reduction to include the psychosocial costs of lacking the culturally specific resources required for full participation in society. The paper also illustrates ways in which poverty can be explored by asking about ill‐being and that children as young as five years are able to address these themes through well‐designed research methods.
Raising Malawi’s Children: Unanticipated Outcomes Associated with Institutionalised Care
Authors: Freidus Andrea
Published: June 2010

Malawian orphans and vulnerable children are becoming increasingly numerous and visible in the media and materials produced by non‐governmental organisations. As a result, orphanages are proliferating to meet their needs. Drawing on data collected in three different orphanages, this paper reports some of the positive and negative outcomes of ‘institutionalising’ children in Malawi. Being designated an orphan is becoming a valued identity for some, and a source of vulnerability and exploitation for others. While institutions address material vulnerabilities, orphans and staff report that they can also lead to increased stigmatisation, struggles over belonging, and the disruption of community and family ties.
The effectiveness of radioisotope synovectomy for chronic synovitis in Turkish paediatric haemophiliacs: Ankara experience
Authors: ALIOGLU B. , OZSOY H. , KOCA G. , SAKAOGULLARI A. , SELVER B. , OZDEMIR M. , DALLAR Y.
Published: June 2010

Summary.  Between January 2006 and December 2009, 37 radioisotope synovectomy (RS) in 18 severe haemophilic patients (factor 8 < 1%) have been performed at our centre. The distribution of joint injected was as follows: rhenium‐186 [Re186], 19 joints (ankles, 8 and elbows, 11) and yttrium‐90 [Y90] 18 joints (knees, 18). Their mean age was 12 years (range: 8–20 years). Mean follow‐up period after procedure was 22.6 months. We preferred to use Y90 for all large joints and Re186 for small joints. Haemophilic patients with grade‐II or III synovitis were selected for RS in our study. Radioisotope synovectomy was performed in eight ankles for seven patients, 11 elbows for seven patients and 18 knees for 13 patients. Mean bleeding counts before the procedure and after the procedure were as follows: Ankles, 3.43 vs. 0.62 (P = 0.002); elbows, 3.12 vs. 0.55 (P = 0.000); and 3.83 vs. 0.62 (P = 0.011). No major complications requiring secondary treatments were observed. In summary, an early RS is the best way to halt the evolution of chronic haemophilia synovitis to devastating haemophilic arthropathy. Radioisotope synovectomy is very effective and safe in the treatment of chronic synovitis of children with haemophilia. Our data confirm the efficacy of RS for the treatment of chronic haemophilic synovitis, which has been previously published by many authors around the world. We highly recommend this procedure for developing countries to prevent joint disabilities. For a better and a healthier generation, RS has to be introduced in all the developing countries.
Nurses’ knowledge and barriers regarding pain management in intensive care units
Authors: Wang Hsiang‐Ling , Tsai Yun‐Fang
Published: June 2010

Aim.  To explore nurses’ knowledge and barriers regarding pain management in intensive care units.

Background.  Pain is a common and treatable condition among intensive care patients. Quality care of these patients depends on the pain knowledge and pain management skills of critical care nurses. However, no single study has explored these nurses’ knowledge of and perceived barriers to pain management in Taiwan.

Design.  A cross‐sectional study.

Method.  Intensive care unit nurses (n = 370) were recruited from 16 hospitals chosen by stratified sampling across Taipei County in Taiwan. Data were collected on nurses’ knowledge of pain management using the Nurses’ Knowledge and Attitudes Survey‐Taiwanese version, on perceived barriers to pain management using a researcher‐developed scale and on background information.

Results.  The overall average correct response rate for the knowledge scale was 53·4%, indicating poor knowledge of pain management. The top barrier to managing pain identified by these nurses was ‘giving proper pain prescription needs doctor’s approval; can’t depend on me’. Knowledge of pain management was significantly and negatively related to perceived barriers to pain management. In addition, scores for knowledge and perceived barriers differed significantly by specific intensive care unit. Knowledge also differed significantly by nurses’ education level, clinical competence level (nursing ladder) and hospital accreditation category.

Conclusion.  Our results indicate an urgent need to strengthen pain education by including case analysis for intensive care nurses in Taiwan.

Relevance to clinical practice.  Pain education should target knowledge deficits and barriers to changing pain management approaches for Taiwanese nurses in intensive care units.
The crystal structures of two salivary cystatins from the tick Ixodes scapularis and the effect of these inhibitors on the establishment of Borrelia burgdorferi infection in a murine model
Authors: Kotsyfakis Michalis , Horka Helena , Salat Jiri , Andersen John F.
Published: June 2010

We have previously demonstrated that two salivary cysteine protease inhibitors from the Borrelia burgdorferi (Lyme disease) vector Ixodes scapularis– namely sialostatins L and L2 – play an important role in tick biology, as demonstrated by the fact that silencing of both sialostatins in tandem results in severe feeding defects. Here we show that sialostatin L2 – but not sialostatin L – facilitates the growth of B. burgdorferi in murine skin. To examine the structural basis underlying these differential effects of the two sialostatins, we have determined the crystal structures of both sialostatin L and L2. This is the first structural analysis of cystatins from an invertebrate source. Sialostatin L2 crystallizes as a monomer with an ‘unusual’ conformation of the N‐terminus, while sialostatin L crystallizes as a domain‐swapped dimer with an N‐terminal conformation similar to other cystatins. Deletion of the ‘unusual’ N‐terminal five residues of sialostatin L2 results in marked changes in its selectivity, suggesting that this region is a particularly important determinant of the biochemical activity of sialostatin L2. Collectively, our results reveal the structure of two tick salivary components that facilitate vector blood feeding and that one of them also supports pathogen transmission to the vertebrate host.
Screening Leishmania donovani‐specific genes required for visceral infection
Authors: Zhang Wen‐Wei , Matlashewski Greg
Published: June 2010

Comparison of the Leishmania infantum genome with Leishmania braziliensis and Leishmania major genomes has identified 25 L. infantum species‐specific genes that are absent or pseudogenes in L. major and L. braziliensis. To determine whether these L. infantum species‐specific genes are involved in visceral Leishmania infection, we cloned the orthologues of 14 L. infantum species‐specific genes from the genetically closely related Leishmania donovani and introduced them into L. major. Two of these L. donovani species‐specific genes were found to significantly increase L. major survival in visceral organs in BALB/c mice. One (orthologue of LinJ28_V3.0340; Ld2834) of these two genes was further investigated. The L. donovani Ld2834 null mutants displayed dramatically reduced virulence in BALB/c mice and were unable to survive in axenic amastigote culture conditions arguing that Ld2834 plays a crucial role in enabling L. donovani survive at the increased temperature typically associated with visceral organs. Ld2834 encodes a 50 kDa protein that is localized in the cytoplasma and has no significant sequence similarity with other known genes. This study validates the importance of comparative genomics for understanding Leishmania species pathology and argues that Leishmania species‐specific genes play important roles in tissue tropism and virulence.
M. tuberculosis intramembrane protease Rip1 controls transcription through three anti‐sigma factor substrates
Authors: Sklar Joseph G. , Makinoshima Hideki , Schneider Jessica S. , Glickman Michael S.
Published: June 2010

Regulated intramembrane proteolysis (RIP) is a mechanism of transmembrane signal transduction that functions through intramembrane proteolysis of substrates. We previously reported that the RIP metalloprotease Rv2869c (Rip1) is a determinant of Mycobacterium tuberculosis (Mtb) cell envelope composition and virulence, but the substrates of Rip1 were undefined. Here we show that Rip1 cleaves three transmembrane anti‐sigma factors: anti‐SigK, anti‐SigL and anti‐SigM, negative regulators of Sigma K, L and M. We show that transcriptional activation of katG in response to phenanthroline requires activation of SigK and SigL by Rip1 cleavage of anti‐SigK and anti‐SigL. We also demonstrate a Rip1‐dependent pathway that activates the genes for the mycolic acid biosynthetic enzyme KasA and the resuscitation promoting factor RpfC, but represses the bacterioferritin encoding gene bfrB. Regulation of these three genes by Rip1 is not reproduced by deletion of Sigma K, L or M, either indicating a requirement for multiple Rip1 substrates or additional arms of the Rip1 pathway. These results identify a branched proteolytic signal transduction system in which a single intramembrane protease cleaves three anti‐sigma factor substrates to control multiple downstream pathways involved in lipid biosynthesis and defence against oxidative stress.
The high affinity iron permease is a key virulence factor required forRhizopus oryzaepathogenesis
Authors: Ibrahim Ashraf S. , Gebremariam Teclegiorgis , Lin Lin , Luo Guanpingsheng , Husseiny Mohamed I. , Skory Christopher D. , Fu Yue , French Samuel W. , Edwards, Jr John E. , Spellberg Brad
Published: June 2010

Rhizopus oryzaeis the most common cause of mucormycosis, an angioinvasive fungal infection that causes more then 50% mortality rate despite first‐line therapy. Clinical and animal model data clearly demonstrate that the presence of elevated available serum iron predisposes the host to mucormycosis. The high affinity iron permease gene (FTR1) is required forR. oryzaeiron transport in iron‐depleted environments. Here we demonstrate thatFTR1is required for full virulence ofR. oryzaein mice. We show thatFTR1is expressed during infection in diabetic ketoacidosis (DKA) mice. In addition, we disruptedFTR1by double cross‐over homologous recombination, but multinucleatedR. oryzaecould not be forced to segregate to a homokaryotic null allele. Nevertheless, a reduction of the relative copy number ofFTR1and inhibition ofFTR1expression by RNAi compromised the ability ofR. oryzaeto acquire ironin vitroand reduced its virulence in DKA mice. Importantly, passive immunization with anti‐Ftr1p immune sera protected DKA mice from infection withR. oryzae. Thus,FTR1is a virulence factor forR. oryzae, and anti‐Ftr1p passive immunotherapy deserves further evaluation as a strategy to improve outcomes of deadly mucormycosis.
The inducer maltotriose binds in the central cavity of the tetratricopeptide‐like sensor domain of MalT, a bacterial STAND transcription factor
Authors: Danot Olivier
Published: June 2010

Signal transduction ATPases with numerous domains (STAND) are sophisticated proteins that integrate several signals and respond by building multimeric platforms allowing signalling in various processes: apoptosis, innate immunity, bacterial metabolism. They comprise a conserved nucleotide oligomerization domain (NOD), which functions as a binary switch that oscillates between the OFF (ADP‐bound) and the ON (ATP‐bound) conformation, and non conserved sensor and effector domains. Transition from the OFF form to the ON form strictly depends on the binding of an inducer to the sensor domain. The interaction of the inducer with this domain was studied in MalT, a model STAND protein. MalT sensor domain has a SUPR (superhelical repeats) fold resembling a cylinder with a central cavity. The cavity was subjected to an alanine‐scanning approach, and the effects of the alanine substitutions on inducer binding and transcription activation were analyzed. This work unambiguously showed that the inducer maltotriose binds inside the cavity, and a patch on the inner surface was proposed to be the primary maltotriose binding‐site. Furthermore, limited proteolysis suggested that maltotriose binding changes the conformation of the sensor domain.
The mycobacteriophage Ms6 encodes a chaperone‐like protein involved in the endolysin delivery to the peptidoglycan
Authors: Catalão Maria João , Gil Filipa , Moniz‐Pereira José , Pimentel Madalena
Published: June 2010

Like most double‐stranded (ds) DNA phages, mycobacteriophage Ms6 uses the holin‐endolysin system to achieve lysis of its host. In addition to endolysin (lysA) and holin (hol) genes, Ms6 encodes three accessory lysis proteins. In this study we investigated the lysis function of Gp1, which is encoded by the gp1 gene that lies immediately upstream of lysA. Escherichia coli lysis was observed after coexpression of LysA and Gp1 in the absence of Ms6 holin. Gp1 does not belong to the holin class of proteins, and we provide evidence that it shares several characteristics with molecular chaperones. We show that Gp1 interacts with LysA, and that this interaction is necessary for LysA delivery to its target. In addition, PhoA fusions showed that, in Mycobacterium smegmatis, LysA is exported to the extracytoplasmic environment in the presence of Gp1. We also show that Gp1 is necessary for efficient M. smegmatis lysis, as Ms6 gp1 deletion results in host lysis defects. We propose that delivery of Ms6 endolysin to the murein layer is assisted by Gp1, a chaperone‐like protein, in a holin‐independent manner.
Guanosine 5′‐diphosphate 3′‐diphosphate (ppGpp) as a negative modulator of polynucleotide phosphorylase activity in a ‘rare’ actinomycete
Authors: Siculella Luisa , Damiano Fabrizio , Di Summa Roberta , Tredici Salvatore M. , Alduina Rosa , Gnoni Gabriele V. , Alifano Pietro
Published: June 2010

With the beginning of the idiophase the highly phosphorylated guanylic nucleotides guanosine 5′‐diphosphate 3′‐diphosphate (ppGpp) and guanosine 5′‐triphosphate 3′‐diphosphate (pppGpp), collectively referred to as (p)ppGpp, activate stress survival adaptation programmes and trigger secondary metabolism in actinomycetes. The major target of (p)ppGpp is the RNA polymerase, where it binds altering the enzyme activity. In this study analysis of the polynucleotide phosphorylase (PNPase)‐encoding gene pnp mRNA, in Nonomuraea sp. ATCC 39727 wild‐type, constitutively stringent and relaxed strains, led us to hypothesize that in actinomycetes (p)ppGpp may modulate gene expression at the level of RNA decay also. This hypothesis was supported by: (i) in vitro evidence that ppGpp, at physiological levels, inhibited both polynucleotide polymerase and phosphorolytic activities of PNPase in Nonomuraea sp., but not in Escherichia coli, (ii) in vivo data showing that the pnp mRNA and the A40926 antibiotic cluster‐specific dpgA mRNA were stabilized during the idiophase in the wild‐type strain but not in a relaxed mutant and (iii) measurement of chemical decay of pulse‐labelled bulk mRNA. The results of biochemical tests suggest competitive inhibition of ppGpp with respect to nucleoside diphosphates in polynucleotide polymerase assays and mixed inhibition with respect to inorganic phosphate when the RNA phosphorolytic activity was determined.