bluuebunny/crossref_metadata_2025 huggingface dataset:
Wheat genotypes differ in potassium accumulation and osmotic adjustment under drought stress
Authors: Damon P. M. , Ma Q. F. , Rengel Z.
Published: July 2011

Potassium (K) is the principal mineral solute contributing to osmotic adjustment (OA) in many crop species, and the magnitude of OA under drought stress may be increased by application of K fertilisers. Genotypic differences in either the capacity for OA under drought stress or the efficiency of K uptake and utilisation by wheat have been separately documented. However, it is not known whether genotypic differences in K uptake and utilisation are linked to differences in OA under drought stress. In this study, we quantified changes in OA in response to variable K fertilisation among five wheat genotypes with contrasting efficiency of K uptake and utilisation.
Fertilisation with K increased OA for most genotypes by increasing K+ uptake and translocation into shoots and its subsequent accumulation in young leaves when drought stress was imposed. Accumulation of K+ in young leaves accounted for 36–51% of OA among the genotypes. The magnitude of OA achieved by genotypes under K fertilisation was highly correlated with the net content of K accumulated in shoots. With K fertilisation, differences in shoot K+ content accounted for 84% of the difference in OA among wheat genotypes. By comparison, for plants without K fertilisation, K+ accumulation in young leaves contributed only 17–28% of OA. At low K supply, the magnitude of OA achieved by genotypes was independent of the content or concentration of K+ in shoots.
Under K-fertilised conditions, genotype Nyabing achieved the highest OA under drought stress, accumulated the highest concentration of K+ in young leaves (–0.87 MPa, accounting for 51% of OA), and had the greatest net K+ content in shoots. Genotype Wyalkatchem accumulated the smallest content of K+ in shoots and the lowest K+ concentration in young leaves (–0.40 MPa, accounting for 38% of OA), and achieved the lowest OA under drought stress. The greatest OA was achieved where high genotypic capacity to take up K was paired with conditions of high soil K availability.
The phylogenetic disposition of Antrodia s.l. (Polyporales, Basidiomycota) from Patagonia, Argentina
Authors: Rajchenberg M. , Gorjón S. P. , Pildain M. B.
Published: July 2011

The aim of the present study was to characterise species of Antrodia s.l. from Patagonia, Argentina, and to determine their phylogenetic relationships by using morphological and cultural features as well as mating systems and ITS sequences. Phylogenetic trees generated from maximum-parsimony, neighbour-joining and Bayesian-inference analyses showed that the Argentinean collections were distributed inside the following three main clades: (1) ‘Antrodia clade’, with Antrodia ramentacea (Berk. & Broome) Donk as a sole representative; (2) ‘Amyloporia clade’, including Amyloporia nothofaginea Rajchenb. & Gorjón sp. nov. and A. stratosa (J.E.Wright & J.R.Deschamps) Rajchenb., Gorjón & Pildain comb. nov.; and (3) ‘Fibroporia clade’, with Fibroporia vaillantii (DC.) Parmasto and F. gossypium (Speg.) Parmasto. ‘Amyloporia’ and ‘Antrodia clades’ did not have strong molecular support; however, they were well defined with a polyphasic approach when other features such as the number of spore nuclei, mating systems and nuclear behaviour were added. Antrodia includes homothallic to bipolar species, with uni- or binucleate spores and normal nuclear behaviour. Amyloporia includes bipolar to tetrapolar species, with uninucleate spores and heterocytic nuclear behaviour. Fibroporia has strong molecular support and includes tetrapolar species, with uninucleate spores and normal nuclear behaviour. Amyloporia nothofaginea is described as a new species and two new combinations in Amyloporia are proposed. A key to the Antrodia s.l. species present in Patagonia is included.
EspR, a key regulator of
Mycobacterium tuberculosis
virulence, adopts a unique dimeric structure among helix-turn-helix proteins
Authors: Rosenberg Oren S. , Dovey Cole , Tempesta Michael , Robbins Rebecca A. , Finer-Moore Janet S. , Stroud Robert M. , Cox Jeffery S.
Published: July 2011

EspR is a transcriptional regulator that activates the ESX-1 secretion system during
Mycobacterium tuberculosis
infection and is critical for pathogenesis. It is unique among DNA-binding proteins as it is secreted as part of a feedback regulatory loop that serves to mitigate transcriptional activity. Here we report the crystal structure of a functional EspR dimer at 2.5-Å resolution. The amino-terminal half of EspR is a helix-turn-helix (HTH) DNA-binding domain and the carboxy terminus consists of a dimerization domain with similarity to the SinR:SinI sporulation regulator of
Bacillus subtilis
. Surprisingly, the HTH domains of EspR are arranged in an unusual conformation in which they are splayed at an oblique angle to each other, suggesting that EspR binds DNA in a profoundly different way than most other known HTH regulators. By mapping the EspR binding sites in the
espACD
promoter, using both in vivo and in vitro binding assays, we show that the EspR operators are located unusually far from the promoter. The EspR dimer binds to these sites cooperatively, but the two “half-sites” contacted by each DNA recognition motif are separated by 177 base pairs. The distinctive structure of EspR and the exceptional arrangement of its operator contacts suggest that it could promote DNA looping in its target promoter. We hypothesize that direct DNA looping mediated by single-site binding of each EspR monomer may facilitate transcriptional control of this important virulence system.
Optical properties in the soft photonic crystals based on ferrofluids
Authors: Fan C Z , Liang E J , Huang J P
Published: July 2011

We theoretically investigate the properties of optical propagation in one-dimensional soft photonic crystals based on ferrofluids using the transfer matrix method. The proposed structure is composed of an alternating ferrofluid layer and a dielectric layer. Ferrofluids are composed of suspended ferromagnetic nanoparticles coated with silver, which has a frequency-dependent dielectric function. Core–shell nanocomposites incorporating an optical signature with magnetic response are particularly useful. The calculated results of dispersion relation show that tunable band gaps can be realized by varying the local magnetic field factor α, the shell thickness parameter t, or the filling fraction ν of the ferrofluid layer. An additional band gap appears in the lower frequency region due to the absorption. These band gaps blue shift when the external magnetic field is enhanced, and red shift when either t or ν is increased. We also extend our analysis to the variation of band width. To meet the requirements of optical devices, such a tunable structure can be used to design optical filters, modulators and waveguides.
An ac susceptibility study in capped Ni/Ni(OH)2 core–shell nanoassemblies: dual peak observations
Authors: Godsell Jeffrey F , Bala Tanushree , Ryan Kevin M. , Roy Saibal
Published: July 2011

In this study, the ac susceptibility (χ′ and χ″) variation with temperature (10–100 K) for oleic acid (OA) capped Ni/Ni(OH)2 core–shell nanoparticle assemblies are reported at frequencies varying from 0.1 to 1000 Hz. Nanoparticle assemblies, with two average particle diameters of ∼34 nm and ∼14 nm, were synthesized using a wet chemical synthesis approach. Two peaks in the ac susceptibility versus temperature curves are clearly discernable for each of the samples. The first, occurring at ∼22 K was attributed to the paramagnetic/antiferromagnetic transition of the Ni(OH)2 present in the shell. The second higher temperature peak was attributed to the superparamagnetic blocking of the pure Ni situated at the core of the nanoparticles. The higher temperature peaks in both the χ′ and χ″ curves were observed to increase with increasing frequency. Thus the Néel and the blocking temperatures for such core–shell nanoassemblies were clearly identified from the ac analysis, whereas they were not discernible (superimposed) even from very low dc (FC/ZFC) field measurements. Interparticle interactions within the assemblies were studied through the fitting of phenomenological laws to the experimental datasets. It is observed that even with an OA capping layer, larger Ni/Ni(OH)2 nanoparticles experience a greater degree of sub-capping layer oxidation thus producing lower magnetic interaction strengths.
Phase separation of monomer in liquid crystal mixtures and surface morphology in polymer-stabilized vertical alignment liquid crystal displays
Authors: Lyu Jae Jin , Kikuchi Hirotsuku , Kim Dae Hyun , Lee Jun Hyup , Kim Kyeong Hyeon , Higuchi Hiroki , Lee Seung Hee
Published: July 2011

The polymer-stabilized vertically aligned (PS-VA) liquid crystal display (LCD) driving mode has high potential for manufacturing low power consuming displays due to the higher transmittance and fast response as compared with the existing patterned vertically aligned and multi-domain vertically aligned modes. In this paper we have investigated the reaction mechanisms of monomer–liquid crystal blends to form a surface pre-tilt angle of liquid crystal in vertical alignment LCD associated with a fishbone electrode structure. The observed sizes of polymer bumps formed on the substrates were found to be dependent on the exposed UV wavelength and were almost equal in both top and bottom substrates. When a large UV wavelength was used, the phase separation mechanism of monomer in PS-VA mode was found nearly isotropic rather than anisotropic in contrast to the previous studies.
Magnetic property effect on transport processes in resistance spot welding
Authors: Wei P S , Wu T H
Published: July 2011

This study investigates the effects of the Curie temperature and magnetic permeability on transport variables, solute distribution and nugget shapes during resistance spot welding. The Curie temperature is the temperature below which a metal or alloy is ferromagnetic with a high magnetic permeability, and above which it is paramagnetic with a small magnetic permeability. The model proposed here accounts for electromagnetic force, heat generation and contact resistance at the faying surface and electrode–workpiece interfaces and bulk resistance in workpieces. Contact resistance includes constriction and film resistances, which are functions of hardness, temperature, electrode force and surface condition. The computed results show that transport variables and nugget shapes can be consistently interpreted from the delay of response time and jump of electric current density as a result of finite magnetic diffusion, rather than through the examination of the variations of dynamic electrical resistance with time. The molten nugget on the faying surface is initiated earlier with increasing magnetic permeability and Curie temperature. A high Curie temperature enhances convection and solute mixing, and readily melts through the workpiece surface near the electrode edge. Any means to reduce the Curie temperature or magnetic permeability, such as adjusting the solute content, can be a good way to control weld quality. This study can also be applied to interpret the contact problems encountered in various electronics and packaging technologies, and so on.
Caldesmon regulates actin dynamics to influence cranial neural crest migration inXenopus
Authors: Nie Shuyi , Kee Yun , Bronner-Fraser Marianne
Published: July 2011

Caldesmon (CaD) is an important actin modulator that associates with actin filaments to regulate cell morphology and motility. Although extensively studied in cultured cells, there is little functional information regarding the role of CaD in migrating cells in vivo. Here we show that nonmuscle CaD is highly expressed in both premigratory and migrating cranial neural crest cells of Xenopus embryos. Depletion of CaD with antisense morpholino oligonucleotides causes cranial neural crest cells to migrate a significantly shorter distance, prevents their segregation into distinct migratory streams, and later results in severe defects in cartilage formation. Demonstrating specificity, these effects are rescued by adding back exogenous CaD. Interestingly, CaD proteins with mutations in the Ca2+-calmodulin–binding sites or ErK/Cdk1 phosphorylation sites fail to rescue the knockdown phenotypes, whereas mutation of the PAK phosphorylation site is able to rescue them. Analysis of neural crest explants reveals that CaD is required for the dynamic arrangements of actin and, thus, for cell shape changes and process formation. Taken together, these results suggest that the actin-modulating activity of CaD may underlie its critical function and is regulated by distinct signaling pathways during normal neural crest migration.
Temporal control of nuclear envelope assembly by phosphorylation of lamin B receptor
Authors: Tseng Li-Chuan , Chen Rey-Huei
Published: July 2011

The nuclear envelope of metazoans disassembles during mitosis and reforms in late anaphase after sister chromatids have well separated. The coordination of these mitotic events is important for genome stability, yet the temporal control of nuclear envelope reassembly is unknown. Although the steps of nuclear formation have been extensively studied in vitro using the reconstitution system from egg extracts, the temporal control can only be studied in vivo. Here, we use time-lapse microscopy to investigate this process in living HeLa cells. We demonstrate that Cdk1 activity prevents premature nuclear envelope assembly and that phosphorylation of the inner nuclear membrane protein lamin B receptor (LBR) by Cdk1 contributes to the temporal control. We further identify a region in the nucleoplasmic domain of LBR that inhibits premature chromatin binding of the protein. We propose that this inhibitory effect is partly mediated by Cdk1 phosphorylation. Furthermore, we show that the reduced chromatin-binding ability of LBR together with Aurora B activity contributes to nuclear envelope breakdown. Our studies reveal for the first time a mechanism that controls the timing of nuclear envelope reassembly through modification of an integral nuclear membrane protein.
Kinesin molecular motor Eg5 functions during polypeptide synthesis
Authors: Bartoli Kristen M. , Jakovljevic Jelena , Woolford John L. , Saunders William S.
Published: July 2011

The kinesin-related molecular motor Eg5 plays roles in cell division, promoting spindle assembly. We show that during interphase Eg5 is associated with ribosomes and is required for optimal nascent polypeptide synthesis. When Eg5 was inhibited, ribosomes no longer bound to microtubules in vitro, ribosome transit rates slowed, and polysomes accumulated in intact cells, suggesting defects in elongation or termination during polypeptide synthesis. These results demonstrate that the molecular motor Eg5 associates with ribosomes and enhances the efficiency of translation.
A view from the NIH bridge: perspectives of a program officer
Authors: Zatz Marion
Published: July 2011

This essay is written from my perspective as a program officer for research and training activities at the National Institute of General Medical Sciences (NIGMS) for almost 27 yr. It gives a bird's-eye view of the job of a program officer, which includes providing advice to applicants and grantees, making funding recommendations, overseeing grantees' progress, facilitating scientific opportunities in specific areas of program responsibility, and shaping NIGMS and National Institutes of Health (NIH) policy. I have highlighted the numerous rewards of serving as a program officer, as well as some of the difficulties. For those who may be considering a position as an NIH program officer now or in the future, I've also described the qualities and qualifications that are important for such a career choice. Finally, this essay addresses some of the challenges for the NIH and the research community in the years ahead as we simultaneously face exciting scientific opportunities and tighter budgets.
Effects of integrin-mediated cell adhesion on plasma membrane lipid raft components and signaling
Authors: Norambuena Andrés , Schwartz Martin A.
Published: July 2011

Anchorage dependence of cell growth, which is mediated by multiple integrin-regulated signaling pathways, is a key defense against cancer metastasis. Detachment of cells from the extracellular matrix triggers caveolin-1–dependent internalization of lipid raft components, which mediates suppression of Rho GTPases, Erk, and phosphatidylinositol 3-kinase in suspended cells. Elevation of cyclic adenosine monophosphate (cAMP) following cell detachment is also implicated in termination of growth signaling in suspended cells. Studies of integrins and lipid rafts, however, examined mainly ganglioside GM1 and glycosylphosphatidylinositol-linked proteins as lipid raft markers. In this study, we examine a wider range of lipid raft components. Whereas many raft components internalized with GM1 following cell detachment, flotillin2, connexin43, and Gαs remained in the plasma membrane. Loss of cell adhesion caused movement of many components from the lipid raft to the nonraft fractions on sucrose gradients, although flotillin2, connexin43, and H-Ras were resistant. Gαs lost its raft association, concomitant with cAMP production. Modification of the lipid tail of Gαs to increase its association with ordered domains blocked the detachment-induced increase in cAMP. These data define the effects of that integrin-mediated adhesion on the localization and behavior of a variety of lipid raft components and reveal the mechanism of the previously described elevation of cAMP after cell detachment.
Condensins I and II are essential for construction of bivalent chromosomes in mouse oocytes
Authors: Lee Jibak , Ogushi Sugako , Saitou Mitinori , Hirano Tatsuya
Published: July 2011

In many eukaryotes, condensins I and II associate with chromosomes in an ordered fashion during mitosis and play nonoverlapping functions in their assembly and segregation. Here we report for the first time the spatiotemporal dynamics and functions of the two condensin complexes during meiotic divisions in mouse oocytes. At the germinal vesicle stage (prophase I), condensin I is present in the cytoplasm, whereas condensin II is localized within the nucleus. After germinal vesicle breakdown, condensin II starts to associate with chromosomes and becomes concentrated onto chromatid axes of bivalent chromosomes by metaphase I. REC8 “glues” chromosome arms along their lengths. In striking contrast to condensin II, condensin I localizes primarily around centromeric regions at metaphase I and starts to associate stably with chromosome arms only after anaphase I. Antibody injection experiments show that condensin functions are required for many aspects of meiotic chromosome dynamics, including chromosome individualization, resolution, and segregation. We propose that the two condensin complexes play distinctive roles in constructing bivalent chromosomes: condensin II might play a primary role in resolving sister chromatid axes, whereas condensin I might contribute to monopolar attachment of sister kinetochores, possibly by assembling a unique centromeric structure underneath.
The budding yeast polo-like kinase Cdc5 regulates the Ndt80 branch of the meiotic recombination checkpoint pathway
Authors: Acosta Isabel , Ontoso David , San-Segundo Pedro A.
Published: July 2011

Defects in chromosome synapsis and/or meiotic recombination activate a surveillance mechanism that blocks meiotic cell cycle progression to prevent anomalous chromosome segregation and formation of aberrant gametes. In the budding yeast zip1 mutant, which lacks a synaptonemal complex component, the meiotic recombination checkpoint is triggered, resulting in extremely delayed meiotic progression. We report that overproduction of the polo-like kinase Cdc5 partially alleviates the meiotic prophase arrest of zip1, leading to the formation of inviable meiotic products. Unlike vegetative cells, we demonstrate that Cdc5 overproduction does not stimulate meiotic checkpoint adaptation because the Mek1 kinase remains activated in zip1 2μ-CDC5 cells. Inappropriate meiotic divisions in zip1 promoted by high levels of active Cdc5 do not result from altered function of the cyclin-dependent kinase (CDK) inhibitor Swe1. In contrast, CDC5 overexpression leads to premature induction of the Ndt80 transcription factor, which drives the expression of genes required for meiotic divisions, including CLB1. We also show that depletion of Cdc5 during meiotic prophase prevents the production of Ndt80 and that CDK activity contributes to the induction of Ndt80 in zip1 cells overexpressing CDC5. Our results reveal a role for Cdc5 in meiotic checkpoint control by regulating Ndt80 function.
RseqFlow: workflows for RNA-Seq data analysis
Authors: Wang Ying , Mehta Gaurang , Mayani Rajiv , Lu Jingxi , Souaiaia Tade , Chen Yangho , Clark Andrew , Yoon Hee Jae , Wan Lin , Evgrafov Oleg V. , Knowles James A. , Deelman Ewa , Chen Ting
Published: July 2011

Summary: We have developed an RNA-Seq analysis workflow for single-ended Illumina reads, termed RseqFlow. This workflow includes a set of analytic functions, such as quality control for sequencing data, signal tracks of mapped reads, calculation of expression levels, identification of differentially expressed genes and coding SNPs calling. This workflow is formalized and managed by the Pegasus Workflow Management System, which maps the analysis modules onto available computational resources, automatically executes the steps in the appropriate order and supervises the whole running process. RseqFlow is available as a Virtual Machine with all the necessary software, which eliminates any complex configuration and installation steps.

Availability and implementation:  http://genomics.isi.edu/rnaseq

Contact:  wangying@xmu.edu.cn; knowles@med.usc.edu; deelman@isi.edu; tingchen@usc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Venous Air Embolism
Authors: Albin Maurice S. , Warner David S.
Published: July 2011

Clinical Considerations Concerning Detection of Venous Air Embolism. By Maurice S. Albin, Robert G. Carroll, Joseph C. Maroon. Neurosurgery 1978; 3:380-84. Abstract used with permission from the Congress of Neurological Surgeons, copyright 1978. Venous air embolism during neurosurgical procedures (detected by Doppler ultrasound and aspiration via a right atrial catheter) was noted in 100 of 400 patients in the sitting position, 5 of 60 patients in the lateral position, 7 of 48 patients in the supine position, and 1 of 10 patients in the monitored prone position. We confirmed venous air embolism in many of these patients by using serial technetium-microaggregated albumin lung scans. Gravitational gradients from the venous portal of entrance to the right side of the heart were as small as 5.0 cm, with aspiration of 200 ml of air occurring. Doppler ultrasonic air bubble detection and aspiration through a previously inserted right atrial catheter are critical factors in the diagnosis and treatment of this condition.
Sevoflurane Protects Ventricular Myocytes from Ca2+Paradox-mediated Ca2+Overload by Blocking the Activation of Transient Receptor Potential Canonical Channels
Authors: Kojima Akiko , Kitagawa Hirotoshi , Omatsu-Kanbe Mariko , Matsuura Hiroshi , Nosaka Shuichi
Published: July 2011

Background

Volatile anesthetics produce cardioprotective action by attenuating cellular Ca2+ overload. The Ca2+ paradox is an important model for studying the mechanisms associated with Ca2+ overload-mediated myocardial injury, and was recently found to be mediated by Ca2+ entry through the transient receptor potential canonical channels upon Ca2+ repletion. This study investigated the effect of sevoflurane on cellular mechanisms underlying the Ca2+ paradox.

Methods

The Ca2+ paradox was examined in fluo-3 or mag-fluo-4-loaded mouse ventricular myocytes using confocal laser scanning microscope, upon Ca2+ repletion after 15 min of Ca2+ depletion in the absence and presence of sevoflurane.

Results

The Ca2+ paradox was evoked in approximately 65% of myocytes upon Ca2+ repletion, as determined by an abrupt elevation of cytosolic Ca2+ accompanied by hypercontracture. The Ca2+ paradox was significantly suppressed by sevoflurane administered for 3 min before and during Ca2+ repletion (Post) or during Ca2+ depletion and repletion (Postlong), and Postlong was more beneficial than Post application. The sarcoplasmic reticulum Ca2+ levels gradually decreased during Ca2+ depletion, and the Ca2+ paradox was readily evoked in myocytes with reduced sarcoplasmic reticulum Ca2+ levels. Postlong but not Post application of sevoflurane prevented decrease in sarcoplasmic reticulum Ca2+ levels by blocking Ca2+ leak through ryanodine receptors. Whole cell patch-clamp recordings revealed that sevoflurane rapidly blocked thapsigargin-induced transient receptor potential canonical currents.

Conclusions

Sevoflurane protects ventricular myocytes from Ca2+ paradox-mediated Ca2+ overload by blocking transient receptor potential canonical channels and by preventing the decrease in sarcoplasmic reticulum Ca2+ levels, which is associated with less activation of transient receptor potential canonical channels.
The effects of NS5A inhibitors on NS5A phosphorylation, polyprotein processing and localization
Authors: Qiu Dike , Lemm Julie A. , O’Boyle Donald R. , Sun Jin-Hua , Nower Peter T. , Nguyen Van , Hamann Lawrence G. , Snyder Lawrence B. , Deon Daniel H. , Ruediger Edward , Meanwell Nicholas A. , Belema Makonen , Gao Min , Fridell Robert A.
Published: July 2011

Hepatitis C virus (HCV) non-structural protein 5A (NS5A) is a multi-functional protein that is expressed in basally phosphorylated (p56) and in hyperphosphorylated (p58) forms. NS5A phosphorylation has been implicated in regulating multiple aspects of HCV replication. We recently reported the identification of a class of compounds that potently inhibit HCV RNA replication by targeting NS5A. Although the precise mechanism of inhibition of these compounds is not well understood, one activity that has been described is their ability to block expression of the hyperphosphorylated form of NS5A. Here, we report that an NS5A inhibitor impaired hyperphosphorylation without affecting basal phosphorylation at the C-terminal region of NS5A. This inhibitor activity did not require NS5A domains II and III and was distinct from that of a cellular kinase inhibitor that also blocked NS5A hyperphosphorylation, results that are consistent with an inhibitor-binding site within the N-terminal region of NS5A. In addition, we observed that an NS5A inhibitor promoted the accumulation of an HCV polyprotein intermediate, suggesting that inhibitor binding to NS5A may occur prior to the completion of polyprotein processing. Finally, we observed that NS5A p56 and p58 separated into different membrane fractions during discontinuous sucrose gradient centrifugation, consistent with these NS5A phosphoforms performing distinct replication functions. The p58 localization pattern was disrupted by an NS5A inhibitor. Collectively, our results suggest that NS5A inhibitors probably impact several aspects of HCV expression and regulation. These findings may help to explain the exceptional potency of this class of HCV replication complex inhibitors.
Avian and mammalian reoviruses use different molecular mechanisms to synthesize their μNS isoforms
Authors: Busch Lisa K. , Rodríguez-Grille Javier , Casal J. Ignacio , Martínez-Costas José , Benavente Javier
Published: July 2011

Previous reports revealed that the M3 gene of both avian and mammalian reoviruses express two isoforms of the non-structural protein μNS in infected cells. The larger isoforms initiate translation at the AUG codon closest to the 5′ end of their respective m3 mRNAs, and were therefore designated μNS. In this study we have performed experiments to identify the molecular mechanisms by which the smaller μNS isoforms are generated. The results of this study confirmed the previous findings indicating that the smaller mammalian reovirus μNS isoform is a primary translation product, the translation of which is initiated at the internal AUG-41 codon of mammalian reovirus m3 mRNA. Our results further revealed that the smaller avian reovirus μNS isoform originates from a specific post-translational cleavage site near the amino terminus of μNS. This cleavage produces a 55 kDa carboxy-terminal protein, termed μNSC, and a 17 kDa amino-terminal polypeptide, designated μNSN. These results allowed us to extend the known avian reovirus protein-encoding capacity to 18 proteins, 12 of which are structural proteins and six of which are non-structural proteins. Our finding that avian and mammalian reoviruses use different mechanisms to express their μNSC isoforms suggests that these isoforms are important for reovirus replication.
Ultracentrifugation deforms unfixed influenza A virions
Authors: Sugita Yukihiko , Noda Takeshi , Sagara Hiroshi , Kawaoka Yoshihiro
Published: July 2011

Negatively stained influenza virions sometimes show irregular morphology and are often referred to as pleomorphic. However, this irregular morphology has not been visualized when ultrathin-section transmission and scanning electron microscopies are used. This study focused on the effects of ultracentrifugation on influenza A virion morphology, as negative staining often involves ultracentrifugation to concentrate or purify virions. The morphologies of unfixed, glutaraldehyde-fixed and osmium tetroxide-fixed virions were quantitatively compared before and after ultracentrifugation, and it was found that, without chemical fixation, approximately 30 % of virions were altered from oval to irregular shapes following ultracentrifugation. By contrast, most glutaraldehyde-fixed virions remained uniformly elliptical, even after ultracentrifugation. When a virus with an 11 aa deletion at the C terminus of its M2 cytoplasmic tail was ultracentrifuged, its morphology was appreciably deformed compared with that of the wild-type virus. These results demonstrate that the native morphology of influenza A virions is regular but is disrupted by ultracentrifugation, and that the cytoplasmic tail of M2 is important for virion integrity.
Phenotypic profiling of the human genome reveals gene products involved in plasma membrane targeting of SRC kinases
Authors: Ritzerfeld Julia , Remmele Steffen , Wang Tao , Temmerman Koen , Brügger Britta , Wegehingel Sabine , Tournaviti Stella , Strating Jeroen R.P.M. , Wieland Felix T. , Neumann Beate , Ellenberg Jan , Lawerenz Chris , Hesser Jürgen , Erfle Holger , Pepperkok Rainer , Nickel Walter
Published: July 2011

SRC proteins are non-receptor tyrosine kinases that play key roles in regulating signal transduction by a diverse set of cell surface receptors. They contain N-terminal SH4 domains that are modified by fatty acylation and are functioning as membrane anchors. Acylated SH4 domains are both necessary and sufficient to mediate specific targeting of SRC kinases to the inner leaflet of plasma membranes. Intracellular transport of SRC kinases to the plasma membrane depends on microdomains into which SRC kinases partition upon palmitoylation. In the present study, we established a live-cell imaging screening system to identify gene products involved in plasma membrane targeting of SRC kinases. Based on siRNA arrays and a human model cell line expressing two kinds of SH4 reporter molecules, we conducted a genome-wide analysis of SH4-dependent protein targeting using an automated microscopy platform. We identified and validated 54 gene products whose down-regulation causes intracellular retention of SH4 reporter molecules. To detect and quantify this phenotype, we developed a software-based image analysis tool. Among the identified gene products, we found factors involved in lipid metabolism, intracellular transport, and cellular signaling processes. Furthermore, we identified proteins that are either associated with SRC kinases or are related to various known functions of SRC kinases such as other kinases and phosphatases potentially involved in SRC-mediated signal transduction. Finally, we identified gene products whose function is less defined or entirely unknown. Our findings provide a major resource for future studies unraveling the molecular mechanisms that underlie proper targeting of SRC kinases to the inner leaflet of plasma membranes.
Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1
Authors: Hu Gangqing , Schones Dustin E. , Cui Kairong , Ybarra River , Northrup Daniel , Tang Qingsong , Gattinoni Luca , Restifo Nicholas P. , Huang Suming , Zhao Keji
Published: July 2011

Enhancers of transcription activate transcription via binding of sequence-specific transcription factors to their target sites in chromatin. In this report, we identify GATA1-bound distal sites genome-wide and find a global reorganization of the nucleosomes at these potential enhancers during differentiation of hematopoietic stem cells (HSCs) to erythrocytes. We show that the catalytic subunit BRG1 of BAF complexes localizes to these distal sites during differentiation and generates a longer nucleosome linker region surrounding the GATA1 sites by shifting the flanking nucleosomes away. Intriguingly, we find that the nucleosome shifting specifically facilitates binding of TAL1 but not GATA1 and is linked to subsequent transcriptional regulation of target genes.
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration
Authors: Wu Weisheng , Cheng Yong , Keller Cheryl A. , Ernst Jason , Kumar Swathi Ashok , Mishra Tejaswini , Morrissey Christapher , Dorman Christine M. , Chen Kuan-Bei , Drautz Daniela , Giardine Belinda , Shibata Yoichiro , Song Lingyun , Pimkin Max , Crawford Gregory E. , Furey Terrence S. , Kellis Manolis , Miller Webb , Taylor James , Schuster Stephan C. , Zhang Yu , Chiaromonte Francesca , Blobel Gerd A. , Weiss Mitchell J. , Hardison Ross C.
Published: July 2011

Interplays among lineage-specific nuclear proteins, chromatin modifying enzymes, and the basal transcription machinery govern cellular differentiation, but their dynamics of action and coordination with transcriptional control are not fully understood. Alterations in chromatin structure appear to establish a permissive state for gene activation at some loci, but they play an integral role in activation at other loci. To determine the predominant roles of chromatin states and factor occupancy in directing gene regulation during differentiation, we mapped chromatin accessibility, histone modifications, and nuclear factor occupancy genome-wide during mouse erythroid differentiation dependent on the master regulatory transcription factor GATA1. Notably, despite extensive changes in gene expression, the chromatin state profiles (proportions of a gene in a chromatin state dominated by activating or repressive histone modifications) and accessibility remain largely unchanged during GATA1-induced erythroid differentiation. In contrast, gene induction and repression are strongly associated with changes in patterns of transcription factor occupancy. Our results indicate that during erythroid differentiation, the broad features of chromatin states are established at the stage of lineage commitment, largely independently of GATA1. These determine permissiveness for expression, with subsequent induction or repression mediated by distinctive combinations of transcription factors.
Enhancing Arabidopsis Leaf Growth by Engineering the BRASSINOSTEROID INSENSITIVE1 Receptor Kinase
Authors: Oh Man-Ho , Sun Jindong , Oh Dong Ha , Zielinski Raymond E. , Clouse Steven D. , Huber Steven C.
Published: July 2011

The BRASSINOSTEROID INSENSITIVE1 (BRI1) receptor kinase has recently been shown to possess tyrosine kinase activity, and preventing autophosphorylation of the tyrosine-831 regulatory site by site-directed mutagenesis enhances shoot growth. In this study, we characterized the increased leaf growth of Arabidopsis (Arabidopsis thaliana) plants expressing BRI1(Y831F)-Flag compared with BRI1-Flag (both driven by the native promoter and expressed in the bri1-5 weak allele background) and provide insights into the possible mechanisms involved. On average, relative leaf growth rate was increased 16% in the Y831F plants (in the bri1-5 background), and the gain of function of the Y831F-directed mutant was dominant in the wild-type background. Leaves were larger as a result of increased cell numbers and had substantially increased vascularization. Transcriptome analysis indicated that genes associated with brassinolide biosynthesis, secondary cell wall biosynthesis and vascular development, and regulation of growth were altered in expression and may contribute to the observed changes in leaf architecture and whole plant growth. Analysis of gas exchange and chlorophyll fluorescence indicated that Y831F mutant plants had higher rates of photosynthesis, and metabolite analysis documented enhanced accumulation of starch, sucrose, and several amino acids, most prominently glycine and proline. These results demonstrate that mutation of BRI1 can enhance photosynthesis and leaf growth/vascularization and may suggest new approaches to increase whole plant carbon assimilation and growth.
Predictors of caregiver burden in caregivers of individuals with dementia
Authors: Kim Heejung , Chang Mido , Rose Karen , Kim Sunha
Published: July 2011

kim h., chang m., rose k. & kim s. (2011) Predictors of caregiver burden in caregivers of individuals with dementia. Journal of Advanced Nursing 68(4), 846–855.

Aims.  This article is a report on a study of the multidimensional predictors of caregiver burden in caregivers of individuals with dementia using nationally representative data.

Background.  Caregiver burden affects the health of both caregivers and their care‐recipients. Although previous studies identified various predictors of caregiver burden, these predictors have not been confirmed in nationally representative population.

Methods.  Data for this secondary analysis was provided by the National Alliance for Caregiving, American Association of Retired Persons. The data were collected through a telephone survey of randomly selected adults in seven states in 2003 (weight adjusted n = 302). Descriptive statistics, inter‐correlation analysis and a hierarchical multiple regression analysis were performed.

Results/findings.  Disease‐related factors were the most significant predictors, explaining 16% of caregiver burden; these were followed by caregiver socio‐demographical factors and caregiving‐related factors (F = 21·28, P < 0·01). Significant individual predictors were impairment of activities of daily living or instrumental activities of daily living, the number of hours of caregiving, use of coping strategies, co‐residence, spousal status and caregiver gender (P < 0·05).

Conclusion.  Impaired function in care‐recipients predicts caregiver burden, and also interacts with demographical‐ and caregiving‐related factors. Thus, it will be beneficial to both care‐recipients and caregivers to target nursing interventions and community services to improve the functional abilities of individuals with dementia.
Stillbirth Collaborative Research Network: design, methods and recruitment experience
Authors: Parker Corette B. , Hogue Carol J. R. , Koch Matthew A. , Willinger Marian , Reddy Uma M. , Thorsten Vanessa R. , Dudley Donald J. , Silver Robert M. , Coustan Donald , Saade George R. , Conway Deborah , Varner Michael W. , Stoll Barbara , Pinar Halit , Bukowski Radek , Carpenter Marshall , Goldenberg Robert ,   for the Stillbirth Collaborative Research Network
Published: July 2011

Parker CB, Hogue CJR, Koch MA, Willinger M, Reddy UM, Thorsten VR, Dudley DJ, Silver RM, Coustan D, Saade GR, Conway D, Varner MW, Stoll B, Pinar H, Bukowski R, Carpenter M, Goldenberg R for the Stillbirth Collaborative Research Network. Stillbirth Collaborative Research Network: design, methods and recruitment experience. Paediatric and Perinatal Epidemiology 2011; 25: 425–435.

The Stillbirth Collaborative Research Network (SCRN) has conducted a multisite, population‐based, case–control study, with prospective enrolment of stillbirths and livebirths at the time of delivery. This paper describes the general design, methods and recruitment experience. The SCRN attempted to enrol all stillbirths and a representative sample of livebirths occurring to residents of pre‐defined geographical catchment areas delivering at 59 hospitals associated with five clinical sites. Livebirths <32 weeks gestation and women of African descent were oversampled. The recruitment hospitals were chosen to ensure access to at least 90% of all stillbirths and livebirths to residents of the catchment areas. Participants underwent a standardised protocol including maternal interview, medical record abstraction, placental pathology, biospecimen testing and, in stillbirths, post‐mortem examination. Recruitment began in March 2006 and was completed in September 2008 with 663 women with a stillbirth and 1932 women with a livebirth enrolled, representing 69% and 63%, respectively, of the women identified. Additional surveillance for stillbirths continued until June 2009 and a follow‐up of the case–control study participants was completed in December 2009.

Among consenting women, there were high consent rates for the various study components. For the women with stillbirths, 95% agreed to a maternal interview, chart abstraction and a placental pathological examination; 91% of the women with a livebirth agreed to all of these components. Additionally, 84% of the women with stillbirths agreed to a fetal post‐mortem examination. This comprehensive study is poised to systematically study a wide range of potential causes of, and risk factors for, stillbirths and to better understand the scope and incidence of the problem.
Hypothalamic–pituitary–adrenal axis suppression in asthmatic children on inhaled and nasal corticosteroids: is the early‐morning serum adrenocorticotropic hormone (ACTH) a useful screening test?
Authors: Zöllner Ekkehard W. , Lombard Carl , Galal Ushma , Hough Stephen , Irusen Elvis , Weinberg Eugene
Published: July 2011

To cite this article: Zöllner EW, Lombard C, Galal U, Hough S, Irusen E, Weinberg E. Hypothalamic–pituitary–adrenal axis suppression in asthmatic children on inhaled and nasal corticosteroids: is the early‐morning serum adrenocorticotropic hormone (ACTH) a useful screening test? Pediatr Allergy Immunol 2011; 22: 614–620.

Background:  Hypothalamic–pituitary–adrenal axis suppression (HPAS) in asthmatic children treated with inhaled corticosteroids (ICS), with or without nasal steroids (NS), may be more common than previously thought. Only dynamic testing will identify children at risk of adrenal crisis. It is impractical to test all asthmatic children for HPAS with a gold standard adrenal function test, i.e. the metyrapone or insulin tolerance test.

Objective:  To determine which clinical or biochemical parameter is the most useful screening test for HPAS in asthmatic children.

Methods:  Twenty‐six asthmatic children, 5–18 yr old, on ICS ± NS, not treated with oral or topical steroids in the preceding year were recruited. Height, weight, height velocity, weight velocity and a change in systolic blood pressure from the recumbent to the standing position (ΔSBP) were recorded. Early‐morning urine for urinary free cortisol (UFC) and urinary cortisol metabolites (UCM) was collected. UFC was analysed by both a chemiluminescent assay and gas chromatography/mass spectrometry (GC‐MS). Morning serum cortisol and adrenocorticotropic hormone (ACTH) levels were measured. The overnight metyrapone test was performed if the fasting morning serum cortisol was >83 nmol/l. HPAS was diagnosed if the ACTH failed to rise >100 pg/ml after metyrapone. Spearman correlation coefficients (r) were calculated between the post‐metyrapone ACTH and each variable. A receiver‐operating characteristics (ROC) curve was drawn for the most promising test, and the diagnostic performance was calculated.

Results:  All clinical and biochemical parameters investigated were weakly and non‐significantly correlated with the post‐metyrapone ACTH, except for the morning serum ACTH (r = 0.68; p <0.001). The best discrimination between those who have and those who do not have HPAS is a morning serum ACTH level of 11.7 pg/ml. This corresponds to a sensitivity of 0.89 (0.57–0.98), a specificity of 0.77 (0.53–0.90), a positive predictive value of 0.67 (0.39–0.87), a negative predictive value of 0.93 (0.69–0.99), an accuracy of 0.81 (0.61–0.94), a positive likelihood ratio of 3.78 (1.68–9.49) and a negative likelihood ratio of 0.15 (0.03–0.60).

Conclusions:  The morning serum ACTH level was found to be the most useful screening test to detect HPAS in this sample of children receiving ICS ± NS. A larger study should be undertaken to refine the diagnostic precision of the morning serum ACTH level.
Safety of pre‐engraftment prophylactic foscarnet administration after allogeneic stem cell transplantation
Authors: Ishiyama K. , Katagiri T. , Ohata K. , Hosokawa K. , Kondo Y. , Yamazaki H. , Takami A. , Nakao S.
Published: July 2011

K. Ishiyama, T. Katagiri, K. Ohata, K. Hosokawa, Y. Kondo, H. Yamazaki, A. Takami, S. Nakao. Safety of pre‐engraftment prophylactic foscarnet administration after allogeneic stem cell transplantation. Transpl Infect Dis 2011. All rights reserved

Abstract: Human herpesvirus‐6 (HHV‐6) is a major cause of limbic encephalitis with a dismal prognosis after allogeneic hematopoietic stem cell transplantation (SCT). Because our previous trial of preemptive therapy with foscarnet sodium (phosphonoformic acid; PFA) failed to prevent HHV‐6 encephalitis, we conducted a prospective study to examine the safety of prophylactic PFA administration and elucidate the changes in the plasma HHV‐6 DNA levels in the early post‐SCT period. Plasma HHV‐6 DNA was measured thrice weekly from day 6. PFA, 90 mg/kg/day, was administered from days 7 to 21 after bone marrow or peripheral blood SCT and to day 25 after umbilical cord blood transplantation. Of the 10 patients enrolled, 2 dropped out of the study, 1 because of early death, and 1 with a low glomerular filtration rate. Grade 3 or greater adverse events occurred in 9 of the 10 prophylactic PFA patients and in 7 of the 10 control patients who had clinical backgrounds similar to the study subjects and underwent SCT during the same period. Neurological disorders developed in none of the study subjects but in 4 of the 10 control patients, including 2 with HHV‐6 encephalitis. HHV‐6 reactivation occurred in 3 of the 10 study subjects. The prophylactic PFA regimen was thus safe and it may reduce the risk of limbic encephalitis, but is not considered to be potent enough to prevent HHV‐6 reactivation.