bluuebunny/crossref_metadata_2025 huggingface dataset:
3D SPH simulations of grain growth in protoplanetary disks
Authors: Laibe Guillaume , Gonzalez Jean-François , Fouchet Laure , Maddison Sarah T.
Published: May 2008

We present the first results of the treatment of grain growth in our 3D, two-fluid (gas+dust) SPH code describing protoplanetary disks. We implement a scheme able to reproduce the variation of grain sizes caused by a variety of physical processes and test it with the analytical expression of grain growth given by Stepinski & Valageas (1997) in simulations of a typical T Tauri disk around a one solar mass star. The results are in agreement with a turbulent growing process and validate the method. We are now able to simulate the grain growth process in a protoplanetary disk given by a more realistic physical description, currently under development. We discuss the implications of the combined effect of grain growth and dust vertical settling and radial migration on subsequent planetesimal formation.
Runaway migration in a multiple-protoplanet system
Authors: Zhang Hui , Zhou Ji-Lin
Published: May 2008

We investigate the migration of two giant planets embedded in a proto-stellar disk. The inner planet(initially located at R10=1) is of 1 Jupiter mass and the outer one(R20=1.5) is of 1 Saturn mass. We find that due to the existence of the inner massive planet, the outer planet can not open a clear gap. Instead of an inward migration and being captured by the mean motion resonance of the inner planet, the outer planet undergoes an outward runaway migration. We conclude that this runaway migration is caused by the co-rotation torque in the co-orbital region of the outer planet and sustained by the wave(flow) driven by the inner massive planet.
Formation and transformation of the 3:1 mean-motion resonance in 55 Cancri System
Authors: Zhou Li-Yong , Ferraz-Mello Sylvio , Sun Yi-Sui
Published: May 2008

We report in this paper the numerical simulations of the capture into the 3:1 mean-motion resonance between the planets b and c in the 55 Cancri system. The results show that this resonance can be obtained by a differential planetary migration. The moderate initial eccentricities, relatively slower migration and suitable eccentricity damping rate increase significantly the probability of being trapped in this resonance. Otherwise, the system crosses the 3:1 commensurability avoiding resonance capture, to be eventually captured into a 2:1 resonance or some other higher-order resonances. After capture into resonance, the system can jump from one orbital configuration to another one if the migration continues, making a large region of the configuration space accessible for a resonance system. These investigations help us understand the diversity of resonance configurations and put some constraints on the early dynamical evolution of orbits in the extra-solar planetary systems.
Orbital stability of planets in binary systems: A new look at old results
Authors: Eberle J. , Cuntz M. , Musielak Z. E.
Published: May 2008

About half of all known stellar systems with Sun-like stars consist of two or more stars, significantly affecting the orbital stability of any planet in these systems. This observational evidence has prompted a large array of theoretical research, including the derivation of mathematically stringent criteria for the orbital stability of planets in stellar binary systems, valid for the “coplanar circular restricted three-body problem”. In the following, we use these criteria to explore the validity of results from previous theoretical studies.
Sensitivity Analysis Applied to Artificial Neural Networks for Forecasting Time Series
Authors: Palmer A. , Montaño J.J. , Franconetti F.J.
Published: May 2008

This paper presents a novel procedure known as sensitivity analysis applied to a multilayer perceptron (MLP), which allows the most relevant lagged terms in time series forecasting to be identified. Second, this paper conducts a comparison of forecasting accuracy between the neural network model resulting from applying the sensitivity analysis to the network model derived from the traditional procedure and the classic ARIMA model – using the time series corresponding to the number of passengers in transit through the Balearic Islands. Our findings demonstrate that a neural network derived from sensitivity analysis provides the greatest forecasting accuracy.
Mantle flow models with core‐mantle boundary constraints and chemical heterogeneities in the lowermost mantle
Authors: Steinberger B. , Holme R.
Published: May 2008

Decorrelation between s‐wave and bulk sound velocities in the lowermost mantle and explicit density models based on seismic tomography give evidence for non‐thermal lateral density variations in the lowermost mantle. Here we implement such variations in a numerical model of mantle flow driven by density anomalies which are derived from seismic tomography. In the lowermost ≈300 km, we either use both s‐wave and bulk sound velocities to infer both thermal mantle density anomalies and non‐thermal heterogeneities, or we assume that regions with s‐wave speed anomalies below −1% have an additional non‐thermal density anomaly. We predefine the shape of the viscosity profile in the upper mantle, transition zone and lower mantle, but absolute values of viscosity in the lithosphere, upper mantle, transition zone and lower mantle are free parameters. We use geoid, radial heat flux profile, viscosity “Haskell” average, core‐mantle boundary (CMB) excess ellipticity, as well as (optionally) long‐wavelength root mean square (RMS) CMB topography and reliable point estimates of CMB topography as constraints to optimize the model in parameter space in a least squares sense. We are able to obtain a reasonable fit to all data constraints. Computed RMS CMB topography is predominantly long‐wavelength and with 1–1.5 km RMS amplitude somewhat larger than the long‐wavelength component inferred from seismology. Geoid variance reduction is 75 to 83% in our preferred parameter range. Best fit models have a viscosity maximum close to 1023 Pas about 600 km above the CMB, and a viscosity drop near the base of the mantle, corresponding to a thermal boundary layer about 300 km thick with temperature increase from ≈2500 to 3500–4000 K.
Retrieval of aerosol single‐scattering properties from diffuse and direct irradiances: Numerical studies
Authors: Kudo Rei , Uchiyama Akihiro , Yamazaki Akihiro , Kobayashi Eriko , Nishizawa Tomoaki
Published: May 2008

Two different methods have been developed to retrieve aerosol single‐scattering albedo ω0(λ) and asymmetry factor g(λ) from the direct and diffuse spectral irradiances measured at the surface. One is the direct method, which assumes the Henyey‐Greenstein phase function and retrieves ω0(λ) and g(λ) directly from the irradiances. The other is the indirect method, which calculates optimum ω0(λ) and g(λ) after roughly retrieving the size distribution and refractive index from the irradiances. Their retrieval accuracies were evaluated from intensive sensitivity tests for water‐soluble, dust, and biomass‐burning models. The retrieval accuracies of ω0(λ) and g(λ) were 0.01 to 0.06 and 0.02 to 0.13 for the direct method, and 0.00 to 0.03 and 0.00 to 0.06 for the indirect method.
Evaluation of the chemical transport model Oslo CTM2 with focus on arctic winter ozone depletion
Authors: Søvde Ole Amund , Gauss Michael , Smyshlyaev Sergei P. , Isaksen Ivar S. A.
Published: May 2008

The global chemical transport model Oslo CTM2, driven by European Centre for Medium‐Range Weather Forecasts international Integrated Forecast System meteorology and including tropospheric and stratospheric chemistry, is described and evaluated against measurements by satellite‐based instruments, ozone sondes, and aircraft. A new heterogeneous chemistry and microphysics scheme capable of reproducing severe ozone depletion events is described. The Oslo CTM2 simulates ozone measurements well, overestimating by less than 20% in the lowermost stratosphere, while underestimating slightly at higher altitudes. In the upper troposphere, the spatial and temporal variation is well simulated, although a 30–50% overestimation is seen. In order to demonstrate ozone depletion in the Arctic by heterogeneous processes, the ozone loss during the cold 2004/2005 Arctic winter stratosphere is compared to the warm 2000/2001 Arctic winter. Enhanced ozone loss is shown to have occurred at eight Arctic stations. From January to March the accumulated ozone loss amounts to up to 1 ppmv, with a maximum ozone loss rate of 32 ppb/d. Ozone sonde measurements are well reproduced for both years.
Small Birth Weight and Later Body Composition and Fat Distribution in Adolescents: The AVENA Study
Authors: Labayen Idoia , Moreno Luis A. , Ruiz Jonatan R. , González‐Gross Marcela , Wärnberg Julia , Breidenassel Christina , Ortega Francisco B. , Marcos Ascensión , Bueno Manuel ,   The AVENA Study Group
Published: May 2008

Objective: To assess the association between birth weight and body composition and fat distribution in adolescents, and to test the possible sex‐specific effect in these relationships.

Methods and Procedures: A total of 1,223 adolescents 13–18.5 years old (553 male adolescents and 670 female adolescents) born at >35 weeks, were selected from a cross‐sectional multicenter study conducted in five Spanish cities in 2000–2002. BMI was calculated from weight and height. Triceps and subscapular skinfold thickness (ST) were measured on the left side, and fat mass (FM) and fat‐free mass (FFM) were estimated according to the equations of Slaughter et al. Subscapular skinfold adjusted by tricipital (ST) and waist circumference were used as markers of central adiposity.

Results: Birth weight Z‐score was positively associated with FFM in female adolescents (P < 0.001), but not in male adolescents, after controlling for age, pubertal stage, gestational age, socioeconomic status, physical activity, and current height (P < 0.001 for interaction between adjusted birth weight Z‐score and sex). Adjusted birth weight Z‐score was inversely associated with central adiposity in male and female adolescents as measured by ST (P = 0.026).

Discussion: These results provide further evidence that gender has an important influence on the programming effect of birth weight on later FFM in adolescents because the effect was only observed in female adolescents. Our results suggest that small size for gestational age at birth could program more central subcutaneous fat deposition in adolescents of both sexes, but further research is needed on this issue.
Alcalase®‐catalysed synthesis of the precursor tetrapeptide N‐benzoylarginylglycylaspartylserinamide (Bz‐RGDS‐NH2) of the cell‐adhesion peptide arginylglycylaspartylserine (RGDS)
Authors: Huang Yi‐Bing , Yang Sen , Cai Yu , Wang Hua , Gao Gui , Wu Xiao‐Xia , Xu Li , Zhang Xue‐Zhong
Published: May 2008

In the present study, a precursor tetrapeptide Bz‐RGDS‐NH2 (N‐benzoylarginylglycylaspartylserinamide) of cell‐adhesion peptide RGDS (arginylglycylaspartylserine) was synthesized by a novel route. First of all, the precursor tripeptide GDS‐NH2 (glycylaspartylserinamide) was synthesized by a chemical method only using aspartic acid and serine at gram scale in four steps. The linkage of the fourth amino acid Bz‐Arg‐OEt (N‐benzoyl‐
L‐arginine ethyl ester) to GDS‐NH2 was completed by an enzymatic method under kinetic control in water‐miscible organic media. An industrial alkaline protease, Alcalase®, with a wide substrate specificity, was used as the catalyst. The effects of organic solvents, pH value, reaction temperature, water content and molar ratio of substrates on the yield of Bz‐RGDS‐NH2 synthesis were examined. The optimum reaction conditions were found to be pH 10.0, 35 °C, 8 h, in an acetonitrile/(Na2CO3/NaHCO3) buffer system (93:7, v/v) with a maximal yield of 65.2%. We found that secondary hydrolysis of the peptide product did not take place in these water‐miscible organic solvents.
A new peroxidase from garlic (Allium sativum) bulb: its use in H2O2 biosensing
Authors: El Ichi Sarra , Abdelghani Adnane , Hadji Imene , Helali Salwa , Limam Ferid , Marzouki M. Nejib
Published: May 2008

Peroxidase POX1 isoenzyme was purified from garlic (Allium sativum L.) bulb by ammonium sulfate precipitation, gel filtration and anion‐exchange chromatography. Native‐PAGE profile showed two isoforms, designated POX1A and POX1B. POX1B seems to be more attractive for biosensor design since its Km (app) for H2O2 is lower than that of POX1A. In addition to its storage and operational stability, POX1B was found to be highly heat‐stable, since almost 70% of its activity was conserved at 60 °C, whereas full activity was retained at 50 and 40 °C for 40 min. The optimal pH was approx. 5 and the optimal temperature was 30 °C. Next, gelatin was used as a matrix for enzyme immobilization on a gold electrode surface and electrochemical measurements were performed by using cyclic voltammetry. POX1B‐based electrodes show great potential for application in H2O2 monitoring of biological samples.
Large‐scale plasmid DNA processing: evidence that cell harvesting and storage methods affect yield of supercoiled plasmid DNA
Authors: Kong Simyee , Rock Cassandra F. , Booth Andrew , Willoughby Nicholas , O'Kennedy Ronan D. , Relton Julian , Ward John M. , Hoare Mike , Levy M. Susana
Published: May 2008

The effect of bacterial‐cell centrifugation and handling on the initial stages of plasmid processing was investigated. Escherichia coli cells containing either a 6 or 20 kb plasmid were grown in 75‐ and 450‐litre bioreactors, and the process yield of the early recovery stages was characterized in terms of SC pDNA (supercoiled plasmid DNA) recovered. In all cases, the cells were totally recovered using either a continuous‐feed, intermittent‐solids‐discharge, disc‐stack centrifuge or a continuous‐feed, batch‐discharge, solid‐bowl centrifuge. The cells were then either processed immediately or stored frozen. The centrifugation method considerably affected the yield of SC pDNA, and there was evidence that the intermittent discharge of cells from a centrifuge operating at high speed led to a sediment containing lysed cells and degraded pDNA. This led to estimated plasmid yield losses of up to 40% as compared with cells recovered from laboratory or solid‐bowl centrifuges, where there is evidently no cell stress on discharge. By inference, the cell stress on feed to either of the continuous centrifuges studied was not implicated in product loss. Freezing of the recovered cells gives a convenient hold stage prior to further processing. In all cases, this extra freeze–thaw stage led to loss of SC pDNA, and this was in addition to the loss attributed to cell lysis during centrifugation discharge. Only average yields can be gained from pilot plant‐scale studies; separate laboratory‐based experiments indicated that this loss of SC pDNA is determined by the time and temperature for which the resuspended cells are held.
Chitosan as a carrier for non‐viral gene transfer in a cystic‐fibrosis cell line
Authors: Nydert Per , Dragomir Anca , Hjelte Lena
Published: May 2008

The gene transfer mediated by chitosan in CFBE41o− (a cystic‐fibrosis bronchial epithelial cell line) and HEK (a human embryonic kidney cell line) has been evaluated. Polyplexes based on chitosan and PEI (polyethyleneimine) using a luciferase and enhanced green fluorescent protein reporter plasmid showed that the transfection efficacy of polyplexes in the CFBE41o− cell line was poor compared with that in HEK cells. In the highly differentiated cystic‐fibrosis bronchial epithelial cell line the narrow‐size‐distributed chitosan shows enhanced transfection at a low pH compared with PEI. The enhanced transfection at lower pH could be a result of damage to the cell surface or changes in the cell‐surface charge, leading to better penetration of the cell membrane.
Secreted expression of human lysozyme in the yeast Pichia pastoris under the direction of the signal peptide from human serum albumin
Authors: Xiong Runsong , Chen Jingjing , Chen Jinchun
Published: May 2008

hLM (human lysozyme) has important potential application as a future safely administered human drug and food additive. To produce secreted rhLM (recombinant hLM) from the yeast Pichia pastoris, the signal peptide from HSA (human serum albumin) was employed to direct secreted expression. On the basis of the vector pPIC3.5k, an overexpression vector, pPIC3.5k‐hLM, carrying the strong promoter AOX1 (aldehyde oxidase 1), the HSA signal peptide, the enterokinase recognition motif, the lysozyme gene and other necessary genetic segments was constructed and this was followed by a series of genetic manipulations. A positive colony was picked off to test its expression pattern. The target protein, rhLM, was obtained from the supernatant and showed a gradual enrichment with the induction time course, reaching its highest level at 72 h. This pattern was identical with that shown by the secreted expression of a heterologous protein directed by Saccharomcyes cerevisiae a‐mating factor prepro‐signal peptide in P. pastoris. After a series of purification processes, including ultrafiltration with a hollow‐fibre membrane module, DEAE‐Sepharose, Sephadex G50 chromatography and enterokinase digestion, the mature protein was characterized by MALDI–TOF‐MS/MS (matrix‐assisted laser‐desorption ionization–time‐of‐flight tandem MS), N‐terminal amino acid sequencing, and Km and Kcat determination. The results confirmed that the rhLM was identical with native hLM. Moreover, the mature protein exhibited in vitro bacteriolytic activity against the Gram‐positive bacterium Micrococcus lysodeikticus and the Gram‐negative bacterium Escherichia coli. Taken together, it appeared that the HSA signal peptide was able direct secretive expression of a heterologous protein in P. pastoris.
Global Sensitivity Analysis for the determination of parameter importance in bio‐manufacturing processes
Authors: Chhatre Sunil , Francis Richard , Newcombe Anthony R. , Zhou Yuhong , Titchener‐Hooker Nigel , King Josh , Keshavarz‐Moore Eli
Published: May 2008

The present paper describes the application of GSA (Global Sensitivity Analysis) techniques to mathematical models of bioprocesses in order to rank inputs such as feed titres, flow rates and matrix capacities for the relative influence that each exerts upon outputs such as yield or throughput. GSA enables quantification of both the impact of individual variables on process outputs, as well as their interactions. These data highlight those attributes of a bioprocess which offer the greatest potential for achieving manufacturing improvements. Whereas previous GSA studies have been limited to individual unit operations, this paper extends the treatment to an entire downstream process and illustrates its utility by application to the production of a Fab‐based rattlesnake antivenom called CroFab™ [(Crotalidae Polyvalent Immune Fab (Ovine); Protherics U.K. Limited]. Initially, hyperimmunized ovine serum containing rattlesnake antivenom IgG (product), other antibodies and albumin is applied to a synthetic affinity ligand adsorbent column to separate the antibodies from the albumin. The antibodies are papain‐digested into Fab and Fc fragments, before concentration by ultrafiltration. Fc, residual IgG and albumin are eliminated by an ion‐exchanger and then CroFab‐specific affinity chromatography is used to produce purified antivenom. Application of GSA to the model of this process showed that product yield was controlled by IgG feed concentration and the synthetic‐material affinity column's capacity and flow rate, whereas product throughput was predominantly influenced by the synthetic material's capacity, the ultrafiltration concentration factor and the CroFab affinity flow rate. Such information provides a rational basis for identifying the most promising strategies for delivering improvements to commercial‐scale biomanufacturing processes.
Comparative effects of natural and synthetic diallyl disulfide on apoptosis of human breast‐cancer MCF‐7 cells
Authors: Jun Zou , Suzuki Makiko , Xiao Jianbo , Wen Jun , Talbot Simon G. , Li Gloria C. , Xu Ming
Published: May 2008

The apoptotic effects of natural (n‐) and synthetic (s‐) DADS (diallyl disulfide; 3,3′‐thiobisprop‐1‐ene) on human breast‐cancer MCF‐7 cells were investigated in vitro. 5‐Fu (5‐fluorouracil) and CTX (cyclophosphamide; Cytoxan) were used as comparative control anticancer agents. After MCF‐7 cells had been treated with the drugs, cell viability, morphological change, apoptosis and changes in the cell cycle were measured. The results indicated that s‐ and n‐DADS had similar cytotoxicities towards human breast‐cancer MCF‐7 cells and showed dose‐dependent and time‐dependent inhibitory effects. Morphological observations and flow‐cytometric results showed that the four drugs (s‐DADS, n‐DADS, CTX and 5‐Fu) induced apoptosis in MCF‐7 cells to different extents. The apoptotic effects of s‐ and n‐DADS were superior to those of 5‐Fu and CTX.
Neuropeptide Y expression, localization and cellular transducing effects in HUVEC
Authors: Silva Antonio P. , Kaufmann Jocelyne E. , Vivancos Cécile , Fakan Stanislav , Cavadas Claudia , Shaw Phillip , Brunner Hans R. , Vischer Ulrich , Grouzmann Eric
Published: May 2008

Background information. NPY (neuropeptide Y) may have an effect on the properties of vascular endothelial cells such as pro‐angiogenic effects and potentiation of noradrenaline‐induced vasoconstriction. In HUVEC (human umbilical‐vein endothelial cells), immunoreactive neuropeptide Y has been detected, but NPY synthesis, storage and secretion have not been studied. The aim of the present study was to establish NPY expression, storage and cellular transducing effects in HUVEC.

Results. HUVEC contain 0.19 fmol of NPY/μg of protein and 0.46 fmol of pro‐NPY/μg of protein, as measured by ELISA. RT (reverse transcriptase)—PCR confirmed the expression of NPY in HUVEC. Immunofluorescence revealed the presence of NPY in small punctate structures, with a fluorescence pattern different from that observed for von Willebrand factor, indicating distinct storage compartments. Double labelling for NPY and Rab3A demonstrated similar granular patterns, with at least partial co‐localization. Electron microscopy showed NPY immunoreactivity in vesicle‐like cytoplasmic structures, of a fine fibrillar texture, as well as in mitochondria and in the nucleus. A similar general distribution pattern was also obtained for Rab3A. Y1 and Y2 receptors were expressed in HUVEC as assessed by RT—PCR, and they were functional since NPY induced a 42 nM intracellular calcium increase within 100 s, representing 22% of the histamine‐induced response. In contrast with histamine, NPY did not induce acute von Willebrand factor secretion.

Conclusions. HUVEC produce, store and respond to NPY, suggesting an autocrine regulatory role for NPY in the endothelium.
Linking nuclear mRNP assembly and cytoplasmic destiny
Authors: Kuersten Scott , Goodwin Elizabeth B.
Published: May 2008

From the very beginning, mRNAs have a complex existence. They are transcribed, capped, spliced, modified at the 3′end, exported from the nucleus, translated, and eventually degraded. These many events not only affect the overall survival and properties of an mRNA, but are also carefully co‐ordinated and integrated with quality control mechanisms that function to ensure that only ‘proper’ mRNAs are translated at the correct developmental time and place. This does not mean that all mRNAs follow a single or uniform path from synthesis to death. Instead, there are diverse means by which the activities of specific mRNAs are regulated, and these controls often depend upon multiple events in the mRNA's life. mRNAs are not found naked in the cell, instead they are part of complex RNPs (ribonucleoproteins) that consist of many factors. These RNPs are highly dynamic structures that change during the lifetime of a given RNA; linking events such as synthesis and processing to the final fate of the mRNA. Here, we will discuss what is known of the assembly of RNPs in general, with specific reference to the myriad of connections between different nuclear events and the cytoplasmic activity of an mRNA. Due to space limitations this review is not comprehensive, instead we focus on specific examples to illustrate these emerging themes in gene expression.
Heat‐shock response down‐regulates interleukin‐18 expression in murine peritoneal macrophages
Authors: Wang Yun , Chang Zongliang
Published: May 2008

Background information. The heat‐shock response is a self‐defence mechanism that protects cells and organisms from a wide range of harmful stresses. Recent studies revealed that it involved the regulation of cytokine expression. Interleukin‐18 (IL‐18) is an important cytokine in mediating immune response.

Results. We studied interferon‐γ (IFN‐γ)‐induced IL‐18 expression in heat‐shock‐treated murine peritoneal macrophages. Our results showed that the heat‐shock response significantly inhibited the expression of IFN‐γ‐induced pro‐inflammatory cytokine IL‐18. Interferon consensus sequence binding protein (ICSBP) is a transcription factor that binds to the promoter of IL‐18 and regulates the transcription of IL‐18. Further research on the down‐regulation mechanism showed that the DNA‐binding activity of ICSBP was greatly reduced by the heat shock response.

Conclusions. These results suggest that the inhibitory effect of heat‐shock response on IL‐18 production in IFN‐γ‐stimulated macrophages is related to the suppression of the binding activity of ICSBP.
Mercury chloride decreases the water permeability of aquaporin‐4‐reconstituted proteoliposomes
Authors: Yukutake Yoshinori , Tsuji Shoji , Hirano Yoshinori , Adachi Takeshi , Takahashi Toshiyuki , Fujihara Kazuo , Agre Peter , Yasui Masato , Suematsu Makoto
Published: May 2008

Background information. Mercurials inhibit AQPs (aquaporins), and site‐directed mutagenesis has identified Cys189 as a site of the mercurial inhibition of AQP1. On the other hand, AQP4 has been considered to be a mercury‐insensitive water channel because it does not have the reactive cysteine residue corresponding to Cys189 of AQP1. Indeed, the osmotic water permeability (Pf) of AQP4 expressed in various types of cells, including Xenopus oocytes, is not inhibited by HgCl2. To examine the direct effects of mercurials on AQP4 in a proteoliposome reconstitution system, His‐tagged rAPR4 (rat AQP4) M23 was expressed in Saccharomyces cerevisiae, purified with an Ni2+‐nitrilotriacetate affinity column, and reconstituted into liposomes with the dilution method.

Results. The water permeability of AQP4 proteoliposomes with or without HgCl2 was measured with a stopped‐flow apparatus. Surprisingly, the Pf of AQP4 proteoliposomes was significantly decreased by 5 μM HgCl2 within 30 s, and this effect was completely reversed by 2‐mercaptoethanol. The dose‐ and time‐dependent inhibitory effects of Hg2+ suggest that the sensitivity to mercury of AQP4 is different from that of AQP1. Site‐directed mutagenesis of six cysteine residues of AQP4 demonstrated that Cys178, which is located at loop D facing the intracellular side, is a target responding to Hg2+. We confirmed that AQP4 is reconstituted into liposome in a bidirectional orientation.

Conclusions. Our results suggest that mercury inhibits the Pf of AQP4 by mechanisms different from those for AQP1 and that AQP4 may be gated by modification of a cysteine residue in cytoplasmic loop D.
Both ERK and JNK are required for enhancement of MD‐2 gene expression during differentiation of HL‐60 cells
Authors: Li Changlin , Yu Yongshen , Wang Yun , Liu Lei , Zhang Min , Sugano Sumio , Wang Zhengguo , Chang Zongliang
Published: May 2008

Background information. MD‐2 is associated with the extracellular domain of TLR4 (Toll‐like receptor 4) and augments TLR4‐dependent LPS (lipopolysaccharide) responses in vitro. Our previous investigation found that PMA‐induced HL‐60 cell differentiation to macrophages is associated largely with TLR2 and CD14 and, to a much lesser extent, with TLR4.

Results. We studied the MD‐2 expression during differentiation of HL‐60 cells induced by PMA. The results showed that PMA, but not VitD3 (1α,25‐dihydroxy‐vitamin D3), strongly induces MD‐2 gene expression by HL‐60 cells in a time‐ and dose‐dependent manner. Treatment with an MEK [MAPK (mitogen‐activated protein kinase)/ERK (extracellular‐signal‐regulated kinase) kinase] inhibitor (PD98059) and a JNK (c‐Jun N‐terminal kinase) inhibitor (SP600125) suppresses PMA‐induced MD‐2 gene expression, whereas impairment of p38 function by treatment with the inhibitor SB203580 has no effect on MD‐2 mRNA. In order to reveal the possible molecular mechanism for such a regulation of MD‐2 gene expression, we cloned and analysed the putative MD‐2 gene promoter. Transient transfection of different deletion mutants demonstrated that the region −185/−171 (5′‐TCCTTTACAGGAAGT‐3′) of the MD‐2 gene promoter is closely related to gene transcription in response to PMA. Additionally, the transcription factor Elk‐1 has been found to bind this specific motif.

Conclusions. These results suggest that ERK and JNK pathways are involved in PMA‐mediated MD‐2 gene expression during HL‐60 cell differentiation, and the activation of the MEK/possible ERK/Elk signal pathway is the mechanism responsible for PMA‐induced MD‐2 gene expression in differentiated HL‐60 cells.
S1‐1 nuclear domains: characterization and dynamics as a function of transcriptional activity
Authors: Inoue Akira , Tsugawa Katsuji , Tokunaga Kazuaki , Takahashi Kenichi P. , Uni Shigehiko , Kimura Masatsugu , Nishio Koji , Yamamoto Naoki , Honda Ken‐ichi , Watanabe Takanori , Yamane Hideo , Tani Tokio
Published: May 2008

Background information. The RNA‐binding protein S1‐1, also called RBM10 (RNA‐binding motif 10), is a paralogue of putative tumour suppressor RBM5 and has been correlated with cancer proliferation and apoptosis. In the present study, we have investigated the cell biology of S1‐1.

Results. In the extranucleolar nucleoplasm, S1‐1 occurred in hundreds of punctate and irregular domains. Some 10–40 of these domains were larger than 0.5 μm and prominent for S1‐1 immunostaining. These domains (S1‐1 nuclear bodies) were commonly present in tissue cells and in cultured cells. When cellular transcription was globally reduced by heat shock, serum starvation, culture at high cell densities or inhibition with RNA polymerase II inhibitors, small S1‐1 domains (S1‐1 granules), with weak immunostaining signals, reduced in number, whereas S1‐1 nuclear bodies became prominent and increased in size. These altered S1‐1 domains were returned to initial states when the cells were placed under normal conditions. Similar to paraspeckles, S1‐1 nuclear bodies occurred closely adjacent to nuclear speckles or IGCs (interchromatin granule clusters), as determined by immunoelectron microscopy. However, the S1‐1 nuclear bodies did not correspond to paraspeckles or IGAZs (interchromatin‐granule‐associated zones), but coincided with TIDRs (transcription‐inactivation‐dependent RNA domains), which we had characterized previously at the RNA level. The enlarged S1‐1 nuclear bodies/TIDRs accumulated the S1‐1 protein and microinjected primary and spliced mRNAs, presumably for later elevation of gene expression. In addition, electron microscopy revealed that S1‐1 was also present on perichromatin fibrils, suggesting the structure of S1‐1 granules seen at higher resolution.

Conclusions. S1‐1 constitutes hundreds of nuclear domains, which dynamically change their structures in a reversible manner. Upon globally reducing RNA polymerase II transcription, S1‐1 nuclear bodies enlarge and decrease in number. They are novel domains different from paraspeckles or IGAZs, despite their similar occurrence adjacent to nuclear speckles. We discuss S1‐1 granules in terms of their association with gene expression. In addition, this is the first report of a TIDR‐localized protein.
Effect of translocator protein (18 kDa)‐ligand binding on neurotransmitter‐induced salivary secretion in rat submandibular glands
Authors: Ostuni Mariano A. , Tumilasci Omar R. , Péranzi Gabriel , Cardoso Estela M. L. , Contreras Liliana N. , Arregger Alejandro L. , Papadopoulos Vassilios , Lacapere Jean‐Jacques
Published: May 2008

Background information. TSPO (translocator protein), previously known as PBR (peripheral‐type benzodiazepine receptor), is a ubiquitous 18 kDa transmembrane protein that participates in diverse cell functions. High‐affinity TSPO ligands are best known for their ability to stimulate cholesterol transport in organs synthesizing steroids and bile salts, although they modulate other physiological functions, including cell proliferation, apoptosis and calcium‐dependent transepithelial ion secretion. In present study, we investigated the localization and function of TSPO in salivary glands.

Results. Immunohistochemical analysis of TSPO in rat salivary glands revealed that TSPO and its endogenous ligand, DBI (diazepam‐binding inhibitor), were present in duct and mucous acinar cells. TSPO was localized to the mitochondria of these cells, whereas DBI was cytosolic. As expected, mitochondrial membrane preparations, which were enriched in TSPO, exhibited a high affinity for the TSPO drug ligand,3H‐labelled PK 11195, as shown byBmaxandKdvalues of 10.0±0.5 pmol/mg and 4.0±1.0 nM respectively. Intravenous perfusion of PK 11195 increased the salivary flow rate that was induced by muscarinic and α‐adrenergic agonists, whereas it had no effect when administered alone. Addition of PK 11195 also increased the K+, Na+, Cl−and protein content of saliva, indicating that this ligand modulated secretion by acini and duct cells.

Conclusions. High‐affinity ligand binding to mitochondrial TSPO modulates neurotransmitter‐induced salivary secretion by duct and mucous acinar cells of rat submandibular glands.
TGFβ1 regulates endothelial cell spreading and hypertrophy through a Rac—p38‐mediated pathway
Authors: Varon Christine , Rottiers Patricia , Ezan Jerome , Reuzeau Edith , Basoni Caroline , Kramer IJsbrand , Génot Elisabeth
Published: May 2008

Background information. TGFβ (transforming growth factor β) is a multifunctional cytokine and a potent regulator of cell growth, migration and differentiation in many cell types. In the vascular system, TGFβ plays crucial roles in vascular remodelling, but the signalling pathways involved remain poorly characterized.

Results. Using the model of porcine aortic endothelial cells, we demonstrated that TGFβ stimulates cellular spreading when cells are on collagen I. TGFβ‐stimulated Rac1–GTP accumulation, which was associated with increased MAPK (mitogen‐activated protein kinase) p38 phosphorylation. Furthermore, ectopic expression of a dominant‐negative Rac mutant, or treatment of the cells with the p38 pharmacological inhibitor SB203580, abrogated TGFβ‐induced cell spreading. Our results demonstrate for the first time that prolonged exposure to TGFβ stimulates endothelial cell hypertrophy and flattening. Collectively, these data indicate that TGFβ‐induced cell spreading and increase in cell surface areas occurs via a Rac—p38‐dependent pathway.

Conclusions. The Rac—p38 pathway may have conceptual implications in pathophysiological endothelial cell responses to TGFβ, such as wound healing or development of atherosclerotic lesions.
Sp1 and Sp3 control constitutive expression of the human NHE2 promoter by interactions with the proximal promoter and the transcription initiation site
Authors: Pearse Ian , Zhu Ying X. , Murray Eleanor J. , Dudeja Pradeep K. , Ramaswamy Krishnamurthy , Malakooti Jaleh
Published: May 2008

We have previously cloned the human Na+/H+ exchanger NHE2 gene and its promoter region. In the present study, the regulatory elements responsible for the constitutive expression of NHE2 were studied. Transient transfection assays revealed that the −40/+150 promoter region contains the core promoter responsible for the optimal promoter activity. A smaller fragment, −10/+40, containing the TIS (transcription initiation site) showed minimal activity. We identified a palindrome that overlaps the TIS and binds to the transcription factors Sp1 and Sp3. Mutations in the 5′ flank of the palindrome abolished the Sp1/Sp3 interaction and reduced promoter activity by approx. 45%. In addition, a conserved GC-box centered at −25 was found to play a critical role in basal promoter activity and also interacted with Sp1 and Sp3. An internal deletion in the GC-box severely reduced the promoter activity. Sp1/Sp3 binding to these elements was established using gel-mobility shift assays, confirmed by chromatin immunoprecipitation and co-transfections in Drosophila SL2 cells. Furthermore, we identified two positive regulatory elements in the DNA region corresponding to the 5′-UTR (5′-untranslated region). The results in the present study indicate that Sp1 and Sp3 are required for constitutive NHE2 expression and that the positive regulatory elements of the 5′-UTR may co-operate with the 5′-flanking region to achieve the optimal promoter activity.
Reactivity and endogenous modification by nitrite and hydrogen peroxide: does human neuroglobin act only as a scavenger?
Authors: Nicolis Stefania , Monzani Enrico , Ciaccio Chiara , Ascenzi Paolo , Moens Luc , Casella Luigi
Published: May 2008

NGB (human neuroglobin), a recently discovered haem protein of the globin family containing a six-co-ordinated haem, is expressed in nervous tissue, but the physiological function of NGB is currently unknown. As well as playing a role in neuronal O2 homoeostasis, NGB is thought to act as a scavenger of reactive species. In the present study, we report on the reactivity of metNGB (ferric-NGB), which accumulates in vivo as a result of the reaction of oxyNGB (oxygenated NGB) with NO, towards NO2− and H2O2. NO2− co-ordination of the haem group accounts for the activity of metNGB in the nitration of phenolic substrates. The two different metNGB forms, with and without the internal disulfide bond between Cys46 (seventh residue on the inter-helix region between helices C and D) and Cys55 (fifth residue on helix D), exhibit different reactivity, the former being more efficient in activating NO2−. The kinetics of the reactions, the NO2−-binding studies and the analysis of the nitrated products from different substrates all support the hypothesis that metNGB is able to generate an active species with the chemical properties of peroxynitrite, at pathophysiological concentrations of NO2− and H2O2. Without external substrates, the targets of the reactive species generated by the metNGB/NO2−/H2O2 system are endogenous tyrosine (resulting in the production of 3-nitrotyrosine) and cysteine (oxidized to sulfinic acid and sulfonic acid) residues. These endogenous modifications were characterized by HPLC-MS/MS (tandem MS) analysis of metNGB after reaction with NO2− and H2O2 under various conditions. The internal S–S bond affects the functional properties of the protein. Therefore metNGB acts not only as scavenger of toxic species, but also as a target of the self-generated reactive species. Self-modification of the protein may be related to or inhibit its postulated neuroprotective activity.
Tumour necrosis factor induces phosphorylation primarily of the nitric-oxide-responsive form of glyoxalase I
Authors: de Hemptinne Virginie , Rondas Dieter , Vandekerckhove Joël , Vancompernolle Katia
Published: May 2008

We have previously shown that TNF (tumour necrosis factor) induces phosphorylation of GLO1 (glyoxalase I), which is required for cell death in L929 cells. In the present paper, we show that the TNF-induced phosphorylation of GLO1 occurs primarily on the NO (nitric oxide)-responsive form of GLO1. In addition, analysis of several cysteine mutants of GLO1 indicated that Cys-138, in combination with either Cys-18 or Cys-19, is a crucial target residue for the NO-mediated modification of GLO1. Furthermore, the NO-donor GSNO (S-nitrosogluthathione) induces NO-mediated modification of GLO1 and enhances the TNF-induced phosphorylation of this NO-responsive form. GSNO also strongly promotes TNF-induced cell death. By the use of pharmacological inhibition of iNOS (inducible NO synthase) and overexpression of mutants of GLO1 that are deficient for the NO-mediated modification, we have shown that the NO-mediated modification of GLO1 is not a requirement for TNF-induced phosphorylation or TNF-induced cell death respectively. In summary, these data suggest that the TNF-induced phosphorylation of GLO1 is the dominant factor for cell death.
Two zinc finger transcription factors, CrzA and SltA, are involved in cation homoeostasis and detoxification in Aspergillus nidulans
Authors: Spielvogel Anja , Findon Helen , Arst Herbert N. , Araújo-Bazán Lidia , Hernández-Ortíz Patricia , Stahl Ulf , Meyer Vera , Espeso Eduardo A.
Published: May 2008

To investigate cation adaptation and homoeostasis in Aspergillus nidulans, two transcription-factor-encoding genes have been characterized. The A. nidulans orthologue crzA of the Saccharomyces cerevisiae CRZ1 gene, encoding a transcription factor mediating gene regulation by Ca2+, has been identified and deleted. The crzA deletion phenotype includes extreme sensitivity to alkaline pH, Ca2+ toxicity and aberrant morphology connected with alterations of cell-wall-related phenotypes such as reduced expression of a chitin synthase gene, chsB. A fully functional C-terminally GFP (green fluorescent protein)-tagged form of the CrzA protein is apparently excluded from nuclei in the absence of added Ca2+, but rapidly accumulates in nuclei upon exposure to Ca2+. In addition, the previously identified sltA gene, which has no identifiable homologues in yeasts, was deleted, and the resulting phenotype includes considerably enhanced toxicity by a number of cations other than Ca2+ and also by alkaline pH. Reduced expression of a homologue of the S. cerevisiae P-type ATPase Na+ pump gene ENA1 might partly explain the cation sensitivity of sltA-null strains. Up-regulation of the homologue of the S. cerevisiae vacuolar Ca2+/H+ exchanger gene VCX1 might explain the lack of Ca2+ toxicity to null-sltA mutants, whereas down-regulation of this gene might be responsible for Ca2+ toxicity to crzA-null mutants. Both crzA and sltA encode DNA-binding proteins, and the latter exerts both positive and negative gene regulation.
Room-temperature-photoinduced magnetism and spin-electronic functions of spinel ferrite with a spin-cluster structure
Authors: Kanki Teruo , Hotta Yasushi , Asakawa Naoki , Seki Munetoshi , Tabata Hitoshi , Kawai Tomoji
Published: May 2008

Room-temperature-photoinduced magnetization (PIM) was observed in spinel ferrite Al0.2Ru0.8Fe2O4 thin films with a spin-cluster-glass structure. Additionally, the films exhibited significant properties as spintronic materials, showing a low saturation magnetization under 0.6μB/unit cell and good conductivity with a high spin polarized electron level of over 75%. A combination of high-temperature PIM and the electronic properties associated with spintronics would generate an area of research and development that utilize the degrees of freedom offered by optical systems in the field of spintronics.
Effect of island overlap on edge localized mode suppression by resonant magnetic perturbations in DIII-D
Authors: Fenstermacher M. E. , Evans T. E. , Osborne T. H. , Schaffer M. J. , Aldan M. P. , deGrassie J. S. , Gohil P. , Joseph I. , Moyer R. A. , Snyder P. B. , Groebner R. J. , Jakubowski M. , Leonard A. W. , Schmitz O. ,   the DIII-D Team
Published: May 2008

Recent DIII-D [J. L. Luxon et al., Nucl. Fusion 43, 1813 (2003)] experiments show a correlation between the extent of overlap of magnetic islands induced in the edge plasma by perturbation coils and complete suppression of Type-I edge localized modes (ELMs) in plasmas with ITER-like electron pedestal collisionality νe*∼0.1, flux surface shape and low edge safety factor (q95≈3.6). With fixed amplitude n=3 resonant magnetic perturbation (RMP), ELM suppression is obtained only in a finite window in the edge safety factor (q95) consistent with maximizing the resonant component of the applied helical field. ELM suppression is obtained over an increasing range of q95 by either increasing the n=3 RMP strength, or by adding n=1 perturbations to “fill in” gaps between islands across the edge plasma. The suppression of Type-I ELMs correlates with a minimum width of the edge region having magnetic islands with Chirikov parameter >1.0, based on vacuum calculations of RMP mode components excluding the plasma response or rotational shielding. The fraction of vacuum magnetic field lines that are lost from the plasma, with connection length to the divertor targets comparable to an electron-ion collisional mean free path, increases throughout the island overlap region in the ELM suppressed case compared with the ELMing case.
Comparison of DNA hydration patterns obtained using two distinct computational methods, molecular dynamics simulation and three-dimensional reference interaction site model theory
Authors: Yonetani Yoshiteru , Maruyama Yutaka , Hirata Fumio , Kono Hidetoshi
Published: May 2008

Because proteins and DNA interact with each other and with various small molecules in the presence of water molecules, we cannot ignore their hydration when discussing their structural and energetic properties. Although high-resolution crystal structure analyses have given us a view of tightly bound water molecules on their surface, the structural data are still insufficient to capture the detailed configurations of water molecules around the surface of these biomolecules. Thanks to the invention of various computational algorithms, computer simulations can now provide an atomic view of hydration. Here, we describe the apparent patterns of DNA hydration calculated by using two different computational methods: Molecular dynamics (MD) simulation and three-dimensional reference interaction site model (3D-RISM) theory. Both methods are promising for obtaining hydration properties, but until now there have been no thorough comparisons of the calculated three-dimensional distributions of hydrating water. This rigorous comparison showed that MD and 3D-RISM provide essentially similar hydration patterns when there is sufficient sampling time for MD and a sufficient number of conformations to describe molecular flexibility for 3D-RISM. This suggests that these two computational methods can be used to complement one another when evaluating the reliability of the calculated hydration patterns.
Control of whistler radiation efficiency of a loop antenna by generation of ambient magnetic field irregularities
Authors: Gushchin M. E. , Korobkov S. V. , Kostrov A. V. , Strikovsky A. V. , Zaboronkova T. M. , Krafft C. , Koldanov V. A.
Published: May 2008

Electrodynamic means for the control of loop antenna radiation efficiency in plasma is proposed, which can be used in the whistler frequency band. The method is based on the generation, without perturbing the plasma density, of localized ambient magnetic field irregularities in the vicinity of the antenna. In order to produce such irregularities, it is suggested to feed the antenna with additional dc current along with the rf current. Experiments performed in a large laboratory magnetoplasma showed that the generation of localized magnetic field enhancements provides the possibility of increasing the amplitude of the whistlers emitted by the loop antenna. Moreover, experiments have shown that the amplification of the whistlers’ signals from the receiving loop antenna fed with additional dc current is observed when a static magnetic field enhancement is generated in the vicinity of the receiver. The experimental data are in good agreement with the theoretical results obtained for comparatively weak ambient magnetic field perturbations.