bluuebunny/crossref_metadata_2025 huggingface dataset:
Rab11b Regulates the Apical Recycling of the Cystic Fibrosis Transmembrane Conductance Regulator in Polarized Intestinal Epithelial Cells
Authors: Silvis Mark R. , Bertrand Carol A. , Ameen Nadia , Golin-Bisello Franca , Butterworth Michael B. , Frizzell Raymond A. , Bradbury Neil A.
Published: February 2009

The cystic fibrosis transmembrane conductance regulator (CFTR), a cAMP/PKA-activated anion channel, undergoes efficient apical recycling in polarized epithelia. The regulatory mechanisms underlying CFTR recycling are understood poorly, yet this process is required for proper channel copy number at the apical membrane, and it is defective in the common CFTR mutant, ΔF508. Herein, we investigated the function of Rab11 isoforms in regulating CFTR trafficking in T84 cells, a colonic epithelial line that expresses CFTR endogenously. Western blotting of immunoisolated Rab11a or Rab11b vesicles revealed localization of endogenous CFTR within both compartments. CFTR function assays performed on T84 cells expressing the Rab11a or Rab11b GDP-locked S25N mutants demonstrated that only the Rab11b mutant inhibited 80% of the cAMP-activated halide efflux and that only the constitutively active Rab11b-Q70L increased the rate constant for stimulated halide efflux. Similarly, RNAi knockdown of Rab11b, but not Rab11a, reduced by 50% the CFTR-mediated anion conductance response. In polarized T84 monolayers, adenoviral expression of Rab11b-S25N resulted in a 70% inhibition of forskolin-stimulated transepithelial anion secretion and a 50% decrease in apical membrane CFTR as assessed by cell surface biotinylation. Biotin protection assays revealed a robust inhibition of CFTR recycling in polarized T84 cells expressing Rab11b-S25N, demonstrating the selective requirement for the Rab11b isoform. This is the first report detailing apical CFTR recycling in a native expression system and to demonstrate that Rab11b regulates apical recycling in polarized epithelial cells.
Caveolin-1–mediated Suppression of Cyclooxygenase-2 via a β-catenin-Tcf/Lef–dependent Transcriptional Mechanism Reduced Prostaglandin E2 Production and Survivin Expression
Authors: Rodriguez Diego A. , Tapia Julio C. , Fernandez Jaime G. , Torres Vicente A. , Muñoz Nicolas , Galleguillos Daniela , Leyton Lisette , Quest Andrew F. G.
Published: February 2009

Augmented expression of cyclooxygenase-2 (COX-2) and enhanced production of prostaglandin E2 (PGE2) are associated with increased tumor cell survival and malignancy. Caveolin-1 is a scaffold protein that has been proposed to function as a tumor suppressor in human cancer cells, although mechanisms underlying this ability remain controversial. Intriguingly, the possibility that caveolin-1 regulates the expression of COX-2 has not been explored. Here we show that augmented caveolin-1 expression in cells with low basal levels of this protein, such as human colon cancer (HT29, DLD-1), breast cancer (ZR75), and embryonic kidney (HEK293T) cells reduced COX-2 mRNA and protein levels and β-catenin-Tcf/Lef and COX-2 gene reporter activity, as well as the production of PGE2 and cell proliferation. Moreover, COX-2 overexpression or PGE2 supplementation increased levels of the inhibitor of apoptosis protein survivin by a transcriptional mechanism, as determined by PCR analysis, survivin gene reporter assays and Western blotting. Furthermore, addition of PGE2 to the medium prevented effects attributed to caveolin-1–mediated inhibition of β-catenin-Tcf/Lef–dependent transcription. Finally, PGE2 reduced the coimmunoprecipitation of caveolin-1 with β-catenin and their colocalization at the plasma membrane. Thus, by reducing COX-2 expression, caveolin-1 interrupts a feedback amplification loop involving PGE2-induced signaling events linked to β-catenin/Tcf/Lef–dependent transcription of tumor survival genes including cox-2 itself and survivin.
Nuclear Shuttling of She2p Couples ASH1 mRNA Localization to its Translational Repression by Recruiting Loc1p and Puf6p
Authors: Shen Zhifa , Paquin Nicolas , Forget Amélie , Chartrand Pascal
Published: February 2009

The transport and localization of mRNAs results in the asymmetric synthesis of specific proteins. In yeast, the nucleocytoplasmic shuttling protein She2 binds the ASH1 mRNA and targets it for localization at the bud tip by recruiting the She3p–Myo4p complex. Although the cytoplasmic role of She2p in mRNA localization is well characterized, its nuclear function is still unclear. Here, we show that She2p contains a nonclassical nuclear localization signal (NLS) that is essential for its nuclear import via the importin α Srp1p. Exclusion of She2p from the nucleus by mutagenesis of its NLS leads to defective ASH1 mRNA localization and Ash1p sorting. Interestingly, these phenotypes mimic knockouts of LOC1 and PUF6, which encode for nuclear RNA-binding proteins that bind the ASH1 mRNA and control its translation. We find that She2p interacts with both Loc1p and Puf6p and that excluding She2p from the nucleus decreases this interaction. Absence of nuclear She2p disrupts the binding of Loc1p and Puf6p to the ASH1 mRNA, suggesting that nuclear import of She2p is necessary to recruit both factors to the ASH1 transcript. This study reveals that a direct coupling between localization and translation regulation factors in the nucleus is required for proper cytoplasmic localization of mRNAs.
The Extracellular Signal-regulated Kinase–Mitogen-activated Protein Kinase Pathway Phosphorylates and Targets Cdc25A for SCFβ-TrCP-dependent Degradation for Cell Cycle Arrest
Authors: Isoda Michitaka , Kanemori Yoshinori , Nakajo Nobushige , Uchida Sanae , Yamashita Katsumi , Ueno Hiroyuki , Sagata Noriyuki
Published: February 2009

The extracellular signal-regulated kinase (ERK) pathway is generally mitogenic, but, upon strong activation, it causes cell cycle arrest by a not-yet fully understood mechanism. In response to genotoxic stress, Chk1 hyperphosphorylates Cdc25A, a positive cell cycle regulator, and targets it for Skp1/Cullin1/F-box protein (SCF)β-TrCPubiquitin ligase-dependent degradation, thereby leading to cell cycle arrest. Here, we show that strong ERK activation can also phosphorylate and target Cdc25A for SCFβ-TrCP-dependent degradation. When strongly activated in Xenopus eggs, the ERK pathway induces prominent phosphorylation and SCFβ-TrCP-dependent degradation of Cdc25A. p90rsk, the kinase downstream of ERK, directly phosphorylates Cdc25A on multiple sites, which, interestingly, overlap with Chk1 phosphorylation sites. Furthermore, ERK itself phosphorylates Cdc25A on multiple sites, a major site of which apparently is phosphorylated by cyclin-dependent kinase (Cdk) in Chk1-induced degradation. p90rsk phosphorylation and ERK phosphorylation contribute, roughly equally and additively, to the degradation of Cdc25A, and such Cdc25A degradation occurs during oocyte maturation in which the endogenous ERK pathway is fully activated. Finally, and importantly, ERK-induced Cdc25A degradation can elicit cell cycle arrest in early embryos. These results suggest that strong ERK activation can target Cdc25A for degradation in a manner similar to, but independent of, Chk1 for cell cycle arrest.
BISEN: Biochemical Simulation Environment
Authors: Vanlier J. , Wu F. , Qi F. , Vinnakota K. C. , Han Y. , Dash R. K. , Yang F. , Beard D. A.
Published: February 2009

Summary: The Biochemical Simulation Environment (BISEN) is a suite of tools for generating equations and associated computer programs for simulating biochemical systems in the MATLAB® computing environment. This is the first package that can generate appropriate systems of differential equations for user-specified multi-compartment systems of enzymes and transporters accounting for detailed biochemical thermodynamics, rapid equilibria of multiple biochemical species and dynamic proton and metal ion buffering.

Availability: The software and a user manual (including several tutorial examples) are available at bbc.mcw.edu/BISEN.

Contact:  dbeard@mcw.edu
PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes
Authors: Pyrkov Timothy V. , Chugunov Anton O. , Krylov Nikolay A. , Nolde Dmitry E. , Efremov Roman G.
Published: February 2009

Summary: The PLATINUM (Protein–Ligand ATtractions Investigation NUMerically) web service is designed for analysis and visualization of hydrophobic/hydrophilic properties of biomolecules supplied as 3D-structures. Furthermore, PLATINUM provides a number of tools for quantitative characterization of the hydrophobic/hydrophilic match in biomolecular complexes e.g. in docking poses. These complement standard scoring functions. The calculations are based on the concept of empirical Molecular Hydrophobicity Potential (MHP).

Availability: The PLATINUM web tool as well as detailed documentation and tutorial are available free of charge for academic users at http://model.nmr.ru/platinum/. PLATINUM requires Java 5 or higher and Adobe Flash Player 9.

Contact:  pyrkov@nmr.ru

Supplementary information:  Supplementary data are available at Bioinformatics online.
Statistical inferences for isoform expression in RNA-Seq
Authors: Jiang Hui , Wong Wing Hung
Published: February 2009

Summary: The development of RNA sequencing (RNA-Seq) makes it possible for us to measure transcription at an unprecedented precision and throughput. However, challenges remain in understanding the source and distribution of the reads, modeling the transcript abundance and developing efficient computational methods. In this article, we develop a method to deal with the isoform expression estimation problem. The count of reads falling into a locus on the genome annotated with multiple isoforms is modeled as a Poisson variable. The expression of each individual isoform is estimated by solving a convex optimization problem and statistical inferences about the parameters are obtained from the posterior distribution by importance sampling. Our results show that isoform expression inference in RNA-Seq is possible by employing appropriate statistical methods.

Contact:  whwong@stanford.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
[Retracted] Evidences of Protective Potentials of Microdoses of Ultra‐High Diluted Arsenic Trioxide in Mice Receiving Repeated Injections of Arsenic Trioxide
Authors: Banerjee Pathikrit , Bhattacharyya Soumya Sundar , Pathak Surajit , Boujedaini Naoual , Belon Philippe , Khuda-Bukhsh Anisur Rahman
Published: February 2009

The present study was undertaken to examine if microdoses of ultra‐high diluted arsenic trioxide (a potentized homeopathic remedy, Arsenicum Album 200C, diluted 10-400 times) have hepatoprotective potentials in mice subjected to repeated injections of arsenic trioxide. Arsenic intoxicated mice were divided into: (i) those receiving Arsenicum Album‐200C daily, (ii) those receiving the same dose of diluted succussed alcohol (Alc 200C) and (iii) another group receiving neither drug nor succussed alcohol. Two other control groups were also maintained: one fed normal diet only and the other receiving normal diet and Alc‐200C. Toxicity biomarkers like aspartate and alanine aminotransferases, glutathione reductase, catalase, succinate dehydrogenase, superoxide dismutase and reduced glutathione contents were periodically assayed keeping the observer “blinded”. Additionally, electron microscopic studies and gelatin zymography for matrix metalloproteinases of liver tissues were made at day 90 and 120. Blood glucose, hemoglobin, estradiol and testosterone contents were also studied. Compared to controls, Arsenicum Album‐200C fed mice showed positive modulations of all parameters studied, thereby providing evidence of protective potentials of the homeopathic drug against chronic arsenic poisoning.
Acupuncture′s Effects in Treating the Sequelae of Acute and Chronic Spinal Cord Injuries: A Review of Allopathic and Traditional Chinese Medicine Literature
Authors: Dorsher Peter T. , McIntosh Peter M.
Published: February 2009

Each year, there are an estimated 12 000 individuals who sustain a spinal cord injury (SCI) in the United States. Improved understanding of the pathophysiology of SCI and its sequelae has over the past 50 years led to the development of medical treatments (especially urologic) that have enhanced short‐ and long‐term survival from these injuries. The prevalence of individuals with SCI in this country is 250 000 individuals; and beyond the incalculable personal consequences of these devastating neurologic injuries, substantial direct and indirect societal costs result from the sequelae of SCI including paralysis, sensory loss, chronic pain, decubiti and bladder and/or bowel incontinence. The purpose of this treatise is to review the allopathic and traditional Chinese medicine (TCM) literature available through MEDLINE, PubMed and eCAM search engines that discuss the potential uses of acupuncture to treat acute and chronic spinal cord injuries and their sequelae, and present the neurophysiologic mechanisms for acupuncture′s beneficial effects. There is evidence that use of electroacupuncture in acute SCI may significantly improve long‐term neurologic recovery from these injuries both in terms of motor, sensory and bowel/bladder function with essentially no risk. Acupuncture may even improve neurourologic function in individuals with chronic SCI, and help with management with chronic pain associated with these injuries.
Specific point mutations in Lactobacillus casei ATCC 27139 cause a phenotype switch from Lac− to Lac+
Authors: Tsai Yu-Kuo , Chen Hung-Wen , Lo Ta-Chun , Lin Thy-Hou
Published: February 2009

Lactose metabolism is a changeable phenotype in strains ofLactobacillus casei. In this study, we found thatL. caseiATCC 27139 was unable to utilize lactose. However, when exposed to lactose as the sole carbon source, spontaneous Lac+clones could be obtained. A gene cluster (lacTEGF–galKETRM) involved in the metabolism of lactose and galactose inL. caseiATCC 27139 (Lac−) and its Lac+revertant (designated strain R1) was sequenced and characterized. We found that only one nucleotide, located in thelacTEGFpromoter (lacTp), of the twolac–galgene clusters was different. The protein sequence identity between thelac–galgene cluster and those reported previously for someL. casei(Lac+) strains was high; namely, 96–100 % identity was found and no premature stop codon was identified. A single point mutation located within thelacTppromoter region was also detected for each of the 41 other independently isolated Lac+revertants ofL. caseiATCC 27139. The revertants could be divided into six classes based on the positions of the point mutations detected. Primer extension experiments conducted on transcription fromlacTprevealed that thelacTppromoter of these six classes of Lac+revertants was functional, while that ofL. caseiATCC 27139 was not. Northern blotting experiments further confirmed that thelacTEGFoperon of strain R1 was induced by lactose but suppressed by glucose, whereas no blotting signal was ever detected forL. caseiATCC 27139. These results suggest that a single point mutation in thelacTppromoter was able to restore the transcription of a fully functionallacTEGFoperon and cause a phenotype switch from Lac−to Lac+forL.caseiATCC 27139.
CpgA, EF-Tu and the stressosome protein YezB are substrates of the Ser/Thr kinase/phosphatase couple, PrkC/PrpC, in Bacillus subtilis
Authors: Absalon Cédric , Obuchowski Michal , Madec Edwige , Delattre Delphine , Holland I. Barry , Séror Simone J.
Published: February 2009

The conservedprpC,prkC,cpgAlocus inBacillus subtilisencodes respectively a Ser/Thr phosphatase, the cognate sensor kinase (containing an external PASTA domain suggested to bind peptidoglycan precursors) and CpgA, a small ribosome-associated GTPase that we have shown previously is implicated in shape determination and peptidoglycan deposition. In this study, in a search for targets of PrkC and PrpC, we showed that,in vitro, CpgA itself is phosphorylated on serine and threonine, and another GTPase, the translation factor EF-Tu, is also phosphorylated by the kinase on the conserved T384 residue. Both substrates are dephosphorylated by PrpCin vitro. In addition, we identified YezB, a 10.3 kDa polypeptide, and a component of the stressosome, as a substrate for both enzymesin vitroand apparentlyin vivo. We propose that the PrpC/PrkC/CpgA system constitutes an important element of a regulatory network involved in the coordination of cell wall expansion and growth inB. subtilis.
Escherichia coli O157 : H7 glutamate- and arginine-dependent acid-resistance systems protect against oxidative stress during extreme acid challenge
Authors: Bearson Bradley L. , Lee In Soo , Casey Thomas A.
Published: February 2009

Micro-organisms may simultaneously encounter multiple stresses in their environment. To investigate the protection that several knownEscherichia coliO157 : H7 acid-resistance systems might provide against both oxidative and acid stress, the addition of diamide, a membrane-permeable thiol-specific oxidizing agent, or hydrogen peroxide were used concurrent with acid challenge at pH 2.5 to determine bacterial survival. The addition of either diamide or hydrogen peroxide decreased bacterial survival in a dose-dependent manner forE. coliO157 : H7 during challenge at pH 2.5 following overnight growth in LB MES pH 5.5 (acid-resistance system 1, AR1). In contrast, the presence of either glutamate or arginine during challenge provided significant protection against diamide- and hydrogen peroxide-induced oxidative stress during pH 2.5 acid challenge. Oxidative stress protection during acid challenge requiredgadCandadiAfor the glutamate- (AR2) and arginine- (AR3) dependent acid-resistance systems, respectively. In addition, maximal protection against oxidative stress in the presence of glutamate required a low external pH (pH 2.5), since pH 5.5 did not protect. This study demonstrates that the glutamate- and arginine-dependent acid-resistance systems ofE. coliO157 : H7 can simultaneously protect against oxidative stress during extreme acid challenge.
Transient responses during hyperosmotic shock in the filamentous fungus Neurospora crassa
Authors: Lew Roger R. , Nasserifar Shanar
Published: February 2009

Fungal cells maintain an internal hydrostatic pressure (turgor) of about 400–500 kPa. In the filamentous fungusNeurospora crassa, the initial cellular responses to hyperosmotic treatment are loss of turgor, a decrease in relative hyphal volume per unit length (within 1 min) and cell growth arrest; all recover over a period of 10–60 min due to increased net ion uptake and glycerol production. The electrical responses to hyperosmotic treatment are a transient depolarization of the potential (within 1 min), followed by a sustained hyperpolarization (after 4 min) to a potential more negative than the initial potential (a driving force for ion uptake). The nature of the transient depolarization was explored in the context of other transient responses to hyperosmotic shock, to determine whether activation of a specific ion permeability or some other rapid change in electrogenic transport was responsible. Changing the ionic composition of the extracellular medium revealed that K+permeability increases and H+permeability declines during the transient depolarization. We suggest that these changes are due to concerted inhibition of the electrogenic H+-ATPase, and an increase in a K+conductance. Knockout mutants of known K+(tok,trk,trm-8,hak-1) and Cl−(aclc-3homologue) channels and transporters had no effect on the transient depolarization, buttrkandhak-1do play a role in osmoadaptation, as does a homologue of a serine kinase regulator of H+-ATPase in yeast, Ptk2.
Exploring the antimicrobial action of a carbon monoxide-releasing compound through whole-genome transcription profiling of Escherichia coli
Authors: Nobre Lígia S. , Al-Shahrour Fátima , Dopazo Joaquin , Saraiva Lígia M.
Published: February 2009

We recently reported that carbon monoxide (CO) has bactericidal activity. To understand its mode of action we analysed the gene expression changes occurring whenEscherichia coli, grown aerobically and anaerobically, is treated with the CO-releasing molecule CORM-2 (tricarbonyldichlororuthenium(II) dimer). Microarray analysis shows that theE. coliCORM-2 response is multifaceted, with a high number of differentially regulated genes spread through several functional categories, namely genes involved in inorganic ion transport and metabolism, regulators, and genes implicated in post-translational modification, such as chaperones. CORM-2 has a higher impact inE. colicells grown anaerobically, as judged by the repression of genes belonging to eight functional classes which are not seen in the response of aerobically CORM-2-treated cells. The biological relevance of the variations caused by CORM-2 was substantiated by studying the CORM-2 sensitivity of selectedE. colimutants. The results show that the deletion of redox-sensing regulators SoxS and OxyR increased the sensitivity to CORM-2 and suggest that while SoxS plays an important role in protection against CORM-2 under both growth conditions, OxyR seems to participate only in the aerobic CORM-2 response. Under anaerobic conditions, we found that the heat-shock proteins IbpA and IbpB contribute to CORM-2 defence since the deletion of these genes increases the sensitivity of the strain. The induction of severalmetgenes and the hypersensitivity to CORM-2 of the ΔmetR, ΔmetIand ΔmetNmutant strains suggest that CO has effects on the methionine metabolism ofE. coli. CORM-2 also affects the transcription of severalE. colibiofilm-related genes and increases biofilm formation inE. coli. In particular, the absence oftqsAorbhsAincreases the resistance ofE. colito CORM-2, and deletion oftsqAleads to a strain that has lost its capacity to form biofilm upon treatment with CORM-2. In spite of the relatively stable nature of the CO molecule, our results show that CO is able to trigger a significant alteration in the transcriptome ofE. coliwhich necessarily has effects in several key metabolic pathways.
Cereulide synthesis in emetic Bacillus cereus is controlled by the transition state regulator AbrB, but not by the virulence regulator PlcR
Authors: Lücking Genia , Dommel Monica K. , Scherer Siegfried , Fouet Agnes , Ehling-Schulz Monika
Published: February 2009

Cereulide, a depsipeptide structurally related to the antibiotic valinomycin, is responsible for the emetic type of gastrointestinal disease caused by Bacillus cereus. Recently, it has been shown that cereulide is produced non-ribosomally by the plasmid-encoded peptide synthetase Ces. Using deletion mutants of the emetic reference strain B. cereus F4810/72, the influence of the well-known transcription factors PlcR, Spo0A and AbrB on cereulide production and on the transcription of the cereulide synthetase gene cluster was investigated. Our data demonstrate that cereulide synthesis is independent of the B. cereus specific virulence regulator PlcR but belongs to the Spo0A-AbrB regulon. Although cereulide production turned out to be independent of sporulation, it required the activity of the sporulation factor Spo0A. The σ
A-promoted transcription of spo0A was found to be crucial for cereulide production, while the σ
H-driven transcription of spo0A did not affect cereulide synthesis. Overexpression of the transition state factor AbrB in B. cereus F4810/72 resulted in a non-toxic phenotype. Moreover, AbrB was shown to bind efficiently to the main promoter region of the ces operon, indicating that AbrB acts as a repressor of cereulide production by negatively affecting ces transcription.
The Borrelia burgdorferi outer-surface protein ErpX binds mammalian laminin
Authors: Brissette Catherine A. , Verma Ashutosh , Bowman Amy , Cooley Anne E. , Stevenson Brian
Published: February 2009

The Lyme disease spirochaete,Borrelia burgdorferi, can invade and persistently infect its hosts' connective tissues. We now demonstrate thatB. burgdorferiadheres to the extracellular matrix component laminin. The surface-exposed outer-membrane protein ErpX was identified as having affinity for laminin, and is the first laminin-binding protein to be identified in a Lyme disease spirochaete. The adhesive domain of ErpX was shown to be contained within a small, unstructured hydrophilic segment at the protein's centre. The sequence of that domain is distinct from any previously identified bacterial laminin adhesin, suggesting a unique mode of laminin binding.
Computer Simulation of the Dynamic Behavior of the Glutathione-Ascorbate Redox Cycle in Chloroplasts
Authors: Valero Edelmira , González-Sánchez María I. , Maciá Hermenegilda , García-Carmona Francisco
Published: February 2009

The glutathione-ascorbate redox pathway in chloroplasts is a complex network of spontaneous, photochemical, and enzymatic reactions for detoxifying hydrogen peroxide. This article presents a comprehensive sensitivity analysis of the system. A model has been constructed to simulate oxidative stress conditions, enabling steady-state concentrations of the metabolites involved in the pathway and photochemical and enzymatic fluxes to be calculated. The model includes an electron source whose flux is distributed among three competitive routes (photogeneration of \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{O}_{2}^{{-}}\) \end{document}, photoreduction of NADP+ to NADPH, and photoreduction of monodehydroascorbate to ascorbate) and that allows the simulation of variations in NADPH concentration with time. Each enzyme considered is introduced in the model, taking into account its particular catalytic mechanism, including the inactivation of ascorbate peroxidase in the presence of low-ascorbate concentrations. Computer simulations pointed to the great sensitivity of the system to the ratio among fluxes corresponding to ascorbate and NADPH photoproduction and NADPH consumption by the Calvin cycle. Under oxidative stress conditions, the model shows a sequential depletion of antioxidant power in chloroplasts in the order NADPH, glutathione, ascorbate and their recovery in the reverse order. Decreasing levels of glutathione reductase, ascorbate peroxidase, and superoxide dismutase led to the irreversible photoinactivation of ascorbate peroxidase and the subsequent increase in hydrogen peroxide concentration, preceded by a maximum in dehydroascorbate reductase activity.
Preferential Up-Regulation of G2/M Phase-Specific Genes by Overexpression of the Hyperactive Form of NtmybA2 Lacking Its Negative Regulation Domain in Tobacco BY-2 Cells
Authors: Kato Kiichi , Gális Ivan , Suzuki Shiori , Araki Satoshi , Demura Taku , Criqui Marie-Claire , Potuschak Thomas , Genschik Pascal , Fukuda Hiroo , Matsuoka Ken , Ito Masaki
Published: February 2009

Many G2/M phase-specific genes in plants contain mitosis-specific activator (MSA) elements, which act as G2/M phase-specific enhancers and bind with R1R2R3-Myb transcription factors. Here, we examined the genome-wide effects of NtmybA2 overexpression, one of the R1R2R3-Myb transcription factors in tobacco (Nicotiana tabacum). We used a custom-made 16-K cDNA microarray for comparative transcriptome analysis of transgenic tobacco BY-2 cell lines that overexpress NtmybA2 or its truncated hyperactive form. The microarray was also used to determine the transcript profile during the cell cycle in synchronized cultures of BY-2 cells. Combined microarray data from transgenic lines and synchronized cells revealed that overexpression of the truncated hyperactive form of NtmybA2, but not its full-length form, preferentially up-regulated many G2/M phase-specific genes in BY-2 cells. We determined promoter sequences of several such up-regulated genes and showed that all contain MSA-like motifs in the proximal regions of their promoters. One of the up-regulated genes, NtE2C, encoding for cyclin-specific ubiquitin carrier proteins, contained a single functional MSA-like motif, which specifically controlled the expression of a reporter gene in the G2/M phase in BY-2 cells. Furthermore, a genomic footprint experiment showed that the MSA element in the NtE2C promoter interacted with nuclear proteins in vivo. Therefore, we propose that the transcription of many G2/M phase-specific genes in tobacco is positively regulated by NtmybA2, in most cases through direct binding to the MSA elements.
An approach to high-throughput X-ray diffraction analysis of combinatorial polycrystalline thin film libraries
Authors: Roncallo S. , Karimi O. , Rogers K. D. , Lane D. W. , Ansari S. A.
Published: February 2009

With the demand for higher rates of discovery in the materials field, characterization techniques that are capable of rapidly and reliably surveying the characteristics of large numbers of samples are essential. A chemical combinatorial approach using thin films can provide detailed phase diagrams without the need to produce multiple, individual samples. This is achieved with compositional gradients forming high-density libraries. Conventional raster scanning of chemical or structural probes is subsequently used to interrogate the libraries. A new, alternative approach to raster scanning is introduced to provide a method of high-throughput data collection and analysis using an X-ray diffraction probe. Libraries are interrogated with an extended X-ray source and the scattering data collected using an area detector. A simple technique of `partitioning' this scattering distribution enables determination of information comparable to conventional raster scanned results but in a dramatically reduced collection time. The technique has been tested using synthetic X-ray scattering distributions and those obtained from contrived samples. In all cases, the partitioning algorithm is shown to be robust and to provide reliable data; discrimination along the library principal axis is shown to be ∼500 µm and the lattice parameter resolution to be ∼10−3 Å mm−1. The limitations of the technique are discussed and future potential applications described.
Direct mapping of fiber diffraction patterns into reciprocal space
Authors: Stribeck Norbert , Nöchel Ulrich
Published: February 2009

On the basis of the concept of Polanyi [Z. Phys.(1921),7, 149–180], the mapping of fiber diffraction patterns into reciprocal space is revisited. The result is a set of concise mapping relations that does not contain any approximations. This set permits the design of a direct method that, in principle, does not require refinement of mapping parameters even for patterns of tilted fibers. The method is unsuitable for diffuse scattering patterns. If inaccuracies of two pixels can be tolerated, a pattern is automatically mapped into reciprocal space in real time. The method is proposed for the processing of the extensive sets of patterns that are recorded in time-resolved wide-angle X-ray diffraction investigations of polymer materials.
Bond valence sum: a new soft chemical constraint forRMCProfile
Authors: Norberg Stefan T. , Tucker Matthew G. , Hull Stephen
Published: February 2009

The implementation of a new soft chemical constraint for the reverse Monte Carlo (RMC) programRMCProfile, based on bond valence sum (BVS) calculations, is described and its advantages for the analysis of `total scattering' diffraction data collected from disordered crystalline systems discussed. The inclusion of the BVS formalism proves particularly valuable in the early stages of the RMC fitting procedure, by avoiding the formation of regions containing chemically unreasonable local configurations which can become frozen in. Furthermore, this approach provides the fitting procedure with additional chemical information to differentiate between cation species that share the same crystallographic sites within the averaged unit cell and possess similar neutron scattering lengths. These issues are illustrated using total neutron scattering data collected at room temperature on the oxide-ion conductor Zr2Y2O7and the nonlinear optical material KTiOPO4.
HAb18G/CD147 inhibits starvation‐induced autophagy in human hepatoma cell SMMC7721 with an involvement of Beclin 1 down‐regulation
Authors: Gou Xingchun , Ru Qiang , Zhang Hongxin , Chen Yanke , Li Ling , Yang Hushan , Xing Jinliang , Chen Zhinan
Published: February 2009

HAb18G/CD147, a transmembrane glycoprotein highly expressed in various types of malignant cells, mainly functions as an inducer of matrix metalloproteinases to promote tumor growth, invasion and metastasis. However, whether there are other mechanisms underlying the role of HAb18G/CD147 in tumor progression remains to be elucidated. In this study, we investigated the functional effects of HAb18G/CD147 on autophagy in hepatoma cell line SMMC7721 using immunofluoscence staining, Western blot and transmission electronmicroscopy. Our data showed that specific small interference RNA (siRNA) considerably down‐regulated the expression of HAb18G/CD147 in SMMC7721 cells at both messenger RNA (mRNA) and protein levels. The down‐regulation of HAb18G/CD147 significantly promoted starvation‐induced autophagy in a dose‐dependent manner. Using trypan blue exclusion assay, we found that HAb18G/CD147 notably enhanced the survival of SMMC7721 cells through inhibiting starvation‐induced autophagy. In addition, we demonstrated that HAb18G/CD147 down‐regulated the expression of autophagy‐regulating protein Beclin 1 in SMMC7721 cells. Furthermore, our data indicated that HAb18G siRNA‐transfected SMMC7721 cells had a significantly decreased level of phosphorylated serine/threonine protein kinase B (pAkt) and the expression of Beclin 1 was inversely associated with the level of pAkt, suggesting that the Class I phosphatidylinositol 3 kinase‐Akt pathway may be involved in the down‐regulation of Beclin 1 by HAb18G/CD147. Overall, we provide the first experimental evidence to show that HAb18G/CD147 may play an important role in the inhibitory regulation of autophagy. Therefore, our data suggest a new molecular mechanism for HAb18G‐mediated hepatoma progression. (Cancer Sci 2009; 100: 837–843)
Isoflavone, polymorphisms in estrogen receptor genes and breast cancer risk in case‐control studies in Japanese, Japanese Brazilians and non‐Japanese Brazilians
Authors: Iwasaki Motoki , Hamada Gerson Shigeaki , Nishimoto Inês Nobuko , Netto Mario Mourão , Motola Jr Juvenal , Laginha Fábio Martins , Kasuga Yoshio , Yokoyama Shiro , Onuma Hiroshi , Nishimura Hideki , Kusama Ritsu , Kobayashi Minatsu , Ishihara Junko , Yamamoto Seiichiro , Hanaoka Tomoyuki , Tsugane Shoichiro
Published: February 2009

Epidemiologic studies have shown an inverse association between isoflavones and breast cancer risk. Because isoflavones bind estrogen receptors, we hypothesized that polymorphisms in the estrogen receptor genes might modify the association between isoflavone intake and breast cancer risk. We conducted hospital‐based case‐control studies of patients aged 20–74 years with primary, incident, histologically confirmed invasive breast cancer, and matched controls from among medical checkup examinees in Nagano, Japan, and from cancer‐free patients in São Paulo, Brazil. A total of 846 pairs (388 Japanese, 79 Japanese Brazilians and 379 non‐Japanese Brazilians) completed validated food frequency questionnaires, and provided blood samples. Five single nucleotide polymorphisms in the estrogen receptor alpha (rs9340799, rs1913474, and rs2234693) and beta (rs4986938 and rs1256049) genes were genotyped. We found no consistent association between the five single nucleotide polymorphisms and breast cancer risk among the three populations. In analyses of combinations of isoflavone intake and single nucleotide polymorphisms, an inverse association between intake and risk was limited to women with the GG genotype of the rs4986938 polymorphism for postmenopausal Japanese (odds ratio for highest versus lowest tertile = 0.47; P for trend = 0.01), Japanese Brazilians (odds ratio for highest versus lowest median = 0.31) and non‐Japanese Brazilians (odds ratio for consumers versus non‐consumers = 0.37) (P for interaction = 0.11, 0.08, and 0.21, respectively). We found no remarkable difference for the other four polymorphisms. Our findings suggest that polymorphisms in the estrogen receptor beta gene may modify the association between isoflavone intake and breast cancer risk. (Cancer Sci 2009; 100: 927–933)
Comparing patients' and healthcare professionals' ADR reports after media attention: the broadcast of a Dutch television programme about the benefits and risks of statins as an example
Authors: Van Hunsel Florence , Passier Anneke , Van Grootheest Kees
Published: February 2009

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• More and more countries accept patient reporting in their spontaneous reporting systems.

• Media exposure about drugs can influence patients and health professionals.

• Evaluation of patient reporting of adverse drug reactions is needed to provide further evidence of its benefits.

WHAT THIS STUDY ADDS

• Patient reporting compared with reporting by health professionals after media attention about statins.

• Patient reports provide additional insight into impact on daily life, the patient–health professional relationship and general worries next to health professionals' reports.

AIMSTo compare adverse drug reaction (ADR) reports from patients and health professionals after the broadcast of a Dutch television consumer programme about the benefits and risks of statins.

METHODSWe performed a quantitative and qualitative analysis on patients' and health professionals' reports of ADRs to statins. These reports were received by the Netherlands Pharmacovigilance Centre Lareb between March 2007 and August 2007. Quantitative data consisted of patient age and gender, number of received reports and characteristics of the report (most frequently reported ADRs, seriousness, drug discontinuation and outcome of the reported reaction). Open text fields in the ADR reporting form were categorized and a content analysis was carried out.

RESULTSMedia attention led to a peak in patient reporting of ADRs but not in reporting by health professionals. There were no differences between patient and health professional reports in seriousness of the ADRs and drug cessation. Patients reported nonrecovery more often than health professionals. The TV programme is mentioned as a reason for drug discontinuation in almost 30 reports. Patients often felt that they did not receive sufficient information and that their concerns were not adequately addressed by healthcare professionals.

CONCLUSIONSMedia attention affects drug use and ADR reporting by patients. Patient reports can provide additional information, making them a useful source of information next to health professional reports. Content analysis provides vital insights into the impact of statins on daily life, and patients' concerns about adverse reactions should be recognized in reports to national pharmacovigilance centres.
Insulin resistance as a predictor of incident asthma‐like symptoms in adults
Authors: Thuesen B. H. , Husemoen L. L. N. , Hersoug L.‐G. , Pisinger C. , Linneberg A.
Published: February 2009

Background
There is accumulating evidence that obesity is associated with an increased risk of asthma. It has been hypothesized that insulin resistance may be involved in obesity‐induced asthma, but till date there is no prospective data on this issue.

Objective
To investigate the association of obesity and insulin resistance with the incidence of asthma‐like symptoms in adults.

Methods
Out of a random sample of 12 934 persons from a general population, 6784 (52.5%) were included and participated in a health examination in 1999–2001. After 5 years they were re‐invited and 4516 (66.6%) participated at follow‐up. At baseline three obesity measures were considered: body mass index, waist circumference, and waist‐to‐hip ratio. In addition, fasting glucose and insulin were measured for determination of insulin resistance. Information on asthma‐like symptoms at baseline and follow‐up were obtained by questionnaires. A total of 3441 participants defined as non‐asthmatic at baseline and with complete information on all the considered variables were included in the analyses. Data were controlled for confounding by sex, age, social status, and smoking.

Results
All obesity measures were associated with incident wheezing and asthma‐like symptoms. In addition, insulin resistance was associated with incident wheezing [odds ratio (OR) 1.87, 95% confidence interval (CI) 1.38–2.54] and asthma‐like symptoms (OR 1.61, 95% CI 1.23–2.10). The effect of insulin resistance was stronger than that of obesity and was independent of sex.

Conclusion
We found that insulin resistance was associated with an increased risk of developing asthma‐like symptoms. This finding supports the hypothesis that obesity and asthma may be linked through inflammatory pathways also involved in insulin resistance.
Effects of livestock breed and grazing pressure on ground‐dwelling arthropods in Cantabrian heathlands
Authors: GARCÍA ROCÍO ROSA , JÁUREGUI BERTA M. , GARCÍA URCESINO , OSORO KOLDO , CELAYA RAFAEL
Published: February 2009

Abstract1. The effects of different goat breeds and grazing pressures on epigeal arachnids (Lycosidae and Opiliones) and ground beetles (Carabidae) were assessed in a heath–gorse shrubland located in the north of the Iberian Peninsula. Three treatments (low grazing pressure with Cashmere breed, high grazing pressure with Cashmere breed, and high grazing pressure with local Celtiberic breed) with three replicates of each treatment were allocated randomly to nine plots.

2. Arthropod fauna abundance, diversity, and species richness were estimated using pitfall trapping over 3 years (2003, 2004, and 2005). Vegetation cover, composition, and height were assessed along transects and above‐ground plant biomass was sampled in quadrats.

3. Lower grazing pressure led to lower herbaceous cover and higher heather cover than high grazing pressure. Overall, it did not enhance arthropod diversity or abundance, but the abundance and species richness of carabids, and abundance of lycosids likePardosa pullata, were higher under high stocking rates, whereas Opiliones were favoured by the low stocking rates. Although it has been assumed that traditional breeds enhance biodiversity, the present study found no significant differences for both arthropod fauna and vegetation between the goat breeds.

4. Arthropod–vegetation relationships were examined by constrained ordination. Fauna assemblages followed a gradient from closed canopy shrubland areas, in the lowest grazing pressure, to grassier open canopy areas resulting from higher grazing pressure, revealing the importance of grazing management as a driver of arthropod community structure of the heathland.
Behavioural activity levels and expression of stress proteins under predation risk in two damselfly species
Authors: SLOS STEFANIE , MEESTER LUC D. , STOKS ROBBY
Published: February 2009

Abstract1. It has become apparent that predators may strongly decrease prey fitness without direct contact with the prey, as they induce the development of defence systems that limit the availability of energy for growth and reproduction. Recent studies suggest that stress proteins may help prey organisms deal with this stress. The pattern is not general, however, and little is known about species differences in physiological traits in coping with predator stress, and covariation of physiological with other antipredator traits.

2. To explore these issues, we quantified levels of constitutive and fish‐induced stress proteins (Hsp60 and Hsp70) and anti‐predator behaviours in larvae of two damselfly species that differ in lifestyle. Both stress proteins were fixed at higher levels inErythromma najas, which has a slow lifestyle, than inLestes sponsa, which has a fast lifestyle. Similarly, anti‐predator behaviours were fixed at safer levels inE. najasthan inL. sponsa.

3. These results suggest that stress proteins may be part of anti‐predator syndromes of damselfly larvae, and there may be trait co‐specialisation between stress proteins and behavioural anti‐predator traits. Studies formally testing these hypotheses in more species may prove rewarding in advancing our understanding of the functional integration of physiological anti‐predator traits in relation to the prey’s lifestyle.
Predator richness has no effect in a diverse marine food web
Authors: O’Connor Mary I. , Bruno John F.
Published: February 2009

In many ecosystems, predator abundance, composition and diversity vary naturally among seasons and habitats. In addition, predator assemblages are changing due to overharvesting, habitat destruction and species invasions.

Predator species composition and richness can influence prey community structure and these effects can cascade to influence plant abundance and composition.

To test the effects of predator presence, composition and species richness on prey abundance, species richness and composition, we conducted three experiments in a subtidal marine food web. Experimental food webs were drawn from species pools of 5–7 predator species, 19–52 prey species, benthic micro‐algae and 5 macro‐algae.

Predators reduced prey abundance in the mesocosm experiment, but this effect was diminished or absent in field experiments. Predator species differed in their effects on prey, but we found no effect of predator richness (via complementarity or selection) on any aspect of prey community structure.

The absence of a predator richness effect could be due to several factors including potentially opposing effects of individual predator species, intraguild predation, or greater importance of colonization relative to competition in structuring prey assemblages. Although predators can have strong top‐down effects in this system, selection or resource‐use complementarity among predators do not affect prey community structure.
No experimental evidence for local competition in the nestling phase as a driving force for density‐dependent avian clutch size
Authors: Nicolaus Marion , Both Christiaan , Ubels Richard , Edelaar Pim , Tinbergen Joost M.
Published: February 2009

In birds, local competition for food between pairs during the nestling phase may affect nestling growth and survival. A decrease in clutch size with an increase in breeding density could be an adaptive response to this competition. To investigate whether breeding density causally affected the clutch size of great tits (Parus major), we manipulated breeding density in three out of eight study plots by increasing nest‐box densities. We expected clutch size in these plots to be reduced compared to that in control plots.

We analysed both the effects of variation in annual mean density (between‐year comparisons) and experimental density (within‐year comparison between plots) on clutch size variation, the occurrence of second broods and nestling growth. We examined within‐female variation in clutch size to determine whether individual responses explain the variation over years.

Over the 11 years, population breeding density increased (from 0·33 to 0·50 pairs ha−1) while clutch size and the occurrence of second broods decreased (respectively from 10·0 to 8·5 eggs and from 0·39 to 0·05), consistent with a negative density‐dependent effect for the whole population. Nestling growth showed a declining but nonsignificant trend over years.

The decline in population clutch size over years was primarily explained by changes occurring within individuals rather than selective disappearance of individuals laying large clutches.

Within years, breeding density differed significantly between manipulated plots (0·16 pairs ha−1vs. 0·77 pairs ha−1) but clutch size, occurrence of second broods and nestling growth were not affected by the experimental treatment, resulting in a discrepancy between the effects of experimental and annual variation in density on reproduction.

We discuss two hypotheses that could explain this discrepancy: (i) the decline in breeding performance over time was not due to density, but resulted from other, unknown factors. (ii) Density did cause the decline in breeding performance, but this was not due to local competition in the nestling phase. Instead, we suggest that competition acting in a different phase (e.g. before egg laying or after fledgling) was responsible for the density effect on clutch size among years.