bluuebunny/crossref_metadata_2025 huggingface dataset:
GPR17 is a negative regulator of the cysteinyl leukotriene 1 receptor response to leukotriene D
4
Authors: Maekawa Akiko , Balestrieri Barbara , Austen K. Frank , Kanaoka Yoshihide
Published: June 2009

The cysteinyl leukotrienes (cys-LTs) are proinflammatory lipid mediators acting on the type 1 cys-LT receptor (CysLT
1
R) to mediate smooth muscle constriction and vascular permeability. GPR17, a G protein-coupled orphan receptor with homology to the P2Y and cys-LT receptors, failed to mediate calcium flux in response to leukotriene (LT) D
4
with stable transfectants. However, in stable cotransfections of 6×His-tagged GPR17 with Myc-tagged CysLT
1
R, the robust CysLT
1
R-mediated calcium response to LTD
4
was abolished. The membrane expression of the CysLT
1
R analyzed by FACS with anti-Myc Ab was not reduced by the cotransfection, yet both LTD
4
-elicited ERK phosphorylation and the specific binding of [
3
H]LTD
4
to microsomal membranes were fully inhibited. CysLT
1
R and GPR17 expressed in transfected cells were coimmunoprecipitated and identified by Western blots, and confocal immunofluorescence microscopy revealed that GPR17 and CysLT
1
R colocalize on the cell surface of human peripheral blood monocytes. Lentiviral knockdown of GPR17 in mouse bone marrow-derived macrophages (BMMΦs) increased both the membrane expression of CysLT
1
R protein by FACS analysis and the LTD
4
-elicited calcium flux in a dose-dependent manner as compared with control BMMΦs, indicating a negative regulatory function of GPR17 for CysLT
1
R in a primary cell. In IgE-dependent passive cutaneous anaphylaxis, GPR17-deficient mice showed a marked and significant increase in vascular permeability as compared with WT littermates, and this vascular leak was significantly blocked by pretreatment of the mice with the CysLT
1
R antagonist, MK-571. Taken together, our findings suggest that GPR17 is a ligand-independent, constitutive negative regulator for the CysLT
1
R that suppresses CysLT
1
R-mediated function at the cell membrane.
Association between aerobic fitness in late pregnancy and duration of labor in nulliparous women
Authors: KARDEL KRISTIN R. , JOHANSEN BJØRN , VOLDNER NANNA , IVERSEN PER OLE , HENRIKSEN TORE
Published: June 2009

It is established that the level of physical activity in the population generally is too low, and data indicate that pregnant women are no exception. Studies of the effects of aerobic fitness on delivery outcomes are limited. In this observational study, we investigated the effect of aerobic fitness on duration of labor in nulliparous women who started labor spontaneously. Maximal oxygen uptake was measured in 40 nulliparous women at 35–37 weeks of gestation. Duration of labor was defined as the time between 3 cm cervical dilation with regular uterine contractions and delivery. The mean (SD) maximal oxygen uptake was 2.1 (0.3) L/min and duration of labor 583 (317) minutes. Duration of labor was inversely associated with maximal oxygen uptake after adjusting for birthweight (p = 0.034). We conclude that measurement of maximal oxygen uptake is safe in pregnancy at 35–37 weeks and that increased aerobic fitness was associated with shorter labor in nulliparous women who started labor spontaneously.
Is there any relation between development of persistent non‐reassuring fetal heart rate pattern and acutely increased uterine artery vascular flow resistance during dinoprostone use in prolonged pregnancies?
Authors: KARCAALTINCABA DENIZ , AKDAG DERYA , KANDEMIR OMER , YALVAC SERDAR , GUVEN EMINE SEDA GUVENDAG , HABERAL ALI
Published: June 2009

Objective. To investigate the relation between changes in Doppler parameters of fetal and uterine arteries and development of persistent non‐reassuring fetal heart rate (FHR) pattern during induction of labor with dinoprostone (Propess®) in pregnancies at ≥41 weeks gestation. Design. Prospective cohort study. Setting. Etlik Zubeyde Hanim Women's Hospital, Turkey. Sample. One hundred forty‐one prolonged pregnancies. Methods. Doppler parameters of umbilical, middle cerebral, and uterine arteries were measured before and 4–6 hours after dinoprostone application between uterine contractions. Non‐reassuring FHR pattern and persistent non‐reassuring FHR pattern criteria were defined based on NICE 2007 guidelines. Women with successful spontaneous vaginal delivery were recruited as a control group (n = 108), while women who underwent cesarean delivery due to persistent non‐reassuring FHR pattern were recruited as a study group (n = 15). Main outcome measures. Prediction of non‐reassuring FHR pattern with Doppler analysis of uterine and fetal arteries. Results. After dinoprostone application there was significant enhancement in uterine artery resistance index (RI) in the study group compared to the control group (p = 0.002). Receiver operating characteristics curve analysis identified a uterine artery RI increase value of 0.11 as the optimal threshold for prediction of persistent non‐reassuring FHR pattern with 73.3% sensitivity and 69.4% specificity. Logistic regression analysis demonstrated that an increase in the uterine artery RI was predictive for persistent non‐reassuring FHR pattern (odds ratio (OR) 4.97; 95% CI 1.5–16.8). Conclusion. Acute increase in uterine artery RI due to dinoprostone use may end with persistent non‐reassuring FHR pattern in prolonged pregnancies. This may allow earlier prediction of persistent non‐reassuring FHR pattern development and risk assessment.
Short and long‐term effects of antenatal corticosteroids assessed in a cohort of 7,827 children born preterm
Authors: ERIKSSON LENA , HAGLUND BENGT , EWALD UWE , ODLIND VIVECA , KIELER HELLE
Published: July 2009

Objective. To study the benefits of antenatal corticosteroids (ACS) in clinical settings and to evaluate the occurrence of long‐term neuro‐sensory effects such as epilepsy and cerebral palsy (CP). Design. Observational population‐based study including all births between gestational weeks 24 and 34 during 1976–1997 in Sweden. Exposure to ACS was evaluated at hospital level. Children were followed up to their ninth birthday. Sample and methods. Seven thousand eight hundred twenty‐seven infants of which 5,632 were exposed to ACS. Data on hospital ACS routines was based on questionnaires and interviews with physicians and pharmacy sales. Outcomes were obtained from the national health registers and assessed according to gender of the child. Logistic regression was used to assess associations. Main outcome measures. Neonatal death, low Apgar score, respiratory distress syndrome (RDS), bronchopulmonary dysplasia (BPD), intraventricular hemorrhage (IVH), retinopathy of prematurity (ROP), CP, and epilepsy. Results. After adjustment, exposed infants had reduced risks of RDS (OR 0.80, 95% CI 0.70–0.92), late neonatal death (OR 0.86, 95% CI 0.57–1.29), BPD (OR 0.87, 95% CI 0.62–1.22), ROP (OR 0.80, 95% CI 0.48–1.32), IVH (OR 0.93, 95% CI 0.67–1.3), and CP (OR 0.82, 95% CI 0.58–1.15). Males had a higher risk of epilepsy (OR 1.74, 95% CI 0.85–3.55) than females (OR 0.50, 95% CI 0.25–1.03). Conclusion. The results confirm the beneficial effect of ACS regarding RDS in clinical settings. Except for a tendency to increased risk of epilepsy among male infants there were no increased risks of neuro‐sensory outcomes.
A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry
Authors: Thompson Reid F. , Suzuki Masako , Lau Kevin W. , Greally John M.
Published: June 2009

Motivation: DNA cytosine methylation is an important epigenetic regulator, critical for mammalian development and the control of gene expression. Numerous techniques using either restriction enzyme or affinity-based approaches have been developed to interrogate cytosine methylation status genome-wide, however these assays must be validated by a more quantitative approach, such as MALDI-TOF mass spectrometry of bisulphite-converted DNA (commercialized as Sequenom's EpiTYPER assay using the MassArray system). Here, we present an R package (‘MassArray’) that assists in assay design and uses the standard Sequenom output file as the input to a pipeline of analyses not available as part of the commercial software. The tools in this package include bisulphite conversion efficiency calculation, sequence polymorphism flagging and visualization tools that combine multiple experimental replicates and create tracks for genome browser viewing.

Contact:  jgreally@aecom.yu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Comparative study on ChIP-seq data: normalization and binding pattern characterization
Authors: Taslim Cenny , Wu Jiejun , Yan Pearlly , Singer Greg , Parvin Jeffrey , Huang Tim , Lin Shili , Huang Kun
Published: June 2009

Motivation: Antibody-based Chromatin Immunoprecipitation assay followed by high-throughput sequencing technology (ChIP-seq) is a relatively new method to study the binding patterns of specific protein molecules over the entire genome. ChIP-seq technology allows scientist to get more comprehensive results in shorter time. Here, we present a non-linear normalization algorithm and a mixture modeling method for comparing ChIP-seq data from multiple samples and characterizing genes based on their RNA polymerase II (Pol II) binding patterns.

Results: We apply a two-step non-linear normalization method based on locally weighted regression (LOESS) approach to compare ChIP-seq data across multiple samples and model the difference using an Exponential-NormalK mixture model. Fitted model is used to identify genes associated with differential binding sites based on local false discovery rate (fdr). These genes are then standardized and hierarchically clustered to characterize their Pol II binding patterns. As a case study, we apply the analysis procedure comparing normal breast cancer (MCF7) to tamoxifen-resistant (OHT) cell line. We find enriched regions that are associated with cancer (P < 0.0001). Our findings also imply that there may be a dysregulation of cell cycle and gene expression control pathways in the tamoxifen-resistant cells. These results show that the non-linear normalization method can be used to analyze ChIP-seq data across multiple samples.

Availability: Data are available at http://www.bmi.osu.edu/~khuang/Data/ChIP/RNAPII/

Contact:  taslim.2@osu.edu; khuang@bmi.osu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Error control variability in pathway-based microarray analysis
Authors: Gold David L. , Miecznikowski Jeffrey C. , Liu Song
Published: June 2009

Motivation: The decision to commit some or many false positives in practice rests with the investigator. Unfortunately, not all error control procedures perform the same. Our problem is to choose an error control procedure to determine a P-value threshold for identifying differentially expressed pathways in high-throughput gene expression studies. Pathway analysis involves fewer tests than differential gene expression analysis, on the order of a few hundred. We discuss and compare methods for error control for pathway analysis with gene expression data.

Results: In consideration of the variability in test results, we find that the widely used Benjamini and Hochberg's (BH) false discovery rate (FDR) analysis is less robust than alternative procedures. BH's error control requires a large number of hypothesis tests, a reasonable assumption for differential gene expression analysis, though not the case with pathway-based analysis. Therefore, we advocate through a series of simulations and applications to real gene expression data that researchers control the number of false positives rather than the FDR.

Availability: Our R package, EPath.omg is available at http://sphhp.buffalo.edu/biostat/research/software.

Contact:  dlgold@buffalo.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
A genetic programming approach for Burkholderia Pseudomallei diagnostic pattern discovery
Authors: Yang Zheng Rong , Lertmemongkolchai Ganjana , Tan Gladys , Felgner Philip L. , Titball Richard
Published: June 2009

Motivation: Finding diagnostic patterns for fighting diseases like Burkholderia pseudomallei using biomarkers involves two key issues. First, exhausting all subsets of testable biomarkers (antigens in this context) to find a best one is computationally infeasible. Therefore, a proper optimization approach like evolutionary computation should be investigated. Second, a properly selected function of the antigens as the diagnostic pattern which is commonly unknown is a key to the diagnostic accuracy and the diagnostic effectiveness in clinical use.

Results: A conversion function is proposed to convert serum tests of antigens on patients to binary values based on which Boolean functions as the diagnostic patterns are developed. A genetic programming approach is designed for optimizing the diagnostic patterns in terms of their accuracy and effectiveness. During optimization, it is aimed to maximize the coverage (the rate of positive response to antigens) in the infected patients and minimize the coverage in the non-infected patients while maintaining the fewest number of testable antigens used in the Boolean functions as possible. The final coverage in the infected patients is 96.55% using 17 of 215 (7.4%) antigens with zero coverage in the non-infected patients. Among these 17 antigens, BPSL2697 is the most frequently selected one for the diagnosis of Burkholderia Pseudomallei. The approach has been evaluated using both the cross-validation and the Jack–knife simulation methods with the prediction accuracy as 93% and 92%, respectively. A novel approach is also proposed in this study to evaluate a model with binary data using ROC analysis.

Contact:  z.r.yang@ex.ac.uk
libAnnotationSBML: a library for exploiting SBML annotations
Authors: Swainston Neil , Mendes Pedro
Published: June 2009

Summary: The Systems Biology Markup Language (SBML) is an established community XML format for the markup of biochemical models. With the introduction of SBML level 2 version 3, specific model entities, such as species or reactions, can now be annotated using ontological terms. These annotations, which are encoded using the resource description framework (RDF), provide the facility to specify definite terms to individual components, allowing software to unambiguously identify such components and thus link the models to existing data resources.

libSBML is an application programming interface library for the manipulation of SBML files. While libSBML provides the facilities for reading and writing such annotations from and to models, it is beyond the scope of libSBML to provide interpretation of these terms. The libAnnotationSBML library introduced here acts as a layer on top of libSBML linking SBML annotations to the web services that describe these ontological terms. Two applications that use this library are described: SbmlSynonymExtractor finds name synonyms of SBML model entities and SbmlReactionBalancer checks SBML files to determine whether specifed reactions are elementally balanced.

Availability:  http://mcisb.sourceforge.net/

Contact:  neil.swainston@manchester.ac.uk
Transcriptional landscape estimation from tiling array data using a model of signal shift and drift
Authors: Nicolas Pierre , Leduc Aurélie , Robin Stéphane , Rasmussen Simon , Jarmer Hanne , Bessières Philippe
Published: June 2009

Motivation: High-density oligonucleotide tiling array technology holds the promise of a better description of the complexity and the dynamics of transcriptional landscapes. In organisms such as bacteria and yeasts, transcription can be measured on a genome-wide scale with a resolution >25 bp. The statistical models currently used to handle these data remain however very simple, the most popular being the piecewise constant Gaussian model with a fixed number of breakpoints.

Results: This article describes a new methodology based on a hidden Markov model that embeds the segmentation of a continuous-valued signal in a probabilistic setting. For a computationally affordable cost, this framework (i) alleviates the difficulty of choosing a fixed number of breakpoints, and (ii) permits retrieving more information than a unique segmentation by giving access to the whole probability distribution of the transcription profile. Importantly, the model is also enriched and accounts for subtle effects such as signal ‘drift’ and covariates. Relevance of this framework is demonstrated on a Bacillus subtilis dataset.

Availability: A software is distributed under the GPL.

Contact:  pierre.nicolas@jouy.inra.fr

Supplementary information:  Supplementary data is available at Bioinformatics online.
The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction
Authors: Huttenhower Curtis , Hibbs Matthew A. , Myers Chad L. , Caudy Amy A. , Hess David C. , Troyanskaya Olga G.
Published: June 2009

Motivation: Rapidly expanding repositories of highly informative genomic data have generated increasing interest in methods for protein function prediction and inference of biological networks. The successful application of supervised machine learning to these tasks requires a gold standard for protein function: a trusted set of correct examples, which can be used to assess performance through cross-validation or other statistical approaches. Since gene annotation is incomplete for even the best studied model organisms, the biological reliability of such evaluations may be called into question.

Results: We address this concern by constructing and analyzing an experimentally based gold standard through comprehensive validation of protein function predictions for mitochondrion biogenesis in Saccharomyces cerevisiae. Specifically, we determine that (i) current machine learning approaches are able to generalize and predict novel biology from an incomplete gold standard and (ii) incomplete functional annotations adversely affect the evaluation of machine learning performance. While computational approaches performed better than predicted in the face of incomplete data, relative comparison of competing approaches—even those employing the same training data—is problematic with a sparse gold standard. Incomplete knowledge causes individual methods' performances to be differentially underestimated, resulting in misleading performance evaluations. We provide a benchmark gold standard for yeast mitochondria to complement current databases and an analysis of our experimental results in the hopes of mitigating these effects in future comparative evaluations.

Availability: The mitochondrial benchmark gold standard, as well as experimental results and additional data, is available at http://function.princeton.edu/mitochondria

Contact:  ogt@cs.princeton.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Effect of piboserod, a 5‐HT4serotonin receptor antagonist, on left ventricular function in patients with symptomatic heart failure
Authors: Kjekshus John K. , Torp‐Pedersen Christian , Gullestad Lars , Køber Lars , Edvardsen Thor , Olsen Inge C. , Sjaastad Ivar , Qvigstad Eirik , Skomedal Tor , Osnes Jan‐Bjørn , Levy Finn Olav
Published: July 2009

Aims

Myocardial 5‐HT4serotonin (5‐HT) receptors are increased and activated in heart failure (HF). Blockade of 5‐HT4receptors reduced left ventricular (LV) remodelling in HF rats. We evaluated the effect of piboserod, a potent, selective, 5‐HT4serotonin receptor antagonist, on LV function in patients with HF.

Methods and results

This was a prospective, double‐blind, parallel group trial in patients with NYHA class II–IV HF and LV ejection fraction (EF) ≤0.35. Patients receiving standard HF treatment were randomized to placebo (n= 70) or piboserod 80 mg (n= 67) for 24 weeks including 4 weeks up titration. The primary endpoint was LVEF measured by cardiac magnetic resonance imaging (MRI). Secondary endpoints were LV volumes, N‐terminal pro‐brain natriuretic peptide, norepinephrine, quality of life, and 6 min walk test. Piboserod significantly increased LVEF by 1.7% vs. placebo (CI 0.3, 3.2,P= 0.020), primarily through reduced end‐systolic volume from 165 to 158 mL (P= 0.060). There was a trend for greater increase in LVEF (2.7%, CI −1.1, 6.6,P= 0.15) in a small subset of patients not on chronic β‐blocker therapy. There was no significant effect on neurohormones, quality of life, or exercise tolerance. Patients on piboserod reported more adverse events, but numbers were too small to identify specific safety issues.

Conclusion

Although patients with chronic HF had a small but significant improvement in LVEF when treated with piboserod for 24 weeks, the result was not reflected in significant changes in other efficacy parameters, and its clinical relevance remains uncertain.

Clinicaltrials.gov, NCT 00421746
Modeling New Party Performance: A Conceptual and Methodological Approach for Volatile Party Systems
Authors: Mustillo Thomas J.
Published: June 2009

This study of new political parties in the Third Wave democracies of Bolivia, Chile, Ecuador, and Venezuela conceptualizes the early life of a party as a developmental phase. The analysis uses latent trajectory modeling to identify five qualitatively distinctive performance profiles, which the author calls “explosive,” “contender,” “flash,” “flat,” and “flop” trajectories. This finding challenges the conventional approaches used in the study of new party performance, where scholars classify parties using subjective criteria, often into the successful/failed dichotomy. In unstable party systems, where we expect greater diversity in the performance profiles of new parties, latent trajectory modeling is preferred because it yields a result more consistent with extant theorizing on new parties. In stable systems, as in the case of Chile, the approaches can yield similar results. Nevertheless, the case of Venezuela (1958–88) demonstrates that even in stable party systems, the modeling approach used here can identify important variation that alternatives might miss.
Structures of three distinct activator–TFIID complexes
Authors: Liu Wei-Li , Coleman Robert A. , Ma Elizabeth , Grob Patricia , Yang Joyce L. , Zhang Yixi , Dailey Gina , Nogales Eva , Tjian Robert
Published: July 2009

Sequence-specific DNA-binding activators, key regulators of gene expression, stimulate transcription in part by targeting the core promoter recognition TFIID complex and aiding in its recruitment to promoter DNA. Although it has been established that activators can interact with multiple components of TFIID, it is unknown whether common or distinct surfaces within TFIID are targeted by activators and what changes if any in the structure of TFIID may occur upon binding activators. As a first step toward structurally dissecting activator/TFIID interactions, we determined the three-dimensional structures of TFIID bound to three distinct activators (i.e., the tumor suppressor p53 protein, glutamine-rich Sp1 and the oncoprotein c-Jun) and compared their structures as determined by electron microscopy and single-particle reconstruction. By a combination of EM and biochemical mapping analysis, our results uncover distinct contact regions within TFIID bound by each activator. Unlike the coactivator CRSP/Mediator complex that undergoes drastic and global structural changes upon activator binding, instead, a rather confined set of local conserved structural changes were observed when each activator binds holo-TFIID. These results suggest that activator contact may induce unique structural features of TFIID, thus providing nanoscale information on activator-dependent TFIID assembly and transcription initiation.
Long noncoding RNAs: functional surprises from the RNA world
Authors: Wilusz Jeremy E. , Sunwoo Hongjae , Spector David L.
Published: July 2009

Most of the eukaryotic genome is transcribed, yielding a complex network of transcripts that includes tens of thousands of long noncoding RNAs with little or no protein-coding capacity. Although the vast majority of long noncoding RNAs have yet to be characterized thoroughly, many of these transcripts are unlikely to represent transcriptional “noise” as a significant number have been shown to exhibit cell type-specific expression, localization to subcellular compartments, and association with human diseases. Here, we highlight recent efforts that have identified a myriad of molecular functions for long noncoding RNAs. In some cases, it appears that simply the act of noncoding RNA transcription is sufficient to positively or negatively affect the expression of nearby genes. However, in many cases, the long noncoding RNAs themselves serve key regulatory roles that were assumed previously to be reserved for proteins, such as regulating the activity or localization of proteins and serving as organizational frameworks of subcellular structures. In addition, many long noncoding RNAs are processed to yield small RNAs or, conversely, modulate how other RNAs are processed. It is thus becoming increasingly clear that long noncoding RNAs can function via numerous paradigms and are key regulatory molecules in the cell.
Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae
Authors: Camblong Jurgi , Beyrouthy Nissrine , Guffanti Elisa , Schlaepfer Guillaume , Steinmetz Lars M. , Stutz Françoise
Published: July 2009

Homology-dependent gene silencing, a phenomenon described as cosuppression in plants, depends on siRNAs. We provide evidence that in Saccharomyces cerevisiae, which is missing the RNAi machinery, protein coding gene cosuppression exists. Indeed, introduction of an additional copy of PHO84 on a plasmid or within the genome results in the cosilencing of both the transgene and the endogenous gene. This repression is transcriptional and position-independent and requires trans-acting antisense RNAs. Antisense RNAs induce transcriptional gene silencing both in cis and in trans, and the two pathways differ by the implication of the Hda1/2/3 complex. We also show that trans-silencing is influenced by the Set1 histone methyltransferase, which promotes antisense RNA production. Finally we show that although antisense-mediated cis-silencing occurs in other genes, trans-silencing so far depends on features specific to PHO84. All together our data highlight the importance of noncoding RNAs in mediating RNAi-independent transcriptional gene silencing.
Egg Incubation and Collection of Painted Turtle Embryos
Authors: Valenzuela Nicole
Published: July 2009

INTRODUCTION

This protocol describes how to incubate painted turtle eggs and collect embryos for gene expression analysis. The same basic protocol can be used to incubate eggs and collect embryos from other turtle species by modifying the incubation temperature to suit the particular developmental needs of each species.
Nested Patch PCR for Highly Multiplexed Amplification of Genomic Loci
Authors: Varley Katherine E. , Mitra Robi D.
Published: July 2009

INTRODUCTION

Nested Patch polymerase chain reaction (PCR) amplifies a large number (greater than 90) of targeted loci from genomic DNA simultaneously in the same reaction. These amplified loci can then be sequenced on a second-generation sequencing machine to detect single nucleotide polymorphisms (SNPs) and mutations. The reaction is highly specific: 90% of sequencing reads match targeted loci. Nested Patch PCR can be performed on many samples in parallel, and by using sample-specific DNA barcodes, these can be pooled and sequenced in a single reaction. Thus, the Nested Patch PCR protocol that is described here provides an easy workflow to identify SNPs and mutations across many targeted loci for many samples in parallel.
Use of Fluorescence In Situ Hybridization and the daime Image Analysis Program for the Cultivation-Independent Quantification of Microorganisms in Environmental and Medical Samples
Authors: Daims Holger
Published: July 2009

INTRODUCTION

Conventional cultivation-based methods to measure microbial abundance are unsuitable for quantifying uncultured microorganisms that constitute the majority of microbial life in most environmental or medical samples. This problem is solved by the quantification approach described here, which combines fluorescence in situ hybridization (FISH) with rRNA-targeted probes and digital image analysis. By measuring the areas of probe-labeled biomass in randomly recorded image pairs, an unbiased estimate of the relative biovolume of the population of interest can be obtained. This approach expresses abundance as “biovolume fraction” (relative to the total biovolume of the whole microbial community). This value equals the share of biochemical reaction space occupied by the quantified population and thus can be more relevant ecologically than absolute cell numbers (e.g., a few large cells can contain the same biovolume as many small cells). Another advantage lies in the complete independence of this method from the morphology of the quantified organisms. Regardless of whether the target microbes occur as single cells in plankton samples, as filaments, or as dense aggregates in biofilms, this cultivation-independent method allows the composition of complex microbial communities to be determined.
Adhesive Micropatterns for Cells: A Microcontact Printing Protocol
Authors: Théry Manuel , Piel Matthieu
Published: July 2009

INTRODUCTION

This protocol describes a simple, fast, and efficient method for making adhesive micropatterns that can be used to control individual cell shape and adhesion patterns. It is based on the use of an elastomeric stamp containing microfeatures to print proteins on the substrate of choice. The process can be subdivided into three parts. First, a silicon master is fabricated, which contains the microfeatures of interest. Once fabricated, the master can be used multiple times to make stamps. Masters with customized patterns can also be purchased commercially. Second, a polydimethylsiloxane (PDMS) stamp is fabricated. Unlike fabrication of the master, this step can be performed without specialized equipment. The PDMS stamp is inked with extracellular matrix proteins. Proteins are printed on a substrate (e.g., a tissue culture polystyrene dish or a glass coverslip covered with a thin layer of polystyrene). The nonprinted areas are back-filled with poly-L-lysine-polyethylene glycol, which renders them resistant to cell adhesion. The production of these micropatterned substrates can be completed in <2 h. The third and final portion of the protocol describes the deposition of cells onto the micropatterned substrate.
Using Progressive Methods for Global Multiple Sequence Alignment
Authors: Mount David W.
Published: July 2009

INTRODUCTION

Finding a global optimal alignment of more than two sequences that includes matches, mismatches, and gaps and that takes into account the degree of variation in all of the sequences at the same time is especially difficult. The dynamic programming algorithm used for optimal alignment of pairs of sequences can be extended to global alignment of three sequences, but for more than three sequences, only a small number of relatively short sequences may be analyzed. Thus, approximate methods are used for global sequence alignment. One class of these methods is progressive global alignment, which starts with an alignment of the most alike sequences and then builds an alignment by adding more sequences. This article introduces three programs that use progressive alignment methodology.
Turnover of Fatty Acids during Natural Senescence of Arabidopsis, Brachypodium, and Switchgrass and in Arabidopsis β-Oxidation Mutants
Authors: Yang Zhenle , Ohlrogge John B.
Published: June 2009

During leaf senescence, macromolecule breakdown occurs and nutrients are translocated to support growth of new vegetative tissues, seeds, or other storage organs. In this study, we determined the fatty acid levels and profiles in Arabidopsis (Arabidopsis thaliana), Brachypodium  distachyon, and switchgrass (Panicum virgatum) leaves during natural senescence. In young leaves, fatty acids represent 4% to 5% of dry weight and approximately 10% of the chemical energy content of the leaf tissues. In all three species, fatty acid levels in leaves began to decline at the onset of leaf senescence and progressively decreased as senescence advanced, resulting in a greater than 80% decline in fatty acids on a dry weight basis. During senescence, Arabidopsis leaves lost 1.6% of fatty acids per day at a rate of 2.1 μg per leaf (0.6 μg mg−1 dry weight). Triacylglycerol levels remained less than 1% of total lipids at all stages. In contrast to glycerolipids, aliphatic surface waxes of Arabidopsis leaves were much more stable, showing only minor reduction during senescence. We also examined three Arabidopsis mutants, acx1acx2, lacs6lacs7, and kat2, which are blocked in enzyme activities of β-oxidation and are defective in lipid mobilization during seed germination. In each case, no major differences in the fatty acid contents of leaves were observed between these mutants and the wild type, indicating that several mutations in β-oxidation that cause reduced breakdown of reserve oil in seeds do not substantially reduce the degradation of fatty acids during leaf senescence.
The Multifunctional Enzyme CYP71B15 (PHYTOALEXIN DEFICIENT3) Converts Cysteine-Indole-3-Acetonitrile to Camalexin in the Indole-3-Acetonitrile Metabolic Network ofArabidopsis thaliana
Authors: Böttcher Christoph , Westphal Lore , Schmotz Constanze , Prade Elke , Scheel Dierk , Glawischnig Erich
Published: July 2009

Accumulation of camalexin, the characteristic phytoalexin of Arabidopsis thaliana, is induced by a great variety of plant pathogens. It is derived from Trp, which is converted to indole-3-acetonitrile (IAN) by successive action of the cytochrome P450 enzymes CYP79B2/B3 and CYP71A13. Extracts from wild-type plants and camalexin biosynthetic mutants, treated with silver nitrate or inoculated with Phytophthora infestans, were comprehensively analyzed by ultra-performance liquid chromatography electrospray ionization quadrupole time-of-flight mass spectrometry. This metabolomics approach was combined with precursor feeding experiments to characterize the IAN metabolic network and to identify novel biosynthetic intermediates and metabolites of camalexin. Indole-3-carbaldehyde and indole-3-carboxylic acid derivatives were shown to originate from IAN. IAN conjugates with glutathione, γ-glutamylcysteine, and cysteine [Cys(IAN)] accumulated in challenged phytoalexin deficient3 (pad3) mutants. Cys(IAN) rescued the camalexin-deficient phenotype of cyp79b2 cyp79b3 and was itself converted to dihydrocamalexic acid (DHCA), the known substrate of CYP71B15 (PAD3), by microsomes isolated from silver nitrate–treated Arabidopsis leaves. Surprisingly, yeast-expressed CYP71B15 also catalyzed thiazoline ring closure, DHCA formation, and cyanide release with Cys(IAN) as substrate. In conclusion, in the camalexin biosynthetic pathway, IAN is derivatized to the intermediate Cys(IAN), which serves as substrate of the multifunctional cytochrome P450 enzyme CYP71B15.
Corrosion studies on the plasma‐sprayed nanostructured titanium dioxide coatings
Authors: Ahmad Z. , Ahsan M.
Published: June 2009

Purpose

The purpose of this paper is to report the resistance of plasma‐sprayed titanium dioxide (TiO2) nanostructured coatings in a corrosive environment.

Design/methodology/approach

Weight loss studies are performed according to ASTM G31 specifications in 3.5 wt% NaCl. Electrochemical polarization resistance measurements are made according to ASTM G59‐91 specifications. Corrosion resistance in a humid and corrosive environment is determined by exposing the samples in a salt spray chamber for 100 h. Microstructural studies are carried out using an atomic force microscope and scanning electron microscope.

Findings

The nanostructured TiO2 coatings offer good resistance to corrosion, as shown by the results of immersion, electrochemical and salt spray studies. The corrosion resistance of the coating is dictated primarily by the geometry of splat lamellae, density of unmelted nanoparticles, magnitude of porosity and surface homogeneity.

Practical implications

The TiO2 nanostructured coatings show promising potential for use as abrasion, wear‐resistant and thermal barrier coatings for service in harsh environments.

Originality/value

The paper relates the corrosion resistance of nanostructured TiO2 coatings to their structure and surface morphology.
Mechanism of degradation of stabilized corrosion‐resistant steel during the welding cycle
Authors: Schmidova Eva , Svanda Pavel , Vesely David , Kalendova Andrea
Published: June 2009

Purpose

The purpose of this paper is to clarify the destabilisation mechanism that occurs with two types of ferritic corrosion‐resistant steel during the welding cycle.

Design/methodology/approach

A series of experimental weld joints was made to verify the actual response of non‐stabilised corrosion‐resistant steel, and of the same steel that had been stabilised by added titanium. The character and extent of the ensuing structural changes were analysed. The essential characteristics of degradation in the heat‐affected zone are evaluated using optical and scanning electron microscopy; individual phases are identified by means of EDX microanalysis. The underlying mechanism for the loss of stability is induced experimentally in several stages; depending on the thermal doping level and interaction with the environment during the welding process, phases of various types are precipitated. These phases subsequently are studied in connection with the original microstructural characteristics of the steel and the induced grain boundary decohesion of the surface layer. The scope and character of the damage are analysed and the results verified by analysing the actual operating damage to the weldment.

Findings

A degradation mechanism of stabilised corrosion‐resistant steel 1.4510 is induced that is associated with destabilisation of titanium phases. The importance is demonstrated of ensuring that a protective atmosphere is maintained during welding, and various phase changes in the surface layers are identified that can delimit the use of appropriate post‐weld passivation procedures.

Practical implications

Identification of the mechanism underlying the damage to the surface layer in welded stabilised ferritic steel will find application in development of welding technology, specifically in designing a technology process and subsequent surface treatment.

Originality/value

The results bring new knowledge of material response of steel 1.4510 under specific material processing conditions; a destabilisation mechanism related to precipitation of several titanium‐containing phases is identified. The result enables the fatigue limit of the welded material as a function of the welding technology employed, which offers increased service life under specific application conditions.
The corrosion of silver in indoor conditions of an assembly process in the microelectronics industry
Authors: Vargas O.L. , Valdez S.B. , Veleva M.L. , Zlatev K.R. , Schorr W.M. , Terrazas G.J.
Published: June 2009

Purpose

The purpose of this paper is to evaluate the corrosion of silver due to hydrogen sulphide pollutant in indoor conditions at a microelectronics plant located in Mexicali, Baja California, a semi‐arid zone in the northwest of Mexico.

Design/methodology/approach

Silver coupons and silver plated on to copper‐lead frames are exposed in the assembly process building of a microelectronics company during a period of 60 days and also in a sheltered test chamber that simulates indoor conditions with ambient concentrations of atmospheric pollutants, temperature and relative humidity (rH). Other exposures are made in the test chamber to study the corrosion behaviour of silver coupons over a duration of 24 months. The corrosion products were analysed using the Scanning Electron Microscope (SEM) and Energy Dispersive X‐ray Spectroscopy (EDS). Corrosion rates were measured by Quartz Crystal Microbalance (QCM) under laboratory‐controlled conditions.

Findings

The presence of silver sulphide corrosion products, dendrites and whiskers is observed on the exposed samples using SEM and EDS analysis.

Practical implications

The paper is designed to establish whether the company, where the exposure is taking place, constituted an indoor environment with outdoor hydrogen sulphide pollutant in sufficient concentration to induce silver corrosion.

Originality/value

The methodology used in this work can be applied to study the indoor corrosion behaviour of other metals, which will be of interest to the microelectronics industry.
Preparation of non‐chromium polymer films on zinc for corrosion protection due to a compound effect between silane and cerium salt
Authors: Fang Da‐jing , Mao Xu‐hui , Zhang Ye‐ming , Chen Zhi‐liang , Liu Min , Gan Fu‐xing
Published: June 2009

Purpose

The purpose of this paper is to study the compound effect between silane and cerium salts in the passivation process of chemical conversion treatment of zinc.

Design/methodology/approach

Chemical conversion treatment using 3‐Glycidoxypropyltrimethoxysilane on zinc is investigated as an alternative treatment to chromate conversion. The surface chemistry of the silane‐treated samples is investigated with mass change measurements, polarization curves, electrochemical impedance spectroscopy (EIS) and the salt spray tests (SST). The surface morphology of samples was studied using a scanning electron microscope.

Findings

The polarization curves, EIS and SST data are in agreement. On the surface of zinc, the silane formed a compound with the cerium, thus enhancing the adhesion and corrosion resistance of the polymer film.

Originality/value

There have been few reports on the compound effects of silanes and cerium salts in the passivation process. The mechanism of this compound effect may be due to the ability of Ce3 + ions to gain access to the interface through tiny cracks or micropores in the cross‐linking structure of GPS polymer films on zinc, and the subsequent oxidation of Ce3 + to Ce4 + by H2O2 may result in a barrier effect between the electrolyte and the metallic substrate.
Inhibition of the corrosion of cold rolled steel in hydrochloric acid solution by Tween‐40
Authors: Xianghong Li , Shuduan Deng , Hui Fu , Taohong Li , Guannan Mu
Published: June 2009

Purpose

The purpose of this paper is to study the inhibition effect of Tween‐40 on the corrosion of cold rolled steel (CRS) in 1.0‐8.0 M HCl over the temperature range of 20‐50°C. It also aims to make an attempt to correlate both thermodynamic parameters and kinetic parameters with the inhibition effect.

Design/methodology/approach

The inhibition efficiencies of Tween‐40 are investigated by weight loss and potentiodynamic polarization methods.

Findings

Tween‐40 acts as a good inhibitor in 1.0 M HCl, and inhibition efficiency increases with the inhibitor concentration, while it decreases with HCl concentration and temperature. The adsorption of inhibitor on the CRS surface obeys the Langmuir adsorption isotherm equation. The inhibition effect is satisfactorily explained by both thermodynamic and kinetic parameters. Polarization curves show that Tween‐40 is a mixed‐type inhibitor in hydrochloric acid.

Originality/value

The experimental data have been treated with adsorption theory and kinetic equations successfully. Both the thermodynamic and kinetic parameters can be obtained, and used in explaining the inhibition effect satisfactorily.
Ethnic wage inequality in Vietnam
Authors: Pham Hung T. , Reilly Barry
Published: June 2009

Purpose

This paper seeks to complement earlier studies on ethnic minority underdevelopment in Vietnam by empirically examining the ethnic wage gap for the wage employed in the Vietnamese labour market, using data from a large‐scale household survey conducted in 2002.

Design/methodology/approach

The paper uses the “index number” decomposition method suggested by Oaxaca to decompose the ethnic wage gap into treatment and endowment effects at both the mean and selected quantiles of the conditional wage distribution.

Findings

The results confirm the existence of an ethnic wage gap in the labour market, though the gap is found to be substantially narrower than the ethnic gap detected using household living standard measures for Vietnam. Decomposition results reveal that the ethnic wage gap is largely attributable to differentials in the returns to endowments, a finding invariant whether the mean or selected quantiles of the conditional wage distribution are examined.

Research limitations/implications

In the absence of feasible alternatives, the paper uses an ad hoc procedure to correct for selectivity into wage employment for the quantile regression models. In addition, due to data constraints with regard to earnings, the paper does not examine the ethnic wage gap for the self‐employed.

Originality/value

The paper is the first to analyse the ethnic wage gap in the Vietnam labour market and one of the few to examine ethnic pay differentials at selected points of the conditional wage distribution using quantile regression analysis.
Inside the “black box” and “HRM”
Authors: Edgar Fiona , Geare Alan
Published: June 2009

Purpose

This paper has two objectives. The first is to see whether “shared values” is an important intermediary, or part of the “black box” (along with organisational commitment and job satisfaction), between HRM practices and firm performance. The second is to assess whether the use of multiple levels of respondents produces different results compared with the usual practice of using senior HRM managers or, in lieu, another senior manager.

Design/methodology/approach

A survey methodology is used to obtain perceptual data on HRM practices and a variety of work‐related attitudes. The sample comprises managers, supervisors and workers from 27 New Zealand firms. Statistical analysis, using SPSS, was performed at the firm and individual level.

Findings

At group‐level there are wide differences in attitudes towards HRM activities. The desirability of using as many respondents as possible, and also respondents from different levels within organisations, was confirmed. “Shared values” is also deemed worthy of inclusion in the “black box” as it relates significantly to perceptions of HRM practices. However, organisational commitment and job satisfaction appear to have a stronger role.

Research limitations/implications

Current writings suggest that certain HRM practices can foster a system of shared values amongst the workforce. The study finds this indeed to be the case at the individual level. However, the supposition that a shared value system significantly contributes to the promotion of other desirable attitudinal outcomes has not been supported by the study's findings. A limitation of the study is that it did not explore the HRM‐firm performance relationship in its entirety. Further research exploring all linkages in this relationship is now required.

Practical implications

The paper concludes that practitioners should be wary of pursuing an agenda that sees the development of a shared value system as the key to superior firm performance. Instead, it is suggested that the values of the organisation should be considered as the foundation from which a set of mutually reinforcing and supportive HRM practices is developed.

Originality/value

The paper provides much needed empirical data on shared values and their role in the HRM‐performance relationship.