bluuebunny/crossref_metadata_2025 huggingface dataset:
A hidden Ising model for ChIP-chip data analysis
Authors: Mo Qianxing , Liang Faming
Published: January 2010

Motivation: Chromatin immunoprecipitation (ChIP) coupled with tiling microarray (chip) experiments have been used in a wide range of biological studies such as identification of transcription factor binding sites and investigation of DNA methylation and histone modification. Hidden Markov models are widely used to model the spatial dependency of ChIP-chip data. However, parameter estimation for these models is typically either heuristic or suboptimal, leading to inconsistencies in their applications. To overcome this limitation and to develop an efficient software, we propose a hidden ferromagnetic Ising model for ChIP-chip data analysis.

Results: We have developed a simple, but powerful Bayesian hierarchical model for ChIP-chip data via a hidden Ising model. Metropolis within Gibbs sampling algorithm is used to simulate from the posterior distribution of the model parameters. The proposed model naturally incorporates the spatial dependency of the data, and can be used to analyze data with various genomic resolutions and sample sizes. We illustrate the method using three publicly available datasets and various simulated datasets, and compare it with three closely related methods, namely TileMap HMM, tileHMM and BAC. We find that our method performs as well as TileMap HMM and BAC for the high-resolution data from Affymetrix platform, but significantly outperforms the other three methods for the low-resolution data from Agilent platform. Compared with the BAC method which also involves MCMC simulations, our method is computationally much more efficient.

Availability: A software called iChip is freely available at http://www.bioconductor.org/.

Contact:  moq@mskcc.org
Antidiabetic Activities ofAbutilon indicum(L.) Sweet Are Mediated by Enhancement of Adipocyte Differentiation and Activation of the GLUT1 Promoter
Authors: Krisanapun Chutwadee , Lee Seong-Ho , Peungvicha Penchom , Temsiririrkkul Rungravi , Baek Seung Joon
Published: January 2010

Abutilon indicum(L.) Sweet is an Asian phytomedicine traditionally used to treat several disorders, including diabetes mellitus. However, molecular mechanisms supporting the antidiabetic effect ofA. indicumL. remain unknown. The aim of this study was to evaluate whether extract ofA. indicumL. improves insulin sensitivity. First, we observed the antidiabetic activity of aqueous extract of the entire plant (leaves, twigs and roots) ofA. indicumL. on postprandial plasma glucose in diabetic rats. The subsequent experiments revealed that butanol fractions of the extract bind to PPARγand activate 3T3‐L1 differentiation. To measure glucose uptake enhanced by insulin‐like activity, we used rat diaphragm incubated with various concentrations of the crude extract and found that the extract enhances glucose consumption in the incubated solution. Our data also indicate that the crude extract and the fractions (water and butanol) did not affect the activity of kinases involved in Akt and GSK‐3βpathways; however, the reporter assay showed that the crude extract could activate glucose transporter 1 (GLUT1) promoter activity. These results suggest that the extract fromA. indicumL. may be beneficial for reducing insulin resistance through its potency in regulating adipocyte differentiation through PPARγagonist activity, and increasing glucose utilization via GLUT1.
Prevalence and pharmacological treatment of left‐ventricular dysfunction in patients undergoing vascular surgery
Authors: Flu Willem‐Jan , van Kuijk Jan‐Peter , Galal Wael , Kuiper Ruud , van de Ven Louis L. , Verhagen Hence J.M. , Bax Jeroen J. , Poldermans Don
Published: January 2010

Aims

This study evaluated the prevalence of left‐ventricular (LV) dysfunction in vascular surgery patients and pharmacological treatment, according ESC guidelines.

Methods and results

Echocardiography was performed pre‐operatively in 1005 consecutive patients. Left ventricular ejection fraction (LVEF) ≤50% defined systolic LV dysfunction. Diastolic LV dysfunction was diagnosed based on E/A‐ratio, pulmonary vein flow, and deceleration time. Optimal pharmacological treatment to improve LV function was considered as: (i) angiotensin‐blocking agent (ACE‐I/ARB) in patients with LVEF ≤40%; (ii) ACE‐I/ARB and β‐blocker in patients with LVEF ≤40% + heart failure symptoms or previous myocardial infarction; and (iii) a diuretic in patients with symptomatic heart failure, regardless of LVEF. Left‐ventricular dysfunction was present in 506 patients (50%), of whom 209 (41%) had asymptomatic diastolic LV dysfunction, 194 (39%) had asymptomatic systolic LV dysfunction, and 103 (20%) had symptomatic heart failure. Treatment with ACE‐I/ARB and/or β‐blocker could be initiated/improved in 67 (34%) of the 199 patients with (a)symptomatic LVEF ≤40%. A diuretic could be initiated in 32 patients (31%) with symptomatic heart failure (regardless of LVEF).

Conclusions

This study demonstrates a high prevalence of LV dysfunction in vascular surgery patients and under‐utilization of ESC recommended pharmacological treatment. Standard pre‐operative evaluation of LV function could be argued based on our results to reduce this observed care gap.
Long‐term association between self‐reported signs and symptoms and heart failure hospitalizations: the Atherosclerosis Risk In Communities (ARIC) Study
Authors: Avery Christy L. , Mills Katherine T. , Chambless Lloyd E. , Chang Patricia P. , Folsom Aaron R. , Mosley Thomas H. , Ni Hanyu , Rosamond Wayne D. , Wagenknecht Lynne , Wood Joy , Heiss Gerardo
Published: January 2010

Aims

Although studies of the accuracy of heart failure (HF) classification scoring systems are available, few have examined their performance when restricted to self‐reported items.

Methods and results

We evaluated the association between a simplified version of the Gothenburg score, a validated HF score comprised of cardiac and pulmonary signs and symptoms and medication use, and incident HF hospitalizations in 15 430 Atherosclerosis Risk in Communities (ARIC) Study participants. Gothenburg scores (range: 0–3) were constructed using self‐reported items obtained at study baseline (1987–89). Incident HF hospitalization over 14.7 years of follow‐up was defined as the first identified hospitalization with an ICD‐9 discharge code of 428 (n = 1668). Self‐reported Gothenburg scores demonstrated very high agreement with the original metric comprised of self‐reported and clinical measures and were directly associated with incident HF hospitalizations: [score = 1: hazard rate ratio (HRR) = 1.23 (1.07–1.42); score = 2: HRR = 2.17 (1.92–2.43); score = 3: HRR = 3.98 (3.37–4.70)].

Conclusion

In a population‐based cohort, self‐reported Gothenburg criteria items were associated with hospitalized HF over a prolonged follow‐up time. The association was also consistent across groups defined by sex and race, suggesting that this simple score deserves further study as a screening tool for the identification of individuals at high risk of HF in resource‐limited settings.
Haemodynamic effects of acute intravenous metoprolol in apical ballooning syndrome with dynamic left ventricular outflow tract obstruction
Authors: Migliore Federico , Bilato Claudio , Isabella Gianbattista , Iliceto Sabino , Tarantini Giuseppe
Published: January 2010

Takotsubo syndrome, also called apical ballooning syndrome, is a clinical entity characterized by transient hypokinesis, akinesis, or dyskinesis of the left ventricular mid‐segments with or without apical involvement, and without obstructive coronary lesions. The contemporary presence of left ventricular outflow tract obstruction (LVOTO), systolic anterior motion of the anterior mitral leaflet, and acute mitral regurgitation might explain the worsening of the heart failure or the occurrence of cardiogenic shock in some patients with apical ballooning syndrome. The use of β‐blockers should improve the LVOTO gradient by reducing basal hypercontractility, increasing left ventricular filling and size, and reducing heart rate. However, clear evidence of the direct haemodynamic effects of β‐blockers is still lacking. We present a case of apical ballooning syndrome complicated by dynamic LVOTO, treated with metoprolol.
The predictive value of stable precursor fragments of vasoactive peptides in patients with chronic heart failure: data from the GISSI‐heart failure (GISSI‐HF) trial
Authors: Masson Serge , Latini Roberto , Carbonieri Emanuele , Moretti Luciano , Rossi Maria Grazia , Ciricugno Santo , Milani Valentina , Marchioli Roberto , Struck Joachim , Bergmann Andreas , Maggioni Aldo P. , Tognoni Gianni , Tavazzi Luigi ,   on behalf of the GISSI‐HF Investigators
Published: January 2010

Aims

Though various neurohormonal systems are concurrently activated during heart failure (HF), their biological effectors are not always easy to measure due to their short life in vivo, instability in biological samples, or very low concentrations. We measured the plasma concentrations of four stable precursor fragments of neurohormonal systems in patients with chronic HF and evaluated their relationship with outcome.

Methods and results

This study was performed in 1237 patients with chronic and stable HF enrolled in the GISSI‐heart failure trial (GISSI‐HF). The following four precursor fragments, mid‐regional pro‐atrial natriuretic peptide (MR‐proANP), mid‐regional pro‐adrenomedullin (MR‐proADM), C‐terminal pro‐endothelin‐1 (CT‐proET‐1) and C‐terminal pro‐vasopressin (CT‐proAVP or copeptin), were measured at randomization and after 3 months. Baseline concentrations were independent predictors of clinical outcome (median follow‐up 3.9 years). The addition of MR‐proANP improved net reclassification for mortality when added to multivariable models based on clinical risk factors alone [net reclassification improvement (NRI) = 0.12, P = 0.0007] or together with NT‐proBNP (NRI = 0.06, P = 0.01). Changes in MR‐proANP concentrations were related to mortality [HR (95% CI) 1.38 (0.99–1.93), P = 0.0614 and 1.58 (1.13–2.21), P = 0.0078 in the middle and highest vs. lowest tertiles], while changes in the other markers were not.

Conclusion

In patients with chronic and stable HF enrolled in a multicentre, randomized, clinical trial, measurement of stable precursor fragments of vasoactive peptides provided prognostic information independent of natriuretic peptides which are currently the best biomarkers for risk stratification.
Proportionally Difficult: Testing for Nonproportional Hazards in Cox Models
Authors: Keele Luke
Published: January 2010

The Cox proportional hazards model is widely used to model durations in the social sciences. Although this model allows analysts to forgo choices about the form of the hazard, it demands careful attention to the proportional hazards assumption. To this end, a standard diagnostic method has been developed to test this assumption. I argue that the standard test for nonproportional hazards has been misunderstood in current practice. This test detects a variety of specification errors, and these specification errors must be corrected before one can correctly diagnose nonproportionality. In particular, unmodeled nonlinearity can appear as a violation of the proportional hazard assumption for the Cox model. Using both simulation and empirical examples, I demonstrate how an analyst might be led astray by incorrectly applying the nonproportionality test.
Switchable genetic oscillator operating in quasi-stable mode
Authors: Strelkowa Natalja , Barahona Mauricio
Published: January 2010

Ring topologies of repressing genes have qualitatively different long-term dynamics if the number of genes is odd (they oscillate) or even (they exhibit bistability). However, these attractors may not fully explain the observed behaviour in transient and stochastic environments such as the cell. We show here that even repressilators possess quasi-stable, travelling wave periodic solutions that are reachable, long-lived and robust to parameter changes. These solutions underlie the sustained oscillations observed in even rings in the stochastic regime, even if these circuits are expected to behave as switches. The existence of such solutions can also be exploited for control purposes: operation of the system around the quasi-stable orbit allows us to turn on and off the oscillations reliably and on demand. We illustrate these ideas with a simple protocol based on optical interference that can induce oscillations robustly both in the stochastic and deterministic regimes.
Alkaliphilus halophilus sp. nov., a strictly anaerobic and halophilic bacterium isolated from a saline lake, and emended description of the genus Alkaliphilus
Authors: Wu Xiao-Yue , Shi Kong-Lan , Xu Xue-Wei , Wu Min , Oren Aharon , Zhu Xu-Fen
Published: January 2010

A novel strictly anaerobic, halophilic and fermentative strain, designated E2RT, was isolated from sediments of Xiaokule salt lake in Xinjiang Province, China. Cells were straight to slightly curved, Gram-stain-positive rods that were motile by means of flagella and formed endospores. Strain E2RT was moderately halophilic and grew optimally in the presence of 7.5 % NaCl, at pH 8.0 and at 32 °C. Substrates used include yeast extract, Casamino acids, tryptone, fructose, sucrose, xylose, ribose, lactate and tartrate. Thiosulfate could be used as an accessory electron acceptor and stimulated growth. The main fermentation products from fructose were formate and acetate. The predominant fatty acids were iso-C15 : 0, iso-C15 : 1 F and iso-C13 : 0. 16S rRNA gene sequence analyses revealed that strain E2RT was related most closely to members of the genus Alkaliphilus (95.5–91.1 % similarity). The G+C content of strain E2RT was 28.5 mol%. Strain E2RT could be differentiated from its closest relatives based on its halophilic nature and its lower DNA G+C content. It could also be differentiated based on its substrate utilization pattern and relatively high levels of iso-C15 : 0. On the basis of these data, strain E2RT is considered to represent a novel species of the genus Alkaliphilus, for which the name Alkaliphilus halophilus sp. nov. is proposed. The type strain is E2RT (=CGMCC 1.5124T =JCM 16124T). An emended description of the genus Alkaliphilus is also provided.
Cohnella xylanilytica sp. nov. and Cohnella terrae sp. nov., xylanolytic bacteria from soil
Authors: Khianngam Saowapar , Tanasupawat Somboon , Akaracharanya Ancharida , Kim Kwang Kyu , Lee Keun Chul , Lee Jung-Sook
Published: January 2010

Two xylan-degrading bacteria, strains MX15-2T and MX21-2T, were isolated from soils collected in Nan province, Thailand. Cells were Gram-reaction-positive, facultatively anaerobic, spore-forming and rod-shaped. They contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The major menaquinone was MK-7. iso-C16 : 0 and anteiso-C15 : 0 were the predominant cellular fatty acids. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and lysyl-phosphatidylglycerol were the major polar lipids. The genomic DNA G+C contents of strains MX15-2T and MX21-2T were 63.0 and 65.1 mol%, respectively. Phylogenetic analysis using 16S rRNA gene sequences showed that strains MX15-2T and MX21-2T were affiliated with the genus Cohnella and were closely related to Cohnella thermotolerans CCUG 47242T, with 96.5 and 95.6 % sequence similarity, respectively. The strains could be clearly distinguished from each other and from all known species of the genus Cohnella based on their physiological and biochemical characteristics as well as their phylogenetic positions and levels of DNA–DNA hybridization. Therefore, these two strains represent novel species of the genus Cohnella, for which the names Cohnella xylanilytica sp. nov. (type strain MX15-2T =KCTC 22294T =PCU 309T =TISTR 1891T) and Cohnella terrae sp. nov. (type strain MX21-2T =KCTC 22295T =PCU 310T =TISTR 1892T) are proposed.
Lactobacillus odoratitofui sp. nov., isolated from stinky tofu brine
Authors: Chao Shiou-Huei , Sasamoto Masae , Kudo Yuko , Fujimoto Junji , Tsai Ying-Chieh , Watanabe Koichi
Published: January 2010

Three Gram-positive-staining strains isolated from fermented stinky tofu brine were rod-shaped, non-motile, asporogenous, facultatively anaerobic, heterofermentative and did not exhibit catalase activity. Comparative analyses of 16S rRNA, rpoA and pheS gene sequences demonstrated that the novel strains were members of the genus Lactobacillus. On the basis of 16S rRNA gene sequence similarity, the type strains of Lactobacillus collinoides (98.6 %), Lactobacillus paracollinoides (98.6 %) and Lactobacillus similis (99.6 %) were the closest neighbours. However, DNA–DNA reassociation values with these strains were less than 10 %. The phenotypic and genotypic features demonstrated that these isolates represent a novel species of the genus Lactobacillus, for which the name Lactobacillus odoratitofui sp. nov. is proposed. The type strain is YIT 11304T (=JCM 15043T =BCRC 17810T =DSM 19909T).
Phylogenetic analysis and delineation of phytoplasmas based on secY gene sequences
Authors: Lee I.-M. , Bottner-Parker K. D. , Zhao Y. , Davis R. E. , Harrison N. A.
Published: January 2010

The secY gene sequence is more variable than that of the 16S rRNA gene. Comparative phylogenetic analyses with 16S rRNA and secY gene sequences from 80 and 83 phytoplasma strains, respectively, were performed to assess the efficacy of these sequences for delineating phytoplasma strains within each 16Sr group. The phylogenetic interrelatedness among phytoplasma taxa inferred by secY gene-based phylogeny was nearly congruent with that inferred by 16S rRNA gene-based phylogeny. Phylogenetic analysis based on the secY gene permitted finer differentiation of phytoplasma strains, however. The secY gene-based phylogeny not only readily resolved 16Sr subgroups within a given 16Sr group, but also delineated distinct lineages irresolvable by 16S rRNA gene-based phylogeny. Such high resolving power makes the secY gene a more useful genetic marker than the 16S rRNA gene for finer differentiation of closely related phytoplasma strains based on RFLP analysis with selected restriction enzymes. Such strains were readily identified by collective secY RFLP patterns. The genetic interrelationships among these strains were determined by pattern similarity coefficients, which coincided with delineations by phylogenetic analysis. This study also revealed two heterogeneous spc operons present in the phytoplasma clade. This latter finding may have significant implications for phytoplasma evolution.
Methanocella arvoryzae sp. nov., a hydrogenotrophic methanogen isolated from rice field soil
Authors: Sakai Sanae , Conrad Ralf , Liesack Werner , Imachi Hiroyuki
Published: January 2010

A novel hydrogenotrophic methanogen, designated strain MRE50T, was isolated from a methanogenic consortium, which was originally established from an Italian rice field soil. Cells were non-motile rods, 1.3–2.8 μm long and 0.4–0.7 μm wide. Coccoid cells were also observed in cultures at the late-exponential phase of growth. Strain MRE50Tgrew at 37–55 °C (optimally at 45 °C), at pH 6–7.8 (optimally at pH 7.0) and in the presence of 0–20 g NaCl l−1. The isolate utilized H2/CO2and formate for growth and methane production. Phylogenetic analyses of the 16S rRNA gene and the methanogen-specific marker genemcrAshowed that strain MRE50Tis affiliated with the orderMethanocellales, previously known as uncultured archaeal group Rice Cluster I. Based on both 16S rRNA gene andmcrAgene sequences, strain MRE50Twas related most closely toMethanocella paludicolaSANAET. Levels of sequence similarity were 92.5 and 86.1 %, respectively, indicating that strains MRE50TandMethanocella paludicolaSANAETrepresent different species within the genusMethanocella. In addition, although these strains shared phenotypic properties including cell morphology and substrate utilization, they differed with respect to susceptibility to antibiotics, and temperature and NaCl ranges for growth. Given the phenotypic differences and the distinct phylogenetic placement of the new isolate relative to the type species of the genusMethanocella, strain MRE50Tis considered to represent a novel species of the genusMethanocella, for which the nameMethanocella arvoryzaesp. nov. is proposed. The type strain is MRE50T(=NBRC 105507T=DSM 22066T).
Paracoccus fistulariae sp. nov., a lipolytic bacterium isolated from bluespotted cornetfish, Fistularia commersonii
Authors: Kim Young-Ok , Kong Hee Jeong , Park Sooyeon , Kang So-Jung , Kim Kyung-Kil , Moon Dae Yeon , Oh Tae-Kwang , Yoon Jung-Hoon
Published: January 2010

A Gram-stain-negative, non-motile, non-spore-forming and short rod- or rod-shaped bacterial strain, designated 22-5T, was isolated from a bluespotted cornetfish, Fistularia commersonii, and subjected to taxonomic study. Strain 22-5T grew optimally at 30 °C and in the presence of 2–5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain 22-5T belonged to the genus Paracoccus and joined the cluster comprising Paracoccus homiensis DD-R11T and Paracoccus zeaxanthinifaciens ATCC 21588T, with which strain 22-5T exhibited 97.4 and 96.9 % 16S rRNA gene sequence similarity, respectively. Strain 22-5T exhibited 94.0–96.6 % 16S rRNA gene sequence similarity with the other type strains of species of the genus Paracoccus. Strain 22-5T contained Q-10 as the predominant menaquinone and C18 : 1
ω7c as the predominant fatty acid. In this study, P. zeaxanthinifaciens KCTC 22688T also contained Q-10 as the predominant isoprenoid quinone. The DNA G+C content of strain 22-5T was 63.6 mol%. Strain 22-5T exhibited 44 and 32 % DNA–DNA relatedness to P. homiensis KACC 11518T and P. zeaxanthinifaciens KCTC 22688T, respectively. On the basis of phenotypic, phylogenetic and genetic data, strain 22-5T is considered to represent a novel species of the genus Paracoccus, for which the name Paracoccus fistulariae sp. nov. is proposed. The type strain is 22-5T (=KCTC 22803T =CCUG 58401T).
MCA1 and MCA2 That Mediate Ca2+ Uptake Have Distinct and Overlapping Roles in Arabidopsis
Authors: Yamanaka Takuya , Nakagawa Yuko , Mori Kendo , Nakano Masataka , Imamura Tomomi , Kataoka Hajime , Terashima Asuka , Iida Kazuko , Kojima Itaru , Katagiri Takeshi , Shinozaki Kazuo , Iida Hidetoshi
Published: January 2010

Ca2+ is important for plant growth and development as a nutrient and a second messenger. However, the molecular nature and roles of Ca2+-permeable channels or transporters involved in Ca2+ uptake in roots are largely unknown. We recently identified a candidate for the Ca2+-permeable mechanosensitive channel in Arabidopsis (Arabidopsis thaliana), named MCA1. Here, we investigated the only paralog of MCA1 in Arabidopsis, MCA2. cDNA of MCA2 complemented a Ca2+ uptake deficiency in yeast cells lacking a Ca2+ channel composed of Mid1 and Cch1. Reverse transcription polymerase chain reaction analysis indicated that MCA2 was expressed in leaves, flowers, roots, siliques, and stems, and histochemical observation showed that an MCA2 promoter::GUS fusion reporter gene was universally expressed in 10-d-old seedlings with some exceptions: it was relatively highly expressed in vascular tissues and undetectable in the cap and the elongation zone of the primary root. mca2-null plants were normal in growth and morphology. In addition, the primary root of mca2-null seedlings was able to normally sense the hardness of agar medium, unlike that of mca1-null or mca1-null mca2-null seedlings, as revealed by the two-phase agar method. Ca2+ uptake activity was lower in the roots of mca2-null plants than those of wild-type plants. Finally, growth of mca1-null mca2-null plants was more retarded at a high concentration of Mg2+ added to medium compared with that of mca1-null and mca2-null single mutants and wild-type plants. These results suggest that the MCA2 protein has a distinct role in Ca2+ uptake in roots and an overlapping role with MCA1 in plant growth.
Photosynthetic Performance and Fertility Are Repressed in GmAOX2b Antisense Soybean
Authors: Chai Tsun-Thai , Simmonds Daina , Day David A. , Colmer Timothy D. , Finnegan Patrick M.
Published: January 2010

The alternative oxidase (AOX) is a cyanide-resistant oxidase that provides an alternative outlet for electrons from the respiratory electron transport chain embedded in the inner membrane of plant mitochondria. Examination of soybean (Glycine max) plants carrying a GmAOX2b antisense gene showed AOX to have a central role in reproductive development and fecundity. In three independently transformed antisense lines, seed set was reduced by 16% to 43%, whereas ovule abortion increased by 1.2- to 1.7-fold when compared with nontransgenic transformation control plants. Reduced fecundity was associated with reductions in whole leaf cyanide-resistant, salicylhydroxamic acid-sensitive respiration and net photosynthesis, but there was no change in total respiration in the dark. The frequency of potential fertilization events was reduced by at least one-third in the antisense plants as a likely consequence of prefertilization defects. Pistils of the antisense plants contained a higher proportion of immature-sized, nonfertile embryo sacs compared with nontransgenic control plants. Increased rates of pollen abortion in vivo and reduced rates of pollen germination in vitro suggested that the antisense gene compromised pollen development and function. Reciprocal crosses between antisense and nontransgenic plants revealed that pollen produced by antisense plants was less active in fertilization. Taken together, the results presented here indicate that AOX expression has an important role in determining normal gametophyte development and function.
Genome-Wide Analysis of Ethylene-Responsive Element Binding Factor-Associated Amphiphilic Repression Motif-Containing Transcriptional Regulators in Arabidopsis
Authors: Kagale Sateesh , Links Matthew G. , Rozwadowski Kevin
Published: January 2010

The ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motif is a transcriptional regulatory motif identified in members of the ethylene-responsive element binding factor, C2H2, and auxin/indole-3-acetic acid families of transcriptional regulators. Sequence comparison of the core EAR motif sites from these proteins revealed two distinct conservation patterns: LxLxL and DLNxxP. Proteins containing these motifs play key roles in diverse biological functions by negatively regulating genes involved in developmental, hormonal, and stress signaling pathways. Through a genome-wide bioinformatics analysis, we have identified the complete repertoire of the EAR repressome in Arabidopsis (Arabidopsis thaliana) comprising 219 proteins belonging to 21 different transcriptional regulator families. Approximately 72% of these proteins contain a LxLxL type of EAR motif, 22% contain a DLNxxP type of EAR motif, and the remaining 6% have a motif where LxLxL and DLNxxP are overlapping. Published in vitro and in planta investigations support approximately 40% of these proteins functioning as negative regulators of gene expression. Comparative sequence analysis of EAR motif sites and adjoining regions has identified additional preferred residues and potential posttranslational modification sites that may influence the functionality of the EAR motif. Homology searches against protein databases of poplar (Populus trichocarpa), grapevine (Vitis vinifera), rice (Oryza sativa), and sorghum (Sorghum bicolor) revealed that the EAR motif is conserved across these diverse plant species. This genome-wide analysis represents the most extensive survey of EAR motif-containing proteins in Arabidopsis to date and provides a resource enabling investigations into their biological roles and the mechanism of EAR motif-mediated transcriptional regulation.
Cross-Kingdom Comparison of Transcriptomic Adjustments to Low-Oxygen Stress Highlights Conserved and Plant-Specific Responses
Authors: Mustroph Angelika , Lee Seung Cho , Oosumi Teruko , Zanetti Maria Eugenia , Yang Huijun , Ma Kelvin , Yaghoubi-Masihi Arbi , Fukao Takeshi , Bailey-Serres Julia
Published: January 2010

High-throughput technology has facilitated genome-scale analyses of transcriptomic adjustments in response to environmental perturbations with an oxygen deprivation component, such as transient hypoxia or anoxia, root waterlogging, or complete submergence. We showed previously that Arabidopsis (Arabidopsis thaliana) seedlings elevate the levels of hundreds of transcripts, including a core group of 49 genes that are prioritized for translation across cell types of both shoots and roots. To recognize low-oxygen responses that are evolutionarily conserved versus species specific, we compared the transcriptomic reconfiguration in 21 organisms from four kingdoms (Plantae, Animalia, Fungi, and Bacteria). Sorting of organism proteomes into clusters of putative orthologs identified broadly conserved responses associated with glycolysis, fermentation, alternative respiration, metabolite transport, reactive oxygen species amelioration, chaperone activity, and ribosome biogenesis. Differentially regulated genes involved in signaling and transcriptional regulation were poorly conserved across kingdoms. Strikingly, nearly half of the induced mRNAs of Arabidopsis seedlings encode proteins of unknown function, of which over 40% had up-regulated orthologs in poplar (Populus trichocarpa), rice (Oryza sativa), or Chlamydomonas reinhardtii. Sixteen HYPOXIA-RESPONSIVE UNKNOWN PROTEIN (HUP) genes, including four that are Arabidopsis specific, were ectopically overexpressed and evaluated for their effect on seedling tolerance to oxygen deprivation. This allowed the identification of HUPs coregulated with genes associated with anaerobic metabolism and other processes that significantly enhance or reduce stress survival when ectopically overexpressed. These findings illuminate both broadly conserved and plant-specific low-oxygen stress responses and confirm that plant-specific HUPs with limited phylogenetic distribution influence low-oxygen stress endurance.
The Significance of Protein Maturation by Plastidic Type I Signal Peptidase 1 for Thylakoid Development in Arabidopsis Chloroplasts
Authors: Shipman-Roston Rebecca L. , Ruppel Nicholas J. , Damoc Catalina , Phinney Brett S. , Inoue Kentaro
Published: January 2010

Thylakoids are the chloroplast internal membrane systems that house light-harvesting and electron transport reactions. Despite the important functions and well-studied constituents of thylakoids, the molecular mechanism of their development remains largely elusive. A recent genetic study has demonstrated that plastidic type I signal peptidase 1 (Plsp1) is vital for proper thylakoid development in Arabidopsis (Arabidopsis thaliana) chloroplasts. Plsp1 was also shown to be necessary for processing of an envelope protein, Toc75, and a thylakoid lumenal protein, OE33; however, the relevance of the protein maturation in both of the two distinct subcompartments for proper chloroplast development remained unknown. Here, we conducted an extensive analysis of the plsp1-null mutant to address the significance of lumenal protein maturation in thylakoid development. Plastids that lack Plsp1 were found to accumulate vesicles of variable sizes in the stroma. Analyses of the mutant plastids revealed that the lack of Plsp1 causes a reduction in accumulation of thylakoid proteins and that Plsp1 is involved in maturation of two additional lumenal proteins, OE23 and plastocyanin. Further immunoblotting and electron microscopy immunolocalization studies showed that OE33 associates with the stromal vesicles of the mutant plastids. Finally, we used a genetic complementation system to demonstrate that accumulation of improperly processed forms of Toc75 in the plastid envelope does not disrupt normal plant development. These results suggest that proper maturation of lumenal proteins may be a key process for correct assembly of thylakoids.
MRL1, a Conserved Pentatricopeptide Repeat Protein, Is Required for Stabilization of rbcL mRNA in Chlamydomonas and Arabidopsis
Authors: Johnson Xenie , Wostrikoff Katia , Finazzi Giovanni , Kuras Richard , Schwarz Christian , Bujaldon Sandrine , Nickelsen Joerg , Stern David B. , Wollman Francis-André , Vallon Olivier
Published: January 2010

We identify and functionally characterize MRL1, a conserved nuclear-encoded regulator of the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase. The nonphotosynthetic mrl1 mutant of Chlamydomonas reinhardtii lacks ribulose-1,5-bisphosphate carboxylase/oxygenase, and the resulting block in electron transfer is partially compensated by redirecting electrons toward molecular oxygen via the Mehler reaction. This allows continued electron flow and constitutive nonphotochemical quenching, enhancing cell survival during illumination in spite of photosystem II and photosystem I photoinhibition. The mrl1 mutant transcribes rbcL normally, but the mRNA is unstable. The molecular target of MRL1 is the 5 ′ untranslated region of rbcL. MRL1 is located in the chloroplast stroma, in a high molecular mass complex. Treatment with RNase or deletion of the rbcL gene induces a shift of the complex toward lower molecular mass fractions. MRL1 is well conserved throughout the green lineage, much more so than the 10 other pentatricopeptide repeat proteins found in Chlamydomonas. Depending upon the organism, MRL1 contains 11 to 14 pentatricopeptide repeats followed by a novel MRL1-C domain. In Arabidopsis thaliana, MRL1 also acts on rbcL and is necessary for the production/stabilization of the processed transcript, presumably because it acts as a barrier to 5 ′ >3 ′ degradation. The Arabidopsis  mrl1 mutant retains normal levels of the primary transcript and full photosynthetic capacity.
The Plastid Isoform of Triose Phosphate Isomerase Is Required for the Postgerminative Transition from Heterotrophic to Autotrophic Growth in Arabidopsis
Authors: Chen Mingjie , Thelen Jay J.
Published: January 2010

During postgerminative seedling establishment, reserves stored during seed filling are mobilized to provide energy and carbon for the growing seedling until autotrophic growth is possible. A plastid isoform of triose phosphate isomerase (pdTPI) plays a crucial role in this transition from heterotrophic to autotrophic growth. A T-DNA insertion in Arabidopsis thaliana pdTPI resulted in a fivefold reduction in transcript, reduced TPI activity, and a severely stunted and chlorotic seedling that accumulated dihydroxyacetone phosphate (DHAP), glycerol, and glycerol-3-phosphate. Methylglyoxal (MG), a by-product of DHAP, also accumulated in the pdtpi mutant. Wild-type seed sown in the presence of any of these four metabolites resulted in a phenocopy of this pdtpi mutant, although MG and DHAP were the most effective based upon dosage. These metabolites (except MG) are by-products of triacylglycerol mobilization and precursors for glycerolipid synthesis, suggesting that lipid metabolism may also be affected. Lipid profiling revealed lower monogalactosyl but higher digalactosyl lipids. It is unclear whether the change in lipid composition is a direct or indirect consequence of the pdtpi mutation, as ribulose-1,5-bis-phosphate carboxylase/oxygenase expression, chloroplast morphology, and starch synthesis are also defective in this mutant. We propose that DHAP and MG accumulation in developing plastids delays the transition from heterotrophic to autotrophic growth, possibly due to MG toxicity.
Cooperation of Multiple Chromatin Modifications Can Generate Unanticipated Stability of Epigenetic States inArabidopsis
Authors: Baubec Tuncay , Dinh Huy Q. , Pecinka Ales , Rakic Branislava , Rozhon Wilfried , Wohlrab Bonnie , von Haeseler Arndt , Scheid Ortrun Mittelsten
Published: January 2010

Epigenetic changes of gene expression can potentially be reversed by developmental programs, genetic manipulation, or pharmacological interference. However, a case of transcriptional gene silencing, originally observed in tetraploid Arabidopsis thaliana plants, created an epiallele resistant to many mutations or inhibitor treatments that activate many other suppressed genes. This raised the question about the molecular basis of this extreme stability. A combination of forward and reverse genetics and drug application provides evidence for an epigenetic double lock that is only alleviated upon the simultaneous removal of both DNA methylation and histone methylation. Therefore, the cooperation of multiple chromatin modifications can generate unanticipated stability of epigenetic states and contributes to heritable diversity of gene expression patterns.
Health status assessment using reverse supply chain data
Authors: Antai Imoh , Mutshinda Crispin M.
Published: January 2010

Purpose

The purpose of this paper is to suggest the use of reverse medical supply chain data to infer changes of a population's health status with regard to a focal disease. It includes a detailed illustration of how health status information can be obtained from drug reverse chains.

Design/methodology/approach

A Bayesian dynamical model linking drug reverse supply chain data to relevant health status indicators with regard to a focal disease is developed. A detailed implementation of the model on computer‐simulated data is considered. The predictive ability of the methodology is also assessed using out‐of‐sample Monte Carlo‐based predictive analysis.

Findings

The results substantiate the good fit of the model to the empirical data.

Research limitations/implications

Difficulty in obtaining actual return data and in selecting appropriate health status indicators. The correspondence disease‐drug is typically not one‐to‐one. Experts' opinion is required in setting up suitable mixing weights as many drugs may inform the health status relative to a given disease and vice versa.

Practical implications

Reverse logistics data may contain potential information, and this is not exclusive to medical chains.

Originality/value

The paper's suggestions tend to reinforce the notion that supply chain data may be used in many unsuspected settings. Solutions to issues of immediate concern in public health require multidisciplinary cooperation, and this paper shows how supply chain management can contribute. It is believed that the potential of reverse chain data in the health status prospect has previously hardly ever been pointed out.
Integration of supply and marketing for a blood service
Authors: Grant David B.
Published: January 2010

Purpose

The blood service sector faces issues with obtaining and retaining loyal donors at one end of its supply chain, a marketing issue, and being efficient and effective in blood and related product delivery to customers at the other end of its supply chain, a supply chain management issue. The purpose of this paper is to present an investigation of these issues and propose the adoption of techniques and technologies from the food processing and retailing sector to address them.

Design/methodology/approach

An exploratory case study with the Scottish National Blood Transfusion Service is used to investigate research questions stemming from extant literature.

Findings

This study finds that a national blood service can achieve better stock management and resource optimisation and better communication with “input” and “output” stakeholders by implementing information flows and integration throughout the supply and marketing chain. It also finds that a national blood service can convince non‐donors to donate and increase donor relationships and loyalty by ensuring internal marketing takes place with its employees who can then inform external stakeholders through their first‐contact relationships.

Research limitations/implications

This study is exploratory, thus empirical research is limited.

Practical implications

This paper validates primary issues in recruiting and retaining blood donors and making blood supply chains more efficient and effective, and proposes the adoption of techniques and technology from other process sectors to overcome these issues. Thus, European national blood services should benefit from implementing suggestions in this research.

Originality/value

This paper adopts a multi‐disciplinary approach across the marketing and supply chain management disciplines to explore issues usually associated with medical and pure sciences.
Employer brand image in a health care organization
Authors: Heilmann Pia A.K.
Published: January 2010

Purpose

The purpose of this paper is to provide an overview concerning employer brand image in a Finnish hospital organization. What is done for recruitment marketing? This study offers some proposals for improving the recruitment process.

Design/methodology/approach

The research is a qualitative case study and the research method used is a group interview. The research questions are approached from an organizational perspective. Background information about the current labour shortage in health care is gathered from the focus hospital organization, from the public media and from the health care trade organizations.

Findings

Very few marketing actions concerning employer image have been done in the focus hospital. There also existed a lack of appropriate recruitment tools and competence. Data systems and the internet have not been fully exploited in the recruitment process. Vacancies are not announced in educational institutes. Career development possibilities are not presented in job advertisements and job‐rotation has not been used in recruitment.

Originality/value

This paper provides useful information for health care managers and researchers concerning the role of employer image in recruiting and the importance of a well‐organized recruitment process.
Managing competitive bidding in the Finnish healthcare sector
Authors: Härkönen Kai , Ulkuniemi Pauliina , Tähtinen Jaana
Published: January 2010

Purpose

The purpose of this paper is to describe the competences needed for managing competitive bidding in the Finnish healthcare and to understand the management of competitive bidding holistically, considering the challenges the management faces from being embedded in focal nets and the wider network.

Design/methodology/approach

The phenomenon is examined from the perspective of networks. This focus acknowledges the fact that competitive bidding changes the dynamics of the network and therefore requires new competences from the actors. The study applies qualitative methods.

Findings

Competitive bidding connects effects, interests, resources and actors together. It changes the dynamics of the net and the network. Thus, new competences are required. Three major competence areas were detected: relationship management competences, net management competences and purchasing competences.

Originality/value

The conclusions shed light on the combination of competences needed in managing competitive bidding in healthcare networks.
The impact of extrinsic and package design attributes on preferences for non‐prescription drugs
Authors: Kauppinen‐Räisänen Hannele
Published: January 2010

Purpose

The purpose of this paper is to examine the influence of extrinsic attributes and package design attributes on consumer preferences of high‐risk products.

Design/methodology/approach

An explorative conjoint analysis is conducted. A small‐scale sample, consisting of 18 consumers, conduct two conjoint tasks for two drug product types, i.e. painkillers and sore throat medicine.

Findings

The impact of the tested attributes varies according to the product type. The intrinsic attribute of taste is valued most in sore throat medicines, followed by colour and producer. Producer and colour are the most valued in painkillers. Colour is the most influential of the design attributes tested. Well‐known producer is perceived as more important in painkillers, whereas in sore throat medicine domestic producers are valued more.

Research limitations/implications

The study is exploratory and limited due to the design with few statistical assumptions and to small‐scale sampling in one country only.

Practical implications

The health care marketers should recognize the impact of package design on consumers' preferences of high‐risk products, such as non‐prescription drug.

Originality/value

There has been little research on the impact of package design attributes such as package colours on consumers in health care marketing.
The effect of competence‐based trust between physicians and administrative executives in healthcare on decision outcomes
Authors: Parayitam Satyanarayana
Published: January 2010

Purpose

Research on strategic decision making has over‐emphasized the importance of competence‐based trust among the team members. Literature on healthcare is silent on the impact of competence‐based trust between the physicians and administrators on decision outcomes. The purpose of this paper is to empirically investigate whether competence‐based trust between physician executives and administrators is beneficial to the healthcare organizations.

Design/methodology/approach

Using a structured instrument, data are collected from top management teams of 109 US hospitals. The participants include both CEOs and administrators and physician executives. The data are analyzed using multiple regression technique to examine the role of competence‐based trust between the physicians and administrative executives in enhancing decision quality, commitment and understanding.

Findings

Results show that competence‐based trust is the key to successful strategic decision making while lack of trust may hinder the effectiveness of decision implementation in healthcare organizations.

Research limitations/implications

Only the healthcare industry is considered. Self‐report measures may have some common method bias and social desirability bias.

Practical implications

This study contributes to both practicing managers as well as to strategic management literature. This study suggests that development and retention of competence‐based trust between the administrators and physicians is essential in making decision‐making process effective and successful.

Originality/value

Though the study represents the US hospitals, to the extent the strategic decision process is similar across the world, the findings can be generalized to other healthcare organizations in the world.
Interview with Suzanne Doyle Morris
Authors: by Juliet Norton Interview
Published: January 2010

Purpose

The purpose of this paper is to present and an interview with Suzanne Doyle Morris, an author, academic, entrepreneur, international speaker and accredited executive coach specialising in strategic career development and leadership coaching for high‐potential executive women.

Design/methodology/approach

The paper takes the form of an interview with Suzanne Doyle Morris her views on encouraging women in the workplace.

Findings

The paper reveals that, in Suzanne Doyle Morris's view, one of the strategies that companies can use to reward high performing women is to offer coaching. Also they could not limiting high profile jobs to those that are willing to work full time.

Originality/value

This is interview provides insights into how companies can encourage women workers to achieve more in the workplace.
The Chinese sensor industry: poised to become world leader?
Authors: Bogue Robert
Published: January 2010

Purpose

The purpose of this paper is to provide an insight into China's burgeoning sensor industry.

Design/methodology/approach

Following an introduction to the Chinese economy and sensor market, this paper considers a number of key sensor applications and technologies and highlights a selection of Chinese sensor manufacturers and their products. It concludes with an overview of the country's sensor research effort.

Findings

This shows that China's sensor market is expanding very rapidly and is being served by a fast‐growing community of manufacturers who are producing large numbers of sensors for physical and chemical variables. The automotive sector is one of the leading users of sensors and is aiding China's micro‐electromechanical system industry. China has a large and active sensor research community.

Originality/value

This paper provides an up‐to‐date review of the Chinese sensor industry, illustrating its very rapid, recent growth and huge future potential.