bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Lab of Their Own: Genomic sovereignty as postcolonial science policy
Authors: Benjamin Ruha 
Published: October 2009

Abstract
This paper analyzes the emergence of ‘genomic sovereignty’ policies as a newly popular way for postcolonial countries to frame their investment in genomics. It identifies three strands in the genealogy of this policy arena—the International Haplotype Mapping Project as a model and foil for postcolonial genomics; an emerging public health genomics field which stands in contrast to Western pursuits of personalized medicine; and North American drug companies increased focus on ethnic drug markets. I conceptualize postcolonial genomics as a nationalist project with contradictory tendencies—unifying and differentiating a diverse body politic, cultivating national scientific and commercial autonomy and dependence upon global knowledge networks and foreign capital. It argues that the ‘strategic calibration’ of socio-political versus biological taxonomies in postcolonial genomics creates two primary challenges for this arena, which I refer to heuristically as dilemmas of mapping and marketing.
Model aggregation: a building-block approach to creating large macromolecular regulatory networks
Authors: Randhawa Ranjit , Shaffer Clifford A. , Tyson John J. 
Published: October 2009

Abstract
Motivation: Models of regulatory networks become more difficult to construct and understand as they grow in size and complexity. Modelers naturally build large models from smaller components that each represent subsets of reactions within the larger network. To assist modelers in this process, we present model aggregation, which defines models in terms of components that are designed for the purpose of being combined.
Results: We have implemented a model editor that incorporates model aggregation, and we suggest supporting extensions to the Systems Biology Markup Language (SBML) Level 3. We illustrate aggregation with a model of the eukaryotic cell cycle ‘engine’ created from smaller pieces.
Availability: Java implementations are available in the JigCell Aggregation Connector. See http://jigcell.biol.vt.edu.
Contact: shaffer@vt.edu
inGAP: an integrated next-generation genome analysis pipeline
Authors: Qi Ji , Zhao Fangqing , Buboltz Anne , Schuster Stephan C. 
Published: October 2009

Abstract
Summary: We develop a novel mining pipeline, Integrative Next-generation Genome Analysis Pipeline (inGAP), guided by a Bayesian principle to detect single nucleotide polymorphisms (SNPs), insertion/deletions (indels) by comparing high-throughput pyrosequencing reads with a reference genome of related organisms. inGAP can be applied to the mapping of both Roche/454 and Illumina reads with no restriction of read length. Experiments on simulated and experimental data show that this pipeline can achieve overall 97% accuracy in SNP detection and 94% in the finding of indels. All the detected SNPs/indels can be further evaluated by a graphical editor in our pipeline. inGAP also provides functions of multiple genomes comparison and assistance of bacterial genome assembly.
Availability: inGAP is available at http://sites.google.com/site/nextgengenomics/ingap
Contact: scs@bx.psu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Simulation-based model selection for dynamical systems in systems and population biology
Authors: Toni Tina , Stumpf Michael P. H. 
Published: October 2009

Abstract
Motivation: Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not straightforward. We therefore require suitable statistical tools that allow us to choose rationally between different mechanistic models of, e.g. signal transduction or gene regulation networks. This is particularly challenging in systems biology where only a small number of molecular species can be assayed at any given time and all measurements are subject to measurement uncertainty.
Results: Here, we develop such a model selection framework based on approximate Bayesian computation and employing sequential Monte Carlo sampling. We show that our approach can be applied across a wide range of biological scenarios, and we illustrate its use on real data describing influenza dynamics and the JAK-STAT signalling pathway. Bayesian model selection strikes a balance between the complexity of the simulation models and their ability to describe observed data. The present approach enables us to employ the whole formal apparatus to any system that can be (efficiently) simulated, even when exact likelihoods are computationally intractable.
Contact: ttoni@imperial.ac.uk; m.stumpf@imperial.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Bayesian model selection for characterizing genomic imprinting effects and patterns
Authors: Yang Runqing , Wang Xin , Wu Zeyuan , Prows Daniel R. , Lin Min 
Published: October 2009

Abstract
Motivation: Although imprinted genes have been ubiquitously observed in nature, statistical methodology still has not been systematically developed for jointly characterizing genomic imprinting effects and patterns. To detect imprinting genes influencing quantitative traits, the least square and maximum likelihood approaches for fitting a single quantitative trait loci (QTL) and Bayesian method for simultaneously modeling multiple QTLs have been adopted in various studies.
Results: In a widely used F2 reciprocal mating population for mapping imprinting genes, we herein propose a genomic imprinting model which describes additive, dominance and imprinting effects of multiple imprinted quantitative trait loci (iQTL) for traits of interest. Depending upon the estimates of the above genetic effects, we categorized imprinting patterns into seven types, which provides a complete classification scheme for describing imprinting patterns. Bayesian model selection was employed to identify iQTL along with many genetic parameters in a computationally efficient manner. To make statistical inference on the imprinting types of iQTL detected, a set of Bayes factors were formulated using the posterior probabilities for the genetic effects being compared. We demonstrated the performance of the proposed method by computer simulation experiments and then applied this method to two real datasets. Our approach can be generally used to identify inheritance modes and determine the contribution of major genes for quantitative variations.
Contact: annie.lin@duke.edu; runqingyang@sjtu.edu.cn
MATICCE: mapping transitions in continuous character evolution
Authors: Hipp Andrew L. , Escudero Marcial 
Published: October 2009

Abstract
Summary: MATICCE is a new software package in the R language for mapping phylogenetic transitions in organismal traits that have continuous distributions. MATICCE integrates over phylogenetic and model uncertainty and provides simulation functions for visualizing evolutionary scenarios based on estimated parameter values.
Availability and Implementation: MATICCE is written in the open source R language and freely available through the Comprehensive R Archive Network (http://cran.r-project.org/web/packages/maticce).
Contact: ahipp@mortonarb.org
MODIFIED VACUOLE PHENOTYPE1 Is an Arabidopsis Myrosinase-Associated Protein Involved in Endomembrane Protein Trafficking
Authors: Agee April E. , Surpin Marci , Sohn Eun Ju , Girke Thomas , Rosado Abel , Kram Brian W. , Carter Clay , Wentzell Adam M. , Kliebenstein Daniel J. , Jin Hak Chul , Park Ohkmae K. , Jin Hailing , Hicks Glenn R. , Raikhel Natasha V. 
Published: October 2009

Abstract
We identified an Arabidopsis (Arabidopsis thaliana) ethyl methanesulfonate mutant, modified vacuole phenotype1-1 (mvp1-1), in a fluorescent confocal microscopy screen for plants with mislocalization of a green fluorescent protein-δ tonoplast intrinsic protein fusion. The mvp1-1 mutant displayed static perinuclear aggregates of the reporter protein. mvp1 mutants also exhibited a number of vacuole-related phenotypes, as demonstrated by defects in growth, utilization of stored carbon, gravitropic response, salt sensitivity, and specific susceptibility to the fungal necrotroph Alternaria brassicicola. Similarly, crosses with other endomembrane marker fusions identified mislocalization to aggregate structures, indicating a general defect in protein trafficking. Map-based cloning showed that the mvp1-1 mutation altered a gene encoding a putative myrosinase-associated protein, and glutathione S-transferase pull-down assays demonstrated that MVP1 interacted specifically with the Arabidopsis myrosinase protein, THIOGLUCOSIDE GLUCOHYDROLASE2 (TGG2), but not TGG1. Moreover, the mvp1-1 mutant showed increased nitrile production during glucosinolate hydrolysis, suggesting that MVP1 may play a role in modulation of myrosinase activity. We propose that MVP1 is a myrosinase-associated protein that functions, in part, to correctly localize the myrosinase TGG2 and prevent inappropriate glucosinolate hydrolysis that could generate cytotoxic molecules.
Grain Unloading of Arsenic Species in Rice
Authors: Carey Anne-Marie , Scheckel Kirk G. , Lombi Enzo , Newville Matt , Choi Yongseong , Norton Gareth J. , Charnock John M. , Feldmann Joerg , Price Adam H. , Meharg Andrew A. 
Published: October 2009

Abstract
Rice (Oryza sativa) is the staple food for over half the world's population yet may represent a significant dietary source of inorganic arsenic (As), a nonthreshold, class 1 human carcinogen. Rice grain As is dominated by the inorganic species, and the organic species dimethylarsinic acid (DMA). To investigate how As species are unloaded into grain rice, panicles were excised during grain filling and hydroponically pulsed with arsenite, arsenate, glutathione-complexed As, or DMA. Total As concentrations in flag leaf, grain, and husk, were quantified by inductively coupled plasma mass spectroscopy and As speciation in the fresh grain was determined by x-ray absorption near-edge spectroscopy. The roles of phloem and xylem transport were investigated by applying a ± stem-girdling treatment to a second set of panicles, limiting phloem transport to the grain in panicles pulsed with arsenite or DMA. The results demonstrate that DMA is translocated to the rice grain with over an order magnitude greater efficiency than inorganic species and is more mobile than arsenite in both the phloem and the xylem. Phloem transport accounted for 90% of arsenite, and 55% of DMA, transport to the grain. Synchrotron x-ray fluorescence mapping and fluorescence microtomography revealed marked differences in the pattern of As unloading into the grain between DMA and arsenite-challenged grain. Arsenite was retained in the ovular vascular trace and DMA dispersed throughout the external grain parts and into the endosperm. This study also demonstrates that DMA speciation is altered in planta, potentially through complexation with thiols.
TheO-Mannosyltransferase PMT4 Is Essential for Normal Appressorium Formation and Penetration inUstilago maydis
Authors: Fernández-Álvarez Alfonso , Elías-Villalobos Alberto , Ibeas José I. 
Published: October 2009

AbstractIn Saccharomyces cerevisiae, the PMT, KRE2/MNT1, and MNN1 mannosyltransferase protein families catalyze the steps of the O-mannosylation pathway, sequentially adding mannoses to target proteins. We have identified members of all three families and analyzed their roles in pathogenesis of the maize smut fungus Ustilago maydis. Furthermore, we have shown that PMT4, one of the three PMT family members in U. maydis, is essential for tumor formation in Zea mays. Significantly, PMT4 seems to be required only for pathogenesis and is dispensable for other aspects of the U. maydis life cycle. We subsequently show that the deletion of pmt4 results in a strong reduction in the frequency of appressorium formation, with the few appressoria that do form lacking the capacity to penetrate the plant cuticle. Our findings suggest that the O-mannosylation pathway plays a key role in the posttranslational modification of proteins involved in the pathogenic development of U. maydis. The fact that PMT homologs are not found in plants may open new avenues for the development of fungal control strategies. Moreover, the discovery of a highly specific requirement for a single O-mannosyltransferase should aid in the identification of the proteins directly involved in fungal plant penetration, thus leading to a better understanding of plant–fungi interactions.
Fleshy Fruit Expansion and Ripening Are Regulated by the Tomato SHATTERPROOF Gene TAGL1
Authors: Vrebalov Julia , Pan Irvin L. , Arroyo Antonio Javier Matas , McQuinn Ryan , Chung MiYoung , Poole Mervin , Rose Jocelyn , Seymour Graham , Grandillo Silvana , Giovannoni James , Irish Vivian F. 
Published: October 2009

Abstract
The maturation and ripening of fleshy fruits is a developmental program that synchronizes seed maturation with metabolism, rendering fruit tissues desirable to seed dispersing organisms. Through RNA interference repression, we show that Tomato AGAMOUS-LIKE1 (TAGL1), the tomato (Solanum lycopersicum) ortholog of the duplicated SHATTERPROOF (SHP) MADS box genes of Arabidopsis thaliana, is necessary for fruit ripening. Tomato plants with reduced TAGL1 mRNA produced yellow-orange fruit with reduced carotenoids and thin pericarps. These fruit are also decreased in ethylene, indicating a comprehensive inhibition of maturation mediated through reduced ACC Synthase 2 expression. Furthermore, ectopic expression of TAGL1 in tomato resulted in expansion of sepals and accumulation of lycopene, supporting the role of TAGL1 in ripening. In Arabidopsis, the duplicate SHP1 and SHP2 MADS box genes regulate the development of separation layers essential for pod shatter. Expression of TAGL1 in Arabidopsis failed to completely rescue the shp1 shp2 mutant phenotypes, indicating that TAGL1 has evolved distinct molecular functions compared with its Arabidopsis counterparts. These analyses demonstrate that TAGL1 plays an important role in regulating both fleshy fruit expansion and the ripening process that together are necessary to promote seed dispersal of fleshy fruit. From this broad perspective, SHP1/2 and TAGL1, while distinct in molecular function, regulate similar activities via their necessity for seed dispersal in Arabidopsis and tomato, respectively.
Domain Swapping to Assess the Mechanistic Basis ofArabidopsisPhototropin 1 Receptor Kinase Activation and Endocytosis by Blue Light
Authors: Kaiserli Eirini , Sullivan Stuart , Jones Matthew A. , Feeney Kevin A. , Christie John M. 
Published: October 2009

AbstractPhototropins (phot1 and phot2) are plasma membrane–associated receptor kinases that respond specifically to blue and UV wavelengths. In addition to a C-terminal Ser/Thr kinase domain, phototropins contain two N-terminal chromophore binding LOV domains that function as photoswitches to regulate a wide range of enzymatic activities in prokaryotes and eukaryotes. Through domain swapping, we show that the photochemical properties of Arabidopsis thaliana phot1 rely on interactions between LOV1 and LOV2, which are facilitated by their intervening linker sequence. Functional analysis of domain-swap proteins supports a mechanism whereby LOV2 acts as a dark-state repressor of phot1 activity both in vitro and in vivo. Moreover, we find a photoactive role for LOV1 in arresting chloroplast accumulation at high light intensities. Unlike LOV2, LOV1 cannot operate as a dark-state repressor, resulting in constitutive receptor autophosphorylation and accelerated internalization from the plasma membrane. Coexpression of active and inactive forms of phot1 demonstrates that autophosphorylation can occur intermolecularly, independent of LOV1, via light-dependent receptor dimerization in vivo. Indeed, transphosphorylation is sufficient to promote phot1 internalization through a clathrin-dependent endocytic pathway triggered primarily by phosphorylation of Ser-851 within the kinase activation loop. The mechanistic implications of these findings in regard to light-driven receptor activation and trafficking are discussed.
A Zinc Finger Transcription Factor ART1 Regulates Multiple Genes Implicated in Aluminum Tolerance in Rice
Authors: Yamaji Naoki , Huang Chao Feng , Nagao Sakiko , Yano Masahiro , Sato Yutaka , Nagamura Yoshiaki , Ma Jian Feng 
Published: October 2009

Abstract
Aluminum (Al) toxicity is the major limiting factor of crop production on acid soils, but some plant species have evolved ways of detoxifying Al. Here, we report a C2H2-type zinc finger transcription factor ART1 (for Al resistance transcription factor 1), which specifically regulates the expression of genes related to Al tolerance in rice (Oryza sativa). ART1 is constitutively expressed in the root, and the expression level is not affected by Al treatment. ART1 is localized in the nucleus of all root cells. A yeast one-hybrid assay showed that ART1 has a transcriptional activation potential and interacts with the promoter region of STAR1, an important factor in rice Al tolerance. Microarray analysis revealed 31 downstream transcripts regulated by ART1, including STAR1 and 2 and a couple of homologs of Al tolerance genes in other plants. Some of these genes were implicated in both internal and external detoxification of Al at different cellular levels. Our findings shed light on comprehensively understanding how plants detoxify aluminum to survive in an acidic environment.
Total phenols and vitamin C contents of Iranian fruits
Authors: Nikniaz Zeinab , Mahdavi Reza , Rafraf Maryam , Jouyban Abolghasem 
Published: October 2009

PurposeThe antioxidant characteristics of fruits can be attributed to their contents of polyphenols and vitamins. Because of the interest in the role of antioxidants in human health, the purpose of this paper is to examine the major compounds associated with antioxidant activity, namely total phenolic and vitamin C contents, of some regularly cultivated and consumed fruits in Iran.Design/methodology/approachIn total, 66 fruits from 22 families were chosen for this study. Terbium sensitized fluorescence assay and spectrophotometric method were used to determine total polyphenol and vitamin C contents respectively. The ANOVA with Tukey post‐hoc test was used for statistical analyses.FindingsThe total mean polyphenol content of fruits was 4.93 ± 2.86 mg QE/100 g that were ranging from 0.8 ± 0.05 to 11.94 ± 0.02 mg QE/100 g with the lowest amount obtained for pear and the highest amount detected in black grape. The polyphenol contents of black grape, sourcherry and pomegranate were significantly higher than those of other fruits (p < 0.001). The total mean vitamin C content of fresh fruits was 18.34 ± 9.77 mg/100 g that were ranging from 57.38 ± 0.02 (strawberry) to 11.44 ± 0.02 (melon) mg/100 g. The vitamin C contents of strawberry was significantly higher than all other fruits (p < 0.001). Despite the differences in the polyphenol and vitamin C contents of various fruits, as a good source of nutritious compounds and functional foods, they can be effective in enhancing health status.Originality/valueThis paper is believed to be the only one which provides information about the polyphenol and vitamin C contents of Iranian fruits. Also, the polyphenol content was measured by using a newly‐developed method.
An exploratory study of students' consumption of non‐alcoholic beverages in Nigeria
Authors: Gbadamosi Ayantunji , Olukayode Iwaloye Ojo , Bamber David 
Published: October 2009

PurposeGiven the diversity which exists among various groups of consumers, the purpose of this paper is to explore students' consumption of non‐alcoholic beverages in Nigeria.Design/methodology/approachThree focus groups and 20 in‐depth interviews were conducted with students in three universities located in Lagos, Nigeria.FindingsInitial findings indicate that these students' consumption of non‐alcoholic beverages is influenced in many ways. Nevertheless, the most striking of these influences are found to be convenience of purchase, along with availability, price, health concerns, and culture/social reasons.Originality/valueThe main contribution of the study lies in the relevance of segmentation, targeting, and positioning activities of business organisations in respect of marketing of non‐alcoholic beverages. Based on the findings, the empirical study will serve as a valuable input to marketers in their planning, analysis, and implementation of appropriate marketing strategies to students vis‐à‐vis the highlighted influences on their consumption of this category of food. It will thus serve as a tool for creating competitive advantage in this prevailing volatile business environment.
Panelists liking of canola (Brassica napus) greens
Authors: Miller‐Cebert Rhona L. , Sistani Nahid A. , Cebert Ernst 
Published: October 2009

PurposeThe purpose of this paper is to describe how three traditional cruciferous vegetables: cabbage (Brassica oleracea var. capitata), collard greens (Brassica oleracea var. acephala) and kale (Brassica oleracea var. viridis) were compared to canola greens through sensory analysis to evaluate panelists' acceptance of canola as a potential source of leafy‐green vegetable.Design/methodology/approachCanola cultivars were grown at Alabama A&M University, Winfred Thomas Agricultural Research Station, Hazel Green, Alabama, and harvested at the rosette stage. Traditional vegetables (cabbage, collard and kale) were obtained from a local food specialty store. All vegetables were washed and refrigerated overnight. On the day of testing, vegetables were chopped uniformly in preparation for cooking. Using a nine‐point hedonic scale, vegetables were rated for color, flavor and texture. Overall preference was rated using most favorite, second favorite and third favorite.FindingsColor of prepared canola was preferred significantly over other vegetables. There was no significant difference in preference based on texture among canola, collard greens and kale, however, cabbage was significantly preferred by panelists for texture and flavor. The rating for color and texture indicated significant difference among age groups. Response for texture and flavor showed a linear relationship (r2 of 0.69) for the model: color texture = flavor, while principal component analysis indicated African‐American females, ages 20‐29 as outliers. The results suggest that canola greens have the appeal of being accepted as an additional tasty Brassica vegetable. Originality/value – This research provides new data on canola as a potential new green leafy vegetable, based on consumer preference.
The influence of socioeconomic status and ethnicity on children's excess body weight
Authors: Costarelli Vassiliki , Manios Yannis 
Published: October 2009

PurposeThe purpose of this paper is to describe and briefly discuss the prevalence of childhood obesity in selected countries of the WHO European Region in relation to socioeconomic status (SES) and ethnic origin. Emphasis was given on the most recent research papers available.Design/methodology/approachA search was performed on relevant papers on “Prevalence of Obesity and Overweight in relation to socio‐economic status and ethnicity” using MEDLINE and the ISI Web of Science. The search was limited to the age range 0‐20 years to the countries of the WHO European Region.FindingsA growing number of studies suggest that children in lower‐income families in developed countries are particularly vulnerable to becoming obese. Plausible explanations for the differences in obesity prevalence in migrant children and children with lower SES include poor diet, limited opportunity for physical activity and differences in the perception of ideal body weight together with possible food security issues. It is important to stress that the rising cost of a healthy diet is of great concern.Originality/valueUnderstanding the prevalence of obesity in children and the social and cultural parameters related to the phenomenon can facilitate the formation of effective public health intervention policies in counteracting childhood obesity.