bluuebunny/crossref_metadata_2025_split huggingface dataset:
IncreasedL-arginine transport via system b0,+ in human proximal tubular cells exposed to albumin
Authors: Ashman Neil , Brunini Tatiana M. , Mann Giovanni E. , Mendes Ribeiro A. Claudio , Yaqoob Muhammad M. 
Published: November 2006

Albumin has complex effects on PTECs (proximal tubular epithelial cells) and is able to stimulate growth or injury depending on its bound moieties. Albumin itself is a mitogen, inducing proliferation through a number of pathways. In PTEC exposed to purified albumin, polyamines are required for entry into the cell cycle and are critical for proliferation. Polyamines are synthesized from L-ornithine (itself derived by the action of arginase on L-arginine), and the transport and availability of L-arginine may thus be important for subsequent polyamine-dependent proliferation. In the present study we investigated radiolabelled cationic amino-acid transport in cultured PTEC exposed to 20 mg/ml ultrapure recombinant human albumin, describing the specific kinetic characteristics of transport and the expression of transporters. L-[3H]Arginine transport capacity in human PTEC is increased after exposure for 24 h to human albumin, mediated by the broad-scope high-affinity system b0,+ and, to a lesser extent, system y+L (but not system y+) transport. Increased transport is associated with increased b0,+-associated transporter expression. Inhibition of phosphoinositide 3-kinase, a key regulator of albumin endocytosis and signalling, inhibited proliferation, but had no effect on the observed increase in transport. PTEC proliferated in response to albumin. L-Lysine, a competitive inhibitor of L-arginine transport, had no effect on albumin-induced proliferation; however, arginine deprivation effectively reversed the albumin-induced proliferation observed. In conclusion, in PTEC exposed to albumin, increased L-arginine transport is mediated by increased transcription and activity of the apical b0,+ transport system. This may make L-arginine available as a substrate for the downstream synthesis of polyamines, but is not critical for cell proliferation.
Blinded Case-Control Study of the Relationship between Human Coronavirus NL63 and Kawasaki Syndrome
Authors: Dominguez Samuel R.  , Anderson Marsha S.  , Glodé Mary P.  , Robinson Christine C.  , Holmes Kathryn V.  
Published: November 2006

Abstract
We conducted a blinded, case-control, retrospective study in pediatric patients hospitalized at The Children’s Hospital, Denver, Colorado, to determine whether human coronavirus (HCoV)–NL63 infection is associated with Kawasaki syndrome (KS). Over the course of a 7-month period, nasopharyngeal-wash samples from 2 (7.7%) of 26 consecutive children with KS and 4 (7.7%) of 52 matched control subjects tested positive for HCoV-NL63 by reverse transcription–polymerase chain reaction. These data suggest that, although HCoV-NL63 was circulating in children in our community during the time of the study, the prevalence of infection with HCoV-NL63 was not greater in patients with KS than in control subjects.
Transcriptome Analysis Reveals a Critical Role ofCHS7andCHS8Genes for Isoflavonoid Synthesis in Soybean Seeds
Authors: Dhaubhadel Sangeeta , Gijzen Mark , Moy Pat , Farhangkhoee Mana 
Published: November 2006

AbstractWe have used cDNA microarray analysis to examine changes in gene expression during embryo development in soybean (Glycine max) and to compare gene expression profiles of two soybean cultivars that differ in seed isoflavonoid content. The analysis identified 5,910 genes that were differentially expressed in both soybean cultivars grown at two different locations for two consecutive years in one of the five different stages of embryo development. An ANOVA analysis with P value &lt; 0.05 and &lt; 0.01 indicated that gene expression changes due to environmental factors are greater than those due to cultivar differences. Most changes in gene expression occurred at the stages when the embryos were at 30 or 70 d after pollination. A significantly larger fraction of genes (48.5%) was expressed throughout the development and showed little or no change in expression. Transcript accumulation for genes related to the biosynthesis of storage components in soybean embryos showed several unique temporal expressions. Expression patterns of several genes involved in isoflavonoid biosynthesis, such as Phenylalanine Ammonia-Lyase, Chalcone Synthase (CHS) 7, CHS8, and Isoflavone Synthase2, were higher at 70 d after pollination in both the cultivars. Thus, expression of these genes coincides with the onset of accumulation of isoflavonoids in the embryos. A comparative analysis of genes involved in isoflavonoid biosynthesis in RCAT Angora (high seed isoflavonoid cultivar) and Harovinton (low seed isoflavonoid cultivar) revealed that CHS7 and CHS8 were expressed at significantly greater level in RCAT Angora than in Harovinton. Our study provides a detailed transcriptome profiling of soybean embryos during development and indicates that differences in the level of seed isoflavonoids between these two cultivars could be as a result of differential expression of CHS7 and CHS8 during late stages of seed development.
MAIZEWALL. Database and Developmental Gene Expression Profiling of Cell Wall Biosynthesis and Assembly in Maize
Authors: Guillaumie Sabine , San-Clemente Hélène , Deswarte Caroline , Martinez Yves , Lapierre Catherine , Murigneux Alain , Barrière Yves , Pichon Magalie , Goffner Deborah 
Published: November 2006

Abstract
An extensive search for maize (Zea mays) genes involved in cell wall biosynthesis and assembly has been performed and 735 sequences have been centralized in a database, MAIZEWALL (http://www.polebio.scsv.ups-tlse.fr/MAIZEWALL). MAIZEWALL contains a bioinformatic analysis for each entry and gene expression data that are accessible via a user-friendly interface. A maize cell wall macroarray composed of a gene-specific tag for each entry was also constructed to monitor global cell wall-related gene expression in different organs and during internode development. By using this macroarray, we identified sets of genes that exhibit organ and internode-stage preferential expression profiles. These data provide a comprehensive fingerprint of cell wall-related gene expression throughout the maize plant. Moreover, an in-depth examination of genes involved in lignin biosynthesis coupled to biochemical and cytological data from different organs and stages of internode development has also been undertaken. These results allow us to trace spatially and developmentally regulated, putative preferential routes of monolignol biosynthesis involving specific gene family members and suggest that, although all of the gene families of the currently accepted monolignol biosynthetic pathway are conserved in maize, there are subtle differences in family size and a high degree of complexity in spatial expression patterns. These differences are in keeping with the diversity of lignified cell types throughout the maize plant.
Combining Expression and Comparative Evolutionary Analysis. TheCOBRAGene Family
Authors: Brady Siobhan M. , Song Shuang , Dhugga Kanwarpal S. , Rafalski J. Antoni , Benfey Philip N. 
Published: November 2006

AbstractPlant cell shape is achieved through a combination of oriented cell division and cell expansion and is defined by the cell wall. One of the genes identified to influence cell expansion in the Arabidopsis (Arabidopsis thaliana) root is the COBRA (COB) gene that belongs to a multigene family. Three members of the AtCOB gene family have been shown to play a role in specific types of cell expansion or cell wall biosynthesis. Functional orthologs of one of these genes have been identified in maize (Zea mays) and rice (Oryza sativa; Schindelman et al., 2001; Li et al., 2003; Brown et al., 2005; Persson et al., 2005; Ching et al., 2006; Jones et al., 2006). We present the maize counterpart of the COB gene family and the COB gene superfamily phylogeny. Most of the genes belong to a family with two main clades as previously identified by analysis of the Arabidopsis family alone. Within these clades, however, clear differences between monocot and eudicot family members exist, and these are analyzed in the context of Type I and Type II cell walls in eudicots and monocots. In addition to changes at the sequence level, gene regulation of this family in a eudicot, Arabidopsis, and a monocot, maize, is also characterized. Gene expression is analyzed in a multivariate approach, using data from a number of sources, including massively parallel signature sequencing libraries, transcriptional reporter fusions, and microarray data. This analysis has revealed that the expression of Arabidopsis and maize COB gene family members is highly developmentally and spatially regulated at the tissue and cell type-specific level, that gene superfamily members show overlapping and unique expression patterns, and that only a subset of gene superfamily members act in response to environmental stimuli. Regulation of expression of the Arabidopsis COB gene family members has highly diversified in comparison to that of the maize COB gene superfamily members. We also identify BRITTLE STALK 2-LIKE 3 as a putative ortholog of AtCOB.
Modification of Leaf Apoplastic pH in Relation to Stomatal Sensitivity to Root-Sourced Abscisic Acid Signals
Authors: Jia Wensuo , Davies William John 
Published: November 2006

Abstract
The confocal microscope was used to determine the pH of the leaf apoplast and the pH of microvolumes of xylem sap. We quantified variation in leaf apoplast and sap pH in relation to changes in edaphic and atmospheric conditions that impacted on stomatal sensitivity to a root-sourced abscisic acid signal. Several plant species showed significant changes in the pH of both xylem sap and the apoplast of the shoot in response to environmental perturbation. Xylem sap leaving the root was generally more acidic than sap in the midrib and the apoplast of the leaf. Increasing the transpiration rate of both intact plants and detached plant parts resulted in more acidic leaf apoplast pHs. Experiments with inhibitors suggested that protons are removed from xylem sap as it moves up the plant, thereby alkalinizing the sap. The more rapid the transpiration rate and the shorter the time that the sap resided in the xylem/apoplastic pathway, the smaller the impact of proton removal on sap pH. Sap pH of sunflower (Helianthus annuus) and Commelina communis did not change significantly as soil dried, while pH of tomato (Lycopersicon esculentum) sap increased as water availability in the soil declined. Increasing the availability of nitrate to roots also significantly alkalinized the xylem sap of tomato plants. This nitrogen treatment had the effect of enhancing the sensitivity of the stomatal response to soil drying. These responses were interpreted as an effect of nitrate addition on sap pH and closure of stomata via an abscisic acid-based mechanism.
Characterization of thePreprotein and Amino Acid TransporterGene Family in Arabidopsis
Authors: Murcha Monika W. , Elhafez Dina , Lister Ryan , Tonti-Filippini Julian , Baumgartner Manuela , Philippar Katrin , Carrie Chris , Mokranjac Dejana , Soll Jürgen , Whelan James 
Published: November 2006

AbstractSeventeen loci encode proteins of the preprotein and amino acid transporter family in Arabidopsis (Arabidopsis thaliana). Some of these genes have arisen from recent duplications and are not in annotated duplicated regions of the Arabidopsis genome. In comparison to a number of other eukaryotic organisms, this family of proteins has greatly expanded in plants, with 24 loci in rice (Oryza sativa). Most of the Arabidopsis and rice genes are orthologous, indicating expansion of this family before monocot and dicot divergence. In vitro protein uptake assays, in vivo green fluorescent protein tagging, and immunological analyses of selected proteins determined either mitochondrial or plastidic localization for 10 and six proteins, respectively. The protein encoded by At5g24650 is targeted to both mitochondria and chloroplasts and, to our knowledge, is the first membrane protein reported to be targeted to mitochondria and chloroplasts. Three genes encoded translocase of the inner mitochondrial membrane (TIM)17-like proteins, three TIM23-like proteins, and three outer envelope protein16-like proteins in Arabidopsis. The identity of Arabidopsis TIM22-like proteins is most likely a protein encoded by At3g10110/At1g18320, based on phylogenetic analysis, subcellular localization, and complementation of a yeast (Saccharomyces cerevisiae) mutant and coexpression analysis. The lack of a preprotein and amino acid transporter domain in some proteins, localization in mitochondria, plastids, or both, variation in gene structure, and the differences in expression profiles indicate that the function of this family has diverged in plants beyond roles in protein translocation.
Genetic Variation Suggests Interaction between Cold Acclimation and Metabolic Regulation of Leaf Senescence
Authors: Masclaux-Daubresse Céline , Purdy Sarah , Lemaitre Thomas , Pourtau Nathalie , Taconnat Ludivine , Renou Jean-Pierre , Wingler Astrid 
Published: November 2006

Abstract
The extent to which leaf senescence is induced by nitrogen deficiency or by sugar accumulation varies between natural accessions of Arabidopsis (Arabidopsis thaliana). Analysis of senescence in plants of the Bay-0 × Shahdara recombinant inbred line (RIL) population revealed a large variation in developmental senescence of the whole leaf rosette, which was in agreement with the extent to which glucose (Glc) induced senescence in the different lines. To determine the regulatory basis of genetic differences in the Glc response, we investigated changes in gene expression using Complete Arabidopsis Transcriptome MicroArray (CATMA) analysis. Genes whose regulation did not depend on the genetic background, as well as genes whose regulation was specific to individual RILs, were identified. In RIL 310, a line that does not show the typical senescence response to Glc, stress response genes, especially those responding to cold stress, were induced by Glc. We therefore tested whether cold acclimation delays senescence by reducing sugar sensitivity. In cold-acclimated plants, leaf senescence was severely delayed and Glc did not induce the typical senescence response. Together, our results suggest that cold acclimation extends rosette longevity by affecting metabolic regulation of senescence, thereby allowing vernalization-dependent plants to survive the winter period. The role of functional chloroplasts and of nitrogen and phosphate availability in this regulation is discussed.
Degradation of Oxidized Proteins by Autophagy during Oxidative Stress in Arabidopsis
Authors: Xiong Yan , Contento Anthony L. , Nguyen Phan Quang , Bassham Diane C. 
Published: November 2006

Abstract
Upon encountering oxidative stress, proteins are oxidized extensively by highly reactive and toxic reactive oxidative species, and these damaged, oxidized proteins need to be degraded rapidly and effectively. There are two major proteolytic systems for bulk degradation in eukaryotes, the proteasome and vacuolar autophagy. In mammalian cells, the 20S proteasome and a specific type of vacuolar autophagy, chaperone-mediated autophagy, are involved in the degradation of oxidized proteins in mild oxidative stress. However, little is known about how cells remove oxidized proteins when under severe oxidative stress. Using two macroautophagy markers, monodansylcadaverine and green fluorescent protein-AtATG8e, we here show that application of hydrogen peroxide or the reactive oxidative species inducer methyl viologen can induce macroautophagy in Arabidopsis (Arabidopsis thaliana) plants. Macroautophagy-defective RNAi-AtATG18a transgenic plants are more sensitive to methyl viologen treatment than wild-type plants and accumulate a higher level of oxidized proteins due to a lower degradation rate. In the presence of a vacuolar H+-ATPase inhibitor, concanamycin A, oxidized proteins were detected in the vacuole of wild-type root cells but not RNAi-AtATG18a root cells. Together, our results indicate that autophagy is involved in degrading oxidized proteins under oxidative stress conditions in Arabidopsis.
Phylogeography of the Western Lyresnake (Trimorphodon biscutatus): testing aridland biogeographical hypotheses across the Nearctic–Neotropical transition
Authors: DEVITT THOMAS J. 
Published: November 2006

AbstractThe Western Lyresnake (Trimorphodon biscutatus) is a widespread, polytypic taxon inhabiting arid regions from the warm deserts of the southwestern United States southward along the Pacific versant of Mexico to the tropical deciduous forests of Mesoamerica. This broadly distributed species provides a unique opportunity to evaluate a priori biogeographical hypotheses spanning two major distinct biogeographical realms (the Nearctic and Neotropical) that are usually treated separately in phylogeographical analyses. I investigated the phylogeography ofT. biscutatususing maximum likelihood and Bayesian phylogenetic analysis of mitochondrial DNA (mtDNA) from across this species’ range. Phylogenetic analyses recovered five well‐supported clades whose boundaries are concordant with existing geographical barriers, a pattern consistent with a model of vicariant allopatric divergence. Assuming a vicariance model, divergence times between mitochondrial lineages were estimated using Bayesian relaxed molecular clock methods calibrated using geological information from putative vicariant events. Divergence time point estimates were bounded by broad confidence intervals, and thus these highly conservative estimates should be considered tentative hypotheses at best. Comparison of mtDNA lineages and taxa traditionally recognized as subspecies based on morphology suggest this taxon is comprised of multiple independent lineages at various stages of divergence, ranging from putative secondary contact and hybridization to sympatry of ‘subspecies’.
When supercolonies collide: territorial aggression in an invasive and unicolonial social insect
Authors: THOMAS MELISSA L. , PAYNE‐MAKRISÂ CHRISTINE M. , SUAREZ ANDREW V. , TSUTSUI NEIL D. , HOLWAY DAVID A. 
Published: November 2006

AbstractSome species of ants possess an unusual form of social organization in which aggression among nests is absent. This type of social organization, called unicoloniality, has been studied in only a handful of species and its evolutionary origins remain unclear. To date, no study has examined behavioural and genetic patterns at points of contact between the massive supercolonies that characterize unicoloniality. Since interactions at territory boundaries influence the costs of aggression and the likelihood of gene flow, such data may illuminate how supercolonies are formed and maintained. Here we provide field data on intraspecific territoriality for a widespread and invasive unicolonial social insect, the Argentine ant (Linepithema humile). We observed abrupt and well‐defined behavioural boundaries at 16 contact zones between three different pairs of supercolonies. We visited nine of these zones weekly during a six‐month period and observed consistent and intense intercolony aggression that resulted in variable, but often large, levels of worker mortality. Microsatellite variation along six transects across territory borders showed that FST values were lower within supercolonies (0.08 ± 0.01 (mean ± SE)) than between supercolonies (0.29 ± 0.01) and that this disparity was especially strong right at territory borders, despite direct and prolonged contact between the supercolonies. Matrix correspondence tests confirmed that levels of aggression and genetic differentiation were significantly correlated, but no relationship existed between geographic distance and either intraspecific aggression or genetic differentiation. Patterns of FST variation indicated high levels of gene flow within supercolonies, but little to no gene flow between them. Overall, these findings are inconsistent with a model of relaxed ecological constraints leading to colony fusion and suggest that environmentally derived cues are not the prime determined of nestmate recognition in field populations of Argentine ants.
Comprehensive genetic analyses reveal evolutionary distinction of a mouse (Zapus hudsonius preblei) proposed for delisting from the US Endangered Species Act
Authors: KING TIM L. , SWITZER JOHN F. , MORRISON CHERYL L. , EACKLES MICHAEL S. , YOUNG COLLEEN C. , LUBINSKI BARBARA A. , CRYAN PAUL 
Published: November 2006

AbstractZapus hudsonius preblei, listed as threatened under the US Endangered Species Act (ESA), is one of 12 recognized subspecies of meadow jumping mice found in North America. Recent morphometric and phylogenetic comparisons amongZ. h. prebleiand neighbouring conspecifics questioned the taxonomic status of selected subspecies, resulting in a proposal to delist theZ. h. prebleifrom the ESA. We present additional analyses of the phylogeographic structure withinZ. hudsoniusthat calls into question previously published data (and conclusions) and confirms the original taxonomic designations. A survey of 21 microsatellite DNA loci and 1380 base pairs from two mitochondrial DNA (mtDNA) regions (control region and cytochromeb) revealed that eachZ. hudsoniussubspecies is genetically distinct. These data do not support the null hypothesis of a homogeneous gene pool among the five subspecies found within the southwestern portion of the species’ range. The magnitude of the observed differentiation was considerable and supported by significant findings for nearly every statistical comparison made, regardless of the genome or the taxa under consideration. Structuring of nuclear multilocus genotypes and subspecies‐specific mtDNA haplotypes corresponded directly with the disjunct distributions of the subspecies investigated. Given the level of correspondence between the observed genetic population structure and previously proposed taxonomic classification of subspecies (based on the geographic separation and surveys of morphological variation), we conclude that the nominal subspecies surveyed in this study do not warrant synonymy, as has been proposed forZ. h. preblei,Z. h. campestris, andZ. h. intermedius.