bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of ArabidopsisratMutants
Authors: Zhu Yanmin , Nam Jaesung , Humara Jaime M. , Mysore Kirankumar S. , Lee Lan-Ying , Cao Hongbin , Valentine Lisa , Li Jingling , Kaiser Anthony D. , Kopecky Andrea L. , Hwang Hau-Hsuan , Bhattacharjee Saikat , Rao Praveen K. , Tzfira Tzvi , Rajagopal Jyothi , Yi HoChul , Veena  , Yadav Badam S. , Crane Yan M. , Lin Kui , Larcher Yves , Gelvin Matthew J.K. , Knue Marnie , Ramos Cynthia , Zhao Xiaowen , Davis Susan J. , Kim Sang-Ic , Ranjith-Kumar C.T. , Choi Yoo-Jin , Hallan Vipin K. , Chattopadhyay Sudip , Sui Xiangzhen , Ziemienowicz Alicja , Matthysse Ann G. , Citovsky Vitaly , Hohn Barbara , Gelvin Stanton B. 
Published: June 2003

AbstractLimited knowledge currently exists regarding the roles of plant genes and proteins in the Agrobacterium tumefaciens-mediated transformation process. To understand the host contribution to transformation, we carried out root-based transformation assays to identify Arabidopsis mutants that are resistant to Agrobacterium transformation (rat mutants). To date, we have identified 126 rat mutants by screening libraries of T-DNA insertion mutants and by using various “reverse genetic” approaches. These mutants disrupt expression of genes of numerous categories, including chromatin structural and remodeling genes, and genes encoding proteins implicated in nuclear targeting, cell wall structure and metabolism, cytoskeleton structure and function, and signal transduction. Here, we present an update on the identification and characterization of these rat mutants.
Strategies for Development of Functionally Equivalent Promoters with Minimum Sequence Homology for Transgene Expression in Plants: cis-Elements in a Novel DNA Context versus Domain Swapping
Authors: Bhullar Simran , Chakravarthy Suma , Advani Sonia , Datta Sudipta , Pental Deepak , Burma Pradeep Kumar 
Published: June 2003

Abstract
The cauliflower mosaic virus 35S (35S) promoter has been extensively used for the constitutive expression of transgenes in dicotyledonous plants. The repetitive use of the same promoter is known to induce transgene inactivation due to promoter homology. As a way to circumvent this problem, we tested two different strategies for the development of synthetic promoters that are functionally equivalent but have a minimum sequence homology. Such promoters can be generated by (a) introducing known cis-elements in a novel or synthetic stretch of DNA or (b) “domain swapping,” wherein domains of one promoter can be replaced with functionally equivalent domains from other heterologous promoters. We evaluated the two strategies for promoter modifications using domain A (consisting of minimal promoter and subdomain A1) of the 35S promoter as a model. A set of modified 35S promoters were developed whose strength was compared with the 35S promoter per se using β-glucuronidase as the reporter gene. Analysis of the expression of the reporter gene in transient assay system showed that domain swapping led to a significant fall in promoter activity. In contrast, promoters developed by placing cis-elements in a novel DNA context showed levels of expression comparable with that of the 35S. Two promoter constructs Mod2A1T and Mod3A1T were then designed by placing the core sequences of minimal promoter and subdomain A1 in divergent DNA sequences. Transgenics developed in tobacco (Nicotiana tabacum) with the two constructs and with 35S as control were used to assess the promoter activity in different tissues of primary transformants. Mod2A1T and Mod3A1T were found to be active in all of the tissues tested, at levels comparable with that of 35S. Further, the expression of the Mod2A1T promoter in the seedlings of the T1 generation was also similar to that of the 35S promoter. The present strategy opens up the possibility of creating a set of synthetic promoters with minimum sequence homology and with expression levels comparable with the wild-type prototype by modifying sequences present between cis-elements for transgene expression in plants.
Expression Pattern of Two Paralogs Encoding Cinnamyl Alcohol Dehydrogenases in Arabidopsis. Isolation and Characterization of the Corresponding Mutants
Authors: Sibout Richard , Eudes Aymerick , Pollet Brigitte , Goujon Thomas , Mila Isabelle , Granier Fabienne , Séguin Armand , Lapierre Catherine , Jouanin Lise 
Published: June 2003

Abstract
Studying Arabidopsis mutants of the phenylpropanoid pathway has unraveled several biosynthetic steps of monolignol synthesis. Most of the genes leading to monolignol synthesis have been characterized recently in this herbaceous plant, except those encoding cinnamyl alcohol dehydrogenase (CAD). We have used the complete sequencing of the Arabidopsis genome to highlight a new view of the complete CAD gene family. Among nine AtCAD genes, we have identified the two distinct paralogs AtCAD-C and AtCAD-D, which share 75% identity and are likely to be involved in lignin biosynthesis in other plants. Northern, semiquantitative restriction fragment-length polymorphism-reverse transcriptase-polymerase chain reaction and western analysis revealed that AtCAD-C and AtCAD-D mRNA and protein ratios were organ dependent. Promoter activities of both genes are high in fibers and in xylem bundles. However, AtCAD-C displayed a larger range of sites of expression than AtCAD-D. Arabidopsis null mutants (Atcad-D and Atcad-C) corresponding to both genes were isolated. CAD activities were drastically reduced in both mutants, with a higher impact on sinapyl alcohol dehydrogenase activity (6% and 38% of residual sinapyl alcohol dehydrogenase activities for Atcad-D and Atcad-C, respectively). Only Atcad-D showed a slight reduction in Klason lignin content and displayed modifications of lignin structure with a significant reduced proportion of conventional S lignin units in both stems and roots, together with the incorporation of sinapaldehyde structures ether linked at Cβ. These results argue for a substantial role of AtCAD-D in lignification, and more specifically in the biosynthesis of sinapyl alcohol, the precursor of S lignin units.
Identification of Glycosylphosphatidylinositol-Anchored Proteins in Arabidopsis. A Proteomic and Genomic Analysis
Authors: Borner Georg H.H. , Lilley Kathryn S. , Stevens Timothy J. , Dupree Paul 
Published: June 2003

Abstract
In a recent bioinformatic analysis, we predicted the presence of multiple families of cell surface glycosylphosphatidylinositol (GPI)-anchored proteins (GAPs) in Arabidopsis (G.H.H. Borner, D.J. Sherrier, T.J. Stevens, I.T. Arkin, P. Dupree [2002] Plant Physiol 129: 486-499). A number of publications have since demonstrated the importance of predicted GAPs in diverse physiological processes including root development, cell wall integrity, and adhesion. However, direct experimental evidence for their GPI anchoring is mostly lacking. Here, we present the first, to our knowledge, large-scale proteomic identification of plant GAPs. Triton X-114 phase partitioning and sensitivity to phosphatidylinositol-specific phospholipase C were used to prepare GAP-rich fractions from Arabidopsis callus cells. Two-dimensional fluorescence difference gel electrophoresis and one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis demonstrated the existence of a large number of phospholipase C-sensitive Arabidopsis proteins. Using liquid chromatography-tandem mass spectrometry, 30 GAPs were identified, including six β-1,3 glucanases, five phytocyanins, four fasciclin-like arabinogalactan proteins, four receptor-like proteins, two Hedgehog-interacting-like proteins, two putative glycerophosphodiesterases, a lipid transfer-like protein, a COBRA-like protein, SKU5, and SKS1. These results validate our previous bioinformatic analysis of the Arabidopsis protein database. Using the confirmed GAPs from the proteomic analysis to train the search algorithm, as well as improved genomic annotation, an updated in silico screen yielded 64 new candidates, raising the total to 248 predicted GAPs in Arabidopsis.
The Monosaccharide Transporter Gene, AtSTP4, and the Cell-Wall Invertase, Atβfruct1, Are Induced in Arabidopsis during Infection with the Fungal Biotroph Erysiphe cichoracearum
Authors: Fotopoulos Vasileios , Gilbert Martin J. , Pittman Jon K. , Marvier Alison C. , Buchanan Aram J. , Sauer Norbert , Hall J.L. , Williams Lorraine E. 
Published: June 2003

Abstract
Powdery mildew fungi are biotrophic pathogens that form a complex interface, the haustorium, between the host plant and the parasite. The pathogen acts as an additional sink, competing with host sinks, resulting in considerable modification of photoassimilate production and partitioning within the host tissue. Here, we examine the factors that may contribute to these changes. We show for the first time in one biotrophic interaction (Arabidopsis/Erysiphe cichoracearum) all of the following responses: Glc uptake in host tissues is enhanced after fungal infection; this coincides with the induction of expression of the monosaccharide transporter gene, Arabidopsis sugar transport protein 4 (AtSTP4), in infected leaves; invertase activity and transcript levels for a cell wall invertase, Atβfruct1, increase substantially in Arabidopsis during attack by this pathogen. Before infection, Arabidopsis plants transformed with an AtSTP4 promoter-β-glucuronidase construct show expression mainly in sink tissues such as roots; after infection, AtSTP4 expression is induced in the mature leaves and increases over the 6-d time period. Sections of infected leaves stained for β-glucuronidase show that AtSTP4 expression is not confined to infected epidermal cells but is also evident in a wider range of cells, including those of the vascular tissue. The results are discussed in relation to the possible coordinated expression of hexose transporters and cell wall invertase in the host response to powdery mildew infection.
Overexpression of AtCPS and AtKS in Arabidopsis Confers Increased ent-Kaurene Production But No Increase in Bioactive Gibberellins
Authors: Fleet Christine M. , Yamaguchi Shinjiro , Hanada Atsushi , Kawaide Hiroshi , David Charles J. , Kamiya Yuji , Sun Tai-ping 
Published: June 2003

Abstract
The plant growth hormone gibberellin (GA) is important for many aspects of plant growth and development. Although most genes encoding enzymes at each step of the GA biosynthetic pathway have been cloned, their regulation is less well understood. To assess how up-regulation of early steps affects the biosynthetic pathway overall, we have examined transgenic Arabidopsis plants that overexpress either AtCPS or AtKS or both. These genes encode the enzymes ent-copalyl diphosphate synthase (CPS) and ent-kaurene synthase, which catalyze the first two committed steps in GA biosynthesis. We find that both CPS and CPS/ent-kaurene synthase overexpressors have greatly increased levels of the early intermediates ent-kaurene and ent-kaurenoic acid, but a lesser increase of later metabolites. These overexpression lines do not exhibit any GA overdose morphology and have wild-type levels of bioactive GAs. Our data show that CPS is limiting for ent-kaurene production and suggest that conversion of ent-kaurenoic acid to GA12 by ent-kaurenoic acid oxidase may be an important rate-limiting step for production of bioactive GA. These results demonstrate the ability of plants to maintain GA homeostasis despite large changes in accumulation of early intermediates in the biosynthetic pathway.
The GMD1 and GMD2 Genes of Arabidopsis Encode Isoforms of GDP-D-Mannose 4,6-Dehydratase with Cell Type-Specific Expression Patterns
Authors: Bonin Christopher P. , Freshour Glenn , Hahn Michael G. , Vanzin Gary F. , Reiter Wolf-Dieter 
Published: June 2003

Abstract
l-Fucose (l-Fuc) is a monosaccharide constituent of plant cell wall polysaccharides and glycoproteins. The committing step in the de novo synthesis of l-Fuc is catalyzed by GDP-d-mannose 4,6-dehydratase, which, in Arabidopsis, is encoded by the GMD1 and GMD2 (MUR1) genes. To determine the functional significance of this genetic redundancy, the expression patterns of both genes were investigated via promoter-β-glucuronidase fusions and immunolocalization of a Fuc-containing epitope. GMD2 is expressed in most cell types of the root, with the notable exception of the root tip where strong expression of GMD1 is observed. Within shoot organs, GMD1::GUS expression is confined to stipules and pollen grains leading to fucosylation of the walls of these cell types in the mur1 mutant. These results suggest that GMD2 represents the major housekeeping gene for the de novo synthesis of GDP-l-Fuc, whereas GMD1 expression is limited to a number of specialized cell types. We conclude that the synthesis of GDP-l-Fuc is controlled in a cell-autonomous manner by differential expression of two isoforms of the same enzyme.
Characterization of green seed, an Enhancer of abi3-1 in Arabidopsis That Affects Seed Longevity
Authors: Clerkx Emile J.M. , Vries Hetty Blankestijn-De , Ruys Gerda J. , Groot Steven P.C. , Koornneef Maarten 
Published: June 2003

Abstract
Seeds are usually stored in physiological conditions in which they gradually lose their viability and vigor depending on storage conditions, storage time, and genotype. Very little is known about the underlying genetics of seed storability and seed deterioration. We analyzed a mutant in Arabidopsis disturbed in seed storability. This mutant was isolated as a grs (green-seeded) mutant in an abi3-1 (abscisic acid 3) mutant background. Genetic and physiological characterization showed that the monogenic grs mutant was not visibly green seeded and mapped on chromosome 4. This enhancer mutation did not affect the ABA sensitivity of seed germination or seed dormancy but was found to affect seed storability and seedling vigor. Seed storability was assessed in a controlled deterioration test, in which the germination capacity of the mutant decreased with the duration of the treatment. The decrease in viability and vigor was confirmed by storing the seeds in two relative humidities (RHs) for a prolonged period. At 60% RH, the mutant lost germinability, but storage at 32% RH showed no decrease of germination although seed vigor decreased. The decrease in viability and vigor could be related to an increase in conductivity, suggesting membrane deterioration. This was not affected by light conditions during imbibition, expected to influence the generation of active oxygen species. During seed maturation, ABI3 regulates several processes: acquiring dormancy and long-term storability and loss of chlorophyll. Our results indicate that GRS is a common regulator in the latter two but not of dormancy/germination.
Arabidopsis Genes Involved in Acyl Lipid Metabolism. A 2003 Census of the Candidates, a Study of the Distribution of Expressed Sequence Tags in Organs, and a Web-Based Database
Authors: Beisson Frédéric , Koo Abraham J.K. , Ruuska Sari , Schwender Jörg , Pollard Mike , Thelen Jay J. , Paddock Troy , Salas Joaquín J. , Savage Linda , Milcamps Anne , Mhaske Vandana B. , Cho Younghee , Ohlrogge John B. 
Published: June 2003

Abstract
The genome of Arabidopsis has been searched for sequences of genes involved in acyl lipid metabolism. Over 600 encoded proteins have been identified, cataloged, and classified according to predicted function, subcellular location, and alternative splicing. At least one-third of these proteins were previously annotated as “unknown function” or with functions unrelated to acyl lipid metabolism; therefore, this study has improved the annotation of over 200 genes. In particular, annotation of the lipolytic enzyme group (at least 110 members total) has been improved by the critical examination of the biochemical literature and the sequences of the numerous proteins annotated as “lipases.” In addition, expressed sequence tag (EST) data have been surveyed, and more than 3,700 ESTs associated with the genes were cataloged. Statistical analysis of the number of ESTs associated with specific cDNA libraries has allowed calculation of probabilities of differential expression between different organs. More than 130 genes have been identified with a statistical probability &gt; 0.95 of preferential expression in seed, leaf, root, or flower. All the data are available as a Web-based database, the Arabidopsis Lipid Gene database (http://www.plantbiology.msu.edu/lipids/genesurvey/index.htm). The combination of the data of the Lipid Gene Catalog and the EST analysis can be used to gain insights into differential expression of gene family members and sets of pathway-specific genes, which in turn will guide studies to understand specific functions of individual genes.
Identification and Characterization of Aluminum Tolerance Loci in Arabidopsis (Landsberg erecta × Columbia) by Quantitative Trait Locus Mapping. A Physiologically Simple But Genetically Complex Trait
Authors: Hoekenga Owen A. , Vision Todd J. , Shaff Jon E. , Monforte Antonio J. , Lee Gung Pyo , Howell Stephen H. , Kochian Leon V. 
Published: June 2003

Abstract
Aluminum (Al) toxicity, which is caused by the solubilization of Al3+ in acid soils resulting in inhibition of root growth and nutrient/water acquisition, is a serious limitation to crop production, because up to one-half of the world's potentially arable land is acidic. To date, however, no Al tolerance genes have yet been cloned. The physiological mechanisms of tolerance are somewhat better understood; the major documented mechanism involves the Al-activated release of Al-binding organic acids from the root tip, preventing uptake into the primary site of toxicity. In this study, a quantitative trait loci analysis of Al tolerance in Arabidopsis was conducted, which also correlated Al tolerance quantitative trait locus (QTL) with physiological mechanisms of tolerance. The analysis identified two major loci, which explain approximately 40% of the variance in Al tolerance observed among recombinant inbred lines derived from Landsberg erecta (sensitive) and Columbia (tolerant). We characterized the mechanism by which tolerance is achieved, and we found that the two QTL cosegregate with an Al-activated release of malate from Arabidopsis roots. Although only two of the QTL have been identified, malate release explains nearly all (95%) of the variation in Al tolerance in this population. Al tolerance in Landsberg erecta × Columbia is more complex genetically than physiologically, in that a number of genes underlie a single physiological mechanism involving root malate release. These findings have set the stage for the subsequent cloning of the genes responsible for the Al tolerance QTL, and a genomics-based cloning strategy and initial progress on this are also discussed.
‘A Matter of Much Contention in the Realm’: Parish Controversies over Communion Bread in Post‐Reformation England
Authors: Haigh Christopher 
Published: June 2003

AbstractIn 1559 the Book of Common Prayer ordered that bread should be used at communion services in English churches, but the royal Injunctions prescribed wafers. At first, Archbishop Parker and most of his bishops tried to enforce wafers, as Queen Elizabeth commanded, but this led to protests from Protestant clergy and some laypeople, who regarded the wafers as popish. After Parker's death in 1575, however, the bishops were more inclined to enforce the use of bread – which led to widespread objections from parishioners who wanted the customary wafers. ‘Bread or wafers’ became a divisive issue in many parts of England, with Protestants refusing wafers when offered and traditionalists refusing bread. By the mid‐1590s, however, most congregations had got used to bread, and after the Canons of 1604 the last of the wafer‐using parishes came into line. Bread had won the day.
Excluded Souls: The Wayward and Excommunicated in Counter‐Reformation Spain
Authors: Tausiet María 
Published: June 2003

AbstractIn the late sixteenth century, one of the main weapons used by the Catholic and Counter‐Reformation church to discipline its faithful was the application of excommunication. In theory this was the gravest spiritual punishment because it meant not only deprivation of the sacraments but also of communication and human relations. However, the abuse of excommunication from the late middle ages onwards led to its discredit and the loss of its former significance. In 1563 the Council of Trent made a decisive move to re‐establish excommunication as a punishment for disobedience, rebelliousness or contumacy, no matter what the reasons were for the contumacy. Detailed analysis of the excommunicated in Counter‐Reformation Spain through the writings of contemporary theologians and the actual policy practised by the two institutions in charge of ecclesiastical justice (episcopal courts and the Inquisition), reveals a picture in which many people were excommunicated not because of their rebelliousness, as the Church claimed, but rather as a result of either their carelessness or indifference or because they practised a kind of religiosity that was alien to the official religion.
Praying by Number: The Confraternity of the Rosary and the English Catholic Community, c.1580–1700
Authors: Dillon Anne 
Published: June 2003

AbstractThe image of the rosary recurs as a constant and familiar sign throughout the sources of Reformation English Catholicism. It rarely elicits comment other than to mark it as an example of a remnant of late medieval devotion, which survived and continued to be practised by the recusant community. This article argues that such impressions of quiescence and continuity are deceptive. The devotion was revised and amended by the Jesuits in the light of Counter‐Reformation initiatives and teaching and specifically adapted to meet the particular conditions they encountered on the English mission. Newly refigured, the rosary was encoded and promoted among English Catholics within the context of the Confraternity of the Rosary. In this way, the Jesuits redeveloped the rosary both as a simple and effective didactic instrument which they used to bring Counter‐Reformation doctrine and practice into the heart of the English Catholic community, and as a symbol of Catholic loyalty to encourage Catholic separation and recusancy.
The Call to Public Service: Entrance, Learning, and Reflection
Authors: Kiel L. Douglas 
Published: June 2003

Books reviewed in this article:Richard P. Nathan, So You Want to Be in Government? Handbook for Appointed Officials in America's GovernmentsKenneth H. Ashworth, Caught between the Dog and the Fireplug, or, How to Survive Public ServiceO.C. McSwite, Invitation to Public Administration