bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Central Role of a SNRK2 Kinase in Sulfur Deprivation Responses
Authors: Gonzalez-Ballester David , Pollock Steve V. , Pootakham Wirulda , Grossman Arthur R. 
Published: March 2008

Abstract
In the absence of sulfur (S), Chlamydomonas reinhardtii increases the abundance of several transcripts encoding proteins associated with S acquisition and assimilation, conserves S amino acids, and acclimates to suboptimal growth conditions. A positive regulator, SAC1 (for sulfur acclimation protein 1), and a negative regulator, SAC3, were shown to participate in the control of these processes. In this study, we investigated two allelic mutants (ars11 and ars44) affected in a gene encoding a SNRK2 (for SNF1-related protein kinase 2) kinase designated SNRK2.1. Like the sac1 mutant, both snrk2.1 mutants were deficient in the expression of S-responsive genes. Furthermore, the mutant cells bleached more rapidly than wild-type cells during S deprivation, although the phenotypes of ars11 and ars44 were not identical: ars11 exhibited a more severe phenotype than either ars44 or sac1. The phenotypic differences between the ars11 and ars44 mutants reflected distinct alterations of SNRK2.1 mRNA splicing caused by insertion of the marker gene. The ars11 phenotype could be rescued by complementation with SNRK2.1 cDNA. In contrast to the nonepistatic relationship between SAC3 and SAC1, characterization of the sac3 ars11 double mutant showed that SNRK2.1 is epistatic to SAC3. These data reveal the crucial regulatory role of SNRK2.1 in the signaling cascade critical for eliciting S deprivation responses in Chlamydomonas. The phylogenetic relationships and structures of the eight members of the SNRK2 family in Chlamydomonas are discussed.
Isolation and Characterization of Mutants of Common Ice Plant Deficient in Crassulacean Acid Metabolism
Authors: Cushman John C. , Agarie Sakae , Albion Rebecca L. , Elliot Stewart M. , Taybi Tahar , Borland Anne M. 
Published: March 2008

AbstractCrassulacean acid metabolism (CAM) is a specialized mode of photosynthesis that improves water use efficiency by shifting part or all of net atmospheric CO2 uptake to the night. Genetic dissection of regulatory and metabolic attributes of CAM has been limited by the difficulty of identifying a reliable phenotype for mutant screening. We developed a novel and simple colorimetric assay to measure leaf pH to screen fast neutron-mutagenized populations of common ice plant (Mesembryanthemum crystallinum), a facultative CAM species, to detect CAM-deficient mutants with limited nocturnal acidification. The isolated CAM-deficient mutants showed negligible net dark CO2 uptake compared with wild-type plants following the imposition of salinity stress. The mutants and wild-type plants accumulated nearly comparable levels of sodium in leaves, but the mutants grew more slowly than the wild-type plants. The mutants also had substantially reduced seed set and seed weight relative to wild type under salinity stress. Carbon-isotope ratios of seed collected from 4-month-old plants indicated that C3 photosynthesis made a greater contribution to seed production in mutants compared to wild type. The CAM-deficient mutants were deficient in leaf starch and lacked plastidic phosphoglucomutase, an enzyme critical for gluconeogenesis and starch formation, resulting in substrate limitation of nocturnal C4 acid formation. The restoration of nocturnal acidification by feeding detached leaves of salt-stressed mutants with glucose or sucrose supported this defect and served to illustrate the flexibility of CAM. The CAM-deficient mutants described here constitute important models for exploring regulatory features and metabolic consequences of CAM.
A Third Phytoene Synthase Is Devoted to Abiotic Stress-Induced Abscisic Acid Formation in Rice and Defines Functional Diversification of Phytoene Synthase Genes
Authors: Welsch Ralf , Wüst Florian , Bär Cornelia , Al-Babili Salim , Beyer Peter 
Published: March 2008

AbstractWe here report on the characterization of a novel third phytoene synthase gene (PSY) in rice (Oryza sativa), OsPSY3, and on the differences among all three PSY genes with respect to the tissue-specific expression and regulation upon various environmental stimuli. The two already known PSYs are under phytochrome control and involved in carotenoid biosynthesis in photosynthetically active tissues and exhibit different expression patterns during chloroplast development. In contrast, OsPSY3 transcript levels are not affected by light and show almost no tissue-specific differences. Rather, OsPSY3 transcripts are up-regulated during increased abscisic acid (ABA) formation upon salt treatment and drought, especially in roots. The simultaneous induction of genes encoding 9-cis-epoxycarotenoid dioxygenases (NCEDs), involved in the initial steps of ABA biosynthesis, indicate that decreased xanthophyll levels are compensated by the induction of the third PSY gene. Furthermore, OsPSY3 and the OsNCEDs investigated were also induced by the application of ABA, indicating positive feedback regulation. The regulatory differences are mirrored by cis-acting elements in the corresponding promoter regions, with light-responsive elements for OsPSY1 and OsPSY2 and an ABA-response element as well as a coupling element for OsPSY3. The investigation of the gene structures and 5′ untranslated regions revealed that OsPSY1 represents a descendant of an ancient PSY gene present in the common ancestor of monocots and dicots. Since the genomic structures of OsPSY2 and OsPSY3 are comparable, we conclude that they originated from the most recent common ancestor, OsPSY1.
Modulation of Nitrosative Stress byS-Nitrosoglutathione Reductase Is Critical for Thermotolerance and Plant Growth inArabidopsis
Authors: Lee Ung , Wie Chris , Fernandez Bernadette O. , Feelisch Martin , Vierling Elizabeth 
Published: March 2008

AbstractNitric oxide (NO) is a key signaling molecule in plants. This analysis of Arabidopsis thaliana HOT5 (sensitive to hot temperatures), which is required for thermotolerance, uncovers a role of NO in thermotolerance and plant development. HOT5 encodes S-nitrosoglutathione reductase (GSNOR), which metabolizes the NO adduct S-nitrosoglutathione. Two hot5 missense alleles and two T-DNA insertion, protein null alleles were characterized. The missense alleles cannot acclimate to heat as dark-grown seedlings but grow normally and can heat-acclimate in the light. The null alleles cannot heat-acclimate as light-grown plants and have other phenotypes, including failure to grow on nutrient plates, increased reproductive shoots, and reduced fertility. The fertility defect of hot5 is due to both reduced stamen elongation and male and female fertilization defects. The hot5 null alleles show increased nitrate and nitroso species levels, and the heat sensitivity of both missense and null alleles is associated with increased NO species. Heat sensitivity is enhanced in wild-type and mutant plants by NO donors, and the heat sensitivity of hot5 mutants can be rescued by an NO scavenger. An NO-overproducing mutant is also defective in thermotolerance. Together, our results expand the importance of GSNOR-regulated NO homeostasis to abiotic stress and plant development.
A MYB Transcription Factor Regulates Very-Long-Chain Fatty Acid Biosynthesis for Activation of the Hypersensitive Cell Death Response inArabidopsis
Authors: Raffaele Sylvain , Vailleau Fabienne , Léger Amandine , Joubès Jérôme , Miersch Otto , Huard Carine , Blée Elisabeth , Mongrand Sébastien , Domergue Frédéric , Roby Dominique 
Published: March 2008

AbstractPlant immune responses to pathogen attack include the hypersensitive response (HR), a form of programmed cell death occurring at invasion sites. We previously reported on Arabidopsis thaliana MYB30, a transcription factor that acts as a positive regulator of a cell death pathway conditioning the HR. Here, we show by microarray analyses of Arabidopsis plants misexpressing MYB30 that the genes encoding the four enzymes forming the acyl-coA elongase complex are putative MYB30 targets. The acyl-coA elongase complex synthesizes very-long-chain fatty acids (VLCFAs), and the accumulation of extracellular VLCFA-derived metabolites (leaf epidermal wax components) was affected in MYB30 knockout mutant and overexpressing lines. In the same lines, a lipid extraction procedure allowing high recovery of sphingolipids revealed changes in VLCFA contents that were amplified in response to inoculation. Finally, the exacerbated HR phenotype of MYB30-overexpressing lines was altered by the loss of function of the acyl-ACP thioesterase FATB, which causes severe defects in the supply of fatty acids for VLCFA biosynthesis. Based on these findings, we propose a model in which MYB30 modulates HR via VLCFAs by themselves, or VLCFA derivatives, as cell death messengers in plants.
The Leaf Epidermome ofCatharanthus roseusReveals Its Biochemical Specialization
Authors: Murata Jun , Roepke Jonathon , Gordon Heather , De Luca Vincenzo 
Published: March 2008

AbstractCatharanthus roseus is the sole commercial source of the monoterpenoid indole alkaloids (MIAs), vindoline and catharanthine, components of the commercially important anticancer dimers, vinblastine and vincristine. Carborundum abrasion technique was used to extract leaf epidermis–enriched mRNA, thus sampling the epidermome, or complement, of proteins expressed in the leaf epidermis. Random sequencing of the derived cDNA library established 3655 unique ESTs, composed of 1142 clusters and 2513 singletons. Virtually all known MIA pathway genes were found in this remarkable set of ESTs, while only four known genes were found in the publicly available Catharanthus EST data set. Several novel MIA pathway candidate genes were identified, as demonstrated by the cloning and functional characterization of loganic acid O-methyltransferase involved in secologanin biosynthesis. The pathways for triterpene biosynthesis were also identified, and metabolite analysis showed that oleanane-type triterpenes were localized exclusively to the cuticular wax layer. The pathways for flavonoid and very-long-chain fatty acid biosynthesis were also located in this cell type. The results illuminate the biochemical specialization of Catharanthus leaf epidermis for the production of multiple classes of metabolites. The value and versatility of this EST data set for biochemical and biological analysis of leaf epidermal cells is also discussed.
Data sources for performing citation analysis: an overview
Authors: Neuhaus Christoph , Daniel Hans‐Dieter 
Published: March 2008

PurposeThe purpose of this paper is to provide an overview of new citation‐enhanced databases and to identify issues to be considered when they are used as a data source for performing citation analysis.Design/methodology/approachThe paper reports the limitations of Thomson Scientific's citation indexes and reviews the characteristics of the citation‐enhanced databases Chemical Abstracts, Google Scholar and Scopus.FindingsThe study suggests that citation‐enhanced databases need to be examined carefully, with regard to both their potentialities and their limitations for citation analysis.Originality/valueThe paper presents a valuable overview of new citation‐enhanced databases in the context of research evaluation.
Use of the Universal Decimal Classification
Authors: Slavic Aida 
Published: March 2008

PurposeThe purpose of this paper is to present a general overview with up‐to‐date information on the Universal Decimal Classification (UDC) use worldwide.Design/methodology/approachThe research combined e‐mail interviews with LIS professionals in 208 countries, literature research and information obtained from UDC distributors/publishers (AENOR, BSI, UDC Consortium). The following categorisation of UDC use was offered: A – dominant system; B – used in some kind of libraries only; or C – rarely used.FindingsThe paper finds that, of the 208 countries contacted and researched through the literature in 2004‐2006, the UDC was found to be used in 124 (60 per cent) of these. In 34 (28 per cent) of the countries researched (in Europe, Asia and Africa), UDC is the main classification system used across national information networks. In 45 (36 per cent) of the countries it is used in certain kinds of libraries. In the remaining 45 (36 per cent) of the countries it is used rarely, in only a few libraries or information centres.Research limitations/implicationsIt was beyond the scope of this research to provide any information regarding the actual number of institutions using UDC in a given country or to give an estimate of the size and number of document collections organised by it. Although a decline in UDC use since the 1980s was reported from a number of countries, it was not possible to measure this accurately.Practical implicationsThe interest shown for using UDC in the organisation of digital collections, information exchange and cross domain and cross collection resource discovery depends on accurate knowledge of its actual usage worldwide. This gives a measure of its global importance and verifies its credentials as an indexing standard. This research, which attempted wider and more systematic coverage than previous surveys, should help clarify the status of UDC and its potential use in the networked environment.Originality/valueThe paper provides up‐to‐date information on the presence of the UDC system across countries and languages.
Author‐rated importance of cited references in biology and psychology publications
Authors: Tang Rong , Safer Martin A. 
Published: March 2008

PurposeThe present study aims to investigate how textual features, depth of citation treatment, reasons for citation, and relationships between citers and citees predict author‐rated citation importance.Design/methodology/approachA total of 49 biology and 50 psychology authors assessed the importance, reason for citation, and relationship to the cited author for each cited reference in his or her own recently published empirical article. Participants performed their evaluations on individualized web‐based surveys.FindingsThe paper finds that certain textual features, such as citation frequency, citation length, and citation location, as well as author‐stated reasons for citation predicted ratings of importance, but the strength of the relationship often depended on citation features in the article as a whole. The relationship between objective citation features and author‐rated importance also tended to be weaker for self‐citations.Research limitations/implicationsThe study sample included authors of relatively long empirical articles with a minimum of 35 cited references. There were relatively few disciplinary differences, which suggests that citation behavior in psychology may be similar to that in natural science disciplines. Future studies should involve authors from other disciplines employing diverse referencing patterns in articles of varying lengths and types.Originality/valueFindings of the study have enabled a comprehensive, profound level of understanding of citation behaviors of biology and psychology authors. It uncovered a number of unique characteristics in authors' citation evaluations, such as article‐level context effects and rule‐ versus affective‐based judgments. The paper suggests possible implications for developing retrieval algorithms based on automatically predicted importance of cited references.
Students' search process and outcome in Medline in writing an essay for a class on evidence‐based medicine
Authors: Huuskonen Saila , Vakkari Pertti 
Published: March 2008

PurposeThe aim of this study is to explore to which extent searching by medical students in Medline produces information items useful for writing an essay measured by precision and relative recall as perceived by the students, the proportion of cited items, and their utilization on four dimensions of the essay writing task evaluated by external assessors. It also aims to study interrelations of search process and outcome.Design/methodology/approachThe study subjects were 42 third year medical students attending a class on Diagnostic and therapy. Searching in Medline was a part of their assignment of essay writing. The data consist of students' printed logs of Medline searches, students' assessments of the usefulness of the references retrieved, a questionnaire concerning the search process, and evaluation scores of the essays given by the teachers of the class. Pearson correlation coefficients were calculated for answering the research questions.FindingsThe paper finds that precision and relative recall were not associated with evaluation scores in three of the four dimensions assessed. Some of the process variables were associated with precision and with assessment scores in two of the four dimensions assessed. Citing rate was negatively associated with recall. It seems that precision and recall are only weakly, if at all, associated to the use of information in the documents retrieved for writing the essay. Precision and relative recall are not associated to the way information in the retrieved items is used for performing the task. Users evidently look for a sufficient number of documents containing enough information for progressing in their task. Precision and recall are not sufficient measures in evaluating IR systems, but they have to be completed by other measures indicating the impact of the system on users’ task performance.Originality/valueThe paper provides useful information on students' information search process.
ANTAEUS “Do mention the war”
Authors: Joint Nicholas 
Published: March 2008

PurposeThis paper aims to explore the relationship between library and information management principles and defence and national security.Design/methodology/approachAn opinion piece based on viewpoints from speakers at the 2007 American Library Association conference held in Washington DC, and on recent US writings on US foreign and defence policy. Findings – That there is a verifiable relationship between library and information management principles and defence and national security. But the exact nature of this relationship is open to dispute, which therefore presents important challenges in professional ethics to librarians. Research limitations/implications – It is impossible to define the moral parameters of professional ethical issue in the abstract. Reflective and sophisticated analysis of ethical issues in the particular contemporary context is an ongoing requirement of LIS research.Practical implicationsIt is important for a fully rounded professional to see the relevance of larger moral, political and social issues to the narrower sphere of their professional practice. Originality/value – This paper gives a starting point for the analysis of information principles in terms of the most recent developments in the international political arena.
MLIS program at Kuwait University
Authors: Rehman Sajjad , Marouf Laila 
Published: March 2008

PurposeThis study aims to analyze the perceptions of the graduates of Master in Library and Information Science (MLIS) program at Kuwait University about coursework, faculty, instructional methods, instructional facilities, fieldwork, comprehensive examination, and research component.Design/methodology/approachA survey instrument was used for electronic administration. Eighty graduates of the MLIS program of Kuwait University were identified as population of the study. Sixty‐seven alumni (86.3 per cent) participated in the survey.FindingsBased on the analysis of 61 usable responses, it was found that the faculty and core courses received highest mean scores for satisfaction whereas elective coursework, fieldwork, and comprehensive examinations received the lowest. Qualitative analysis of the participants revealed that the alumni wished broadening the breadth of the elective coursework and fundamental changes in fieldwork and comprehensive examination. Many of them were quite critical of instructional methods and facilities.Research limitations/implicationsResults cannot be generalized to other graduate programs. Yet, these provide procedural guidance and insights about the way these studies of perception can be conducted.Practical implicationsThis input can be meaningfully applied in further development of the MLIS program.Originality/valueIt is original research that carries value for the assessment of graduate programs of library and information studies.
Enticing teenagers into the library
Authors: Snowball Clare 
Published: March 2008

PurposeChildren and teenagers are the future adult users of libraries, and how they are treated in our libraries, particularly school and public libraries, can cement lifelong memories and habits in these young people. This paper aims to address this issue.Design/methodology/approachThe following paper is a review of the literature on young people's, particularly teenagers’ use (or lack thereof) of libraries, the importance of library use and methods to encourage library use in young people.FindingsDespite the findings from some of the literature that teenagers are less likely to visit libraries, there were many services and programmes in libraries that aim to reverse this trend.Research limitations/implicationsSome of the literature is peer‐reviewed, but selected pieces were written by librarians in the field about their interactions with young people in their libraries. Although the latter cannot be generalised to all young people, they are important in providing examples of what occurs in some cases and what might be replicated in other settings.Originality/valueEncouraging young people to visit and enjoy libraries can be a rewarding experience and is important in creating the next generation of library users.
Why should not they benefit from rare books?
Authors: Torre Meredith E. 
Published: March 2008

PurposeSpecial collections departments are predominately portrayed or perceived as a place for researchers rather than as a means for enhancing the learning experience for the undergraduate student. The very nature of rare books and manuscripts means that arguments to discourage their heavy use prevail. The purpose of this paper is to address this issue.Design/methodology/approachThis paper reviews these perceptions, considers why such perceptions continue to thrive, and provides examples in which the image of special collections departments can be refashioned into a more inclusive environment for the undergraduate student.FindingsThere are extraordinary barriers that face the average undergraduate experience with rare books at most academic institutions. Librarians of special collections departments and other primary resource collections can play a fundamental role in making these collections accessible to the undergraduate student.Originality/valueThis paper reexamines the notion that special collections should have limited use due to conservation concerns and demonstrates that using fragile materials may serve as a good opportunity to reflect on the collection's conservational health.