bluuebunny/crossref_metadata_2025_split huggingface dataset:
The tail pigmentation pattern of C57BL/6J mice affects nociception/pain quantification in the tail flick test
Authors: Wen Ting , Ansonoff Michael A. , Pintar John E. 
Published: September 2008

ABSTRACTThe heat radiant tail flick test is commonly used to quantify nociception and pain levels. Likewise, the C57BL/6J strain of mice is frequently used in pain‐related studies as transgenic mice are often backcrossed onto this background. C57BL/6J mice naturally develop non‐pigmented patches of variable length on the distal part of the tail that could conceivably modify the response latency in tail flick assays. Here we find that these non‐pigmented regions, in a position‐independent manner, significantly increase the response latency in the heat radiant tail flick assay, but not the warm water immersion test. This finding demonstrates that the extent of pigmentation, and not other potential variables between pigmented and non‐pigmented skin, affects radiant heat tail flick latency, and should be considered in the design of pain‐related studies using mice with variable tail pigmentation.
Establishing a New Animal Model for the Study of Laryngeal Biology and Disease: An Anatomic Study of the Mouse Larynx
Authors: Thomas Lisa B. , Stemple Joseph C. , Andreatta Richard D. , Andrade Francisco H. 
Published: September 2008

PurposeAnimal models have contributed greatly to the study of voice, permitting the examination of laryngeal biology and the testing of surgical, medical, and behavioral interventions. Various models have been used. However, until recently, the mouse(Mus musculus) has not been used in laryngeal research, and features of the mouse larynx have not been defined. Therefore, the purpose of this study was to qualitatively describe mouse laryngeal anatomy in relation to known human anatomy.MethodsLarynges of 7 C57BL mice were examined and photographed under stereotactic and light microscopy.ResultsThe authors found that mouse laryngeal organization was similar to that of humans. The hyoid bone and epiglottal, thyroid, cricoid, and arytenoid cartilages were identified. An additional cartilage was present ventrally. Thyroarytenoid, posterior cricoarytenoid, lateral cricoarytenoid, and cricothyroid muscles were grossly positioned as in humans. Interarytenoid muscles were not present; however, a functional counterpart was identified.ConclusionsThe authors provide an initial description of mouse laryngeal anatomy. Because of its amenability to genetic engineering, the mouse is the premiere model for the study of disease and the testing of interventions. Introduction of the mouse model for laryngeal study offers a tool for the study of normal laryngeal cell biology and tissue response to disease processes.
Optimal stepwise experimental design for pairwise functional interaction studies
Authors: Casey Fergal P. , Cagney Gerard , Krogan Nevan J. , Shields Denis C. 
Published: September 2008

AbstractMotivation: Pairwise experimental perturbation is increasingly used to probe gene and protein function because these studies offer powerful insight into the activity and regulation of biological systems. Symmetric two-dimensional datasets, such as pairwise genetic interactions are amenable to an optimally designed measurement procedure because of the equivalence of cases and conditions where fewer experimental measurements may be required to extract the underlying structure.Results: We show that optimal experimental design can provide improvements in efficiency when collecting data in an iterative manner. We develop a method built on a statistical clustering model for symmetric data and the Fisher information uncertainty estimates, and we also provide simple heuristic approaches that have comparable performance. Using yeast epistatic miniarrays as an example, we show that correct assignment of the major subnetworks could be achieved with &lt;50% of the measurements in the complete dataset. Optimization is likely to become critical as pairwise functional studies extend to more complex mammalian systems where all by all experiments are currently intractable.Contact: fergal.p.casey@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online.
Empirically modelling the potential effects of changes in temperature and prey availability on the growth of cod larvae in UK shelf seas
Authors: Pitois Sophie G. , Fox Clive J. 
Published: September 2008

Abstract
Pitois, S. G., and Fox, C. J. 2008. Empirically modelling the potential effects of changes in temperature and prey availability on the growth of cod larvae in UK shelf seas. – ICES Journal of Marine Science, 65: 1559–1572. It has been hypothesized that changes in zooplankton community structure over the past four decades led to reduced growth and survival of prerecruit Atlantic cod (Gadus morhua) and that this was a key factor underlying poor year classes, contributing to stock collapse, and inhibiting the recovery of stocks around the UK. To evaluate whether observed changes in plankton abundance, species composition and temperature could have led to periods of poorer growth of cod larvae, we explored the effect of prey availability and temperature on early larval growth using an empirical trophodynamic model. Prey availability was parameterized using species abundance data from the Continuous Plankton Recorder. Our model suggests that the observed changes in plankton community structure in the North Sea may have had less impact on cod larval growth, at least for the first 40 days following hatching, than previously suggested. At least in the short term, environmental and prey conditions should be able to sustain growth of cod larvae and environmental changes acting on this early life stage should not limit stock recovery.
Impact of PsbTc on Forward and Back Electron Flow, Assembly, and Phosphorylation Patterns of Photosystem II in Tobacco
Authors: Umate Pavan , Fellerer Christine , Schwenkert Serena , Zoryan Mikael , Eichacker Lutz A. , Sadanandam Abbagani , Ohad Itzhak , Herrmann Reinhold G. , Meurer Jörg 
Published: September 2008

Abstract
Photosystem II (PSII) of oxygen-evolving cyanobacteria, algae, and land plants mediates electron transfer from the Mn4Ca cluster to the plastoquinone pool. It is a dimeric supramolecular complex comprising more than 30 subunits per monomer, of which 16 are bitopic or peripheral, low-molecular-weight components. Directed inactivation of the plastid gene encoding the low-molecular-weight peptide PsbTc in tobacco (Nicotiana tabacum) does not prevent photoautotrophic growth. Mutant plants appear normal green, and levels of PSII proteins are not affected. Yet, PSII-dependent electron transport, stability of PSII dimers, and assembly of PSII light-harvesting complexes (LHCII) are significantly impaired. PSII light sensitivity is moderately increased and recovery from photoinhibition is delayed, leading to faster D1 degradation in ΔpsbTc under high light. Thermoluminescence emission measurements revealed alterations of midpoint potentials of primary/secondary electron-accepting plastoquinone of PSII interaction. Only traces of CP43 and no D1/D2 proteins are phosphorylated, presumably due to structural changes of PSII in ΔpsbTc. In striking contrast to the wild type, LHCII in the mutant is phosphorylated in darkness, consistent with its association with PSI, indicating an increased pool of reduced plastoquinone in the dark. Finally, our data suggest that the secondary electron-accepting plastoquinone of PSII site, the properties of which are altered in ΔpsbTc, is required for oxidation of reduced plastoquinone in darkness in an oxygen-dependent manner. These data present novel aspects of plastoquinone redox regulation, chlororespiration, and redox control of LHCII phosphorylation.
Transcriptional Profiling of Mature Arabidopsis Trichomes Reveals That NOECK Encodes the MIXTA-Like Transcriptional Regulator MYB106
Authors: Jakoby Marc J. , Falkenhan Doris , Mader Michael T. , Brininstool Ginger , Wischnitzki Elisabeth , Platz Nicole , Hudson Andrew , Hülskamp Martin , Larkin John , Schnittger Arp 
Published: September 2008

Abstract
Leaf hairs (trichomes) of Arabidopsis (Arabidopsis thaliana) have been extensively used as a model to address general questions in cell and developmental biology. Here, we lay the foundation for a systems-level understanding of the biology of this model cell type by performing genome-wide gene expression analyses. We have identified 3,231 genes that are up-regulated in mature trichomes relative to leaves without trichomes, and we compared wild-type trichomes with two mutants, glabra3 and triptychon, that affect trichome morphology and physiology in contrasting ways. We found that cell wall-related transcripts were particularly overrepresented in trichomes, consistent with their highly elaborated structure. In addition, trichome expression maps revealed high activities of anthocyanin, flavonoid, and glucosinolate pathways, indicative of the roles of trichomes in the biosynthesis of secondary compounds and defense. Interspecies comparisons revealed that Arabidopsis trichomes share many expressed genes with cotton (Gossypium hirsutum) fibers, making them an attractive model to study industrially important fibers. In addition to identifying physiological processes involved in the development of a specific cell type, we also demonstrated the utility of transcript profiling for identifying and analyzing regulatory gene function. One of the genes that are differentially expressed in fibers is the MYB transcription factor GhMYB25. A combination of transcript profiling and map-based cloning revealed that the NOECK gene of Arabidopsis encodes AtMYB106, a MIXTA-like transcription factor and homolog of cotton GhMYB25. However, in contrast to Antirrhinum, in which MIXTA promotes epidermal cell outgrowth, AtMYB106 appears to function as a repressor of cell outgrowth in Arabidopsis.
Alterations in Cytosolic Glucose-Phosphate Metabolism Affect Structural Features and Biochemical Properties of Starch-Related Heteroglycans
Authors: Fettke Joerg , Nunes-Nesi Adriano , Alpers Jessica , Szkop Michal , Fernie Alisdair R. , Steup Martin 
Published: September 2008

AbstractThe cytosolic pools of glucose-1-phosphate (Glc-1-P) and glucose-6-phosphate are essential intermediates in several biosynthetic paths, including the formation of sucrose and cell wall constituents, and they are also linked to the cytosolic starch-related heteroglycans. In this work, structural features and biochemical properties of starch-related heteroglycans were analyzed as affected by the cytosolic glucose monophosphate metabolism using both source and sink organs from wild-type and various transgenic potato (Solanum tuberosum) plants. In leaves, increased levels of the cytosolic phosphoglucomutase (cPGM) did affect the cytosolic heteroglycans, as both the glucosyl content and the size distribution were diminished. By contrast, underexpression of cPGM resulted in an unchanged size distribution and an unaltered or even increased glucosyl content of the heteroglycans. Heteroglycans prepared from potato tubers were found to be similar to those from leaves but were not significantly affected by the level of cPGM activity. However, external glucose or Glc-1-P exerted entirely different effects on the cytosolic heteroglycans when added to tuber discs. Glucose was directed mainly toward starch and cell wall material, but incorporation into the constituents of the cytosolic heteroglycans was very low and roughly reflected the relative monomeric abundance. By contrast, Glc-1-P was selectively taken up by the tuber discs and resulted in a fast increase in the glucosyl content of the heteroglycans that quantitatively reflected the level of the cytosolic phosphorylase activity. Based on 14C labeling experiments, we propose that in the cytosol, glucose and Glc-1-P are metabolized by largely separated paths.
High Glycolate Oxidase Activity Is Required for Survival of Maize in Normal Air
Authors: Zelitch Israel , Schultes Neil P. , Peterson Richard B. , Brown Patrick , Brutnell Thomas P. 
Published: September 2008

Abstract
A mutant in the maize (Zea mays) Glycolate Oxidase1 (GO1) gene was characterized to investigate the role of photorespiration in C4 photosynthesis. An Activator-induced allele of GO1 conditioned a seedling lethal phenotype when homozygous and had 5% to 10% of wild-type GO activity. Growth of seedlings in high CO2 (1%–5%) was sufficient to rescue the mutant phenotype. Upon transfer to normal air, the go1 mutant became necrotic within 7 d and plants died within 15 d. Providing [1-14C]glycolate to leaf tissue of go1 mutants in darkness confirmed that the substrate is inefficiently converted to 14CO2, but both wild-type and GO-deficient mutant seedlings metabolized [1-14C]glycine similarly to produce [14C]serine and 14CO2 in a 1:1 ratio, suggesting that the photorespiratory pathway is otherwise normal in the mutant. The net CO2 assimilation rate in wild-type leaves was only slightly inhibited in 50% O2 in high light but decreased rapidly and linearly with time in leaves with low GO. When go1 mutants were shifted from high CO2 to air in light, they accumulated glycolate linearly for 6 h to levels 7-fold higher than wild type and 11-fold higher after 25 h. These studies show that C4 photosynthesis in maize is dependent on photorespiration throughout seedling development and support the view that the carbon oxidation pathway evolved to prevent accumulation of toxic glycolate.
A Protracted and Dynamic Maturation Schedule UnderliesArabidopsisLeaf Development
Authors: Efroni Idan , Blum Eyal , Goldshmidt Alexander , Eshed Yuval 
Published: September 2008

AbstractLeaf development has been monitored chiefly by following anatomical markers. Analysis of transcriptome dynamics during leaf maturation revealed multiple expression patterns that rise or fall with age or that display age-specific peaks. These were used to formulate a digital differentiation index (DDI) based on a set of selected markers with informative expression during leaf ontogeny. The leaf-based DDI reliably predicted the developmental state of leaf samples from diverse sources and was independent of mitotic cell division transcripts or propensity of specific cell types. When calibrated by informative root markers, the same algorithm accurately diagnosed dissected root samples. We used the DDI to characterize plants with reduced activities of multiple CINCINNATA (CIN)-TCP (TEOSINTE BRANCHED1, CYCLOIDEA, PCF) growth regulators. These plants had giant curled leaves made up of small cells with abnormal shape, low DDI scores, and low expression of mitosis markers, depicting the primary role of CIN-TCPs as promoters of differentiation. Delayed activity of several CIN-TCPs resulted in abnormally large but flat leaves with regular cells. The application of DDI has therefore portrayed the CIN-TCPs as heterochronic regulators that permit the development of a flexible and robust leaf form through an ordered and protracted maturation schedule.
Genetic Analysis Reveals That C19-GA 2-Oxidation Is a Major Gibberellin Inactivation Pathway inArabidopsis
Authors: Rieu Ivo , Eriksson Sven , Powers Stephen J. , Gong Fan , Griffiths Jayne , Woolley Lindsey , Benlloch Reyes , Nilsson Ove , Thomas Stephen G. , Hedden Peter , Phillips Andrew L. 
Published: September 2008

AbstractBioactive hormone concentrations are regulated both at the level of hormone synthesis and through controlled inactivation. Based on the ubiquitous presence of 2β-hydroxylated gibberellins (GAs), a major inactivating pathway for the plant hormone GA seems to be via GA 2-oxidation. In this study, we used various approaches to determine the role of C19-GA 2-oxidation in regulating GA concentration and GA-responsive plant growth and development. We show that Arabidopsis thaliana has five C19-GA 2-oxidases, transcripts for one or more of which are present in all organs and at all stages of development examined. Expression of four of the five genes is subject to feed-forward regulation. By knocking out all five Arabidopsis C19-GA 2-oxidases, we show that C19-GA 2-oxidation limits bioactive GA content and regulates plant development at various stages during the plant life cycle: C19-GA 2-oxidases prevent seed germination in the absence of light and cold stimuli, delay the vegetative and floral phase transitions, limit the number of flowers produced per inflorescence, and suppress elongation of the pistil prior to fertilization. Under GA-limited conditions, further roles are revealed, such as limiting elongation of the main stem and side shoots. We conclude that C19-GA 2-oxidation is a major GA inactivation pathway regulating development in Arabidopsis.
Civilisation and its disconnects
Authors: Hunt Robin 
Published: September 2008

PurposeThis paper aims to explore some initial and necessarily broad ideas about the effects of the world wide web on our methods of understanding and trusting, online and off.Design/methodology/approachThe paper considers the idea of trust via some of the revolutionary meanings inherent in the world wide web at its public conception in 1994, and some of its different meanings now. It does so in the context of the collaborative reader‐writer Web2.0 (of today), and also through a brief exploration of our relationship to the grand narratives (and some histories) of the post‐war West. It uses a variety of formal approaches taken from information science, literary criticism, philosophy, history, and journalism studies – together with some practical analysis based on 15 years as a web practitioner and content creator. It is a starting point.FindingsThis paper suggests that a pronounced effect of the world wide web is the further atomising of many once‐shared Western post‐war narratives, and the global democratising of doubt as a powerful though not necessarily helpful epistemological tool. The world wide web is the place that most actively demonstrates contemporary doubt.Research limitations/implicationsThis is the starting place for a piece of larger cross‐faculty (and cross‐platform) research into the arena of trust and doubt. In particular, the relationship of concepts such as news, event, history and myth with the myriad content platforms of new media, the idea of the digital consumer, and the impact of geography on knowledge that is enshrined in the virtual. This paper attempts to frame a few of the initial issues inherent in the idea of “trust” in the digital age and argues that without some kind of shared aesthetics of narrative judgment brought about through a far broader public understanding of (rather than an interpretation of) oral, visual, literary and multi‐media narratives, stories and plots, we cannot be said to trust many types of knowledge – not just in philosophical terms but also in our daily actions and behaviours.Originality/valueThis paper initiates debate about whether the creation of a new academic “space” in which cross‐faculty collaborations into the nature of modern narrative (in terms of production and consumption; producers and consumers) might be able to help us to understand more of the social implications of the collaborative content produced for consumption on the world wide web.
Information‐seeking behaviour of physicists and astronomers
Authors: Jamali Hamid R. , Nicholas David 
Published: September 2008

PurposeThe study aims to examines two aspects of information seeking behaviour of physicists and astronomers including methods applied for keeping up‐to‐date and methods used for finding articles. The relationship between academic status and research field of users with their information seeking behaviour was investigated.Design/methodology/approachData were gathered using a questionnaire survey of PhD students and staff of the Department of Physics and Astronomy at University College London; 114 people (47.1 per cent response rate) participated in the survey.FindingsThe study reveals differences among subfields of physics and astronomy in terms of information‐seeking behaviour, highlights the need for and the value of looking at narrower subject communities within disciplines for a deeper understanding of the information behaviour of scientists.Originality/valueThe study is the first to deeply investigate intradisciplinary dissimilarities of information‐seeking behaviour of scientists in a discipline. It is also an up‐to‐date account of information seeking behaviour of physicists and astronomers.
Iranian women in science: a gender study of scientific productivity in an Islamic country
Authors: Mozaffarian Mehrnoush , Jamali Hamid R. 
Published: September 2008

PurposeThe aim of the paper is to explore and test gender differences in the authorship of Iranian journal articles.Design/methodology/approachA list of articles published by Iranian authors in ISI journals in 2003 was obtained from the Web of Science. The names of authors were searched in a specific database as well as the web to find their first names and hence their gender. The articles were then broken down by gender and subject category. International collaborations of the authors were also investigated.FindingsThe productivity of female authors at the individual level as measured by article per author share was lower than male authors. In total, females accounted for 6 per cent and males for 94 per cent of the articles published in 2003. A chi‐square test showed that female contribution was significantly lower than expected.Originality/valueThe study is the first to investigate gender participation in scientific productivity in Iran and most likely in a Muslim country. The article highlights the need for qualitative studies on the gender aspect of scientific productivity in Muslim countries.
Transition and people with learning disabilities
Authors: Williams Peter 
Published: September 2008

PurposeThe paper's purpose is to describe the information content of web sites developed by and for people with learning disabilities around the theme of transition from school to adulthood.Design/methodology/approachThe paper adopts a content analysis approach, in which subject experts evaluate user‐generated content produced as part of a project on inclusion and people with learning disabilities.FindingsDespite being only one theme of a number pertaining to transition, leisure, entertainment and hobby‐related information dominated the web sites. Other issues elicited included that of writing about one's personal experiences providing limited information of use to others, the key role of carers/supporters in information provision, and some material being too difficult for people with learning disabilities to understand.Practical implicationsThe paper shows that for the information service to be valuable and relevant to the target audience, much training and considerable time investment are required for both people with learning disabilities and their supporters. The practice of creating and uploading information on to the web site holds benefits to the creator beyond mere information provision.Originality/valueThe development of information services for people with learning disabilities by the service users themselves is an important innovation. This paper points out how such an inclusive approach could work in the future.