bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of two‐pore‐domain (K2P) potassium leak channels by the tyrosine kinase inhibitor genistein
Authors: Gierten J , Ficker E , Bloehs R , Schlömer K , Kathöfer S , Scholz E , Zitron E , Kiesecker C , Bauer A , Becker R , Katus H A , Karle C A , Thomas D 
Published: June 2008

Background and purpose:Two‐pore‐domain potassium (K2P) channels mediate potassium background (or ‘leak’) currents, controlling excitability by stabilizing membrane potential below firing threshold and expediting repolarization. Inhibition of K2Pcurrents permits membrane potential depolarization and excitation. As expected for key regulators of excitability, leak channels are under tight control from a plethora of stimuli. Recently, signalling via protein tyrosine kinases (TKs) has been implicated in ion channel modulation. The objective of this study was to investigate TK regulation of K2Pchannels.Experimental approach:The two‐electrode voltage clamp technique was used to record K2Pcurrents inXenopusoocytes. In addition, K2Pchannels were studied in Chinese hamster ovary (CHO) cells using the whole‐cell patch clamp technique.Key results:Here, we report inhibition of human K2P3.1 (TASK‐1) currents by the TK antagonist, genistein, inXenopusoocytes (IC50=10.7 μM) and in CHO cells (IC50=12.3 μM). The underlying molecular mechanism was studied in detail. hK2P3.1 was not affected by genistin, an inactive analogue of genistein. Perorthovanadate, an inhibitor of tyrosine phosphatase activity, reduced the inhibitory effect of genistein. Current reduction was voltage independent and did not require channel protonation at position H98 or phosphorylation at the single TK phosphorylation site, Y323. Among functional hK2Pfamily members, genistein also reduced K2P6.1 (TWIK‐2), K2P9.1 (TASK‐3) and K2P13.1 (THIK‐1) currents, respectively.Conclusions and implications:Modulation of K2Pchannels by the TK inhibitor, genistein, represents a novel molecular mechanism to alter background K+currents.British Journal of Pharmacology(2008)154, 1680–1690; doi:10.1038/bjp.2008.213; published online 2 June 2008
Potential role of 2,2'-biphenylquinones in the carcinogenic/anti-cancer activity of dioxins
Authors: Rayne Sierra 
Published: May 2008

AbstractModes of carcinogenicity for the well-known environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) have been investigated over the past several decades. However, the mechanisms underlying TCDD carcinogenicity are still unclear. Recent work also suggests TCDD may have anti-cancer activity. Based on established photochemical generation of reactive 2,2'-biphenylquinone intermediates from dioxins, a novel toxicological mechanism for TCDD that may be operative is proposed. 2,2'-Biphenylquinones may be obtained via biochemical activation of dioxins such as TCDD, and these intermediates may play a role in expressing both the carcinogenic and anti-cancer activities of this important contaminant class. The broader research community is encouraged to consider this potential new mechanism for dioxin toxicology in the design of future studies, the positive or negative findings from which will supplement the datasets developed by previous and current research groups.
Web-based design and evaluation of T-cell vaccine candidates
Authors: Thurmond James , Yoon Hyejin , Kuiken Carla , Yusim Karina , Perkins Simon , Theiler James , Bhattacharya Tanmoy , Korber Bette , Fischer Will 
Published: May 2008

Abstract
Summary: We present a suite of on-line tools to design candidate vaccine proteins, and to assess antigen potential, using coverage of k-mers (as proxies for potential T-cell epitopes) as a metric. The vaccine design tool uses the recently published ‘mosaic’ method to generate protein sequences optimized for coverage of high-frequency k-mers; the coverage-assessment tools facilitate coverage comparisons for any potential antigens. To demonstrate these tools, we designed mosaic protein sets for B-clade HIV-1 Gag, Pol and Nef, and compared them to antigens used in a recent human vaccine trial.
Availability: http://hiv.lanl.gov/content/sequence/MOSAIC/
Contact: wfischer@lanl.gov
Supplementary information: Supplementary data are available at ftp://ftp-t10.lanl.gov/pub/btk/WebToolsData
Sparse kernel methods for high-dimensional survival data
Authors: Evers Ludger , Messow Claudia-Martina 
Published: May 2008

AbstractSparse kernel methods like support vector machines (SVM) have been applied with great success to classification and (standard) regression settings. Existing support vector classification and regression techniques however are not suitable for partly censored survival data, which are typically analysed using Cox's proportional hazards model. As the partial likelihood of the proportional hazards model only depends on the covariates through inner products, it can be ‘kernelized’. The kernelized proportional hazards model however yields a solution that is dense, i.e. the solution depends on all observations. One of the key features of an SVM is that it yields a sparse solution, depending only on a small fraction of the training data. We propose two methods. One is based on a geometric idea, where—akin to support vector classification—the margin between the failed observation and the observations currently at risk is maximised. The other approach is based on obtaining a sparse model by adding observations one after another akin to the Import Vector Machine (IVM). Data examples studied suggest that both methods can outperform competing approaches.Availability: Software is available under the GNU Public License as an R package and can be obtained from the first author's website http://www.maths.bris.ac.uk/~maxle/software.htmlContact: l.evers@bris.ac.uk
Phenotypic Analysis of Arabidopsis Mutants: Auxin Hormone Response
Authors: Estelle Mark 
Published: June 2008

INTRODUCTIONThe hormone auxin is transported directionally through the plant body to effect a variety of morphological processes. In the embryo, auxin is required in the early stages of development to establish the bilateral axis of the developing embryo. Later, it participates in vascular element patterning and differentiation, lateral organ outgrowth in the root and shoot, and local growth responses to external stimuli such as light and gravity. A convenient way to measure auxin response, described in this protocol, is to monitor the effects of auxins or of auxin transport inhibitors on root growth.
Selectable Tolerance to Herbicides by Mutated Acetolactate Synthase Genes Integrated into the Chloroplast Genome of Tobacco
Authors: Shimizu Masanori , Goto Maki , Hanai Moeko , Shimizu Tsutomu , Izawa Norihiko , Kanamoto Hirosuke , Tomizawa Ken-Ichi , Yokota Akiho , Kobayashi Hirokazu 
Published: May 2008

AbstractStrategies employed for the production of genetically modified (GM) crops are premised on (1) the avoidance of gene transfer in the field; (2) the use of genes derived from edible organisms such as plants; (3) preventing the appearance of herbicide-resistant weeds; and (4) maintaining transgenes without obstructing plant cell propagation. To this end, we developed a novel vector system for chloroplast transformation with acetolactate synthase (ALS). ALS catalyzes the first step in the biosynthesis of the branched amino acids, and its enzymatic activity is inhibited by certain classes of herbicides. We generated a series of Arabidopsis (Arabidopsis thaliana) mutated ALS (mALS) genes and introduced constructs with mALS and the aminoglycoside 3′-adenyltransferase gene (aadA) into the tobacco (Nicotiana tabacum) chloroplast genome by particle bombardment. Transplastomic plants were selected using their resistance to spectinomycin. The effects of herbicides on transplastomic mALS activity were examined by a colorimetric assay using the leaves of transplastomic plants. We found that transplastomic G121A, A122V, and P197S plants were specifically tolerant to pyrimidinylcarboxylate, imidazolinon, and sulfonylurea/pyrimidinylcarboxylate herbicides, respectively. Transplastomic plants possessing mALSs were able to grow in the presence of various herbicides, thus affirming the relationship between mALSs and the associated resistance to herbicides. Our results show that mALS genes integrated into the chloroplast genome are useful sustainable markers that function to exclude plants other than those that are GM while maintaining transplastomic crops. This investigation suggests that the resistance management of weeds in the field amid growing GM crops is possible using (1) a series of mALSs that confer specific resistance to herbicides and (2) a strategy that employs herbicide rotation.
The Arabidopsis Phosphatidylinositol 3-Kinase Is Important for Pollen Development
Authors: Lee Yuree , Kim Eun-Sook , Choi Yunjung , Hwang Inwhan , Staiger Christopher J. , Chung Yong-Yoon , Lee Youngsook 
Published: May 2008

AbstractPhosphatidylinositol 3-kinase has been reported to be important for normal plant growth. To characterize the role of the enzyme further, we attempted to isolate Arabidopsis (Arabidopsis thaliana) plants that do not express the gene, but we could not recover homozygous mutant plants. The progeny of VPS34/vps34 heterozygous plants, harboring a T-DNA insertion, showed a segregation ratio of 1:1:0 for wild-type, heterozygous, and homozygous mutant plants, indicating a gametophytic defect. Genetic transmission analysis showed that the abnormal segregation ratio was due to failure to transmit the mutant allele through the male gametophyte. Microscopic observation revealed that 2-fold higher proportions of pollen grains in heterozygous plants than wild-type plants were dead or showed reduced numbers of nuclei. Many mature pollen grains from the heterozygous plants contained large vacuoles even until the mature pollen stage, whereas pollen from wild-type plants contained many small vacuoles beginning from the vacuolated pollen stage, which indicated that vacuoles in many of the heterozygous mutant pollen did not undergo normal fission after the first mitotic division. Taken together, our results suggest that phosphatidylinositol 3-kinase is essential for vacuole reorganization and nuclear division during pollen development.
Comparative Analysis of Divergent and Convergent Gene Pairs and Their Expression Patterns in Rice, Arabidopsis, andPopulus
Authors: Krom Nicholas , Ramakrishna Wusirika 
Published: May 2008

AbstractComparative analysis of the organization and expression patterns of divergent and convergent gene pairs in multiple plant genomes can identify patterns that are shared by more than one species or are unique to a particular species. Here, we study the coexpression and interspecies conservation of divergent and convergent gene pairs in three plant species: rice (Oryza sativa), Arabidopsis (Arabidopsis thaliana), and black cottonwood (Populus trichocarpa). Strongly correlated expression levels between divergent and convergent genes were found to be quite common in all three species, and the frequency of strong correlation appears to be independent of intergenic distance. Conservation of divergent or convergent arrangement among these species appears to be quite rare. However, conserved arrangement is significantly more frequent when the genes display strongly correlated expression levels or have one or more Gene Ontology (GO) classes in common. A correlation between intergenic distance in divergent and convergent gene pairs and shared GO classes was observed, in varying degrees, in rice and Populus but not in Arabidopsis. Furthermore, multiple GO classes were either overrepresented or underrepresented in Arabidopsis and Populus gene pairs, while only two GO classes were underrepresented in rice divergent gene pairs. Three cis-regulatory elements common to both Arabidopsis and rice were overrepresented in the intergenic regions of strongly correlated divergent gene pairs compared to those of noncorrelated pairs. Our results suggest that shared as well as unique mechanisms operate in shaping the organization and function of divergent and convergent gene pairs in different plant species.
MAPK Signaling Regulates Nitric Oxide and NADPH Oxidase-Dependent Oxidative Bursts inNicotiana benthamiana
Authors: Asai Shuta , Ohta Kohji , Yoshioka Hirofumi 
Published: May 2008

AbstractNitric oxide (NO) and reactive oxygen species (ROS) act as signals in innate immunity in plants. The radical burst is induced by INF1 elicitin, produced by the oomycete pathogen Phytophthora infestans. NO ASSOCIATED1 (NOA1) and NADPH oxidase participate in the radical burst. Here, we show that mitogen-activated protein kinase (MAPK) cascades MEK2-SIPK/NTF4 and MEK1-NTF6 participate in the regulation of the radical burst. NO generation was induced by conditional activation of SIPK/NTF4, but not by NTF6, in Nicotiana benthamiana leaves. INF1- and SIPK/NTF4-mediated NO bursts were compromised by the knockdown of NOA1. However, ROS generation was induced by either SIPK/NTF4 or NTF6. INF1- and MAPK-mediated ROS generation was eliminated by silencing Respiratory Burst Oxidase Homolog B (RBOHB), an inducible form of the NADPH oxidase. INF1-induced expression of RBOHB was compromised in SIPK/NTF4/NTF6-silenced leaves. These results indicated that INF1 regulates NOA1-mediated NO and RBOHB-dependent ROS generation through MAPK cascades. NOA1 silencing induced high susceptibility to Colletotrichum orbiculare but not to P. infestans; conversely, RBOHB silencing decreased resistance to P. infestans but not to C. orbiculare. These results indicate that the effects of the radical burst on the defense response appear to be diverse in plant–pathogen interactions.
XAP5 CIRCADIAN TIMEKEEPERCoordinates Light Signals for Proper Timing of Photomorphogenesis and the Circadian Clock inArabidopsis
Authors: Martin-Tryon Ellen L. , Harmer Stacey L. 
Published: May 2008

AbstractNumerous, varied, and widespread taxa have an internal circadian clock that allows anticipation of rhythmic changes in the environment. We have identified XAP5 CIRCADIAN TIMEKEEPER (XCT), an Arabidopsis thaliana gene important for light regulation of the circadian clock and photomorphogenesis. XCT is essential for proper clock function: xct mutants display a shortened circadian period in all conditions tested. Interestingly, XCT plays opposite roles in plant responses to light depending both on trait and wavelength. The clock in xct plants is hypersensitive to red but shows normal responses to blue light. By contrast, inhibition of hypocotyl elongation in xct is hyposensitive to red light but hypersensitive to blue light. Finally, XCT is important for ribulose-1,5-bisphosphate carboxylase/oxygenase production and plant greening in response to light. This novel combination of phenotypes suggests XCT may play a global role in coordinating growth in response to the light environment. XCT contains a XAP5 domain and is well conserved across diverse taxa, suggesting it has a common function in higher eukaryotes. Downregulation of the XCT ortholog in Caenorhabditis elegans is lethal, suggesting that studies in Arabidopsis may be instrumental to understanding the biochemical activity of XCT.
Biochemical Networks and Epistasis Shape theArabidopsis thalianaMetabolome
Authors: Rowe Heather C. , Hansen Bjarne Gram , Halkier Barbara Ann , Kliebenstein Daniel J. 
Published: May 2008

AbstractGenomic approaches have accelerated the study of the quantitative genetics that underlie phenotypic variation. These approaches associate genome-scale analyses such as transcript profiling with targeted phenotypes such as measurements of specific metabolites. Additionally, these approaches can help identify uncharacterized networks or pathways. However, little is known about the genomic architecture underlying data sets such as metabolomics or the potential of such data sets to reveal networks. To describe the genetic regulation of variation in the Arabidopsis thaliana metabolome and test our ability to integrate unknown metabolites into biochemical networks, we conducted a replicated metabolomic analysis on 210 lines of an Arabidopsis population that was previously used for targeted metabolite quantitative trait locus (QTL) and global expression QTL analysis. Metabolic traits were less heritable than the average transcript trait, suggesting that there are differences in the power to detect QTLs between transcript and metabolite traits. We used statistical analysis to identify a large number of metabolite QTLs with moderate phenotypic effects and found frequent epistatic interactions controlling a majority of the variation. The distribution of metabolite QTLs across the genome included 11 QTL clusters; 8 of these clusters were associated in an epistatic network that regulated plant central metabolism. We also generated two de novo biochemical network models from the available data, one of unknown function and the other associated with central plant metabolism.
Prepenetration Apparatus Assembly Precedes and Predicts the Colonization Patterns of Arbuscular Mycorrhizal Fungi within the Root Cortex of BothMedicago truncatulaandDaucus carota
Authors: Genre Andrea , Chabaud Mireille , Faccio Antonella , Barker David G. , Bonfante Paola 
Published: May 2008

AbstractArbuscular mycorrhizas (AM) are widespread, ancient endosymbiotic associations that contribute significantly to soil nutrient uptake in plants. We have previously shown that initial fungal penetration of the host root is mediated via a specialized cytoplasmic assembly called the prepenetration apparatus (PPA), which directs AM hyphae through the epidermis (Genre et al., 2005). In vivo confocal microscopy studies performed on Medicago truncatula and Daucus carota, host plants with different patterns of AM colonization, now reveal that subsequent intracellular growth across the root outer cortex is also PPA dependent. On the other hand, inner root cortical colonization leading to arbuscule development involves more varied and complex PPA-related mechanisms. In particular, a striking alignment of polarized PPAs can be observed in adjacent inner cortical cells of D. carota, correlating with the intracellular root colonization strategy of this plant. Ultrastructural analysis of these PPA-containing cells reveals intense membrane trafficking coupled with nuclear enlargement and remodeling, typical features of arbusculated cells. Taken together, these findings imply that prepenetration responses are both conserved and modulated throughout the AM symbiosis as a function of the different stages of fungal accommodation and the host-specific pattern of root colonization. We propose a model for intracellular AM fungal accommodation integrating peri-arbuscular interface formation and the regulation of functional arbuscule development.
A Transporter Regulating Silicon Distribution in Rice Shoots
Authors: Yamaji Naoki , Mitatni Namiki , Ma Jian Feng 
Published: May 2008

Abstract
Rice (Oryza sativa) accumulates very high concentrations of silicon (Si) in the shoots, and the deposition of Si as amorphous silica helps plants to overcome biotic and abiotic stresses. Here, we describe a transporter, Lsi6, which is involved in the distribution of Si in the shoots. Lsi6 belongs to the nodulin-26 intrinsic protein III subgroup of aquaporins and is permeable to silicic acid. Lsi6 is expressed in the leaf sheath and leaf blades as well as in the root tips. Cellular localization studies revealed that Lsi6 is found in the xylem parenchyma cells of the leaf sheath and leaf blades. Moreover, Lsi6 showed polar localization at the side facing toward the vessel. Knockdown of Lsi6 did not affect the uptake of Si by the roots but resulted in disordered deposition of silica in the shoots and increased excretion of Si in the guttation fluid. These results indicate that Lsi6 is a transporter responsible for the transport of Si out of the xylem and subsequently affects the distribution of Si in the leaf.
Work‐family conflict and career success: the effects of domain‐specific determinants
Authors: Ballout Hassan I. 
Published: May 2008

PurposeDespite widespread acknowledgement that work‐family conflict and career success are salient issues that impact individual wellbeing and organizational effectiveness, there is little research that studies how the two concepts are related. The purpose of this paper is to develop and present a tentative framework for understanding the relationships among antecedents of interrole conflict between work and family and career success.Design/methodology/approachDrawing on existing theoretical and empirical evidence the paper develops and presents a conceptual framework of the relationships between domain‐specific variables, work‐family conflict, and career success. The paper also presents propositions based on the relationships suggested by the framework.FindingsThe framework suggests that individual‐specific variables will be more likely to predict family‐to‐work conflict and perceived career success, while work‐specific variables will be more likely to predict work‐to‐family conflict and perceived career success. It also suggests that such domain‐specific variables influence both work‐family conflict and career success.Research limitations/implicationsFuture research should examine empirically the linkages suggested by this framework, along with other domain‐specific and, perhaps, cultural‐specific variables that may explain or predict dimensions of organizational cultures that are most relevant to the types of work‐family conflict and to indicators of career success. The paper suggests that employees and employers would be well advised to identify appropriate strategies for balancing work and non‐work domains in such a way that employees strive to perform work and family roles successfully, and employers ensure that employees have the necessary “infrastucture” and tailored‐made family supportive programs to encourage them to achieve dual‐success: success in family relationships and success in careers.Originality/valueThis paper makes a valuable contribution to both the work‐family conflict and career success literatures by being one of the first to examine the effects of domain‐specific characteristics on the relationships between these important organizational concepts and by revealing that managing work‐family conflict and career decision making is relevant for employees, employers, and career consultants.
Occupational communities and cruise tourism: testing a theory
Authors: Lee‐Ross Darren 
Published: May 2008

PurposeThis study aims to advance and test an argument for the existence of a particular type of organizational culture on board cruise tourism vessels known as an occupational community.Design/methodology/approachThe paper used a questionnaire instrument developed from earlier related studies.FindingsA strong occupational culture was identified for hospitality workers (n=72) amongst a sample of cruise ships. These communities were found to be more acute on longer duration voyages than day trips with individuals being attracted to opportunities for socialization provided by the work situation rather than the occupation itself.Practical implicationsCruise directors/hospitality managers will need to understand how occupational communities and espoused organizational cultures impact on each other to maintain positive on‐board employee attitudes, effectiveness and efficiency.Originality/valueThe novel occupational view of on‐board hospitality work could provide a much‐needed new understanding of employee attitudes and behaviors in the twenty‐first century.