bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic variation in the arachidonate 5-lipoxygenase-activating protein (ALOX5AP) is associated with myocardial infarction in the German population
Authors: Linsel-Nitschke Patrick , Götz Anika , Medack Anja , König Inke R. , Bruse Petra , Lieb Wolfgang , Mayer Björn , Stark Klaus , Hengstenberg Christian , Fischer Marcus , Baessler Andrea , Ziegler Andreas , Schunkert Heribert , Erdmann Jeanette
Published: May 2008

Genetic variation in the genes ALOX5AP (arachidonate 5-lipoxygenase-activating protein) and LTA4H (leukotriene A4 hydrolase) has previously been shown to contribute to the risk of MI (myocardial infarction) and stroke in Icelandic and Scottish populations. Both genes encode proteins playing a role in the synthesis of the pro-inflammatory leukotriene B mediators, possibly providing a link between MI and inflammation. The aim of the present study was to investigate whether these associations could be confirmed in a large study of German MI patients. Two previously described four SNP (single nucleotide polymorphism) haplotypes of the ALOX5AP gene (termed haplotype A and B) and one SNP (rs2660899) of the LTA4H gene conferring the greatest risk of MI in previous studies were genotyped in 1211 unrelated MI cases from the German MI Family Study and in 1015 healthy married-in spouses serving as controls. Haplotype B in the ALOX5AP gene was associated with an increased risk of MI in the German population, confirming previously reported associations of this haplotype with CAD (coronary artery disease) in populations from Scotland and Italy. No association with the risk of MI was detected for haplotype A of the ALOX5AP gene or for SNP rs2660899 representing the LTA4H gene. In conclusion, haplotype B of the ALOX5AP gene is associated with an increased risk of MI in a large German study. The present study is the third independent report from a European population describing an increased risk of CAD for carriers of haplotype B of the ALOX5AP gene, which substantiates further a role of this gene in the pathogenesis of CAD in Europeans.
Significant immunomodulatory effects of Pseudomonas aeruginosa quorum-sensing signal molecules: possible link in human sepsis
Authors: Boontham Pisake , Robins Adrian , Chandran Palanichamy , Pritchard David , Cámara Miguel , Williams Paul , Chuthapisith Suebwong , McKechnie Alasdair , Rowlands Brian J. , Eremin Oleg
Published: May 2008

Pathogenic bacteria use quorum-sensing signal molecules to co-ordinate the expression of virulence genes. Animal-based studies have demonstrated the immunomodulatory effects of quorum-sensing signal molecules. In the present study, we have examined the impact of these molecules on normal human immune function in vitro and compared this with immune changes in patients with sepsis where quorum-sensing signal molecules were detected in the sera of patients. Quorum-sensing signal molecules inhibited normal dendritic cell and T-cell activation and proliferation, and down-regulated the expression of co-stimulatory molecules on dendritic cells; in MLDCRs (mixed lymphocyte dendritic cell reactions), secretion of IL (interleukin)-4 and IL-10 was enhanced, but TNF-α (tumour necrosis factor-α), IFN-γ (interferon-γ) and IL-6 was reduced. Quorum-sensing signal molecules induced apoptosis in dendritic cells and CD4+ cells, but not CD8+ cells. Dendritic cells from patients with sepsis were depleted and ex vivo showed defective expression of co-stimulatory molecules and dysfunctional stimulation of allogeneic T-lymphocytes. Enhanced apoptosis of dendritic cells and differential CD4+ Th1/Th2 (T-helper 1/2) cell apoptotic rate, and modified Th1/Th2 cell cytokine profiles in MLDCRs were also demonstrated in patients with sepsis. The pattern of immunological changes in patients with sepsis mirrors the effects of quorum-sensing signal molecules on responses of immune cells from normal individuals in vitro, suggesting that quorum-sensing signal molecules should be investigated further as a cause of immune dysfunction in sepsis.
Multidisciplinary Approach to Congenital Multiple Arterio-Porto-Caval Malformation: Case Report
Authors: Senyuz Osman Faruk , Ceylan Yavuz , Gedikbasi Ali , Oztarhan Kazim , Sahin Bilge , Bingol Banu , Kurugoglu Sebuh
Published: May 2008

A case of intrahepatic arteriovenous malformation connected with umbilical, hepatic, portal, and arterial systems in a fetus diagnosed at 36 weeks of gestation is presented. Prenatal color Doppler ultrasonography in the fetal liver demonstrated complicated vascular connections fed by arterial and portal branches. Postnatal color Doppler, power Doppler, 3D power Doppler, abdominal multidetector computed tomography (MDCT), and angiography CT verified the prenatal diagnoses. Extended right hepatectomy was performed successfully on postnatal day 19.
‘Tactical’ Living: A Situated Study of Teenagers' Negotiations around and Interactions with Living Room Media
Authors: Tutt Dylan
Published: May 2008

This paper examines everyday living room interactions in which teenage household members conduct ‘tactical’ play in order to temporarily gain access to, and disrupt, the dominant, domestic codes of living room media. The practices of individuals are interpreted, through Michel de Certeau's language of ‘tactics’, as struggles or a series of opportunistic actions which can often reforge these codes of living, precisely because the house ‘rules' are not fixed or deterministic in practice. In these tactical performances of self, the use of media is enmeshed in a host of situated and symbolic action, reaffirming how media and face-to-face interactions are multiply and closely entwined in everyday living room life. This video ethnographic work examines such instances of teenagers appealing to ‘house’ rules and demonstrating domestic helpfulness in order to gain access to media, and the tethering of media to objects through the routine practice of ‘markers' and ‘stalls’.
Community Participation, Rights, and Responsibilities: The Governmentality of Sustainable Development Policy in Australia
Authors: Summerville Jennifer A , Adkins Barbara A , Kendall Gavin
Published: May 2008

This paper explores how participative democratic principles, specifically, ideas of community participation in decision-making processes, are framed as community rights and/or responsibilities in sustainable development policy at different levels of government. In doing this, the paper examines the contribution of the governmentality perspective to an understanding of the nature of relationships involved in regulation through community. The paper first briefly reviews key tenets of ‘Third Way’ politics and the alternative view proffered by critiques from the governmentality perspective. It then turns to an analysis of how techniques of rights and responsibilities are implicit in the language of sustainable development policy at three levels: global (Agenda 21), national (Australian national policy-Australian national strategy for ecologically sustainable development), and regional (Queensland regional policy—Draft South East Queensland Regional Plan). Finally, we consider some implications of our application of a governmentality perspective for how we understand government, community and community participation, and sustainable development. In doing so, we argue that neither community, nor sustainable development, can be separated from the techniques of rights and responsibilities that enable ‘government at a distance’.
Spatial Correspondence and Relation Correspondence: Grouping Factors That Influence Perception of the Ternus Display
Authors: Petersik J Timothy , Rice Curran M
Published: May 2008

We cite two different perceptual-correspondence principles whose emphasis can help to disambiguate the otherwise ambiguous Ternus display in apparent movement (a display that can alternately be seen in one of two possible configurations). One of these principles is spatial correspondence, which emphasizes the maintenance of similar stimulus elements in given locations over time. The other principle is relation correspondence, which emphasizes the maintenance of the inter-organization of stimulus elements across frames. Each of four experiments reported here made use of a different stimulus feature (eg element color or element texture) to emphasize these different correspondence principles in Ternus displays. As predicted, an emphasis upon spatial correspondence resulted in an increase in reports of element movement compared to a featureless control condition. Emphasis on relation correspondence resulted in an increase in reports of group movement. Extensions and limitations of the use of these principles to explain apparent movement are discussed.
Proteasomal adaptation to environmental stress links resistance to proteotoxicity with longevity in
Caenorhabditis elegans
Authors: Yun Chi , Stanhill Ariel , Yang Yun , Zhang Yuhong , Haynes Cole M. , Xu Chong-Feng , Neubert Thomas A. , Mor Adam , Philips Mark R. , Ron David
Published: May 2008

The burden of protein misfolding is believed to contribute to aging. However, the links between adaptations to conditions associated with protein misfolding and resistance to the time-dependent attrition of cellular function remain poorly understood. We report that worms lacking
aip-1
, a homologue of mammalian AIRAP (arsenic-inducible proteasomal 19S regulatory particle-associated protein), are not only impaired in their ability to resist exposure to arsenite but also exhibit shortened lifespan and hypersensitivity to misfolding-prone proteins under normal laboratory conditions. Mammals have a second, constitutively expressed AIRAP-like gene (AIRAPL) that also encodes a proteasome-interacting protein, which shares with AIRAP the property of enhancing peptide accessibility to the proteasome's active site. Genetic rescue experiments suggest that features common to the constitutively expressed worm AIP-1 and mammalian AIRAPL (but missing in the smaller, arsenite-inducible AIRAP) are important to lifespan extension. In worms, a single AIRAP-related protein links proteasomal adaptation to environmental stress with resistance to both proteotoxic insults and maintenance of animal life span under normal conditions.
Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics
Authors: Pernthaler Annelie , Dekas Anne E. , Brown C. Titus , Goffredi Shana K. , Embaye Tsegereda , Orphan Victoria J.
Published: May 2008

Microorganisms play a fundamental role in the cycling of nutrients and energy on our planet. A common strategy for many microorganisms mediating biogeochemical cycles in anoxic environments is syntrophy, frequently necessitating close spatial proximity between microbial partners. We are only now beginning to fully appreciate the diversity and pervasiveness of microbial partnerships in nature, the majority of which cannot be replicated in the laboratory. One notable example of such cooperation is the interspecies association between anaerobic methane oxidizing archaea (ANME) and sulfate-reducing bacteria. These consortia are globally distributed in the environment and provide a significant sink for methane by substantially reducing the export of this potent greenhouse gas into the atmosphere. The interdependence of these currently uncultured microbes renders them difficult to study, and our knowledge of their physiological capabilities in nature is limited. Here, we have developed a method to capture select microorganisms directly from the environment, using combined fluorescencein situhybridization and immunomagnetic cell capture. We used this method to purify syntrophic anaerobic methane oxidizing ANME-2c archaea and physically associated microorganisms directly from deep-sea marine sediment. Metagenomics, PCR, and microscopy of these purified consortia revealed unexpected diversity of associated bacteria, includingBetaproteobacteriaand a second sulfate-reducingDeltaproteobacterialpartner. The detection of nitrogenase genes within the metagenome and subsequent demonstration of15N2incorporation in the biomass of these methane-oxidizing consortia suggest a possible role in new nitrogen inputs by these syntrophic assemblages.
Modulation of brassinosteroid-regulated gene expression by jumonji domain-containing proteins ELF6 and REF6 in
Arabidopsis
Authors: Yu Xiaofei , Li Li , Li Lei , Guo Michelle , Chory Joanne , Yin Yanhai
Published: May 2008

Plant steroid hormones, brassinosteroids (BRs), are of great importance for plant growth and development. BRs signal through a cell surface receptor kinase, BRI1, and a GSK3-like kinase, BIN2, to regulate the BES1/BZR1 family of transcription factors, which directly bind to target gene promoters to activate or repress gene expression and mediate BR responses. To understand how BES1 regulates target gene expression, we identified two BES1-interacting proteins, ELF6 (early flowering 6) and its homolog REF6 (relative of early flowering 6), both of which are Jumonji N/C (JmjN/C) domain-containing proteins and were previously found to regulate flowering time. The interactions between BES1 and ELF6/REF6 were confirmed by GST pull-down and BiFC (bimolecular fluorescence complementation) experiments. Mutations in
ELF6
or
REF6
genes in
Arabidopsis
lead to BR-related phenotypes, including impaired cell elongation and reduced expression of BR target genes. Chromatin immunoprecipitation (ChIP) experiments indicated that histone 3 lysine 9 (H3K9) methylation status was changed in
elf6
and
ref6
mutants, consistent with recent findings that many Jmj proteins are histone demethylases. Our results demonstrate that BES1 recruits other transcriptional regulators such as ELF6 and REF6 to regulate target gene expression and coordinate BR responses with other developmental processes such as control of flowering time. Jmj domain-containing histone demethylases are involved in gene expression in many developmental processes and diseases, but how these proteins affect specific pathways is not well understood. Thus, our study establishes an important mechanism by which Jmj domain proteins modulate specific gene expression by interacting with pathway-specific transcription factors such as BES1.
A high field side pellet penetration depth scaling derived for ASDEX Upgrade
Authors: Belonohy E. , Kardaun O.J.W.F. , Fehér T. , Gál K. , Kálvin S. , Kocsis G. , Lackner K. , Lang P.T. , Neuhauser J.
Published: May 2008

Refuelling of fusion plasmas by the injection of frozen hydrogen isotope pellets from the magnetic high field side (HFS) rather than from the low field side (LFS) increases the fuelling efficiency due to the gradBdrift accelerating the ablatant material in the positive major radius direction, thus towards the centre of the plasma. The HFS pellet fuelling is therefore presently established as the main fuelling scenario for ITER. This paper describes an HFS pellet database developed at the ASDEX Upgrade tokamak and the HFS penetration depth scaling derived by statistical analysis performed on the dataset. Also a comparison is made with the existing empirical LFS penetration depth scaling and theoretical models.
Microbial genotype–phenotype mapping by class association rule mining
Authors: Tamura Makio , D'haeseleer Patrik
Published: May 2008

Motivation: Microbial phenotypes are typically due to the concerted action of multiple gene functions, yet the presence of each gene may have only a weak correlation with the observed phenotype. Hence, it may be more appropriate to examine co-occurrence between sets of genes and a phenotype (multiple-to-one) instead of pairwise relations between a single gene and the phenotype. Here, we propose an efficient class association rule mining algorithm, netCAR, in order to extract sets of COGs (clusters of orthologous groups of proteins) associated with a phenotype from COG phylogenetic profiles and a phenotype profile. netCAR takes into account the phylogenetic co-occurrence graph between COGs to restrict hypothesis space, and uses mutual information to evaluate the biconditional relation.

Results: We examined the mining capability of pairwise and multiple-to-one association by using netCAR to extract COGs relevant to six microbial phenotypes (aerobic, anaerobic, facultative, endospore, motility and Gram negative) from 11 969 unique COG profiles across 155 prokaryotic organisms. With the same level of false discovery rate, multiple-to-one association can extract about 10 times more relevant COGs than one-to-one association. We also reveal various topologies of association networks among COGs (modules) from extracted multiple-to-one correlation rules relevant with the six phenotypes; including a well-connected network for motility, a star-shaped network for aerobic and intermediate topologies for the other phenotypes. netCAR outperforms a standard CAR mining algorithm, CARapriori, while requiring several orders of magnitude less computational time for extracting 3-COG sets.

Availability: Source code of the Java implementation is available as Supplementary Material at the Bioinformatics online website, or upon request to the author.

Contact:  makio323@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
HSEpred: predict half-sphere exposure from protein sequences
Authors: Song Jiangning , Tan Hao , Takemoto Kazuhiro , Akutsu Tatsuya
Published: May 2008

Motivation: Half-sphere exposure (HSE) is a newly developed two-dimensional solvent exposure measure. By conceptually separating an amino acid's sphere in a protein structure into two half spheres which represent its distinct spatial neighborhoods in the upward and downward directions, the HSE-up and HSE-down measures show superior performance compared with other measures such as accessible surface area, residue depth and contact number. However, currently there is no existing method for the prediction of HSE measures from sequence data.

Results: In this article, we propose a novel approach to predict the HSE measures and infer residue contact numbers using the predicted HSE values, based on a well-prepared non-homologous protein structure dataset. In particular, we employ support vector regression (SVR) to quantify the relationship between HSE measures and protein sequences and evaluate its prediction performance. We extensively explore five sequence-encoding schemes to examine their effects on the prediction performance. Our method could achieve the correlation coefficients of 0.72 and 0.68 between the predicted and observed HSE-up and HSE-down measures, respectively. Moreover, contact number can be accurately predicted by the summation of the predicted HSE-up and HSE-down values, which has further enlarged the application of this method. The successful application of SVR approach in this study suggests that it should be more useful in quantifying the protein sequence–structure relationship and predicting the structural property profiles from protein sequences.

Availability: The prediction webserver and supplementary materials are accessible at http://sunflower.kuicr.kyoto-u.ac.jp/~sjn/hse/

Contact:  sjn@kuicr.kyoto-u.ac.jp; takutsu@kuicr.kyoto-u.ac.jp

Supplementary Information:  Supplementary data are available at Bioinformatics online.
PatMaN: rapid alignment of short sequences to large databases
Authors: Prüfer Kay , Stenzel Udo , Dannemann Michael , Green Richard E. , Lachmann Michael , Kelso Janet
Published: May 2008

Summary: We present a tool suited for searching for many short nucleotide sequences in large databases, allowing for a predefined number of gaps and mismatches. The commandline-driven program implements a non-deterministic automata matching algorithm on a keyword tree of the search strings. Both queries with and without ambiguity codes can be searched. Search time is short for perfect matches, and retrieval time rises exponentially with the number of edits allowed.

Availability: The C++ source code for PatMaN is distributed under the GNU General Public License and has been tested on the GNU/Linux operating system. It is available from http://bioinf.eva.mpg.de/patman.

Contact:  pruefer@eva.mpg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
lumi: a pipeline for processing Illumina microarray
Authors: Du Pan , Kibbe Warren A. , Lin Simon M.
Published: May 2008

Summary: Illumina microarray is becoming a popular microarray platform. The BeadArray technology from Illumina makes its preprocessing and quality control different from other microarray technologies. Unfortunately, most other analyses have not taken advantage of the unique properties of the BeadArray system, and have just incorporated preprocessing methods originally designed for Affymetrix microarrays. lumi is a Bioconductor package especially designed to process the Illumina microarray data. It includes data input, quality control, variance stabilization, normalization and gene annotation portions. In specific, the lumi package includes a variance-stabilizing transformation (VST) algorithm that takes advantage of the technical replicates available on every Illumina microarray. Different normalization method options and multiple quality control plots are provided in the package. To better annotate the Illumina data, a vendor independent nucleotide universal identifier (nuID) was devised to identify the probes of Illumina microarray. The nuID annotation packages and output of lumi processed results can be easily integrated with other Bioconductor packages to construct a statistical data analysis pipeline for Illumina data.

Availability: The lumi Bioconductor package, www.bioconductor.org

Contact:  dupan@northwestern.edu
Effects of gear characteristics on the presence of bigeye tuna (Thunnus obesus) in the catches of the purse-seine fishery of the eastern Pacific Ocean
Authors: Lennert-Cody Cleridy E. , Roberts Jason J. , Stephenson Richard J.
Published: May 2008

Lennert-Cody, C. E., Roberts, J. J., and Stephenson, R. J. 2008. Effects of gear characteristics on the presence of bigeye tuna (Thunnus obesus) in the catches of the purse-seine fishery of the eastern Pacific Ocean. – ICES Journal of Marine Science, 65: 970–978. Overfishing of bigeye tuna in the eastern Pacific Ocean has motivated a search for a practical means of reducing the catch of bigeye tuna in mixed species aggregations. To explore the effects of gear characteristics on the catch of bigeye tuna, a classification algorithm for the presence/absence of bigeye tuna catch in purse-seine sets on floating objects is developed, using the tree-based method, random forests. Although the location of the set was the strongest determinant of bigeye tuna catch with these data, bigeye tuna in some areas were more likely to be caught on floating objects with greater underwater depths and with deeper purse-seines. Misclassified sets that caught bigeye tuna were concentrated within certain vessels, suggesting the existence of additional vessel effects. Results indicate that fishers may avoid catching bigeye tuna in some areas by changing the depth of the material hanging from the floating object and the actual fishing depth of the purse-seine, or by moving to other fishing areas. Nonetheless, given the complexity of configuring a purse-seine, and the difficulties associated with monitoring compliance with gear regulations, fishery-wide gear restrictions would be problematic.
Partial melting in an upwelling mantle column
Authors: Hewitt I.J , Fowler A.C
Published: May 2008

Decompression melting of hot upwelling rock in the mantle creates a region of partial melt comprising a porous solid matrix through which magma rises buoyantly. Magma transport and the compensating matrix deformation are commonly described by two-phase compaction models, but melt production is less often incorporated. Melting is driven by the necessity to maintain thermodynamic equilibrium between mineral grains in the partial melt; the position and amount of partial melting that occur are thus thermodynamically determined. We present a consistent model for the ascent of a one-dimensional column of rock and provide solutions that reveal where and how much partial melting occurs, the positions of the boundaries of the partial melt being determined by conserving energy across them. Thermodynamic equilibrium of the boundary between partial melt and the solid lithosphere requires a boundary condition on the effective pressure (solid pressure minus melt pressure), which suggests that large effective stresses, and hence fracture, are likely to occur near the base of the lithosphere. Matrix compaction, melt separation and temperature in the partially molten region are all dependent on the effective pressure, a fact that can lead to interesting oscillatory boundary-layer structures.
The impact of experimentally elevated energy expenditure on oxidative stress and lifespan in the short-tailed field voleMicrotus agrestis
Authors: Selman Colin , McLaren Jane S , Collins Andrew R , Duthie Garry G , Speakman John R
Published: May 2008

Life-history theory assumes that animal life histories are a consequence of trade-offs between current activities and future reproductive performance or survival, because resource supply is limited. Empirical evidence for such trade-offs in the wild are common, yet investigations of the underlying mechanisms are rare. Life-history trade-offs may have both physiological and ecological mediated costs. One hypothesized physiological mechanism is that elevated energy metabolism may increase reactive oxygen species production, leading to somatic damage and thus compromising future survival. We investigated the impact of experimentally elevated energy expenditure on oxidative damage, protection and lifespan in short-tailed field voles (Microtus agrestis) maintained in captivity to remove any confounding ecological factor effects. Energy expenditure was elevated via lifelong cold exposure (7±2°C), relative to siblings in the warm (22±2°C). No treatment effect on cumulative mortality risk was observed, with negligible effects on oxidative stress and antioxidant protection. These data suggest that in captive animals physiologically mediated costs on life history do not result from increased energy expenditure and consequent elevations in oxidative stress and reduced survival.
Functional Characterization of HFR1, a High-MannoseN-Glycan-Specific Wheat Lectin Induced by Hessian Fly Larvae
Authors: Subramanyam Subhashree , Smith David F. , Clemens James C. , Webb Mary A. , Sardesai Nagesh , Williams Christie E.
Published: May 2008

We previously cloned and characterized a novel jacalin-like lectin gene from wheat (Triticum aestivum) plants that responds to infestation by Hessian fly (Mayetiola destructor) larvae, a major dipteran pest of this crop. The infested resistant plants accumulated higher levels of Hfr-1 (for Hessian fly-responsive gene 1) transcripts compared with uninfested or susceptible plants. Here, we characterize the soluble and active recombinant His6-HFR1 protein isolated from Escherichia coli. Functional characterization of the protein using hemagglutination assays revealed lectin activity. Glycan microarray-binding assays indicated strong affinity of His6-HFR1 to Manα1-6(Manα1-3)Man trisaccharide structures. Resistant wheat plants accumulated high levels of HFR1 at the larval feeding sites, as revealed by immunodetection, but the avirulent larvae were deterred from feeding and consumed only small amounts of the lectin. Behavioral studies revealed that avirulent Hessian fly larvae on resistant plants exhibited prolonged searching and writhing behaviors as they unsuccessfully attempted to establish feeding sites. During His6-HFR1 feeding bioassays, Drosophila melanogaster larvae experienced significant delays in growth and pupation, while percentage mortality increased with progressively higher concentrations of His6-HFR1 in the diet. Thus, HFR1 is an antinutrient to dipteran larvae and may play a significant role in deterring Hessian fly larvae from feeding on resistant wheat plants.
An External δ-Carbonic Anhydrase in a Free-Living Marine Dinoflagellate May Circumvent Diffusion-Limited Carbon Acquisition
Authors: Lapointe Mathieu , MacKenzie Tyler D.B. , Morse David
Published: May 2008

The oceans globally constitute an important sink for carbon dioxide (CO2) due to phytoplankton photosynthesis. However, the marine environment imposes serious restraints to carbon fixation. First, the equilibrium between CO2 and bicarbonate (HCO3  −) is pH dependent, and, in normal, slightly alkaline seawater, [CO2] is typically low (approximately 10 μ  m). Second, the rate of CO2 diffusion in seawater is slow, so, for any cells unable to take up bicarbonate efficiently, photosynthesis could become carbon limited due to depletion of CO2 from their immediate vicinity. This may be especially problematic for those dinoflagellates using a form II Rubisco because this form is less oxygen tolerant than the usually found form I enzyme. We have identified a carbonic anhydrase (CA) from the free-living marine dinoflagellate Lingulodinium polyedrum that appears to play a role in carbon acquisition. This CA shares 60% sequence identity with δ-class CAs, isoforms so far found only in marine algae. Immunoelectron microscopy indicates that this enzyme is associated exclusively with the plasma membrane. Furthermore, this enzyme appears to be exposed to the external medium as determined by whole-cell CA assays and vectorial labeling of cell surface proteins with 125I. The fixation of 14CO2 is strongly pH dependent, suggesting preferential uptake of CO2 rather than HCO3  −, and photosynthetic rates decrease in the presence of 1 mm acetazolamide, a non-membrane-permeable CA inhibitor. This constitutes the first CA identified in the dinoflagellates, and, taken together, our results suggest that this enzyme may help to increase CO2 availability at the cell surface.
Involvement of CBF Transcription Factors in Winter Hardiness in Birch
Authors: Welling Annikki , Palva E. Tapio
Published: May 2008

Cold acclimation of plants involves extensive reprogramming of gene expression. In Arabidopsis (Arabidopsis thaliana), three cold-inducible transcriptional activators designated CBF1 to -3/DREB1a to -c have been shown to play an important regulatory role in this acclimation process. Similarly to Arabidopsis, boreal zone trees can increase their freezing tolerance (FT) in response to low temperature during the growing season. However, maximal FT of these trees requires short daylength-induced dormancy development followed by exposure to both low and freezing temperatures. To elucidate the molecular basis of FT in overwintering trees, we characterized the role of birch (Betula pendula) CBF transcription factors in the cold acclimation process. We identified four putative CBF orthologs in a birch expressed sequence tag collection designated BpCBF1 to -4. Ectopic expression of birch CBFs in Arabidopsis resulted in constitutive expression of endogenous CBF target genes and increased FT of nonacclimated transgenic plants. In addition, these plants showed stunted growth and delayed flowering, typical features for CBF-overexpressing plants. Expression analysis in birch showed that BpCBF1 to -4 are low temperature responsive but differentially regulated in dormant and growing plants, the expression being delayed in dormant tissues. Freeze-thaw treatment, simulating wintertime conditions in nature, resulted in strong induction of BpCBF genes during thawing, followed by induction of a CBF target gene, BpLTI36. These results suggest that in addition to their role in cold acclimation during the growing season, birch CBFs appear to contribute to control of winter hardiness in birch.
The Arabidopsis Halophytic RelativeThellungiella halophilaTolerates Nitrogen-Limiting Conditions by Maintaining Growth, Nitrogen Uptake, and Assimilation
Authors: Kant Surya , Bi Yong-Mei , Weretilnyk Elizabeth , Barak Simon , Rothstein Steven J.
Published: May 2008

A comprehensive knowledge of mechanisms regulating nitrogen (N) use efficiency is required to reduce excessive input of N fertilizers while maintaining acceptable crop yields under limited N supply. Studying plant species that are naturally adapted to low N conditions could facilitate the identification of novel regulatory genes conferring better N use efficiency. Here, we show that Thellungiella halophila, a halophytic relative of Arabidopsis (Arabidopsis thaliana), grows better than Arabidopsis under moderate (1 mm nitrate) and severe (0.4 mm nitrate) N-limiting conditions. Thellungiella exhibited a lower carbon to N ratio than Arabidopsis under N limitation, which was due to Thellungiella plants possessing higher N content, total amino acids, total soluble protein, and lower starch content compared with Arabidopsis. Furthermore, Thellungiella had higher amounts of several metabolites, such as soluble sugars and organic acids, under N-sufficient conditions (4 mm nitrate). Nitrate reductase activity and NR2 gene expression in Thellungiella displayed less of a reduction in response to N limitation than in Arabidopsis. Thellungiella shoot GS1 expression was more induced by low N than in Arabidopsis, while in roots, Thellungiella GS2 expression was maintained under N limitation but was decreased in Arabidopsis. Up-regulation of NRT2.1 and NRT3.1 expression was higher and repression of NRT1.1 was lower in Thellungiella roots under N-limiting conditions compared with Arabidopsis. Differential transporter gene expression was correlated with higher nitrate influx in Thellungiella at low 15NO3  − supply. Taken together, our results suggest that Thellungiella is tolerant to N-limited conditions and could act as a model system to unravel the mechanisms for low N tolerance.
A Pathogenic Fungi Diphenyl Ether Phytotoxin Targets Plant Enoyl (Acyl Carrier Protein) Reductase
Authors: Dayan Franck E. , Ferreira Daneel , Wang Yan-Hong , Khan Ikhlas A. , McInroy John A. , Pan Zhiqiang
Published: May 2008

Cyperin is a natural diphenyl ether phytotoxin produced by several fungal plant pathogens. At high concentrations, this metabolite inhibits protoporphyrinogen oxidase, a key enzyme in porphyrin synthesis. However, unlike its herbicide structural analogs, the mode of action of cyperin is not light dependent, causing loss of membrane integrity in the dark. We report that this natural diphenyl ether inhibits Arabidopsis (Arabidopsis thaliana) enoyl (acyl carrier protein) reductase (ENR). This enzyme is also sensitive to triclosan, a synthetic antimicrobial diphenyl ether. Whereas cyperin was much less potent than triclosan on this target site, their ability to cause light-independent disruption of membrane integrity and inhibition of ENR is similar at their respective phytotoxic concentrations. The sequence of ENR is highly conserved within higher plants and a homology model of Arabidopsis ENR was derived from the crystal structure of the protein from Brassica napus. Cyperin mimicked the binding of triclosan in the binding pocket of ENR. Both molecules were stabilized by the π-π stacking interaction between one of their phenyl rings and the nicotinamide ring of the NAD+. Furthermore, the side chain of tyrosine is involved in hydrogen bonding with a phenolic hydroxy group of cyperin. Therefore, cyperin may contribute to the virulence of the pathogens by inhibiting ENR and destabilizing the membrane integrity of the cells surrounding the point of infection.
The Effect of Iron on the Primary Root Elongation of Arabidopsis during Phosphate Deficiency
Authors: Ward James T. , Lahner Brett , Yakubova Elena , Salt David E. , Raghothama Kashchandra G.
Published: May 2008

Root architecture differences have been linked to the survival of plants on phosphate (P)-deficient soils, as well as to the improved yields of P-efficient crop cultivars. To understand how these differences arise, we have studied the root architectures of P-deficient Arabidopsis (Arabidopsis thaliana Columbia-0) plants. A striking aspect of the root architecture of these plants is that their primary root elongation is inhibited when grown on P-deficient medium. Here, we present evidence suggesting that this inhibition is a result of iron (Fe) toxicity. When the Fe concentration in P-deficient medium is reduced, we observe elongation of the primary root without an increase in P availability or a corresponding change in the expression of P deficiency-regulated genes. Recovery of the primary root elongation is associated with larger plant weights, improved ability to take up P from the medium, and increased tissue P content. This suggests that manipulating Fe availability to a plant could be a valuable strategy for improving a plant's ability to tolerate P deficiency.
The Stomata of the Fern Adiantum capillus-veneris Do Not Respond to CO2 in the Dark and Open by Photosynthesis in Guard Cells
Authors: Doi Michio , Shimazaki Ken-ichiro
Published: May 2008

The stomata of the fern Adiantum capillus-veneris lack a blue light-specific opening response but open in response to red light. We investigated this light response of Adiantum stomata and found that the light wavelength dependence of stomatal opening matched that of photosynthesis. The simultaneous application of red (2 μmol m−2 s−1) and far-red (50 μmol m−2 s−1) light synergistically induced stomatal opening, but application of only one of these wavelengths was ineffective. Adiantum stomata did not respond to CO2 in the dark; the stomata neither opened under a low intercellular CO2 concentration nor closed under high intercellular CO2 concentration. Stomata in Arabidopsis (Arabidopsis thaliana), which were used as a control, showed clear sensitivity to CO2. In Adiantum, stomatal conductance showed much higher light sensitivity when the light was applied to the lower leaf surface, where stomata exist, than when it was applied to the upper surface. This suggests that guard cells likely sensed the light required for stomatal opening. In the epidermal fragments, red light induced both stomatal opening and K+ accumulation in guard cells, and both of these responses were inhibited by a photosynthetic inhibitor, 3-(3,4-dichlorophenyl)-1,1-dimethylurea. The stomatal opening was completely inhibited by CsCl, a K+ channel blocker. In intact fern leaves, red light-induced stomatal opening was also suppressed by 3-(3,4-dichlorophenyl)-1,1-dimethylurea. These results indicate that Adiantum stomata lack sensitivity to CO2 in the dark and that stomatal opening is driven by photosynthetic electron transport in guard cell chloroplasts, probably via K+ uptake.
An Evaluation of the Basis and Consequences of a Stay-Green Mutation in thenavel negraCitrus Mutant Using Transcriptomic and Proteomic Profiling and Metabolite Analysis
Authors: Alós Enriqueta , Roca María , Iglesias Domingo José , Mínguez-Mosquera Maria Isabel , Damasceno Cynthia Maria Borges , Thannhauser Theodore William , Rose Jocelyn Kenneth Campbell , Talón Manuel , Cercós Manuel
Published: May 2008

A Citrus sinensis spontaneous mutant, navel negra (nan), produces fruit with an abnormal brown-colored flavedo during ripening. Analysis of pigment composition in the wild-type and nan flavedo suggested that typical ripening-related chlorophyll (Chl) degradation, but not carotenoid biosynthesis, was impaired in the mutant, identifying nan as a type C stay-green mutant. nan exhibited normal expression of Chl biosynthetic and catabolic genes and chlorophyllase activity but no accumulation of dephytylated Chl compounds during ripening, suggesting that the mutation is not related to a lesion in any of the principal enzymatic steps in Chl catabolism. Transcript profiling using a citrus microarray indicated that a citrus ortholog of a number of SGR (for STAY-GREEN) genes was expressed at substantially lower levels in nan, both prior to and during ripening. However, the pattern of catabolite accumulation and SGR sequence analysis suggested that the nan mutation is distinct from those in previously described stay-green mutants and is associated with an upstream regulatory step, rather than directly influencing a specific component of Chl catabolism. Transcriptomic and comparative proteomic profiling further indicated that the nan mutation resulted in the suppressed expression of numerous photosynthesis-related genes and in the induction of genes that are associated with oxidative stress. These data, along with metabolite analyses, suggest that nan fruit employ a number of molecular mechanisms to compensate for the elevated Chl levels and associated photooxidative stress.
Hydrophile scanning as a complement to alanine scanning for exploring and manipulating protein–protein recognition: Application to the Bim BH3 domain
Authors: Boersma Melissa D. , Sadowsky Jack D. , Tomita York A. , Gellman Samuel H.
Published: May 2008

Alanine scanning has been widely employed as a method of identifying side chains that play important roles in protein–protein and protein–peptide interactions. Here we show how an analogous and complementary technique, hydrophile scanning, can provide additional insight on such interactions. Mutation of a wild‐type residue to alanine removes most of the side‐chain atoms, and the effect of this removal is typically interpreted to indicate contribution of the deleted side chain to the stability of the complex. Hydrophile scanning involves systematic mutation of wild‐type residues to a cationic or anionic residue (lysine or glutamic acid, in this case). We find that the results of these mutations provide insights on interactions between polypeptide surfaces that are complementary to the information obtained via alanine scanning. We have applied this technique to a peptide that corresponds to the BH3 domain of the pro‐apoptotic protein Bim. The wild‐type Bim BH3 domain binds strongly to the anti‐apoptotic proteins Bcl‐xL and Mcl‐1. Combining information from the alanine, lysine, and glutamic acid scans has enabled us to identify Bim BH3 domain mutants containing only two or three sequence changes that bind very selectively either to Bcl‐xL or Mcl‐1. Our findings suggest that hydrophile scanning may prove to be a broadly useful tool for revealing sources of protein–protein recognition and for engineering selectivity into natural sequences
The structural basis of proteolytic activation of bovine glutamate dehydrogenase
Authors: Carrigan John B. , Engel Paul C.
Published: May 2008

In this work, we re‐examine the previously reported phenomenon of the creation of a superactive glutamate dehydrogenase by proteolytic modification by chymotrypsin and explore the various discrepancies that came to light during those studies. We find that superactivation is caused by cleavage at the N terminus of the protein and not the C‐terminal allosteric site, as has previously been suggested. N‐terminal sequencing reveals that TLCK‐treated chymotrypsin cleaves bovine glutamate dehydrogenase at phenylalanine 10. We suggest that trypsin contamination in nontreated chymotrypsin may have led to the production of the larger 4–5 kDa digestion product, previously misinterpreted as having caused the activation. In line with some previous studies, we can confirm that GTP inhibition is attenuated to some extent by the proteolysis, while ADP activation is almost abolished. Utilizing the recently solved structures of bovine glutamate dehydrogenase, we illustrate the cleavage points.
On the head morphology ofTetraphalerus, the phylogeny of Archostemata and the basal branching events in Coleoptera
Authors: Beutel Rolf G. , Ge Si‐qin , Hörnschemeyer Thomas
Published: May 2008

Internal and external features ofTetraphalerus bruchiwere studied using X‐ray microtomography (µ‐CT) and other techniques, and head structures were described in detail. µ‐Ct is highly efficient for the assessment of anatomical data. A data matrix with 90 morphological characters of recent and fossil beetles was analyzed with different approaches (parsimony, Bayesian analysis). The results of the parsimony analysis resulted in the following branching pattern: (†Tshekardocoleidae + (†Permocupedidae, †Rhombocoleidae + (†Triadocupedidae + ((Adephaga + (Myxophaga + Polyphaga))) + Archostemata s.str. [including Jurodidae]))).Sikhotealiniais placed as sister group of †Jurodes(Jurodidae), and Jurodidae as sister group of the remaining Archostemata (Bayesian analysis) or of a clade comprising Micromalthidae, Crowsoniellidae, †Ademosynidae, †Schizophoridae and †Catiniidae. The monophyly of Ommatidae and Cupedidae is well supported andPriacmais placed as the sister group of all other Cupedidae. Important events in the early evolution of Coleoptera are the shortening of the elytra and the transformation of the elytral venation (Coleoptera excluding †Tshekardocoleidae), the formation of a closed subelytral space (Coleoptera excluding †Tshekardocoleidae and †Permocupedidae), the reduction of two apical antennomeres, and the loss of the broad prothoracic postcoxal bridge (Coleoptera excluding †Tshekardocoleidae, †Permocupedidae and †Rhombocoleidae). Plesiomorphic features preserved in extant Archostemata are the tuberculate cuticle, the elytral pattern with parallel longitudinal ribs and window punctures, a mesoventrite with a transverse ridge, triangular mesocoxae with a distinct meron, and the exposed metatrochantin. The fossils included in the analyses do not only contribute to the reconstruction of character evolution but also influence the branching pattern. An understanding of the major evolutionary events in Coleoptera would not be possible without considering the rich fossil record of Permian and Mesozoic beetles.

© The Willi Hennig Society 2007.
Presumed interaction of fusidic acid with simvastatin
Authors: Burtenshaw A. J. , Sellors G. , Downing R.
Published: May 2008

A 63‐year‐old man was admitted 6 weeks after an elective abdominal aortic aneurysm repair following which methicillin resistant Staphylococcus aureus (MRSA) had been cultured from the aneurysmal sac. He had been commenced on a course of fusidic acid at discharge in addition to his ongoing statin prescription and presented 4 weeks later with symptoms consistent with rhabdomyolysis. Severe rhabdomyolysis was confirmed and despite prolonged and complicated critical care management, his treatment was unsuccessful. Extensive investigations ruled out other known causes of this clinical presentation and failed to identify any other precipitating cause of rhabdomyolysis. We believe the most likely cause was hepatic inhibition of the CYP3A4 hepatic isoenzyme by fusidic acid resulting in an acute severe rise in plasma simvastatin level and extensive myocellular damage. Increasing MRSA colonisation and infection rates together with increased statin usage have the potential to increase the incidence of this presumed drug interaction.
Fatal peri‐operative acute tumour lysis syndrome precipitated by dexamethasone
Authors: McDonnell C. , Barlow R. , Campisi P. , Grant R. , Malkin D.
Published: May 2008

A 3‐year‐old patient presented for elective adenotonsillectomy to treat symptomatic obstructive sleep apnoea. The patient had not been assessed at a pre‐operative anaesthesia clinic but had undergone uneventful general anaesthesia twice in the previous two years. An uneventful operative course was complicated by the development of clinical instability over the first 6 h postoperatively culminating in cardiorespiratory arrest. Subsequent investigation demonstrated the acute development of tumour lysis syndrome in the setting of a new onset, undiagnosed acute leukaemia. The patient died on the third postoperative day. The use of dexamethasone for prophylaxis against postoperative nausea and vomiting was the likely aetiology of the acute tumour lysis syndrome in this case. This is the first documented peri‐operative death due to tumour lysis syndrome after adminstration of dexamethasone. We discuss the various problems encountered with this case and review the recent literature and case reports on tumour lysis syndrome in the operating theatre.