bluuebunny/crossref_metadata_2025 huggingface dataset:
Spherical carbon liquids generated in a low pressure CH4∕Ar plasma
Authors: Feng Zongbao , Kono Akihiko , Nagai Tatsuzo , Shoji Fumiya
Published: May 2007

The authors present a study on spherical carbon particles of micron sizes grown in the plasma sheath as spherical liquids that can be agglomerated by capillary force based on the Laplace pressure. In addition, it is suggested that those spherical carbon liquids with negative charges that are levitating in the sheath region begin to display a collective behavior of Coulomb crystals.
Self-organized pattern formation of an atmospheric pressure plasma jet in a dielectric barrier discharge configuration
Authors: Nie Qiu-Yue , Ren Chun-Sheng , Wang De-Zhen , Li Shou-Zhe , Zhang Jia-Liang , Kong M. G.
Published: May 2007

This letter reports the observation of self-organized patterns formed in a 29mm wide atmospheric pressure plasma jet. By altering the gas flow rate and/or the applied voltage, the plasma jet is seen to have at least three different modes, namely, a diffuse-looking discharge, a self-organized discharge, and an unstable discharge with randomly occurring plasma channels. The self-organized discharge mode is characterized by several bright plasma channels embedded in a diffuse and dim plasma background. These plasma channels are regularly spaced from each other and their self-organized patterns are shown to evolve abruptly.
The A-kinase anchoring protein (AKAP)-Lbc-signaling complex mediates α1 adrenergic receptor-induced cardiomyocyte hypertrophy
Authors: Appert-Collin Aline , Cotecchia Susanna , Nenniger-Tosato Monique , Pedrazzini Thierry , Diviani Dario
Published: May 2007

In response to various pathological stresses, the heart undergoes a pathological remodeling process that is associated with cardiomyocyte hypertrophy. Because cardiac hypertrophy can progress to heart failure, a major cause of lethality worldwide, the intracellular signaling pathways that control cardiomyocyte growth have been the subject of intensive investigation. It has been known for more than a decade that the small molecular weight GTPase RhoA is involved in the signaling pathways leading to cardiomyocyte hypertrophy. Although some of the hypertrophic pathways activated by RhoA have now been identified, the identity of the exchange factors that modulate its activity in cardiomyocytes is currently unknown. In this study, we show that AKAP-Lbc, an A-kinase anchoring protein (AKAP) with an intrinsic Rho-specific guanine nucleotide exchange factor activity, is critical for activating RhoA and transducing hypertrophic signals downstream of α1-adrenergic receptors (ARs). In particular, our results indicate that suppression of AKAP-Lbc expression by infecting rat neonatal ventricular cardiomyocytes with lentiviruses encoding AKAP-Lbc-specific short hairpin RNAs strongly reduces both α1-AR-mediated RhoA activation and hypertrophic responses. Interestingly, α1-ARs promote AKAP-Lbc activation via a pathway that requires the α subunit of the heterotrimeric G protein G12. These findings identify AKAP-Lbc as the first Rho-guanine nucleotide exchange factor (GEF) involved in the signaling pathways leading to cardiomyocytes hypertrophy.
Nitric oxide inhibits Shiga-toxin synthesis by enterohemorrhagic
Escherichia coli
Authors: Vareille Marjolaine , de Sablet Thibaut , Hindré Thomas , Martin Christine , Gobert Alain P.
Published: May 2007

Shiga-toxin (Stx) is the cardinal virulence factor of enterohemorrhagic
Escherichia coli
(EHEC). The genes encoding Stx are carried by a lambdoid phage integrated in the bacterial genome and are fully expressed after a bacterial SOS response induced by DNA-damaging agents. Because nitric oxide (NO) is an essential mediator of the innate immune response of infected colonic mucosa, we aimed to determine its role in Stx production by EHEC. Here we demonstrate that chemical or cellular sources of NO inhibit spontaneous and mitomycin C-induced
stx
mRNA expression and Stx synthesis, without altering EHEC viability. The synthesis of
stx
phage is also reduced by NO. This inhibitory effect apparently occurs through the NO-mediated sensitization of EHEC because mutation of the NO sensor nitrite-sensitive repressor results in loss of NO inhibiting activity on
stx
expression. Thus our findings identify NO as an inhibitor of
stx
expressing-phage propagation and Stx release and thus as a potential protective factor limiting the development of hemolytic syndromes.
Rab11A Controls the Biogenesis of Birbeck Granules by Regulating Langerin Recycling and Stability
Authors: Uzan-Gafsou Stéphanie , Bausinger Huguette , Proamer Fabienne , Monier Solange , Lipsker Dan , Cazenave Jean-Pierre , Goud Bruno , de la Salle Henri , Hanau Daniel , Salamero Jean
Published: May 2007

The extent to which Rab GTPases, Rab-interacting proteins, and cargo molecules cooperate in the dynamic organization of membrane architecture remains to be clarified. Langerin, a recycling protein accumulating in the Rab11-positive compartments of Langerhans cells, induces the formation of Birbeck granules (BGs), which are membrane subdomains of the endosomal recycling network. We investigated the role of Rab11A and two members of the Rab11 family of interacting proteins, Rip11 and RCP, in Langerin traffic and the biogenesis of BGs. The overexpression of a dominant-negative Rab11A mutant or Rab11A depletion strongly influenced Langerin traffic and stability and the formation of BGs, whereas modulation of other Rab proteins involved in dynamic regulation of the endocytic-recycling pathway had no effect. Impairment of Rab11A function led to a missorting of Langerin to lysosomal compartments, but inhibition of Langerin degradation by chloroquine did not restore the formation of BGs. Loss of RCP, but not of Rip11, also had a modest, but reproducible effect on Langerin stability and BG biogenesis, pointing to a role for Rab11A–RCP complexes in these events. Our results show that Rab11A and Langerin are required for BG biogenesis, and they illustrate the role played by a Rab GTPase in the formation of a specialized subcompartment within the endocytic-recycling system.
Mechanism Underlying the Iron-dependent Nuclear Export of the Iron-responsive Transcription Factor Aft1p inSaccharomyces cerevisiae
Authors: Ueta Ryo , Fujiwara Naoko , Iwai Kazuhiro , Yamaguchi-Iwai Yuko
Published: May 2007

Aft1p is an iron-responsive transcriptional activator that plays a central role in maintaining iron homeostasis in Saccharomyces cerevisiae. Aft1p is regulated primarily by iron-induced shuttling of the protein between the nucleus and cytoplasm, but its nuclear import is not regulated by iron. Here, we have shown that the nuclear export of Aft1p is promoted in the presence of iron and that Msn5p is the nuclear export receptor (exportin) for Aft1p. Msn5p recognizes Aft1p in the iron-replete condition. Phosphorylation of S210 and S224 in Aft1p, which is not iron dependent, and the iron-induced intermolecular interaction of Aft1p are both essential for its recognition by Msn5p. Mutation of Cys291 of Aft1p to Phe, which causes Aft1p to be retained in the nucleus and results in constitutive activation of Aft1-target genes, disrupts the intermolecular interaction of Aft1p. Collectively, these results suggest that iron induces a conformational change in Aft1p, in which Aft1p Cys291 plays a critical role, and that, in turn, Aft1p is recognized by Msn5p and exported into the cytoplasm in an iron-dependent manner.
Phosphatidylinositol-4,5 Bisphosphate Produced by PIP5KIγ Regulates Gelsolin, Actin Assembly, and Adhesion Strength of N-Cadherin Junctions
Authors: El Sayegh T. Y. , Arora P. D. , Ling K. , Laschinger C. , Janmey P. A. , Anderson R. A. , McCulloch C. A.
Published: May 2007

Phosphoinositides regulate several actin-binding proteins but their role at intercellular adhesions has not been defined. We found that phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) was generated at sites of N-cadherin–mediated intercellular adhesion and was a critical regulator of intercellular adhesion strength. Immunostaining for PI(4,5)P2or transfection with GFP-PH-PLCδ showed that PI(4,5)P2was enriched at sites of N-cadherin adhesions and this enrichment required activated Rac1. Isoform-specific immunostaining for type I phosphatidylinositol 4-phosphate 5 kinase (PIP5KI) showed that PIP5KIγ was spatially associated with N-cadherin–Fc beads. Association of PIP5KIγ with N-cadherin adhesions was in part dependent on the activation of RhoA. Transfection with catalytically inactive PIP5KIγ blocked the enrichment of PI(4,5)P2around beads. Catalytically inactive PIP5KIγ or a cell-permeant peptide that mimics and competes for the PI(4,5)P2-binding region of the actin-binding protein gelsolin inhibited incorporation of actin monomers in response to N-cadherin ligation and reduced intercellular adhesion strength by more than twofold. Gelsolin null fibroblasts transfected with a gelsolin severing mutant containing an intact PI(4,5)P2binding region, demonstrated intercellular adhesion strength similar to wild-type transfected controls. We conclude that PIP5KIγ-mediated generation of PI(4,5)P2at sites of N-cadherin contacts regulates intercellular adhesion strength, an effect due in part to PI(4,5)P2-mediated regulation of gelsolin.
Canonical Interaction of Cyclin G–associated Kinase with Adaptor Protein 1 Regulates Lysosomal Enzyme Sorting
Authors: Kametaka Satoshi , Moriyama Kengo , Burgos Patricia V. , Eisenberg Evan , Greene Lois E. , Mattera Rafael , Bonifacino Juan S.
Published: May 2007

The adaptor protein 1 (AP1) complex is a heterotetramer that participates in cargo sorting into clathrin-coated vesicles at the trans-Golgi network (TGN) and endosomes. The γ subunit of AP1 possesses a C-terminal “ear” domain that recruits a cohort of accessory proteins through recognition of a shared canonical motif, ΨG[PDE][ΨLM] (where Ψ is an aromatic residue). The physiological relevance of these ear-motif interactions, however, remains to be demonstrated. Here we report that the cyclin G–associated kinase (GAK) has two sequences fitting this motif, FGPL and FGEF, which mediate binding to the AP1-γ-ear domain in vitro. Mutation of both γ-ear–binding sequences or depletion of AP1-γ by RNA interference (RNAi) decreases the association of GAK with the TGN in vivo. Depletion of GAK by RNAi impairs the sorting of the acid hydrolase, cathepsin D, to lysosomes. Importantly, expression of RNAi-resistant GAK restores the lysosomal sorting of cathepsin D in cells depleted of endogenous GAK, whereas expression of a similar construct bearing mutations in both γ-ear–binding sequences fails to correct the sorting defect. Thus, interactions between the ΨG[PDE][ΨLM]-motif sequences in GAK and the AP1-γ-ear domain are critical for the recruitment of GAK to the TGN and the function of GAK in lysosomal enzyme sorting.
Immobilization of the Type XIV Myosin Complex inToxoplasma gondii
Authors: Johnson Terezina M. , Rajfur Zenon , Jacobson Ken , Beckers Con J.
Published: May 2007

The substrate-dependent movement of apicomplexan parasites such as Toxoplasma gondii and Plasmodium sp. is driven by the interaction of a type XIV myosin with F-actin. A complex containing the myosin-A heavy chain, a myosin light chain, and the accessory protein GAP45 is attached to the membranes of the inner membrane complex (IMC) through its tight interaction with the integral membrane glycoprotein GAP50. For the interaction of this complex with F-actin to result in net parasite movement, it is necessary that the myosin be immobilized with respect to the parasite and the actin with respect to the substrate the parasite is moving on. We report here that the myosin motor complex of Toxoplasma is firmly immobilized in the plane of the IMC. This does not seem to be accomplished by direct interactions with cytoskeletal elements. Immobilization of the motor complex, however, does seem to require cholesterol. Both the motor complex and the cholesterol are found in detergent-resistant membrane domains that encompass a large fraction of the inner membrane complex surface. The observation that the myosin XIV motor complex of Toxoplasma is immobilized within this cholesterol-rich membrane likely extends to closely related pathogens such as Plasmodium and possibly to other eukaryotes.
Acetylcholinesterase Mobility and Stability at the Neuromuscular Junction of Living Mice
Authors: Martinez-Pena y Valenzuela Isabel , Akaaboune Mohammed
Published: May 2007

Acetylcholinesterase (AChE) is an enzyme that terminates acetylcholine neurotransmitter function at the synaptic cleft of cholinergic synapses. However, the mechanism by which AChE number and density are maintained at the synaptic cleft is poorly understood. In this work, we used fluorescence recovery after photobleaching, photo-unbinding, and quantitative fluorescence imaging to investigate the surface mobility and stability of AChE at the adult innervated neuromuscular junction of living mice. In wild-type synapses, we found that nonsynaptic (perisynaptic and extrasynaptic) AChEs are mobile and gradually recruited into synaptic sites and that most of the trapped AChEs come from the perijunctional pool. Selective labeling of a subset of synaptic AChEs within the synapse by using sequential unbinding and relabeling with different colors of streptavidin followed by time-lapse imaging showed that synaptic AChEs are nearly immobile. At neuromuscular junctions of mice deficient in α-dystrobrevin, a component of the dystrophin glycoprotein complex, we found that the density and distribution of synaptic AChEs are profoundly altered and that the loss rate of AChE significantly increased. These results demonstrate that nonsynaptic AChEs are mobile, whereas synaptic AChEs are more stable, and that α-dystrobrevin is important for controlling the density and stability of AChEs at neuromuscular synapses.
Short oligonucleotide probes containing G-stacks display abnormal binding affinity on Affymetrix microarrays
Authors: Wu Chunlei , Zhao Haitao , Baggerly Keith , Carta Roberto , Zhang Li
Published: May 2007

Motivation: In microarray experiments, probe design is critical to the specific and accurate measurement of target concentrations. Current designs select suitable probes through in silico scanning of transcriptome/genome based on first principles. However, due to lack of tools, the observed microarray data have not been used to assess the performance of individual probes to provide feedback to improve future designs.

Result: In this study, we describe a probe performance assessment method based on the concordance of the observed signals from probes that share common targets. Using this method, we found that probes containing multiple guanines in a row (G-stacks) have abnormal binding behavior compared with other probes, both in gene expression assays and genotyping assays using Affymetrix microarrays. These probes are less likely to covary with other probes that interrogate the same genes. Moreover, we found that these probes are much more likely to produce outliers when fitting the observed signals according to the positional dependent nearest neighbor model, which gives reasonable estimates of binding affinity for most other probes. These results suggest that probes containing G-stacks tend to have increased cross hybridization signals and reduced target-specific hybridization signals, presumably due to multiplex binding forming G-quartet structures. Our findings are expected to be useful in microarray design and data analysis.

Availability: URL: http://odin.mdacc.tmc.edu/~zhangli/PerfectMatch/contains the computer program for calculating correlations of neighboring probes.

Contact: lzhangli@mdanderson.org

Supplementary information: Bioinformatics online or http://odin.mdacc.tmc.edu/~zhangli/G-stack
Mining co-regulated gene profiles for the detection of functional associations in gene expression data
Authors: Gyenesei Attila , Wagner Ulrich , Barkow-Oesterreicher Simon , Stolte Etzard , Schlapbach Ralph
Published: May 2007

Motivation: Association pattern discovery (APD) methods have been successfully applied to gene expression data. They find groups of co-regulated genes in which the genes are either up- or down-regulated throughout the identified conditions. These methods, however, fail to identify similarly expressed genes whose expressions change between up- and down-regulation from one condition to another. In order to discover these hidden patterns, we propose the concept of mining co-regulated gene profiles. Co-regulated gene profiles contain two gene sets such that genes within the same set behave identically (up or down) while genes from different sets display contrary behavior. To reduce and group the large number of similar resulting patterns, we propose a new similarity measure that can be applied together with hierarchical clustering methods.

Results: We tested our proposed method on two well-known yeast microarray data sets. Our implementation mined the data effectively and discovered patterns of co-regulated genes that are hidden to traditional APD methods. The high content of biologically relevant information in these patterns is demonstrated by the significant enrichment of co-regulated genes with similar functions. Our experimental results show that the Mining Attribute Profile (MAP) method is an efficient tool for the analysis of gene expression data and competitive with bi-clustering techniques.

Contact:  ulrich.wagner@fgcz.ethz.ch

Supplementary information: Supplementary data and an executable demo program of the MAP implementation are freely available at http://www.fgcz.ch/publications/map
Exploring sequence-structure relationships in the tyrosine kinome space: functional classification of the binding specificity mechanisms for cancer therapeutics
Authors: Verkhivker Gennady M.
Published: May 2007

Motivation: Evolutionary and structural conservation patterns shared by more than 500 of identified protein kinases have led to complex sequence-structure relationships of cross-reactivity for kinase inhibitors. Understanding the molecular basis of binding specificity for protein kinases family, which is the central problem in discovery of cancer therapeutics, remains challenging as the inhibitor selectivity is not readily interpreted from chemical proteomics studies, neither it is easily discernable directly from sequence or structure information. We present an integrated view of sequence-structure-binding relationships in the tyrosine kinome space in which evolutionary analysis of the kinases binding sites is combined with computational proteomics profiling of the inhibitor–protein interactions. This approach provides a functional classification of the binding specificity mechanisms for cancer agents targeting protein tyrosine kinases.

Results: The proposed functional classification of the kinase binding specificities explores mechanisms in which structural plasticity of the tyrosine kinases and sequence variation of the binding-site residues are linked with conformational preferences of the inhibitors in achieving effective drug binding. The molecular basis of binding specificity for tyrosine kinases may be largely driven by conformational adaptability of the inhibitors to an ensemble of structurally different conformational states of the enzyme, rather than being determined by their phylogenetic proximity in the kinome space or differences in the interactions with the variable binding-site residues. This approach provides a fruitful functional linkage between structural bioinformatics analysis and disease by unraveling the molecular basis of kinase selectivity for the prominent kinase drugs (Imatinib, Dasatinib and Erlotinib) which is consistent with structural and proteomics experiments.

Contact:  verk@ku.edu or gverkhiv@ucsd.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
READING WALTER BENJAMIN'S CONCEPT OF THE RUIN IN VICTOR HUGO'S
NOTRE-DAME DE PARIS
Authors: Stephens Bradley
Published: May 2007

Walter Benjamin's readings of modernity are repeatedly strained by the tension he identifies between demystification and the drive towards the mythic. How are we to awaken from ‘ideological dream-states’ and engage with an indeterminate reality without positing the unity of an integrated whole to begin with? I suggest that Hugo's
Notre-Dame de Paris
yields a compelling perspective on this dilemma. Hugo never denies the lure of myths in his novel, simply their possibility, recognising that they remain as irresistible as they are incredible. He energises the opposition between artifice and actuality, proposing that man can only oscillate between both the ideal and the real, even though he cannot overcome their incompatibility. This dynamic is observed upon Notre-Dame herself. Her hybrid edifice bears the mark of bygone values, yet as such stands as a monument to the transformative sweep of time. In turn, Hugo teases yet simultaneously refuses any absolute narrative viewpoint, stressing both the limitations of language and his own subjectivity. What makes this reading less an exercise of intellectual indulgence than a matter of critical urgency is Benjamin's widely overlooked attraction towards Hugo as a modernist writer. Indeed, the novel deploys two key tools of Benjamin's thinking: allegory, to expose meaning as arbitrary, and the ruin, which preserves the image of a history that is no more. I explore Hugo's representation of both novel and cathedral as realms of contrast, not integration, so as to make a productive return to the dilemmas Benjamin encounters.
EXHIBITING PAIN: SOPHIE CALLE'S
DOULEUR EXQUISE
Authors: Jordan Shirley Ann
Published: May 2007

This article focuses on the relationship between the subjective and the collective in the work of project artist Sophie Calle through a ‘virtual visit’ to her mixed-media installation
Douleur exquise
(1984–2003). Through detailed analysis of the intricate systems of narrative in and between the installation's three parts, it assesses the contribution of Calle's project to two phenomena which are of central importance to cultural production in France and beyond at the start of the twenty-first century. The first is a fascination with
l'intime
and with punctures or shifts in the public/private boundary, and the article explores how
Douleur exquise
develops Calle's customary handling of autofictional tensions and the exposure of self and other. The second is our obsessive memorial imperative, a cultural development to which Calle has not yet formally been linked. The article argues that Calle's installation demonstrates an anthropological interest in cultural constructions of suffering, mourning practices and memorial artefacts. Finally, it suggests that
Douleur exquise
self-consciously invites us to respond to it as a new kind of monument, one appropriate to process-driven project art. This, the article defines as a ‘soft monument’.
Synergistic Interaction ofSweet potato chlorotic stunt virus(Crinivirus) with Carla-, Cucumo-, Ipomo-, and Potyviruses Infecting Sweet Potato
Authors: Untiveros Milton , Fuentes Segundo , Salazar Luis F.
Published: May 2007

Co-infection of Sweet potato chlorotic stunt virus (SPCSV, genus Crinivirus) with Sweet potato feathery mottle virus (SPFMV, genus Potyvirus) results in sweet potato virus disease (SPVD), a synergistic disease that is widely distributed in the sweet potato (Ipomoea batatas) growing regions of the world. Since both SPCSV and SPFMV are common and often detected as part of multiple co-infections of severely diseased plants, the occurrence of synergistic interactions with other viruses was investigated. Data from this study show that SPCSV, but not SPFMV, can cause synergistic diseases in sweet potato with all viruses tested, including members of the genus Potyvirus (Sweet potato latent virus, Sweet potato mild speckling virus), Ipomovirus (Sweet potato mild mottle virus), Cucumovirus (Cucumber mosaic virus), and putative members of the genus Carlavirus (Sweet potato chlorotic fleck virus and C-6 virus). The synergism was expressed as an increase in the severity of symptoms, virus accumulation, viral movement in plants, and as an effect on yield of storage roots. The presence of a third different virus in plants affected with SPVD increased the severity of symptoms even further compared with SPVD alone. There was a positive correlation between increase in virus accumulation and symptom expression in double and triple SPCSV-associated co-infections. The epidemiological implications of the results are discussed.
Curtobacterium flaccumfaciens pv. beticola, A New Pathovar of Pathogens in Sugar Beet
Authors: Chen Yong-Fang , Yin Yan-Ni , Zhang Xiao-Mei , Guo Jian-Hua
Published: May 2007

Bacterial leaf spot of sugar beet was first discovered in 1995 in Inner Mongolia of China. The pathogen was shown to be a bacterium with properties of gram-positive bacteria: small irregular rods, lateral flagella, aerobic, and catalase-positive. The colonies of sugar beet strains produced a pale-yellow pigment. The optimum temperature for the bacteria to grow was 24 to 27°C. The bacteria could utilize a wide range of organic compounds, including hydrolyzed casein, starch, esculin and Tween 80, and released H2S from cysteine, cystine, and Na2S2O3·5H2O, but could not produce urease, oxidase, or indole. The cell wall peptidoglycan was based on ornithine (type B2β). The predominant menaquinone was MK-9. Polar lipids contained several glycosyldiacyl-glycerols. The DNA G+C content of a type strain of the new pathovar, T30T, was 67.5%. DNA-DNA homology between T30T and Curtobacterium flaccumfaciens pv. flaccumfaciens (International Collection of Micro-Organisms from Plants, New Zealand [ICMP] 2584) was 70.1%. The new pathovar and C. flaccumfaciens pv. flaccumfaciens had 99.9% identity in DNA sequence of 16S rRNA. Close genetic relatedness was observed for the representatives of the species Curtobacterium flaccumfaciens, but a low level of similarity between the different pathovars was found. Based on these physiological, biochemical, chemotaxonomic, phylogenetic, and genetic characteristics, we demonstrate that the pathogen represents a new pathovar of C. flaccumfaciens, for which we propose the name Curtobacterium flaccumfaciens pv. beticola pv. nov. The type strain is T30T (=ATCC BAA-144T).
Response of Soybean Cultivars to Bean pod mottle virus Infection
Authors: Ziems Amy D. , Giesler Loren J. , Graef George L. , Redinbaugh Margaret G. , Vacha Jean L. , Berry SueAnn , Madden Laurence V. , Dorrance Anne E.
Published: May 2007

Bean pod mottle virus (BPMV) has become increasingly common in soybean throughout the north-central region of the United States. Yield loss assessments on southern soybean germplasm have reported reductions ranging from 3 to 52%. Currently, no soybean cultivars have been identified with resistance to BPMV. The objective of this study was to determine the impact of BPMV infection on soybean cultivars representing a broad range of northern soybean germ-plasm by comparing inoculated and noninoculated soybean plants in paired row studies. In all, 30 and 24 cultivars were evaluated in Nebraska (NE) in which soybean plants were inoculated at the V3 to V4 growth stage. Eleven cultivars from public and breeding lines were inoculated at the VC and R5 to R6 growth stages in Ohio (OH). Disease severity, yield, and percent seed coat mottling were assessed at both locations, whereas protein and oil content also were assessed at NE. Yield and percent seed coat mottling was significantly reduced following inoculation at the VC (OH) and V3 to V4 (NE) growth stages. In addition, seed oil and protein composition were impacted in 1 of the 2 years of the study. This study demonstrates that substantial yield losses can occur in soybean due to BPMV infection. In addition, protein and oil may be affected depending on the environment during the production season.
Characterization of Pythium spp. Associated with Corn and Soybean Seed and Seedling Disease in Ohio
Authors: Broders K. D. , Lipps P. E. , Paul P. A. , Dorrance A. E.
Published: May 2007

Cool, moist conditions in combination with minimum tillage, earlier planting, and recent shifts in commercial fungicide seed-treatment active ingredients have led to an increase in corn (Zea mays) and soybean (Glycine max) seedling establishment problems. This situation resulted in an investigation of Pythium spp. associated with seed and seedling diseases. Samples of diseased corn and soybean seedlings were collected from 42 production fields in Ohio. All isolates of Pythium recovered were identified to species using morphological and molecular techniques and evaluated in an in vitro pathogenicity assay on both corn and soybean seed, and a subset of the isolates was tested for sensitivity to fungicides currently used as seed treatments. Eleven species and two distinct morphological groups of Pythium were identified, of which six species were moderately to highly pathogenic on corn seed and nine species were highly pathogenic on soybean seed. There was significant variation (P < 0.05) in sensitivity to mefenoxam, azoxystrobin, trifloxystrobin, and captan both across and within species. Multiple species of Pythium had the capacity to reduce germination of both corn and soybean seed. Results indicated that mefenoxam, azoxystrobin, trifloxystrobin, or captan, when used individually, may not inhibit all pathogenic species of Pythium found in Ohio soils.
Letter Code System of Nomenclature for Puccinia graminis f. sp. avenae
Authors: Fetch T. G. , Jin Y.
Published: May 2007

Current systems that describe the virulence phenotype in Puccinia graminis f. sp. avenae lack a systematic approach for the naming of races or to provide easily made comparisons of virulence among races. A new nomenclature system that simply and systematically characterizes virulence in P. graminis f. sp. avenae is described. The new system has the distinct advantage of providing easily seen relationships among races in contrast to previous nomenclature systems. This allows for easier interpretation of virulence relationships in the oat stem rust population and provides a large amount of virulence information with a minimum of written characters. This system uses single-gene differential lines with the resistance genes Pg1, Pg2, Pg3, Pg4, Pg6, Pg8, Pg9, Pg10, Pg12, Pg13, Pg15, and Pg16, grouped into three subsets of four lines in sequential Pg gene order. By grouping in sequential gene number order, the relationship of the new system to the “standard” system is easily seen. Each race is designated by a three-letter code, based on the seedling reaction (low or high) on 12 differential lines. The letter code nomenclature system is open ended and can be updated easily as new differential genes are identified. This system simply and precisely describes the virulence phenotypes of isolates of P. graminis f. sp. avenae, and allows for easily made comparisons of virulence of isolates collected over time and across geographical locations worldwide.
First Report of Damping-Off and Leaf Spot Caused by Cylindrocladium scoparium on Different Accessions of Bottlebrush Cuttings in Italy
Authors: Polizzi G. , Vitale A. , Aiello D. , Dimartino M. A. , Parlavecchio G.
Published: May 2007

In May of 2006, approximately 10,000 cuttings of bottlebrushes (Callistemon cvs. Laevis, Hannah Ray, Kings Park Special, Masotti Mini Red, and Rose Opal with either C. viminalis (Soland. ex Gaertn.) Cheel. [excluded] or C. citrinus (Curtis) Skeels as one parent) grown in a nursery in eastern Sicily (Italy) exhibited severe disease symptoms including damping-off, leaf spots, and collar and root rot. Initially, the infections were detected on approximately 30% of the cuttings, but by late September 2006, 70% of the plants had symptoms. A Cylindrocladium sp. was consistently isolated from the diseased portions of plants onto potato dextrose agar. To determine the species, single-conidial isolates of the fungus were cultured on carnation leaf agar (CLA) for 7 days at 25°C with 12 h of light/dark conditions. Only the mycelia and spores growing on the carnation leaves were examined with a light microscope, and the isolates were identified as Cylindrocladium scoparium Morgan (teleomorph Calonectria morganii Crous, Alfenas & M.J. Wingf.) on the basis of their pyriform to broadly ellipsoidal terminal vesicles, conidiophore branching pattern, and conidia (1). In addition, the ability of the colonies to mate with South African tester strains of C. scoparium (2,3) confirmed the identification. Koch's postulates were fulfilled by inoculating 10 cuttings for each bottlebrush accession with a spore suspension (105 conidia per ml) of one isolate of the pathogen (DISTEF-GCs7) obtained from 14-day-old single-spore colonies grown on CLA at 24°C under fluorescent cool white lights with 12 h of light/dark. Following inoculation, all plants were maintained in plastic bags in a growth chamber at 25 ± 1°C and 90 to 95% relative humidity. The same number of cuttings was used as a control. Damping-off, crown root rot, and leaf spots symptoms identical to those observed in the nursery appeared within 5 to 20 days. No symptoms were detected on the control plants. C. scoparium was reisolated from the artificially infected tissues. The isolate, used in the pathogenicity proof, was deposited at the Fungal Biodiversity Centre, Centraalbureau voor Schimmelcultures (Accession No. CBS 120930). The presence of C. scoparium was detected for the first time in Italy on mastic tree in 2005 (3). To our knowledge, this is the first report of C. scoparium on bottlebrush in Italy and it represents the first information about the susceptibility of these Callistemon cultivar accessions to the fungus and confirms the spread of the pathogen in Sicilian ornamental nurseries.

References: (1) P. W. Crous. Taxonomy and Pathology of Cylindrocladium (Calonectria) and Allied Genera. The American Phytopathological Society, St. Paul MN, 2002. (2) P. W. Crous and M. J. Wingfield. Mycotaxon 51:341, 1994. (3) G. Polizzi et al. Plant Dis. 90:1110, 2006.
First Report of Phytoplasmas Associated with the Degeneration Syndrome of Artichoke in Catalonia (Spain)
Authors: Batlle A. , Sabaté J. , Laviña A.
Published: May 2007

Spain is the second largest producer of artichoke (Cynara scolymus L.) in the world with 230,000 tons produced annually. The region of Catalonia, located in northeast Spain, has 3,500 ha dedicated to this crop. Low yield and degeneration anomalies are widespread problems in the Mediterranean area. The degeneration syndrome results in curled leaves and late development of capitulum. The association of this syndrome with different viruses such as Artichoke degeneration virus (ADV), Artichoke latent virus (ALV), Broad bean wilt virus (BBWV), Cucumber mosaic virus (CMV), and many others was not conclusive. Other studies indicated that this phenomenon could be related to a regression of the cultivar toward the species of origin, the wild cardoon (C. cardunculus L. var. sylvestris). The distribution of degenerated plants in the principal artichoke-growing areas of Catalonia together with the presence of plants with normal and degenerated tissues in the same plant suggested the presence of phytoplasmas. Samples from 30 symptomatic and 30 asymptomatic plants of cv. Blanca de Tudela were collected in February of 2006 from different areas of Catalonia and analyzed by PCR amplification of phytoplasma DNA. DNA for PCR analyses was prepared from leaf petioles and midribs according to the Ahrens and Seemüller procedure (1). Nested-PCR was carried out with rRNA primer pairs P1/P7 and fU5/rU3 (2,3). Alternatively, nested-PCR, with primers Tuf 1 f/r in the first step and Tuf AY f/r in the second, amplifying a DNA fragment of the elongation gene Tu of the phytoplasmas belonging to Aster yellows and stolbur groups was conducted (4). Results showed a high correlation between presence of symptoms and phytoplasma detection. Phytoplasmas were detected in 100% of the symptomatic plants (30 of 30) and only in one of the asymptomatic plants. The restriction fragment length profiles of Tuf AY amplicons with HpaII showed two different patterns, the most important belonging to the aster yellows (16SrI) group phytoplasma and the other to the stolbur (16SrXII) group phytoplasma. To our knowledge, this is the first time that phytoplasmas have been detected in artichoke and associated with degeneration of this crop.

References: (1) U. Ahrens and E. Seemüller. Phytopathology 82:828, 1992. (2) S. Deng and C. Hiruki. J. Microbiol. Methods 14:53, 1991. (3) K. H. Lorenz et al. Phytopathology 85:771, 1995. (4) B. Schneider et al. Microbiology 143:3381, 1997.
Histopathology of Infection and Colonization of Susceptible and Resistant Port-Orford-Cedar by Phytophthora lateralis
Authors: Oh Eunsung , Hansen Everett M.
Published: May 2007

Port-Orford-cedar (POC) root disease, caused by Phytophthora lateralis, continues to kill POC in landscape plantings and natural forests in western North America. POC trees resistant to P. lateralis have been identified and propagated. Cytological observations of P. lateralis in susceptible and resistant roots and stems were made with light and transmission electron microscopy to identify resistance mechanisms. No differences in infection pathway and initial colonization were observed between susceptible and resistant roots, although there were differences in the rate and extent of development. Germ tubes formed appressoria, and penetration hyphae grew either between or directly through epidermal cell walls; inter- and intracellular hyphae colonized the root cortex. In susceptible roots, hyphae penetrated into the vascular system within 48 h of inoculation. In contrast, hyphae in roots of resistant seedlings grew more slowly in cortical cells and were not observed to penetrate to the vascular tissues. In resistant roots, infection was marked by general thickening of cortical cell walls, wall appositions around penetrating hyphae, collapse of cortical cells, and accumulation of osmophillic granules around hyphae. In susceptible stems, hyphae grew inter- and intracellularly in all cells of the secondary phloem except fiber cells, but were concentrated in sieve and parenchyma cells in the functional phloem. The pattern of penetration and colonization of hyphae was similar in the resistant stems, except that hyphae were found in the fiber cells of the xylem. In resistant stems, there were fewer hyphae in the functional phloem, and cytological changes such as damaged nuclei and disintegrated cytoplasm were evident. Structural changes in resistant stems included collapsed cells, wall thickening, secretory bodies, apposition of electron dense materials, and crystals in cell walls.
Molecular and Biological Characterization of Tomato chlorotic mottle virus Suggests that Recombination Underlies the Evolution and Diversity of Brazilian Tomato Begomoviruses
Authors: Ribeiro Simone G. , Martin Darren P. , Lacorte Cristiano , Simões Isabella C. , Orlandini Deborah R. S. , Inoue-Nagata Alice K.
Published: May 2007

Tomato chlorotic mottle virus (ToCMoV) is an emerging begomovirus species widely distributed throughout tomato-growing regions of Brazil. ToCMoV appears to have expanded its geographic range recently, invading tomato-growing areas that were free of begomovirus infection before 2004. We have determined the first complete genome sequence of an infectious ToCMoV genome (isolate BA-Se1), which is the first begomovirus species isolated in the northeast of Brazil. When introduced by particle bombardment into tomato, the cloned ToCMoV-[BA-Se1] DNA-A and DNA-B components caused typical chlorotic mottle symptoms. The cloned virus was whitefly-transmissible and, although it was infectious in hosts such as Nicotiana benthamiana, pepper, tobacco, and Nicandra physaloides, it was unable to infect Arabidopsis thaliana, bean, N. glutinosa, and Datura metel. Sequence and biological analyses indicate that ToCMoV-[BA-Se1] is a typical New World begomovirus sp. requiring both DNA-A and DNA-B components to establish systemic infections. Although evidence of multiple recombination events was detected within the ToCMoV-[BA-Se1] DNA-A, they apparently occurred relatively long ago, implying that recombination probably has not contributed to the recent emergence of this species.
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution
Authors: Kensche Philip R , van Noort Vera , Dutilh Bas E , Huynen Martijn A
Published: May 2007

The gap between the amount of genome information released by genome sequencing projects and our knowledge about the proteins' functions is rapidly increasing. To fill this gap, various ‘genomic-context’ methods have been proposed that exploit sequenced genomes to predict the functions of the encoded proteins. One class of methods, phylogenetic profiling, predicts protein function by correlating the phylogenetic distribution of genes with that of other genes or phenotypic characteristics. The functions of a number of proteins, including ones of medical relevance, have thus been predicted and subsequently confirmed experimentally. Additionally, various approaches to measure the similarity of phylogenetic profiles and to account for the phylogenetic bias in the data have been proposed. We review the successful applications of phylogenetic profiling and analyse the performance of various profile similarity measures with a set of one microsporidial and 25 fungal genomes. In the fungi, phylogenetic profiling yields high-confidence predictions for the highest and only the highest scoring gene pairs illustrating both the power and the limitations of the approach. Both practical examples and theoretical considerations suggest that in order to get a reliable and specific picture of a protein's function, results from phylogenetic profiling have to be combined with other sources of evidence.
Conformal mappings to a doubly connected polycircular arc domain
Authors: Crowdy D.G , Fokas A.S
Published: May 2007

The explicit construction of the conformal mapping of a concentric annulus to a doubly connected polygonal domain was first reported by Akhiezer in 1928. The construction of an analogous formula for the case of a polycircular arc domain, i.e. for a doubly connected domain whose boundaries are a union of circular arc segments, has remained an important open problem. In this paper, we present this explicit formula. We first introduce a new method for deriving the classical formula of Akhiezer and then show how to generalize the method to the case of a doubly connected polycircular arc domain. As an analytical check of the formula, a special exact solution for a doubly connected polycircular arc mapping is derived and compared with that obtained from the more general construction. As an illustrative example, a doubly connected polycircular arc domain arising in a classic potential flow problem considered in the last century by Lord Rayleigh is considered in detail.
Genetic analysis reveals promiscuity among female cheetahs
Authors: Gottelli Dada , Wang Jinliang , Bashir Sultana , Durant Sarah M
Published: May 2007

Cheetahs (
Acinonyx jubatus
) have a combination of ranging patterns and social system that is unique in mammals, whereby male coalitions occupy small territories less than 10% of the home range of solitary females. This study uses non-invasive genetic sampling of a long-term study population of cheetah in the Serengeti National Park in Tanzania to infer the mating system. Individual cheetah genotypes at up to 13 microsatellite loci were obtained from 171 faecal samples. A statistical method was adapted to partition the cubs within each litter (
n
=47) into full-sibling clusters and to infer the father of each cluster using these loci. Our data showed a high rate of multiple paternity in the population; 43% of litters with more than one cub were fathered by more than one male. The results also demonstrated that female fidelity was low, and provided some evidence that females chose to mate with unrelated males within an oestrus cycle. The low rate of paternity assignments indicated that males living outside the study area contributed substantially to the reproduction of the cheetah population.
Fisheries in the Southern Ocean: an ecosystem approach
Authors: Kock Karl-Hermann , Reid Keith , Croxall John , Nicol Stephen
Published: May 2007

The Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) is bound by its Article II, 3 to follow an ecosystem approach to management. This approach has been extended to the application of a precautionary approach in the late 1980s. In our review, we deal primarily with the science-related aspects of CCAMLR and its development towards an ecosystem approach to the management of the living resources of the Southern Ocean. To assist the Commission in meeting its objectives, as set out in Article II, 3, the Scientific Committee established the CCAMLR Ecosystem Monitoring Programme to detect possible effects of krill fishing on the performance of top-level predators, such as albatrosses, penguins, petrels and fur seals. Fisheries in the Southern Ocean followed the fate of other fisheries worldwide in which target species were depleted to low level one after the other. Currently, two types of fisheries are open: the longline fisheries on Patagonian toothfish (
Dissostichus eleginoides
) and Antarctic toothfish (
Dissostichus mawsoni
) and the trawl fisheries on mackerel icefish (
Champsocephalus gunnari
). Both fisheries are managed in a single-species context, however, with conservation measures in place to protect by-catch species, such as rattails (Macrouridae) and skates and rays (Rajidae). Two major problems still exist in fisheries in the Southern Ocean: the by-catch of birds in longline fisheries primarily in the Indian Ocean and the high level of IUU fishing again in the Indian Ocean. Both, the by-catch of birds and high IUU catches undermine the credibility of CCAMLR to safeguard the marine living resources in the Southern Ocean.
Treatment of thoracic esophageal carcinoma invading adjacent structures
Authors: Seto Yasuyuki , Chin Keisho , Gomi Kotaro , Kozuka Takuyo , Fukuda Takashi , Yamada Kazuhiko , Matsubara Toshiki , Tokunaga Masanori , Kato Yo , Yafune Akifumi , Yamaguchi Toshiharu
Published: May 2007

T4 esophageal cancer is defined as the tumor invading adjacent structures, using tumor–node–metastasis (TNM) staging. For clinically T4 thoracic esophageal carcinoma, multimodality therapy, that is, neoadjuvant chemoradiotherapy (CRT) followed by surgery or definitive CRT, has generally been performed. However, the prognosis of patients with these tumors remains poor. Another strategy is needed to achieve curative treatment. In the present article, the treatment strategies employed to date are reviewed. Furthermore, the strategies for these malignancies are reassessed, based on our experiences. R1/2 and R0 resections are regarded as those with residual and no tumor after surgery. The present data show that patients who underwent R1/2 resection after neoadjuvant CRT experienced little survival benefit, while complete response (CR) cases after definitive CRT had comparatively better results. Therefore, curative surgery should not be attempted without down‐staging, and definitive CRT should be the initial treatment. Then surgery is indicated for the eradication of residual cancer cells. Close surveillance is essential for early detection of relapse even after CR, because the operation will gradually become increasingly difficult due to post‐CRT fibrosis. In conclusion, multimodality therapy consists of definitive CRT followed by R0 resection, which can be the treatment of choice for T4 esophageal carcinoma. These challenging treatments have the potential to constitute the most effective therapeutic strategy. (Cancer Sci 2007; 98: 937–942)