bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovering motif pairs at interaction sites from protein sequences on a proteome-wide scale
Authors: Li Haiquan , Li Jinyan , Wong Limsoon 
Published: January 2006

Abstract
Motivation: Protein–protein interaction, mediated by protein interaction sites, is intrinsic to many functional processes in the cell. In this paper, we propose a novel method to discover patterns in protein interaction sites. We observed from protein interaction networks that there exist a kind of significant substructures called interacting protein group pairs, which exhibit an all-versus-all interaction between the two protein-sets in such a pair. The full-interaction between the pair indicates a common interaction mechanism shared by the proteins in the pair, which can be referred as an interaction type. Motif pairs at the interaction sites of the protein group pairs can be used to represent such interaction type, with each motif derived from the sequences of a protein group by standard motif discovery algorithms. The systematic discovery of all pairs of interacting protein groups from large protein interaction networks is a computationally challenging problem. By a careful and sophisticated problem transformation, the problem is solved using efficient algorithms for mining frequent patterns, a problem extensively studied in data mining.
Results: We found 5349 pairs of interacting protein groups from a yeast interaction dataset. The expected value of sequence identity within the groups is only 7.48%, indicating non-homology within these protein groups. We derived 5343 motif pairs from these group pairs, represented in the form of blocks. Comparing our motifs with domains in the BLOCKS and PRINTS databases, we found that our blocks could be mapped to an average of 3.08 correlated blocks in these two databases. The mapped blocks occur 4221 out of total 6794 domains (protein groups) in these two databases. Comparing our motif pairs with iPfam consisting of 3045 interacting domain pairs derived from PDB, we found 47 matches occurring in 105 distinct PDB complexes. Comparing with another putative domain interaction database InterDom, we found 203 matches.
Availability:
Contact: jinyan@i2r.a-star.edu.sg
Supplementary information: and Bioinformatics online.
A novel domain suggests a ciliary function for ASPM, a brain size determining gene
Authors: Ponting Chris P. 
Published: January 2006

Abstract
The N-terminal domain of abnormal spindle-like microcephaly-associated protein (ASPM) is identified as a member of a novel family of ASH (ASPM, SPD-2, Hydin) domains. These domains are present in proteins associated with cilia, flagella, the centrosome and the Golgi complex, and in Hydin and OCRL whose deficiencies are associated with hydrocephalus and Lowe oculocerebrorenal syndrome, respectively. Genes encoding ASH domains thus represent good candidates for primary ciliary dyskinesias. ASPM has been proposed to function in neurogenesis and to be a major determinant of cerebral cortical size in humans. Support for this hypothesis stems from associations between mutations in ASPM and primary microcephaly, and from the rapid evolution of ASPM during recent hominid evolution. The identification of the ASH domain family instead indicates possible roles for ASPM in sperm flagellar or in ependymal cells' cilia. ASPM's rapid evolution may thus reflect selective pressures on ciliary function, rather than pressures on mitosis during neurogenesis.
Contact: chris.ponting@anat.ox.ac.uk
Thermodynamics of RNA–RNA binding
Authors: Mückstein Ulrike , Tafer Hakim , Hackermüller Jörg , Bernhart Stephan H. , Stadler Peter F. , Hofacker Ivo L. 
Published: January 2006

Abstract
Background: Reliable prediction of RNA–RNA binding energies is crucial, e.g. for the understanding on RNAi, microRNA–mRNA binding and antisense interactions. The thermodynamics of such RNA–RNA interactions can be understood as the sum of two energy contributions: (1) the energy necessary to ‘open’ the binding site and (2) the energy gained from hybridization.
Methods: We present an extension of the standard partition function approach to RNA secondary structures that computes the probabilities Pu[i, j] that a sequence interval [i, j] is unpaired.
Results: Comparison with experimental data shows that Pu[i, j] can be applied as a significant determinant of local target site accessibility for RNA interference (RNAi). Furthermore, these quantities can be used to rigorously determine binding free energies of short oligomers to large mRNA targets. The resource consumption is comparable with a single partition function computation for the large target molecule. We can show that RNAi efficiency correlates well with the binding energies of siRNAs to their respective mRNA target.
Availability: RNAup will be distributed as part of the Vienna RNA Package,
Contact: ivo@tbi.univie.ac.at
Enhancing instance-based classification with local density: a new algorithm for classifying unbalanced biomedical data
Authors: Plant Claudia , Böhm Christian , Tilg Bernhard , Baumgartner Christian 
Published: January 2006

AbstractMotivation: Classification is an important data mining task in biomedicine. In particular, classification on biomedical data often claims the separation of pathological and healthy samples with highest discriminatory performance for diagnostic issues. Even more important than the overall accuracy is the balance of a classifier, particularly if datasets of unbalanced class size are examined.Results: We present a novel instance-based classification technique which takes both information of different local density of data objects and local cluster structures into account. Our method, which adopts the basic ideas of density-based outlier detection, determines the local point density in the neighborhood of an object to be classified and of all clusters in the corresponding region. A data object is assigned to that class where it fits best into the local cluster structure. The experimental evaluation on biomedical data demonstrates that our approach outperforms most popular classification methods.Availability: The algorithm LCF is available for testing underContact: christian.baumgartner@umit.at
The generation of mono-energetic electron beams from ultrashort pulse laser–plasma interactions
Authors: Mangles S.P.D , Krushelnick K , Najmudin Z , Wei M.S , Walton B , Gopal A , Dangor A.E , Fritzler S , Murphy C.D , Thomas A.G.R , Mori W.B , Gallacher J , Jaroszynski D , Norreys P.A , Viskup R 
Published: January 2006

The physics of the interaction of high-intensity laser pulses with underdense plasma depends not only on the interaction intensity but also on the laser pulse length. We show experimentally that as intensities are increased beyond 10
20
W cm
−2
the peak electron acceleration increases beyond that which can be produced from single stage plasma wave acceleration and it is likely that direct laser acceleration mechanisms begin to play an important role. If, alternatively, the pulse length is reduced such that it approaches the plasma period of a relativistic electron plasma wave, high-power interactions at much lower intensity enable the generation of quasi-mono-energetic beams of relativistic electrons.
High-intensity laser-driven proton acceleration: influence of pulse contrast
Authors: McKenna Paul , Lindau Filip , Lundh Olle , Neely David , Persson Anders , Wahlström Claes-Göran 
Published: January 2006

Proton acceleration from the interaction of ultra-short laser pulses with thin foil targets at intensities greater than 10
18
W cm
−2
is discussed. An overview of the physical processes giving rise to the generation of protons with multi-MeV energies, in well defined beams with excellent spatial quality, is presented. Specifically, the discussion centres on the influence of laser pulse contrast on the spatial and energy distributions of accelerated proton beams. Results from an ongoing experimental investigation of proton acceleration using the 10 Hz multi-terawatt Ti : sapphire laser (35 fs, 35 TW) at the Lund Laser Centre are discussed. It is demonstrated that a window of amplified spontaneous emission (ASE) conditions exist, for which the direction of proton emission is sensitive to the ASE-pedestal preceding the peak of the laser pulse, and that by significantly improving the temporal contrast, using plasma mirrors, efficient proton acceleration is observed from target foils with thickness less than 50 nm.
Function and Characterization of Starch Synthase I Using Mutants in Rice
Authors: Fujita Naoko , Yoshida Mayumi , Asakura Noriko , Ohdan Takashi , Miyao Akio , Hirochika Hirohiko , Nakamura Yasunori 
Published: January 2006

Abstract
Four starch synthase I (SSI)-deficient rice (Oryza sativa) mutant lines were generated using retrotransposon Tos17 insertion. The mutants exhibited different levels of SSI activities and produced significantly lower amounts of SSI protein ranging from 0% to 20% of the wild type. The mutant endosperm amylopectin showed a decrease in chains with degree of polymerization (DP) 8 to 12 and an increase in chains with DP 6 to 7 and DP 16 to 19. The degree of change in amylopectin chain-length distribution was positively correlated with the extent of decrease in SSI activity in the mutants. The structural changes in the amylopectin increased the gelatinization temperature of endosperm starch. Chain-length analysis of amylopectin in the SSI band excised from native-polyacrylamide gel electrophoresis/SS activity staining gel showed that SSI preferentially synthesized DP 7 to 11 chains by elongating DP 4 to 7 short chains of glycogen or amylopectin. These results show that SSI distinctly generates DP 8 to 12 chains from short DP 6 to 7 chains emerging from the branch point in the A or B1 chain of amylopectin. SSI seemingly functions from the very early through the late stage of endosperm development. Yet, the complete absence of SSI, despite being a major SS isozyme in the developing endosperm, had no effect on the size and shape of seeds and starch granules and the crystallinity of endosperm starch, suggesting that other SS enzymes are probably capable of partly compensating SSI function. In summary, this study strongly suggested that amylopectin chains are synthesized by the coordinated actions of SSI, SSIIa, and SSIIIa isoforms.
A Role for Mitochondria in the Establishment and Maintenance of the Maize Root Quiescent Center
Authors: Jiang Keni , Ballinger Tracy , Li Daisy , Zhang Shibo , Feldman Lewis 
Published: January 2006

AbstractMitochondria in the oxidizing environment of the maize (Zea mays) root quiescent center (QC) are altered in function, but otherwise structurally normal. Compared to mitochondria in the adjacent, rapidly dividing cells of the proximal root tissues, mitochondria in the QC show marked reductions in the activities of tricarboxylic acid cycle enzymes. Pyruvate dehydrogenase activity was not detected in the QC. Use of several mitochondrial membrane potential (ΔΨm) sensing probes indicated a depolarization of the mitochondrial membrane in the QC, which suggests a reduction in the capacity of QC mitochondria to generate ATP and NADH. We postulate that modifications of mitochondrial function are central to the establishment and maintenance of the QC.
Effects of Feeding Spodoptera littoralis on Lima Bean Leaves. III. Membrane Depolarization and Involvement of Hydrogen Peroxide
Authors: Maffei Massimo E. , Mithöfer Axel , Arimura Gen-Ichiro , Uchtenhagen Hannes , Bossi Simone , Bertea Cinzia M. , Cucuzza Laura Starvaggi , Novero Mara , Volpe Veronica , Quadro Stefano , Boland Wilhelm 
Published: January 2006

Abstract
In response to herbivore (Spodoptera littoralis) attack, lima bean (Phaseolus lunatus) leaves produced hydrogen peroxide (H2O2) in concentrations that were higher when compared to mechanically damaged (MD) leaves. Cellular and subcellular localization analyses revealed that H2O2 was mainly localized in MD and herbivore-wounded (HW) zones and spread throughout the veins and tissues. Preferentially, H2O2 was found in cell walls of spongy and mesophyll cells facing intercellular spaces, even though confocal laser scanning microscopy analyses also revealed the presence of H2O2 in mitochondria/peroxisomes. Increased gene and enzyme activations of superoxide dismutase after HW were in agreement with confocal laser scanning microscopy data. After MD, additional application of H2O2 prompted a transient transmembrane potential (V m) depolarization, with a V m depolarization rate that was higher when compared to HW leaves. In transgenic soybean (Glycine max) suspension cells expressing the Ca2+-sensing aequorin system, increasing amounts of added H2O2 correlated with a higher cytosolic calcium ([Ca2+]cyt) concentration. In MD and HW leaves, H2O2 also triggered the increase of [Ca2+]cyt, but MD-elicited [Ca2+]cyt increase was more pronounced when compared to HW leaves after addition of exogenous H2O2. The results clearly indicate that V m depolarization caused by HW makes the membrane potential more positive and reduces the ability of lima bean leaves to react to signaling molecules.
GOLD HULL AND INTERNODE2 Encodes a Primarily Multifunctional Cinnamyl-Alcohol Dehydrogenase in Rice
Authors: Zhang Kewei , Qian Qian , Huang Zejun , Wang Yiqin , Li Ming , Hong Lilan , Zeng Dali , Gu Minghong , Chu Chengcai , Cheng Zhukuan 
Published: January 2006

Abstract
Lignin content and composition are two important agronomic traits for the utilization of agricultural residues. Rice (Oryza sativa) gold hull and internode phenotype is a classical morphological marker trait that has long been applied to breeding and genetics study. In this study, we have cloned the GOLD HULL AND INTERNODE2 (GH2) gene in rice using a map-based cloning approach. The result shows that the gh2 mutant is a lignin-deficient mutant, and GH2 encodes a cinnamyl-alcohol dehydrogenase (CAD). Consistent with this finding, extracts from roots, internodes, hulls, and panicles of the gh2 plants exhibited drastically reduced CAD activity and undetectable sinapyl alcohol dehydrogenase activity. When expressed in Escherichia coli, purified recombinant GH2 was found to exhibit strong catalytic ability toward coniferaldehyde and sinapaldehyde, while the mutant protein gh2 completely lost the corresponding CAD and sinapyl alcohol dehydrogenase activities. Further phenotypic analysis of the gh2 mutant plants revealed that the p-hydroxyphenyl, guaiacyl, and sinapyl monomers were reduced in almost the same ratio compared to the wild type. Our results suggest GH2 acts as a primarily multifunctional CAD to synthesize coniferyl and sinapyl alcohol precursors in rice lignin biosynthesis.
Characterization of low phosphorus insensitive Mutants Reveals a Crosstalk between Low Phosphorus-Induced Determinate Root Development and the Activation of Genes Involved in the Adaptation of Arabidopsis to Phosphorus Deficiency
Authors: Sánchez-Calderón Lenin , López-Bucio José , Chacón-López Alejandra , Gutiérrez-Ortega Abel , Hernández-Abreu Esmeralda , Herrera-Estrella Luis 
Published: January 2006

Abstract
Low phosphorus (P) availability is one of the most limiting factors for plant productivity in many natural and agricultural ecosystems. Plants display a wide range of adaptive responses to cope with low P stress, which generally serve to enhance P availability in the soil and to increase its uptake by roots. In Arabidopsis (Arabidopsis thaliana), primary root growth inhibition and increased lateral root formation have been reported to occur in response to P limitation. To gain knowledge of the genetic mechanisms that regulate root architectural responses to P availability, we designed a screen for identifying Arabidopsis mutants that fail to arrest primary root growth when grown under low P conditions. Eleven low phosphorus insensitive (lpi) mutants that define at least four different complementation groups involved in primary root growth responses to P availability were identified. The lpi mutants do not show the typical determinate developmental program induced by P stress in the primary root. Other root developmental aspects of the low P rescue system, including increased root hair elongation and anthocyanin accumulation, remained unaltered in lpi mutants. In addition to the insensitivity of primary root growth inhibition, when subjected to P deprivation, lpi mutants show a reduced induction in the expression of several genes involved in the P starvation rescue system (PHOSPHATE TRANSPORTER 1 and 2, PURPLE ACID PHOSPHATASE 1, ACID PHOSPHATASE 5, and INDUCED BY PHOSPHATE STARVATION 1). Our results provide genetic support for the role of P as an important signal for postembryonic root development and root meristem maintenance and show a crosstalk in developmental and biochemical responses to P deprivation.
Phytochrome B Represses Teosinte Branched1 Expression and Induces Sorghum Axillary Bud Outgrowth in Response to Light Signals
Authors: Kebrom Tesfamichael H. , Burson Byron L. , Finlayson Scott A. 
Published: January 2006

Abstract
Light is one of the environmental signals that regulate the development of shoot architecture. Molecular mechanisms regulating shoot branching by light signals have not been investigated in detail. Analyses of light signaling mutants defective in branching provide insight into the molecular events associated with the phenomenon. It is well documented that phytochrome B (phyB) mutant plants display constitutive shade avoidance responses, including increased plant height and enhanced apical dominance. We investigated the phyB-1 mutant sorghum (Sorghum bicolor) and analyzed the expression of the sorghum Teosinte Branched1 gene (SbTB1), which encodes a putative transcription factor that suppresses bud outgrowth, and the sorghum dormancy-associated gene (SbDRM1), a marker of bud dormancy. Buds are formed in the leaf axils of phyB-1; however, they enter into dormancy soon after their formation. The dormant state of phyB-1 buds is confirmed by the high level of expression of the SbDRM1 gene. The level of SbTB1 mRNA is higher in the buds of phyB-1 compared to wild type, suggesting that phyB mediates the growth of axillary shoots in response to light signals in part by regulating the mRNA abundance of SbTB1. These results are confirmed by growing wild-type seedlings with supplemental far-red light that induces shade avoidance responses. We hypothesize that active phyB (Pfr) suppresses the expression of the SbTB1 gene, thereby inducing bud outgrowth, whereas environmental conditions that inactivate phyB allow increased expression of SbTB1, thereby suppressing bud outgrowth.
Cinnamate Metabolism in Ripening Fruit. Characterization of a UDP-Glucose:Cinnamate Glucosyltransferase from Strawberry
Authors: Lunkenbein Stefan , Bellido MariLuz , Aharoni Asaph , Salentijn Elma M.J. , Kaldenhoff Ralf , Coiner Heather A. , Muñoz-Blanco Juan , Schwab Wilfried 
Published: January 2006

Abstract
Strawberry (Fragaria × ananassa) fruit accumulate (hydroxy)cinnamoyl glucose (Glc) esters, which may serve as the biogenetic precursors of diverse secondary metabolites, such as the flavor constituents methyl cinnamate and ethyl cinnamate. Here, we report on the isolation of a cDNA encoding a UDP-Glc:cinnamate glucosyltransferase (Fragaria × ananassa glucosyltransferase 2 [FaGT2]) from ripe strawberry cv Elsanta that catalyzes the formation of 1-O-acyl-Glc esters of cinnamic acid, benzoic acid, and their derivatives in vitro. Quantitative real-time PCR analysis indicated that FaGT2 transcripts accumulate to high levels during strawberry fruit ripening and to lower levels in flowers. The levels in fruits positively correlated with the in planta concentration of cinnamoyl, p-coumaroyl, and caffeoyl Glc. In the leaf, high amounts of Glc esters were detected, but FaGT2 mRNA was not observed. The expression of FaGT2 is negatively regulated by auxin, induced by oxidative stress, and by hydroxycinnamic acids. Although FaGT2 glucosylates a number of aromatic acids in vitro, quantitative analysis in transgenic lines containing an antisense construct of FaGT2 under the control of the constitutive 35S cauliflower mosaic virus promoter demonstrated that the enzyme is only involved in the formation of cinnamoyl Glc and p-coumaroyl Glc during ripening.
Nitrogen controls in planta expression of Cladosporium fulvum Avr9 but no other effector genes
Authors: THOMMA BART P. H. J. , BOLTON MELVIN D. , CLERGEOT PIERRE‐HENRI , DE WIT PIERRE J. G. M. 
Published: January 2006

SUMMARYDuring growth on its host tomato, the apoplast‐colonizing fungal pathogen Cladosporium fulvum secretes several effector proteins. The expression of the Avr9 gene encoding one of these effector proteins has previously been shown to be strongly induced in vitro during nitrogen deprivation. This led to the hypothesis that expression of additional effector genes in C. fulvum could be triggered by nitrogen starvation conditions that are encountered in the host. We now show that expression of most effectors is not affected by varying levels of nitrogen supplementation in vitro. In addition, we demonstrate that the nitrogen response regulator Nrf1 only regulates Avr9 expression during infection of the host, whereas none of the other known effectors is significantly controlled by this transcription factor in planta. Deletion of Nrf1, but not of Avr9, significantly reduces C. fulvum virulence. Therefore, it is concluded that Nrf1 controls, in addition to Avr9, unidentified effector genes that are required for full virulence of C. fulvum.
The phytopathogen Rhodococcus fascians breaks apical dominance and activates axillary meristems by inducing plant genes involved in hormone metabolism
Authors: SIMÓN‐MATEO CARMEN , DEPUYDT STEPHEN , DE OLIVEIRA MANES CARMEM LARA , CNUDDE FILIP , HOLSTERS MARCELLE , GOETHALS KOEN , VEREECKE DANNY 
Published: January 2006

SUMMARY Rhodococcus fascians is a Gram‐positive bacterium that interacts with many plant species and induces multiple shoots through a combination of activation of dormant axillary meristems and de novo meristem formation. Although phenotypic analysis of the symptoms of infected plants clearly demonstrates a disturbance of the phytohormonal balance and an activation of the cell cycle, the actual mechanism of symptom development and the targets of the bacterial signals are unknown. To elucidate the molecular pathways that are responsive to R. fascians infection, differential display was performed on Nicotiana tabacum as a host. Four differentially expressed genes could be identified that putatively encode a senescence‐associated protein, a gibberellin 2‐oxidase, a P450 monooxygenase and a proline dehydrogenase. The differential expression of the three latter genes was confirmed on infected Arabidopsis thaliana plants by quantitative reverse transcription polymerase chain reactions, supporting their general function in R. fascians‐induced symptom development. The role of these genes in hormone metabolism, especially of gibberellin and abscisic acid, in breaking apical dominance and in activating axillary meristems, which are processes associated with symptom development, is discussed.