bluuebunny/crossref_metadata_2025_split huggingface dataset:
TFBS identification based on genetic algorithm with combined representations and adaptive post-processing
Authors: Chan Tak-Ming , Leung Kwong-Sak , Lee Kin-Hong 
Published: December 2007

Abstract
Motivation: Identification of transcription factor binding sites (TFBSs) plays an important role in deciphering the mechanisms of gene regulation. Recently, GAME, a Genetic Algorithm (GA)-based approach with iterative post-processing, has shown superior performance in TFBS identification. However, the basic GA in GAME is not elaborately designed, and may be trapped in local optima in real problems. The feature operators are only applied in the post-processing, but the final performance heavily depends on the GA output. Hence, both effectiveness and efficiency of the overall algorithm can be improved by introducing more advanced representations and novel operators in the GA, as well as designing the post-processing in an adaptive way.
Results: We propose a novel framework GALF-P, consisting of Genetic Algorithm with Local Filtering (GALF) and adaptive post-processing techniques (-P), to achieve both effectiveness and efficiency for TFBS identification. GALF combines the position-led and consensus-led representations used separately in current GAs and employs a novel local filtering operator to get rid of false positives within an individual efficiently during the evolutionary process in the GA. Pre-selection is used to maintain diversity and avoid local optima. Post-processing with adaptive adding and removing is developed to handle general cases with arbitrary numbers of instances per sequence. GALF-P shows superior performance to GAME, MEME, BioProspector and BioOptimizer on synthetic datasets with difficult scenarios and real test datasets. GALF-P is also more robust and reliable when further compared with GAME, the current state-of-the-art approach.
Availability: http://www.cse.cuhk.edu.hk/~tmchan/GALFP/
Contact: tmchan@cse.cuhk.edu.hk
Supplementary information: Supplementary data are available at Bioinformatics online.
Growth of white anglerfish (Lophius piscatorius) tagged in the Northeast Atlantic, and a review of age studies on anglerfish
Authors: Landa Jorge , Duarte Rafael , Quincoces Iñaki 
Published: December 2007

Abstract
Landa, J., Duarte, R., and Quincoces, I. 2008. Growth of white anglerfish (Lophius piscatorius) tagged in the Northeast Atlantic, and a review of age studies on anglerfish. – ICES Journal of Marine Science, 65: 72–80. Growth of white anglerfish was estimated from the results of a tagging study in south European waters. In all, 1326 fish, caught by bottom trawl and gillnet commercial vessels and on trawl surveys, were tagged from 1995 to 2004; 50 were recovered, and a growth rate of 13.6 cm year−1 was estimated from the four fish at liberty long enough to allow extrapolation of the growth rate to an annual period. Growth patterns were reviewed based on available studies of growth verification of white anglerfish in Atlantic waters, including another tag-recapture study, length-frequency of catches, and microstructure analysis of hard parts. The growth rate estimated from these studies showed many similarities, and an overall growth pattern was estimated: growth rate = 18.24e–0.015length. A von Bertalanffy growth curve fitted to all data yielded the parameter values L∞ = 140 cm and k = 0.11. This growth rate is faster than estimated recently using illicia for age estimation, but similar to that found in the first studies that used illicia and sectioned otoliths. Current estimates of growth based on illicia, which are used in assessing the northern European stock of white anglerfish, seem to be underestimated.
Environmental Effects on Oxygen Isotope Enrichment of Leaf Water in Cotton Leaves
Authors: Ripullone Francesco , Matsuo Naoko , Stuart-Williams Hilary , Wong Suan Chin , Borghetti Marco , Tani Makoto , Farquhar Graham 
Published: December 2007

Abstract
The oxygen isotope enrichment of bulk leaf water (Δb) was measured in cotton (Gossypium hirsutum) leaves to test the Craig-Gordon and Farquhar-Gan models under different environmental conditions. Δb increased with increasing leaf-to-air vapor pressure difference (VPd) as an overall result of the responses to the ratio of ambient to intercellular vapor pressures (e a/e i) and to stomatal conductance (g s). The oxygen isotope enrichment of lamina water relative to source water \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(({\bar{{\Delta}}}_{1}),\) \end{document} which increased with increasing VPd, was estimated by mass balance between less enriched water in primary veins and enriched water in the leaf. The Craig-Gordon model overestimated Δb (and \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \({\bar{{\Delta}}}_{1}),\) \end{document} as expected. Such discrepancies increased with increase in transpiration rate (E), supporting the Farquhar-Gan model, which gave reasonable predictions of Δb and \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \({\bar{{\Delta}}}_{1}\) \end{document} with an L of 7.9 mm, much less than the total radial effective length L r of 43 mm. The fitted values of L for \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \({\bar{{\Delta}}}_{1}\) \end{document} of individual leaves showed little dependence on VPd and temperature, supporting the assumption that the Farquhar-Gan formulation is relevant and useful in describing leaf water isotopic enrichment.
The ACA10 Ca2+-ATPase Regulates Adult Vegetative Development and Inflorescence Architecture in Arabidopsis
Authors: George Lynn , Romanowsky Shawn M. , Harper Jeffrey F. , Sharrock Robert A. 
Published: December 2007

AbstractThe Arabidopsis (Arabidopsis thaliana) compact inflorescence (cif) genotype causes altered adult vegetative development and a reduction in elongation of inflorescence internodes resulting in formation of floral clusters. The cif trait requires both a recessive mutation, cif1, and the activity of a naturally occurring dominant allele of an unlinked gene, CIF2D. We show here that the pseudoverticillata mutation is allelic with cif1 and that the product of the CIF1 gene is ACA10, a member of the large family of P-type Ca2+-ATPases found in higher plants. T-DNA insertion mutations in ACA10, but not in the two other Arabidopsis plasma membrane Ca2+-ATPase-encoding genes, ACA8 and ACA9, cause a cif phenotype when combined with the dominant CIF2D modifier allele. Therefore, ACA10 has a unique function in regulating adult phase growth and inflorescence development. The wild-type ACA8 and ACA10 mRNAs are present at similar levels, and the two promoter-β-glucuronidase fusion transgenes show very similar expression patterns. Moreover, transformation of the cif mutant with an extra copy of the ACA8 gene, which causes overexpression of the ACA8 transcript, can complement the cif phenotype. This suggests that these two Ca2+ pump genes have distinct but related activities and that their differential functions can be altered by relatively small changes in their patterns or levels of expression. The correspondence between cif1 and mutations in ACA10 establishes a genetic link between calcium transport, vegetative phase change, and inflorescence architecture.
Altered Profile of Secondary Metabolites in the Root Exudates of Arabidopsis ATP-Binding Cassette Transporter Mutants
Authors: Badri Dayakar V. , Loyola-Vargas Victor M. , Broeckling Corey D. , De-la-Peña Clelia , Jasinski Michal , Santelia Diana , Martinoia Enrico , Sumner Lloyd W. , Banta Lois M. , Stermitz Frank , Vivanco Jorge M. 
Published: December 2007

Abstract
Following recent indirect evidence suggesting a role for ATP-binding cassette (ABC) transporters in root exudation of phytochemicals, we identified 25 ABC transporter genes highly expressed in the root cells most likely to be involved in secretion processes. Of these 25 genes, we also selected six full-length ABC transporters and a half-size transporter for in-depth molecular and biochemical analyses. We compared the exuded root phytochemical profiles of these seven ABC transporter mutants to those of the wild type. There were three nonpolar phytochemicals missing in various ABC transporter mutants compared to the wild type when the samples were analyzed by high-performance liquid chromatography-mass spectrometry. These data suggest that more than one ABC transporter can be involved in the secretion of a given phytochemical and that a transporter can be involved in the secretion of more than one secondary metabolite. The primary and secondary metabolites present in the root exudates of the mutants were also analyzed by gas chromatography-mass spectrometry, which allowed for the identification of groups of compounds differentially found in some of the mutants compared to the wild type. For instance, the mutant Atpdr6 secreted a lower level of organic acids and Atmrp2 secreted a higher level of amino acids as compared to the wild type. We conclude that the release of phytochemicals by roots is partially controlled by ABC transporters.
Identification, Biochemical Characterization, and Subcellular Localization of Allantoate Amidohydrolases from Arabidopsis and Soybean
Authors: Werner Andrea K. , Sparkes Imogen A. , Romeis Tina , Witte Claus-Peter 
Published: December 2007

Abstract
Allantoate amidohydrolases (AAHs) hydrolize the ureide allantoate to ureidoglycolate, CO2, and two molecules of ammonium. Allantoate degradation is required to recycle purine-ring nitrogen in all plants. Tropical legumes additionally transport fixed nitrogen via allantoin and allantoate into the shoot, where it serves as a general nitrogen source. AAHs from Arabidopsis (Arabidopsis thaliana; AtAAH) and from soybean (Glycine max; GmAAH) were cloned, expressed in planta as StrepII-tagged variants, and highly purified from leaf extracts. Both proteins form homodimers and release 2 mol ammonium/mol allantoate. Therefore, they can truly be classified as AAHs. The kinetic constants determined and the half-maximal activation by 2 to 3 μ m manganese are consistent with allantoate being the in vivo substrate of manganese-loaded AAHs. The enzymes were strongly inhibited by micromolar concentrations of fluoride as well as by borate, and by millimolar concentrations of l-asparagine and l-aspartate but not d-asparagine. l-Asparagine likely functions as competitive inhibitor. An Ataah T-DNA mutant, unable to grow on allantoin as sole nitrogen source, is rescued by the expression of StrepII-tagged variants of AtAAH and GmAAH, demonstrating that both proteins are functional in vivo. Similarly, an allantoinase (aln) mutant is rescued by a tagged AtAln variant. Fluorescent fusion proteins of allantoinase and both AAHs localize to the endoplasmic reticulum after transient expression and in transgenic plants. These findings demonstrate that after the generation of allantoin in the peroxisome, plant purine degradation continues in the endoplasmic reticulum.
The Contribution of Photosynthesis to the Red Light Response of Stomatal Conductance
Authors: Baroli Irene , Price G. Dean , Badger Murray R. , von Caemmerer Susanne 
Published: December 2007

Abstract
To determine the contribution of photosynthesis on stomatal conductance, we contrasted the stomatal red light response of wild-type tobacco (Nicotiana tabacum ‘W38’) with that of plants impaired in photosynthesis by antisense reductions in the content of either cytochrome b 6 f complex (anti-b/f plants) or Rubisco (anti-SSU plants). Both transgenic genotypes showed a lowered content of the antisense target proteins in guard cells as well as in the mesophyll. In the anti-b/f plants, CO2 assimilation rates were proportional to leaf cytochrome b 6 f content, but there was little effect on stomatal conductance and the rate of stomatal opening. To compare the relationship between photosynthesis and stomatal conductance, wild-type plants and anti-SSU plants were grown at 30 and 300 μmol photon m−2 s−1 irradiance (low light and medium light [ML], respectively). Growth in ML increased CO2 assimilation rates and stomatal conductance in both genotypes. Despite the significantly lower CO2 assimilation rate in the anti-SSU plants, the differences in stomatal conductance between the genotypes were nonsignificant at either growth irradiance. Irrespective of plant genotype, stomatal density in the two leaf surfaces was 2-fold higher in ML-grown plants than in low-light-grown plants and conductance normalized to stomatal density was unaffected by growth irradiance. We conclude that the red light response of stomatal conductance is independent of the concurrent photosynthetic rate of the guard cells or of that of the underlying mesophyll. Furthermore, we suggest that the correlation of photosynthetic capacity and stomatal conductance observed under different light environments is caused by signals largely independent of photosynthesis.
Pectin Methyl Esterase Inhibits Intrusive and Symplastic Cell Growth in Developing Wood Cells ofPopulus
Authors: Siedlecka Anna , Wiklund Susanne , Péronne Marie-Amélie , Micheli Fabienne , Leśniewska Joanna , Sethson Ingmar , Edlund Ulf , Richard Luc , Sundberg Björn , Mellerowicz Ewa J. 
Published: December 2007

AbstractWood cells, unlike most other cells in plants, grow by a unique combination of intrusive and symplastic growth. Fibers grow in diameter by diffuse symplastic growth, but they elongate solely by intrusive apical growth penetrating the pectin-rich middle lamella that cements neighboring cells together. In contrast, vessel elements grow in diameter by a combination of intrusive and symplastic growth. We demonstrate that an abundant pectin methyl esterase (PME; EC 3.1.1.11) from wood-forming tissues of hybrid aspen (Populus tremula × tremuloides) acts as a negative regulator of both symplastic and intrusive growth of developing wood cells. When PttPME1 expression was up- and down-regulated in transgenic aspen trees, the PME activity in wood-forming tissues was correspondingly altered. PME removes methyl ester groups from homogalacturonan (HG) and transgenic trees had modified HG methylesterification patterns, as demonstrated by two-dimensional nuclear magnetic resonance and immunostaining using PAM1 and LM7 antibodies. In situ distributions of PAM1 and LM7 epitopes revealed changes in pectin methylesterification in transgenic trees that were specifically localized in expanding wood cells. The results show that en block deesterification of HG by PttPME1 inhibits both symplastic growth and intrusive growth. PttPME1 is therefore involved in mechanisms determining fiber width and length in the wood of aspen trees.
Two Distinct Forms ofM-Locus Protein Kinase Localize to the Plasma Membrane and Interact Directly withS-Locus Receptor Kinase to Transduce Self-Incompatibility Signaling inBrassica rapa
Authors: Kakita Mitsuru , Murase Kohji , Iwano Megumi , Matsumoto Tomohito , Watanabe Masao , Shiba Hiroshi , Isogai Akira , Takayama Seiji 
Published: December 2007

AbstractMany flowering plants possess systems of self-incompatibility (SI) to prevent inbreeding. In Brassica, SI recognition is controlled by the multiallelic gene complex (S-haplotypes) at the S-locus, which encodes both the male determinant S-locus protein 11 (SP11/SCR) and the female determinant S-receptor kinase (SRK). Upon self-pollination, the S-haplotype–specific interaction between the pollen-borne SP11 and the cognate stigmatic SRK receptor induces SI signaling in the stigmatic papilla cell and results in rejection of the self-pollen. Our genetic analysis of a self-compatible mutant revealed the involvement of a cytoplasmic protein kinase, M-locus protein kinase (MLPK), in the SI signaling, but its exact physiological function remains unknown. In this study, we identified two different MLPK transcripts, MLPKf1 and MLPKf2, which are produced using alternative transcriptional initiation sites and encode two isoforms that differ only at the N termini. While MLPKf1 and MLPKf2 exhibited distinct expression profiles, both were expressed in papilla cells. MLPKf1 localizes to the plasma membrane through its N-terminal myristoylation motif, while MLPKf2 localizes to the plasma membrane through its N-terminal hydrophobic region. Although both MLPKf1 and MLPKf2 could independently complement the mlpk/mlpk mutation, their mutant forms that lack the plasma membrane localization motifs failed to complement the mutation. Furthermore, a bimolecular fluorescence complementation assay revealed direct interactions between SRK and the MLPK isoforms in planta. These results suggest that MLPK isoforms localize to the papilla cell membrane and interact directly with SRK to transduce SI signaling.
Interaction between SGT1 and Cytosolic/Nuclear HSC70 Chaperones Regulates Arabidopsis Immune Responses
Authors: Noël Laurent D. , Cagna Giuseppe , Stuttmann Johannes , Wirthmüller Lennart , Betsuyaku Shigeyuki , Witte Claus-Peter , Bhat Riyaz , Pochon Nathalie , Colby Thomas , Parker Jane E. 
Published: December 2007

Abstract
The conserved eukaryotic protein SGT1 (for Suppressor of G2 allele of skp1) has characteristics of an HSP90 (for heat shock protein 90 kD) cochaperone and in plants regulates hormone responses and Resistance gene–triggered immunity. We affinity-purified SGT1-interacting proteins from Arabidopsis thaliana leaf extracts and identified by mass spectrometry cytosolic heat shock cognate 70 (HSC70) chaperones as the major stable SGT1 interactors. Arabidopsis SGT1a and SGT1b proteins associate with HSC70 in vivo and distribute with HSC70 in the cytosol and nucleus. An intact C-terminal SGT1-specific (SGS) domain that is required for all known SGT1b functions in immunity and development is needed for HSC70 interaction and for the nuclear accumulation of SGT1b. Interaction assays of transiently expressed proteins or their domains in Nicotiana benthamiana point to a role of SGT1 as a HSC70 cofactor. Expression of two HSC70 isoforms is upregulated by pathogen challenge, and while loss of function of individual cytosolic HSC70 genes has no defense phenotype, HSC70-1 overexpression disables resistance to virulent and avirulent pathogens. Moreover, mutations in SGT1b lead to a similar degree of heat shock tolerance as deregulation of HSC70-1. We conclude that an HSC70-SGT1 chaperone complex is important for multiple plant environmental responses and that the evolutionarily conserved SGS domain of SGT1 is a key determinant of the HSC70–SGT1 association.
Cytokinin Regulates Type-A Arabidopsis Response Regulator Activity and Protein Stability via Two-Component Phosphorelay
Authors: To Jennifer P.C. , Deruère Jean , Maxwell Bridey B. , Morris Veronica F. , Hutchison Claire E. , Ferreira Fernando J. , Schaller G. Eric , Kieber Joseph J. 
Published: December 2007

Abstract
The plant hormone cytokinin regulates many aspects of growth and development. Cytokinin signaling involves His kinase receptors that perceive cytokinin and transmit the signal via a multistep phosphorelay similar to bacterial two-component signaling systems. The final targets of this phosphorelay are a set of Arabidopsis thaliana Response Regulator (ARR) proteins containing a receiver domain with a conserved Asp phosphorylation site. One class of these, the type-A ARRs, are negative regulators of cytokinin signaling that are rapidly transcriptionally upregulated in response to cytokinin. In this study, we tested the role of phosphorylation in type-A ARR function. Our results indicate that phosphorylation of the receiver domain is required for type-A ARR function and suggest that negative regulation of cytokinin signaling by the type-A ARRs most likely involves phosphorylation-dependent interactions. Furthermore, we show that a subset of the type-A ARR proteins are stabilized in response to cytokinin in part via phosphorylation. These studies shed light on the mechanism by which type-A ARRs act to negatively regulate cytokinin signaling and reveal a novel mechanism by which cytokinin controls type-A ARR function.
A CRM Domain Protein Functions Dually in Group I and Group II Intron Splicing in Land Plant Chloroplasts
Authors: Asakura Yukari , Barkan Alice 
Published: December 2007

AbstractThe CRM domain is a recently recognized RNA binding domain found in three group II intron splicing factors in chloroplasts, in a bacterial protein that associates with ribosome precursors, and in a family of uncharacterized proteins in plants. To elucidate the functional repertoire of proteins with CRM domains, we studied CFM2 (for CRM Family Member 2), which harbors four CRM domains. RNA coimmunoprecipitation assays showed that CFM2 in maize (Zea mays) chloroplasts is associated with the group I intron in pre-trnL-UAA and group II introns in the ndhA and ycf3 pre-mRNAs. T-DNA insertions in the Arabidopsis thaliana ortholog condition a defective-seed phenotype (strong allele) or chlorophyll-deficient seedlings with impaired splicing of the trnL group I intron and the ndhA, ycf3-int1, and clpP-int2 group II introns (weak alleles). CFM2 and two previously described CRM proteins are bound simultaneously to the ndhA and ycf3-int1 introns and act in a nonredundant fashion to promote their splicing. With these findings, CRM domain proteins are implicated in the activities of three classes of catalytic RNA: group I introns, group II introns, and 23S rRNA.
Cytokinins Act Directly on Lateral Root Founder Cells to Inhibit Root Initiation
Authors: Laplaze Laurent , Benkova Eva , Casimiro Ilda , Maes Lies , Vanneste Steffen , Swarup Ranjan , Weijers Dolf , Calvo Vanessa , Parizot Boris , Herrera-Rodriguez Maria Begoña , Offringa Remko , Graham Neil , Doumas Patrick , Friml Jiri , Bogusz Didier , Beeckman Tom , Bennett Malcolm 
Published: December 2007

AbstractIn Arabidopsis thaliana, lateral roots are formed from root pericycle cells adjacent to the xylem poles. Lateral root development is regulated antagonistically by the plant hormones auxin and cytokinin. While a great deal is known about how auxin promotes lateral root development, the mechanism of cytokinin repression is still unclear. Elevating cytokinin levels was observed to disrupt lateral root initiation and the regular pattern of divisions that characterizes lateral root development in Arabidopsis. To identify the stage of lateral root development that is sensitive to cytokinins, we targeted the expression of the Agrobacterium tumefaciens cytokinin biosynthesis enzyme isopentenyltransferase to either xylem-pole pericycle cells or young lateral root primordia using GAL4-GFP enhancer trap lines. Transactivation experiments revealed that xylem-pole pericycle cells are sensitive to cytokinins, whereas young lateral root primordia are not. This effect is physiologically significant because transactivation of the Arabidopsis cytokinin degrading enzyme cytokinin oxidase 1 in lateral root founder cells results in increased lateral root formation. We observed that cytokinins perturb the expression of PIN genes in lateral root founder cells and prevent the formation of an auxin gradient that is required to pattern lateral root primordia.