bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Porphyrin‐Based Photocatalytic System for Terpenoids Production from (R)‐(+)‐Limonene
Authors: Trytek Mariusz , Fiedurek Jan , Radzki Stanisław 
Published: December 2006

AbstractA porphyrin‐based photoexcited system has been revealed to be an efficient catalyst for d‐limonene biotransformation under mild conditions and using molecular oxygen or/and H2O2 as oxidants. The influence of the oxidant, the wavelength of visible light, and the photoexcitation time on the catalytic system were studied for limonene oxidation with 5,10,15,20‐tetraphenylporphyrin (H2TPP) as a catalyst. This porphyrin‐catalyzed oxidation of limonene to three main products identified as carvone, an unknown product with a verbenone‐like mass spectrum (1), and a (1 S,4 R)‐ p‐mentha‐2,8‐diene 1‐hydroperoxide (2). The highest conversion yield of these products was achieved at a very high molar ratio of H2TPP to limonene. The dependence of the biotransformation yield on the kind of solvent with different acceptor/donor electron properties was also investigated. Ethyl alcohol proved to be the best among the considered additives used for the reaction. Limonene photooxidation was not significantly dependent on wavelengths of visible light. It was concluded by UV‐vis experiments that the reaction proceeds via a free‐radical or/and molecular mechanism. Additional evidence for its radical nature was obtained from reactivity investigations. Maximal yield of carvone was obtained in the medium containing 90% of the substrate, within the period of 18 to 36 h of exposition to sunlight.
MotifScorer: using a compendium of microarrays to identify regulatory motifs
Authors: Brilli Matteo , Fani Renato , Lió Pietro 
Published: December 2006

AbstractSummary: We describe MotifScorer, a program for systematic genome-wide identification of transcription sites. The program uses a compendium of gene expression microarrays and implements state-of-art partial least squares (PLSs) based regression and stepwise regression procedures. Candidate motifs from the upstream sequences of groups of co-regulated genes are identified and assigned a score using genomic background models and available motif finding tools. The use of a large library of expression data allows statistical comparative analysis of the specificity of motifs identified in different conditions.Availability: MotifScorer, which is written in Java and Matlab, manual and example files are available from the authors.Contact: pl219@cam.ac.uk
Visualization of genomic aberrations using Affymetrix SNP arrays
Authors: Müller André , Holzmann Karlheinz , Kestler Hans A. 
Published: December 2006

AbstractMotivation: DNA copy number aberrations are frequently found in different types of cancer. Recent developments of microarray-based approaches have broadened the knowledge on number and structure of such aberrations. High-density single nucleotide polymorphism (SNP) microarrays provide an extremely high resolution with up to 500 000 SNPs per genome. Owing to the enormous amount of data the detection of common aberrations in large datasets is a great challenge. We describe a novel open source software tool—IdeogramBrowser—which was specifically designed for use with the Affymetrix SNP arrays. It provides an interactive karyotypic visualization of multiple aberration profiles and direct links to GeneCards. Visualization of consensus regions together with gene representation allows the explorative assessment of the data.Availability: IdeogramBrowser and its source code are freely available under a creative commons license and can be obtained from .  IdeogramBrowser is a platform independent Java application.Contact: hans.kestler@uni-ulm.de
Vectors and Agrobacterium Hosts for Arabidopsis Transformation
Authors: Weigel Detlef , Glazebrook Jane 
Published: December 2006

INTRODUCTIONArabidopsis can be stably transformed using Agrobacterium tumefaciens-mediated transfer of T-DNA. A. tumefaciens is a soil-dwelling bacterium that transforms normal plant cells into tumor-forming cells by inserting a piece of bacterial DNA (the transfer, or “T,” DNA) into the plant cell genome. The T-DNA, which is flanked by left- and right-border (LB and RB) sequences, resides on a tumor-inducing (Ti) plasmid. The Ti plasmid also carries many of the transfer functions for mobilizing the T-DNA. This article provides a brief discussion of the principles of T-DNA transformation, including consideration of T-DNA vectors and their hosts.
Gene Delivery by Direct Injection (Microinjection) Using a Pulsed-Flow System
Authors: Dean David A. 
Published: December 2006

INTRODUCTIONThis protocol describes a method for pulsed-flow microinjection using the Eppendorf FemtoJet injector and Eppendorf InjectMan; this is the most common type of pulsed-flow microinjection system currently being used. The advantage of this type of system over a controlled-flow system is that much more control is available over the injection parameters, reducing variability in injections. In addition, the system allows a diagonal insertion of the needle into the cell, causing a direct piercing of the cell. This is fast and may do less damage to the cell than a traditional system, in which the cell is briefly distorted before it is pierced.
PCR Analysis of Agrobacterium
Authors: Wigge Phil 
Published: December 2006

INTRODUCTIONBecause transformation of Arabidopsis is a relatively long-winded process, it is a good idea to verify the presence of the T-DNA plasmid in the Agrobacterium strain before proceeding with transformation experiments. This protocol describes a method to determine the presence of plasmid DNA in an Agrobacterium culture. Compared to selection of transformed Agrobacterium, which can be ambiguous and normally takes several days for resistant colonies to appear, the approach described here is both rapid and accurate.
Helianthus Nighttime Conductance and Transpiration Respond to Soil Water But Not Nutrient Availability
Authors: Howard Ava R. , Donovan Lisa A. 
Published: December 2006

Abstract
We investigated the response of Helianthus species nighttime conductance (g night) and transpiration (E night) to soil nutrient and water limitations in nine greenhouse studies. The studies primarily used wild Helianthus annuus, but also included a commercial and early domesticate of H. annuus and three additional wild species (Helianthus petiolaris Nutt., Helianthus deserticola Heiser, and Helianthus anomalus Blake). Well-watered plants of all species showed substantial g night (0.023–0.225 mol m−2 s−1) and E night (0.29–2.46 mmol m−2 s−1) measured as instantaneous gas exchange. Based on the potential for transpiration to increase mass flow of mobile nutrients to roots, we hypothesized that g night and E night would increase under limiting soil nutrients but found no evidence of responses in all six studies testing this. Based on known daytime responses to water limitation, we hypothesized that g night and E night would decrease when soil water availability was limited, and results from all four studies testing this supported our hypothesis. We also established that stomatal conductance at night was on average 5 times greater than cuticular conductance. Additionally, g night and E night varied nocturnally and across plant reproductive stages while remaining relatively constant as leaves aged. Our results further the ability to predict conditions under which nighttime water loss will be biologically significant and demonstrate that for Helianthus, g night can be regulated.
Transposition-Based Plant Transformation
Authors: Yan Hua , Rommens Caius M. 
Published: December 2006

Abstract
Agrobacterium T-DNAs were used to deliver transposable Dissociation (Ds) elements into the nuclei of potato (Solanum tuberosum) cells. A double-selection system was applied to enrich for plants that only contained a transposed Ds element. This system consisted of a positive selection for the neomycin phosphotransferase (nptII) gene positioned within Ds followed by a negative selection against stable integration of the cytosine deaminase (codA) gene-containing T-DNA. Sixteen of 29 transgenic plants were found to contain a transposed element while lacking any superfluous T-DNA sequences. The occurrence of this genotype indicates that Ds elements can transpose from relatively short extrachromosomal DNA molecules into the plant genome. The frequency of single-copy Ds transformation was determined at 0.3%, which is only about 2.5-fold lower than the potato transformation frequency for backbone-free and single-copy T-DNAs. Because of the generally high expression levels of genes positioned within transposed elements, the new transformation method may find broad applicability to crops that are accessible to Agrobacterium T-DNA transfer.
Enzymatic Evidence for the Key Role of Arginine in Nitrogen Translocation by Arbuscular Mycorrhizal Fungi
Authors: Cruz Cristina , Egsgaard Helge , Trujillo Carmen , Ambus Per , Requena Natalia , Martins-Loução Maria Amélia , Jakobsen Iver 
Published: December 2006

Abstract
Key enzymes of the urea cycle and 15N-labeling patterns of arginine (Arg) were measured to elucidate the involvement of Arg in nitrogen translocation by arbuscular mycorrhizal (AM) fungi. Mycorrhiza was established between transformed carrot (Daucus carota) roots and Glomus intraradices in two-compartment petri dishes and three ammonium levels were supplied to the compartment containing the extraradical mycelium (ERM), but no roots. Time courses of specific enzyme activity were obtained for glutamine synthetase, argininosuccinate synthetase, arginase, and urease in the ERM and AM roots. 15NH4 + was used to follow the dynamics of nitrogen incorporation into and turnover of Arg. Both the absence of external nitrogen and the presence of l-norvaline, an inhibitor of Arg synthesis, prevented the synthesis of Arg in the ERM and resulted in decreased activity of arginase and urease in the AM root. The catabolic activity of the urea cycle in the roots therefore depends on Arg translocation from the ERM. 15N labeling of Arg in the ERM was very fast and analysis of its time course and isotopomer pattern allowed estimation of the translocation rate of Arg along the mycelium as 0.13 μg Arg mg−1 fresh weight h−1. The results highlight the synchronization of the spatially separated reactions involved in the anabolic and catabolic arms of the urea cycle. This synchronization is a prerequisite for Arg to be a key component in nitrogen translocation in the AM mycelium.
Oviposition by Pierid Butterflies Triggers Defense Responses in Arabidopsis
Authors: Little Dawn , Gouhier-Darimont Caroline , Bruessow Friederike , Reymond Philippe 
Published: December 2006

Abstract
Insect eggs represent a threat for the plant as hatching larvae rapidly start with their feeding activity. Using a whole-genome microarray, we studied the expression profile of Arabidopsis (Arabidopsis thaliana) leaves after oviposition by two pierid butterflies. For Pieris brassicae, the deposition of egg batches changed the expression of hundreds of genes over a period of 3 d after oviposition. The transcript signature was similar to that observed during a hypersensitive response or in lesion-mimic mutants, including the induction of defense and stress-related genes and the repression of genes involved in growth and photosynthesis. Deposition of single eggs by Pieris rapae caused a similar although much weaker transcriptional response. Analysis of the jasmonic acid and salicylic acid mutants coi1-1 and sid2-1 indicated that the response to egg deposition is mostly independent of these signaling pathways. Histochemical analyses showed that egg deposition is causing a localized cell death, accompanied by the accumulation of callose, and the production of reactive oxygen species. In addition, activation of the pathogenesis-related1∷β-glucuronidase reporter gene correlated precisely with the site of egg deposition and was also triggered by crude egg extract. This study provides molecular evidence for the detection of egg deposition by Arabidopsis plants and suggests that oviposition causes a localized response with strong similarity to a hypersensitive response.
Cell Death Suppressor Arabidopsis Bax Inhibitor-1 Is Associated with Calmodulin Binding and Ion Homeostasis
Authors: Ihara-Ohori Yuri , Nagano Minoru , Muto Shoshi , Uchimiya Hirofumi , Kawai-Yamada Maki 
Published: December 2006

Abstract
Cell death suppressor Bax inhibitor-1 (BI-1), an endoplasmic reticulum membrane protein, exists in a wide range of organisms. The split-ubiquitin system, overlay assay, and bimolecular fluorescence complementation analysis demonstrated that Arabidopsis (Arabidopsis thaliana) BI-1 (AtBI-1) interacted with calmodulin in yeast (Saccharomyces cerevisiae) and in plant cells. Furthermore, AtBI-1 failed to rescue yeast mutants lacking Ca2+ ATPase (Pmr1 or Spf1) from Bax-induced cell death. Pmr1 and Spf1, p-type ATPases localized at the inner membrane, are believed to be involved in transmembrane movement of calcium ions in yeast. Thus, the presence of intact Ca2+ ATPases was essential for AtBI-1-mediated cell death suppression in yeast. To investigate the effect of AtBI-1 on calcium homeostasis, we evaluated sensitivity against cyclopiazonic acid (CPA), an inhibitor of sarcoplasmic/endoplasmic reticulum Ca2+ ATPase in AtBI-1-overexpressing or knock-down transgenic Arabidopsis plants. These plants demonstrated altered CPA or ion stress sensitivity. Furthermore, AtBI-1-overexpressing cells demonstrated an attenuated rise in cytosolic calcium following CPA or H2O2 treatment, suggesting that AtBI-1 affects ion homeostasis in plant cell death regulation.
MEKK1 Is Required for flg22-Induced MPK4 Activation in Arabidopsis Plants
Authors: Suarez-Rodriguez Maria Cristina , Adams-Phillips Lori , Liu Yidong , Wang Huachun , Su Shih-Heng , Jester Peter J. , Zhang Shuqun , Bent Andrew F. , Krysan Patrick J. 
Published: December 2006

Abstract
The Arabidopsis (Arabidopsis thaliana) gene MEKK1 encodes a mitogen-activated protein kinase kinase kinase that has been implicated in the activation of the map kinases MPK3 and MPK6 in response to the flagellin elicitor peptide flg22. In this study, analysis of plants carrying T-DNA knockout alleles indicated that MEKK1 is required for flg22-induced activation of MPK4 but not MPK3 or MPK6. Experiments performed using a kinase-impaired version of MEKK1 (K361M) showed that the kinase activity of MEKK1 may not be required for flg22-induced MPK4 activation or for other macroscopic FLS2-mediated responses. MEKK1 may play a structural role in signaling, independent of its protein kinase activity. mekk1 knockout mutants display a severe dwarf phenotype, constitutive callose deposition, and constitutive expression of pathogen response genes. This dwarf phenotype was largely rescued by introduction into mekk1 knockout plants of either the MEKK1 (K361M) construct or a nahG transgene that degrades salicylic acid. When treated with pathogenic bacteria, the K361M plants were slightly more susceptible to an avirulent strain of Pseudomonas syringae and showed a delayed hypersensitive response, suggesting a role for MEKK1 kinase activity in this aspect of plant disease resistance. Our results indicate that MEKK1 acts upstream of MPK4 as a negative regulator of pathogen response pathways, a function that may not require MEKK1's full kinase activity.
Ca2+-Dependent and -Independent Abscisic Acid Activation of Plasma Membrane Anion Channels in Guard Cells of Nicotiana tabacum
Authors: Marten Holger , Konrad Kai R. , Dietrich Petra , Roelfsema M. Rob G. , Hedrich Rainer 
Published: December 2006

Abstract
Drought induces stomatal closure, a response that is associated with the activation of plasma membrane anion channels in guard cells, by the phytohormone abscisic acid (ABA). In several species, this response is associated with changes in the cytoplasmic free Ca2+ concentration. In Vicia faba, however, guard cell anion channels activate in a Ca2+-independent manner. Because of potential differences between species, Nicotiana tabacum guard cells were studied in intact plants, with simultaneous recordings of the plasma membrane conductance and the cytoplasmic free Ca2+ concentration. ABA triggered transient rises in cytoplasmic Ca2+ in the majority of the guard cells (14 out of 19). In seven out of 14 guard cells, the change in cytoplasmic free Ca2+ closely matched the activation of anion channels, while the Ca2+ rise was delayed in seven other cells. In the remaining five cells, ABA stimulated anion channels without a change in the cytoplasmic Ca2+ level. Even though ABA could activate anion channels in N. tabacum guard cells independent of a rise in the cytoplasmic Ca2+ concentration, patch clamp experiments showed that anion channels in these cells are stimulated by elevated Ca2+ in an ATP-dependent manner. Guard cells thus seem to have evolved both Ca2+-independent and -dependent ABA signaling pathways. Guard cells of N. tabacum apparently utilize both pathways, while ABA signaling in V. faba seems to be restricted to the Ca2+-independent pathway.
The Plant Structure Ontology, a Unified Vocabulary of Anatomy and Morphology of a Flowering Plant
Authors: Ilic Katica , Kellogg Elizabeth A. , Jaiswal Pankaj , Zapata Felipe , Stevens Peter F. , Vincent Leszek P. , Avraham Shulamit , Reiser Leonore , Pujar Anuradha , Sachs Martin M. , Whitman Noah T. , McCouch Susan R. , Schaeffer Mary L. , Ware Doreen H. , Stein Lincoln D. , Rhee Seung Y. 
Published: December 2006

AbstractFormal description of plant phenotypes and standardized annotation of gene expression and protein localization data require uniform terminology that accurately describes plant anatomy and morphology. This facilitates cross species comparative studies and quantitative comparison of phenotypes and expression patterns. A major drawback is variable terminology that is used to describe plant anatomy and morphology in publications and genomic databases for different species. The same terms are sometimes applied to different plant structures in different taxonomic groups. Conversely, similar structures are named by their species-specific terms. To address this problem, we created the Plant Structure Ontology (PSO), the first generic ontological representation of anatomy and morphology of a flowering plant. The PSO is intended for a broad plant research community, including bench scientists, curators in genomic databases, and bioinformaticians. The initial releases of the PSO integrated existing ontologies for Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and rice (Oryza sativa); more recent versions of the ontology encompass terms relevant to Fabaceae, Solanaceae, additional cereal crops, and poplar (Populus spp.). Databases such as The Arabidopsis Information Resource, Nottingham Arabidopsis Stock Centre, Gramene, MaizeGDB, and SOL Genomics Network are using the PSO to describe expression patterns of genes and phenotypes of mutants and natural variants and are regularly contributing new annotations to the Plant Ontology database. The PSO is also used in specialized public databases, such as BRENDA, GENEVESTIGATOR, NASCArrays, and others. Over 10,000 gene annotations and phenotype descriptions from participating databases can be queried and retrieved using the Plant Ontology browser. The PSO, as well as contributed gene associations, can be obtained at www.plantontology.org.
The RiceTapetum Degeneration RetardationGene Is Required for Tapetum Degradation and Anther Development
Authors: Li Na , Zhang Da-Sheng , Liu Hai-Sheng , Yin Chang-Song , Li Xiao-xing , Liang Wan-qi , Yuan Zheng , Xu Ben , Chu Huang-Wei , Wang Jia , Wen Tie-Qiao , Huang Hai , Luo Da , Ma Hong , Zhang Da-Bing 
Published: December 2006

AbstractIn flowering plants, tapetum degeneration is proposed to be triggered by a programmed cell death (PCD) process during late stages of pollen development; the PCD is thought to provide cellular contents supporting pollen wall formation and to allow the subsequent pollen release. However, the molecular basis regulating tapetum PCD in plants remains poorly understood. We report the isolation and characterization of a rice (Oryza sativa) male sterile mutant tapetum degeneration retardation (tdr), which exhibits degeneration retardation of the tapetum and middle layer as well as collapse of microspores. The TDR gene is preferentially expressed in the tapetum and encodes a putative basic helix-loop-helix protein, which is likely localized to the nucleus. More importantly, two genes, Os CP1 and Os c6, encoding a Cys protease and a protease inhibitor, respectively, were shown to be the likely direct targets of TDR through chromatin immunoprecipitation analyses and the electrophoretic mobility shift assay. These results indicate that TDR is a key component of the molecular network regulating rice tapetum development and degeneration.
Taxes and the Efficiency‐Rent Extraction Trade‐off
Authors: ARYA ANIL , GLOVER JONATHAN , MITTENDORF BRIAN 
Published: December 2006

AbstractThis paper presents an adverse selection model in which progressive taxation enhances productive efficiency by encouraging a principal (buyer) to be less aggressive in contracting with an agent (seller). Wary of padded cost budgets, the buyer employs a hurdle‐rate procurement policy. With a low cost hurdle, the buyer keeps greater profits when transactions are undertaken but trade occurs less often. While the hurdle is unaffected by a flat tax, a progressive tax tilts the buyer's preference: the buyer's benefit from a lower hurdle becomes less pronounced, since the marginal increase in his profits is muted in after‐tax terms. The result is increased trade and the possibility of Pareto improvements.
The Private Provision of Public Goods under Uncertainty: A Symmetric‐Equilibrium Approach
Authors: KEENAN DONALD C. , KIM ILTAE , WARREN RONALD S. 
Published: December 2006

AbstractVarious studies have examined whether increased uncertainty about the non‐Nash response of others to an individual's voluntary contribution to a public good affects that individual's contribution so as to mitigate the free‐rider problem. We extend this single‐agent approach to the analysis of a symmetric equilibrium. We provide conditions on group size and endogenous relative risk aversion that imply increased equilibrium contributions in response to greater uncertainty about the productivity of each individual's contribution to the actual level of the public good. These results enable us to broaden the circumstances in which the theory predicts that increased uncertainty reduces free riding.
CRITICAL CARE ISSUES FOR THE NEPHROLOGIST: Renal Replacement Therapy in the Treatment of Acute Renal Failure—Intermittent and Continuous
Authors: John Stefan , Eckardt Kai‐Uwe 
Published: December 2006

AbstractRenal replacement therapy (RRT) is increasingly used in intensive care as acute renal failure (ARF) is a common and constantly increasing complication in this setting. Different forms of RRT such as intermittent hemodialysis, continuous hemofiltration, or hybrid forms, which combine advantages of both, are available and will be discussed in this article. As a general survival benefit for neither method has been demonstrated, it is the task of the nephrologist or intensivist to choose the RRT strategy that is most advantageous for each individual patient. The choice of RRT might depend not only on the underlying disease, the time course of the disease, the etiology of ARF, the actual clinical status of the patient but also on the resources available and the cost of therapy. An adequate dose of RRT seems to result in improved survival in patients with ARF. However, clear guidelines on the dose of RRT and the timing of initiation are still lacking. Moreover, it will be discussed whether patients with sepsis and septic shock benefit from early RRT initiation, the use of increased RRT doses, and increased removal of inflammatory mediators by RRT.