Journal of Pesticide Science
Online ISSN : 1349-0923
Print ISSN : 1348-589X
ISSN-L : 0385-1559
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Volume 31, Issue 3
Displaying 1-24 of 24 articles from this issue
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Special topic: Applications of omics-technologies to the agricultural and environmental sciences
Reviews
  • Metabolomics: Methodologies and applications in the environmental sciences
    Ching Yu Lin, Mark R. Viant, Ronald S. Tjeerdema
    2006 Volume 31 Issue 3 Pages 245-251
    Published: 2006
    Released on J-STAGE: August 24, 2006
    DOIhttps://doi.org/10.1584/jpestics.31.245
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    Environmental metabolomics is an emerging approach for examining metabolic fingerprints, or profiles, in biological systems exposed to environmental stress. In conjunction with other “omics” techniques, such as genomics, transcriptomics, and proteomics, it has been used to study the biochemical impacts of xenobiotics and disease. The approach analyzes changes in the concentrations of metabolites, which are the precursors and products of enzymatic activity, and then attempts to associate these changes with biological function and/or regulation. Environmental scientists have recently applied such techniques to suggest biomarkers for the risk assessment of chemicals and for diagnosing diseases in wild animals. Furthermore, this approach can in principle allow scientists to better understand the underlying mechanisms of action of toxic compounds in the environment. In this review the methodologies used in metabolomics are briefly discussed along with several examples from the environmental sciences, including biomarker development and risk assessment of toxicant exposure, metabolic responses to environmental stressors, and disease diagnosis and monitoring.
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  • Applications of genomic technologies to the study of organochlorine pesticide-induced reproductive toxicity in fish
    Natàlia Garcia-Reyero, Nancy D. Denslow
    2006 Volume 31 Issue 3 Pages 252-262
    Published: 2006
    Released on J-STAGE: August 24, 2006
    DOIhttps://doi.org/10.1584/jpestics.31.252
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    Microarrays and real time PCR are two molecular methods that are gaining acceptance for ecotoxicology. They will help sort out the complex biochemical pathways that are targeted by exposure of organisms to organochlorine pesticides (OCPs) and other toxicants and may point to the ways that these compounds affect development, reproduction and susceptibility to disease. OCPs are a large group of structurally diverse compounds that are present around the globe and are known to be highly persistent pollutants, for which mechanistic toxicity information is lacking. Genomic technologies such as these will help identify and monitor toxicity and help develop subsequent environmental policies.
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  • Enlistment of omics technologies in the fight against malaria: Panacea or Pandora's Box?
    C. Nelson Hayes, Åsa M. Wheelock, Johan Normark, Mats Wahlgren, ...
    2006 Volume 31 Issue 3 Pages 263-272
    Published: 2006
    Released on J-STAGE: August 24, 2006
    DOIhttps://doi.org/10.1584/jpestics.31.263
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    Plasmodium spp, the causative agent of malaria, imposes an enormous cost on the developing world. Current methods are inadequate for long-term management and eradication, and new treatments are desperately needed. The modern arsenal of “omics” technologies appears to offer a promising approach to engineering a long-term solution to malaria. However, because funding for malaria research is chronically limited, the potential results of omics methodologies must be examined to address whether the investment is justified. This review provides an overview of a suite of omics-related technologies in terms of their potential contribution to the field of malaria research.
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  • Structure–activity relationships and pathway analysis of biological degradation processes
    Tadashi Kadowaki, Craig E. Wheelock, Masahiro Hattori, Susumu Goto, Mi ...
    2006 Volume 31 Issue 3 Pages 273-281
    Published: 2006
    Released on J-STAGE: August 24, 2006
    DOIhttps://doi.org/10.1584/jpestics.31.273
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    (Q)SARs estimate biological activity; however these models are insufficient to fully understand and predict the ADME-Tox processes of small molecules in biological systems. By integrating (Q)SARs with biological databases, the predictive capability of these models can be significantly improved. However, the techniques and methods for integrated analysis have not yet been sufficiently developed for these combined systems. In this review, we discuss standard (Q)SAR methods and biological database construction as well as provide an example of how SAR and metabolic pathway analysis can be combined to examine the biological degradation processes of endocrine disrupting chemicals.
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  • G-language System as a platform for large-scale analysis of high-throughput omics data
    Kazuharu Arakawa, Masaru Tomita
    2006 Volume 31 Issue 3 Pages 282-288
    Published: 2006
    Released on J-STAGE: August 24, 2006
    DOIhttps://doi.org/10.1584/jpestics.31.282
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    The advent of high-throughput measurement technologies has resulted in the rapid accumulation of “omics” information including genome, transcriptome, proteome, and metabolome data. This increase in data acquisition has lead to a demand for an efficient computational platform for in silico analysis. The G-language software suite provides a comprehensive workbench for large-scale omics research and systems biology. The suite includes a bioinformatics research framework G-language Genome Analysis Environment, which contains a Gene Prediction Accuracy Classification benchmarking tool for the quantification of the sensitivity of genome informatics analysis methods to genome annotation completeness. Omics data processed in this environment can be visualized with KEGG-based pathway mapping web service, and Genome-based Modeling System enables automatic prototyping of metabolic pathway models from the genome. The software suite covers various domains of omics, with the goal of integrating all of these data for research into systems biology.
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Commentaries
  • The VANTED software system for transcriptomics, proteomics and metabolomics analysis
    Christian Klukas, Björn H. Junker, Falk Schreiber
    2006 Volume 31 Issue 3 Pages 289-292
    Published: 2006
    Released on J-STAGE: August 24, 2006
    DOIhttps://doi.org/10.1584/jpestics.31.289
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    Current research in biology generates data sets of increasing size that are very difficult to manage and analyze manually. Bioinformatics tools are necessary to facilitate statistical analysis and visualization of the data. While multiple tools exist for this purpose, they are often limited to specific kinds of data or allow only certain types of analyses. Recently, we have reported on the development of VANTED, a software system that allows mapping of multi-dimensional data sets onto relevant biological networks. VANTED provides a variety of functions for network editing, data mapping and processing, statistical analysis, and visualization. This review summarizes the main features of VANTED.
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  • KaPPA-View for integrating quantitative transcriptomic and metabolomic data on plant metabolic pathway maps
    Nozomu Sakurai, Daisuke Shibata
    2006 Volume 31 Issue 3 Pages 293-295
    Published: 2006
    Released on J-STAGE: August 24, 2006
    DOIhttps://doi.org/10.1584/jpestics.31.293
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    With advanced technologies in DNA array, vast amounts of transcriptome data have been produced and state-of-the-art mass spectrometers have contributed to the massive production of metabolome data. Interpretation of the metabolome data in conjunction with the transcriptome data is one of the major concerns associated with research into identifying metabolism-related gene function. The web-based tool KaPPA-View was developed for representing quantitative data for individual transcripts and/or metabolites on plant metabolic pathway maps. The presentation of data in this manner facilitates a good grasp of the transcripts and metabolites, leading to hypotheses of gene function in the metabolic pathway being examined. Here, we comment on a practical use of this omics tool.
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  • Overview of KEGG applications to omics-related research
    Kiyoko F. Aoki-Kinoshita
    2006 Volume 31 Issue 3 Pages 296-299
    Published: 2006
    Released on J-STAGE: August 24, 2006
    DOIhttps://doi.org/10.1584/jpestics.31.296
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    KEGG (Kyoto Encyclopedia of Genes and Genomes) is a bioinformatics resource for analyzing cells and organisms from not only the genomic perspective but also a high-level perspective, integrating together genomic, chemical and network information. Accessible from http://www.genome.jp/, it basically consists of four databases: PATHWAY, GENES, LIGAND and BRITE. The KEGG PATHWAY database provides pathway diagrams, represented as networks of interactions that occur in the cell. These can be viewed according to organism or as generic “reference” maps. KEGG GENES is the collection of genes that are found in the complete genomes that are registered in KEGG. It serves as the repository of genes linked from the pathway diagrams. KEGG LIGAND is a database of compounds, glycans, reactions and enzymes. Finally, KEGG BRITE contains the KEGG Orthology, or KO, which is a manually curated identification system of gene orthologs. It also contains classifications of chemical compounds and enzymatic reactions. KO has become an indispensable tool for the functional annotation of new genomes, and it plays a key part in the KAAS (KEGG Automatic Annotation Server) tool.
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  • Technical problems and practical operations in plant metabolomics
    Takeshi Bamba, Eiichiro Fukusaki
    2006 Volume 31 Issue 3 Pages 300-304
    Published: 2006
    Released on J-STAGE: August 24, 2006
    DOIhttps://doi.org/10.1584/jpestics.31.300
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    A metabolomics experiment consists of several complicated technical elements with each step (‘cultivation of organisms,’ ‘sampling,’ ‘sample preparation,’ ‘analysis,’ ‘data conversion,’ and ‘informatics’) potentially giving rise to experimental error. In order to perform metabolomics studies, it is necessary to understand the method limitations in detail and recognize possible problems at each step. Here, we review a number of technical problems associated with plant metabolomics and describe some practical knowledge for experimental design.
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Original Articles
  • Synthesis and herbicidal activity of 2-acylimino-3-phenyl-1,3-thiazolines—A new family of bleaching herbicides—
    Yuzuru Sanemitsu, Shinichi Kawamura, Junichi Satoh, Tadasi Katayama, S ...
    2006 Volume 31 Issue 3 Pages 305-310
    Published: 2006
    Released on J-STAGE: August 24, 2006
    DOIhttps://doi.org/10.1584/jpestics.31.305
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    A novel series of substituted 2-acylimino-1,3-thiazolines was synthesized and their herbicidal activity against upland weeds and selectivity against crops was assessed. The structure–activity relationships were probed by substitution of the thiazoline nucleus and/or an imino group. Highest activity was seen with compounds which contain two substituents: a methyl group at the 5-position of the thiazoline nucleus and a trifluoroacetyl or a difluoroacetyl group on an imino moiety. Among the compounds examined, 2-(N-difluoroacetylimino)-5-methyl-3-(3-trifluoromethylphenyl)-1,3-thiazoline applied at rates between 62.5 and 125 g a.i./ha, showed excellent broad-spectrum pre-emergence herbicidal activity against grass and broadleaf weeds without injury to cotton.
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  • Synthesis of (+)-(S)-isorobinal together with its antipod, a cyclic monoterpene functioning as the sex pheromone of Rhizoglyphus setosus and its distribution among Astigmata
    Nobuhiro Shimizu, Atsuko Mizoguchi, Kenjiro Murakami, Koji Noge, Naoki ...
    2006 Volume 31 Issue 3 Pages 311-315
    Published: 2006
    Released on J-STAGE: August 24, 2006
    DOIhttps://doi.org/10.1584/jpestics.31.311
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    Both compounds, (+)-(S)- and (−)-(R)-4-isopropenyl-3-oxo-1-cyclohexene-1-carbaldehyde [(+)-(S)- and (−)-(R)-isorobinal, (S)- and (R)-1, [α]D28 +51° (c=1.0, CHCl3) and [α]D25 −45° (c=1.3, CHCl3), 95% ee and 88% ee], were synthesized in seven steps starting from (R)- and (S)-perillyl alcohol [(R)- and (S)-2] available commercially. Isorobinal (1) is distributed among seven species of Astigmata among 61 species examined. (S)-Isorobinal [(S)-1], known as the female sex pheromone of Rhizoglyphus setosus, was confirmed in two other Rhizoglyphus species, while its biological function remained obscure against each species. In the other four species, not only its configuration but also its function has not yet been determined.
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  • Comparative effects of rootstock and scion on dieldrin and endrin uptake by grafted cucumber (Cucumis sativus)
    Takashi Otani, Nobuyasu Seike
    2006 Volume 31 Issue 3 Pages 316-321
    Published: 2006
    Released on J-STAGE: August 24, 2006
    DOIhttps://doi.org/10.1584/jpestics.31.316
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    We examined the effect of grafting on dieldrin and endrin uptake from soil into cucumber plants. We compared the concentrations of dieldrin and endrin in aerial tissues of 10 varieties of Cucurbita spp. and 23 varieties of cucumber (Cucumis sativus L.) grown in a drin-contaminated soil. We chose four varieties each of Cucurbita spp. and cucumber, made up of 16 combinations of grafted plants by combining the Cucurbita spp. as rootstocks and the cucumber as scions, and then compared the dieldrin and endrin concentrations in the aerial tissues of the grafted plants. The results of our grafting trials indicated that dieldrin and endrin concentrations in the grafted plants were influenced mainly by rootstock varieties.
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  • Aerobic metabolism and adsorption of pyrethroid insecticide imiprothrin in soil
    Yusuke Suzuki, Jun Yoshimura, Toshiyuki Katagi
    2006 Volume 31 Issue 3 Pages 322-328
    Published: 2006
    Released on J-STAGE: August 24, 2006
    DOIhttps://doi.org/10.1584/jpestics.31.322
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    Imiprothrin, a unique type of pyrethroid having an imidazolidinyl ring in its alcohol moiety, was rapidly degraded in two aerobic U.S. soils. The half-lives of biologically active trans isomer were estimated by assuming the first-order kinetics to be 1.6–2.5 days, shorter than those of the cis isomer (3.3–12.5 days). The primary metabolic pathway was ester cleavage followed by instantaneous elimination of a hydroxylmethyl group from the alcohol moiety to form PGH (1-propargylimidazolidine-2,4-dione). The opening of the imidazolidinyl ring with subsequent release of the carbamoyl group resulted in the formation of PG (N-propargylglycine). The soil adsorption coefficients (Koc) of the trans isomer, the main component of imiprothrin (80%), to the two soils were determined to be 376 and 428 (ml/g o.c.) by the batch equilibrium method and these lower values as compared with other pyrethroids were likely to stem from the hydrophilic character of the alcohol moiety. Based on the metabolic half-lives and Koc values, the groundwater concentration of imiprothrin was calculated to be 0.039 μg/L by using the screening simulation model SCI-GROW known to give a conservative groundwater concentration. This significant lower concentration clearly indicates that imiprothrin is most unlikely to contaminate the groundwater, mainly due to its rapid degradation in soil.
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  • Thiadiazole carboxylic acid moiety of tiadinil, SV-03, induces systemic acquired resistance in tobacco without salicylic acid accumulation
    Michiko Yasuda, Miyuki Kusajima, Masami Nakajima, Katsumi Akutsu, Tosh ...
    2006 Volume 31 Issue 3 Pages 329-334
    Published: 2006
    Released on J-STAGE: August 24, 2006
    DOIhttps://doi.org/10.1584/jpestics.31.329
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    Systemic acquired resistance (SAR) is a potent innate immunity system in plants that is effective against a broad range of pathogens and induced through the salicylic acid (SA)-mediated pathway. Here we have characterized the SAR induction activity of 4-methyl-1,2,3-thiadiazole-5-carboxylic acid (SV-03) identified as a metabolite of tiadinil in rice. Soil drench application of SV-03 induces a broad range of disease resistance and PR gene expression in tobacco. Further analyses using NahG transgenic tobacco plants indicate that SV-03-induced resistance enhancement does not require SA. Therefore, it is suggested that SV-03 induced SAR by triggering signaling at the same level as or downstream of SA accumulation.
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Notes
  • Ultrastructural effects of pyridalyl, an insecticidal agent, on epidermal cells of Spodoptera litura larvae and cultured insect cells Sf9
    Shigeru Saito, Takafumi Yoshioka, Kimitoshi Umeda
    2006 Volume 31 Issue 3 Pages 335-338
    Published: 2006
    Released on J-STAGE: August 24, 2006
    DOIhttps://doi.org/10.1584/jpestics.31.335
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    The ultrastructural effects of pyridalyl on the epidermal cells of S. litura larvae and cultured Sf9 cells were observed. In epidermal cells, hydropic degeneration containing swollen mitochondria, dilated rough endoplasmic reticulum, dilated Golgi apparatus, shrunken nuclei and increase of unidentified clear granules appeared 6 hr after treatment. In Sf9 cells, swelling of mitochondria was observed 4–6 hr after treatment, and then the cells finally entered hydropic degeneration. Since the time course of such ultrastructural changes was parallel to that of poisoning symptoms in the larvae, these effects were thought to be related with insecticidal action.
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  • Influence of vegetable and mineral oils on the efficacy of some post-emergence herbicides for grass weed control in wheat
    Fabio Stagnari, Andrea Onofri, Gino Covarelli
    2006 Volume 31 Issue 3 Pages 339-343
    Published: 2006
    Released on J-STAGE: August 24, 2006
    DOIhttps://doi.org/10.1584/jpestics.31.339
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    Two field experiments in central Italy on wheat showed that the application rate of clodinafop-propargyl could be significantly reduced to 1/2 of the labelled rate to control oats and canarygrass, with no loss in weed control efficacy. This reduction was favoured by the use of mineral or vegetable oil, with no apparent differences. No rate reduction of clodinafop-propargyl was possible for ryegrass, which needed at least the labelled rate plus vegetable or mineral oil to be satisfactorily controlled. A mixture of diclofop-methyl+fenoxaprop-p-ethyl could be effectively used only against oats controlled at 2/3 of the labelled rate. This mixture did not prove effective against canarygrass, while it was effective against ryegrass only when applied at the maximum labelled rate mixed with vegetable or mineral oil.
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PART II (IN JAPANESE)
The Society Award Lecture
Original Article (with abstract in English)
Abstracts for Original Articles
Commentary
Letter to Members
Symposia
Obituary
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