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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Frédéric Chevallier; Pierre Regnier; Julia Pongratz; Atul K. Jain; +30 Authors

    Abstract. Regional land carbon budgets provide insights on the spatial distribution of the land uptake of atmospheric carbon dioxide, and can be used to evaluate carbon cycle models and to define baselines for land-based additional mitigation efforts. The scientific community has been involved in providing observation-based estimates of regional carbon budgets either by downscaling atmospheric CO2 observations into surface fluxes with atmospheric inversions, by using inventories of carbon stock changes in terrestrial ecosystems, by upscaling local field observations such as flux towers with gridded climate and remote sensing fields or by integrating data-driven or process-oriented terrestrial carbon cycle models. The first coordinated attempt to collect regional carbon budgets for nine regions covering the entire globe in the RECCAP-1 project has delivered estimates for the decade 2000–2009, but these budgets were not comparable between regions, due to different definitions and component fluxes reported or omitted. The recent recognition of lateral fluxes of carbon by human activities and rivers, that connect CO2 uptake in one area with its release in another also requires better definition and protocols to reach harmonized regional budgets that can be summed up to the globe and compared with the atmospheric CO2 growth rate and inversion results. In this study, for the international initiative RECCAP-2 coordinated by the Global Carbon Project, which aims as an update of regional carbon budgets over the last two decades based on observations, for 10 regions covering the globe, with a better harmonization that the precursor project, we provide recommendations for using atmospheric inversions results to match bottom-up carbon accounting and models, and we define the different component fluxes of the net land atmosphere carbon exchange that should be reported by each research group in charge of each region. Special attention is given to lateral fluxes, inland water fluxes and land use fluxes.

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    https://doi.org/10.5194/gmd-20...
    Article . 2020 . Peer-reviewed
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    Geoscientific Model Development (GMD)
    Article . 2022 . Peer-reviewed
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    Geoscientific Model Development (GMD)
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    Wageningen Staff Publications
    Article . 2022
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    https://dx.doi.org/10.60692/vq...
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      https://doi.org/10.5194/gmd-20...
      Article . 2020 . Peer-reviewed
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      Geoscientific Model Development (GMD)
      Article . 2022 . Peer-reviewed
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      Geoscientific Model Development (GMD)
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      MPG.PuRe
      Article . 2020
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Wageningen Staff Publications
      Article . 2022
      License: CC BY
      https://dx.doi.org/10.60692/vq...
      Other literature type . 2020
      Data sources: Datacite
      https://dx.doi.org/10.60692/am...
      Other literature type . 2020
      Data sources: Datacite
      https://dx.doi.org/10.60692/bz...
      Other literature type . 2022
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      https://dx.doi.org/10.60692/zf...
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  • Authors: Yuichi Nakahara; Tomoo Funayama; Takashi Okuda; Masahiko Watanabe; +7 Authors

    Anhydrobiotic larvae of Polypedilum vanderplanki are known to show an extremely high tolerance against a range of stresses. We have recently reported that this insect withstands exposure to high doses of gamma-rays (linear energy transfer [LET] 0.2 keV/microm). However, its tolerance against high LET radiation remains unknown. The aim of this study is to characterize the tolerance to high-LET radiations of P. vanderplanki.Larval survival and subsequent metamorphoses were compared between anhydrobiotic (dry) and non-anhydrobiotic (wet) samples after exposure to 1 - 7000 Gy of three types of heavy ions delivered from the azimuthally varying field (AVF) cyclotron with LET values ranging from 16.2 - 321 keV/microm. The tolerance against 4He ions was also compared among three chironomid species.At all LET values measured, dry larvae consistently showed greater radiation tolerance than hydrated larvae, perhaps due to the presence of high concentrations of the disaccharide trehalose in anhydrobiotic animals, and the radiation-induced damage became evident at lower doses as development progressed. Relative biological effectiveness (RBE) values based on the median inhibitory doses reached a maximum at 116 keV/microm (12C), and the maximum RBE clearly increased as development progressed. Lower D0 (dose to reduce survival from relative value 1.00 - 0.37 on the exponential part of the survival curve), and higher Dq (quasi-threshold dose) were found in individuals exposed to 4He ions, compared to gamma-rays, and in P. vanderplanki larvae compared to non-anhydrobiotic chironomids.Anhydrobiosis potentiates radiation tolerance in terms of larval survival, pupation and adult emergence of P. vanderplanki exposed to high-LET radiations as well as to low-LET radiation. P. vanderplanki larvae might have more efficient DNA damage repair after radiation than other chironomid species.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Athanasios Ragkos; Kentaro Hayashi; João Serra; Hideaki Shibata; +4 Authors

    Sustainable nitrogen (N) management in agriculture is one of the most important issues affecting the environmental performance of modern agriculture. It is actually well perceived that coordinated efforts and holistic approaches are required to regulate N use by farmers. The purpose of this study was to provide an initial examination of stakeholders’ views in Japan regarding N use in agriculture and challenges to increase its sustainability. The analysis was based on a questionnaire study of five types of stakeholders (farmers, advisors, researchers, suppliers, policy makers). By means of multivariate analysis techniques it was revealed that consensus was lacking either in the acknowledgment of the causes and effects of unsustainable N management or in the challenges that need to be addressed. N losses from farms and the effects of N use were perceived but not conceived equally by all stakeholders. Organic farming and mandatory measures were the most controversial challenges, while those involving awareness, training and advisory were the most popular. This study cannot provide safe conclusions that can be generalized in the Japanese context, but it indicates domains where further research is required and orientations for future policy design towards more sustainable N use.

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    Sustainability
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Yasuaki Hijioka; Ronald C. Estoque; Takuya Togawa; Makoto Ooba;

    The conceptualization of the Shared Socioeconomic Pathways (SSPs) framework represented a major leap in scenario development in the context of global environmental change and sustainability, providing significant advances from the previous scenario frameworks-especially the Intergovernmental Panel on Climate Change (IPCC) Special Report on Emissions Scenarios. It is highly likely that the SSP concept, along with its scenario narratives and their respective results, including land-use change projections, will play a substantial role in the forthcoming Sixth Assessment Report by the IPCC. Here, we offer some insights that could make the SSPs' projected future changes in global land use more comprehensive and also help improve the interpretability of such projections. For example, instead of focusing on the quantity of each land-use class at various time points which results only in a net change when change is detected between time points, we recommend that the projected gross gains and gross losses in each land-use class across all scenarios should also be considered. Overall, the insights presented could also help pave the way for stronger collaboration between the SSP-climate science community and the land system science community; such collaboration is much needed in addressing the challenges of global environmental change towards a climate-resilient sustainable development pathway.

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    AMBIO
    Article . 2020 . Peer-reviewed
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  • Authors: Shin-ichi Nagaoka; Keishi Ohara; Yu Kanesaki; Kouichi Abe; +3 Authors

    The reaction rates (ks) of vitamin E (alpha-, beta-, gamma-, delta-tocopherols, TocH), ubiquinol-10, and related antioxidants (tocol, ubiquinol-0, and hydroquinone) with aroxyl (ArO(.-)) radical have been measured in micellar solution by stopped-flow spectrophotometer. The ks values increased in the order of hydroquinone < tocol < delta-TocH < ubiquinol-0 < gamma-TocH approximately beta-TocH < ubiquinol-10 < alpha-TocH at pH 4 approximately 8. The antioxidants which have lower oxidation potentials showed higher reactivities. The ks values of alpha-, beta-, gamma-, delta-tocopherol, and tocol remained constant between pH 4 and 10, and decreased rapidly at pH 11 approximately 12 by increasing pH value. From the pH dependence of ks values, the pKa values (= 13.1 approximately 12.6) have been determined for these tocopherols. The ks values of ubiquinol-10 also remained constant between pH 4 and 9, and increased rapidly at pH 9.5. Ubiquinol-10 is dibasic acid and can exist in three different molecular forms, depending on the pH value. By comparing the ks values with the mole fraction of each molecular form of ubiquinol-10, the reaction rate ks1 (= 1.21 x 10(5) M(-1)s(-1)) for the undissociated form, ks2 (= 1.04 x 10(6) M(-1)s(-1)) for monoanion and ks3 (= 0 M(-1)s(-1)) for dianion, and the pKa1 and pKa2 values (= 11.4 and 12.7) were determined. The ks2 value is 8.6 times as large as the ks1 value. Similar analyses were performed for ubiquinol-0 and hydroquinone. It was found that the relative ratio of ks values (100:21:20:2.9) of alpha-, beta-, gamma-, delta-tocopherols in micellar dispersion has good correlation with the relative biopotency ratios for rat fetal resorption, rat hemeolysis, and chicken muscle dystrophy. The relative antioxidant activities of alpha-tocopherol and ubiquinol-10 have been discussed based on the ks values obtained and their concentrations in serum and several tissues (heart, muscle, liver, kidney, and brain).

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    Authors: Maki Kawai-Yamada; Ichiro Kasajima; Kentaro Takahara; Toshio Yamamoto; +3 Authors

    Nonphotochemical quenching (NPQ) regulates energy conversion in photosystem II and protects plants from photoinhibition. Here we analyze NPQ capacity in a number of rice cultivars. NPQ was strongly induced under medium and high light intensities in rice leaves. Japonica cultivars generally showed higher NPQ capacities than Indica cultivars when we measured a rice core collection. We mapped NPQ regulator and identified a locus ( qNPQ1-2 ) that seems to be responsible for the difference in NPQ capacity between Indica and Japonica. One of the two rice PsbS homologues ( OsPsbS1 ) was found within the qNPQ1-2 region. PsbS protein was not accumulated in the leaf blade of the mutant harboring transferred DNA insertion in OsPsbS1 . NPQ capacity increased as OsPsbS1 expression increased in a series of transgenic lines ectopically expressing OsPsbS1 in an Indica cultivar. Indica cultivars lack a 2.7-kb region at the point 0.4 kb upstream of the OsPsbS1 gene, suggesting evolutionary discrimination of this gene.

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    Proceedings of the National Academy of Sciences
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      Proceedings of the National Academy of Sciences
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    Authors: Akihiro Kuroshima; Hiroshi Ohinata; Shyamal Kumar Saha; Mitsuru Moriya;

    Interference by lipids with fluorometric assay of DNA in adipose tissues using Hoechst 33258 was investigated. Mixed glycerides shifted the emission maximum of standard DNA and induced a dose-dependent increase in fluorescence intensity. Glycerides in the samples containing a known concentration of DNA yielded erroneously higher DNA concentrations. The DNA concentrations obtained from acetone-defatted white and brown adipose tissues (WAT and BAT) were lower than those of non-defatted ones, while DNA content did not differ in low lipid-containing skeletal muscle between defatted and non-defatted samples, indicating that large amounts of lipids interfere with DNA measurement using Hoechst 33258 and that acetone defatting is a simple method to avoid this interference. Using this defatting method, the cellularity of WAT and BAT was estimated in rats under various experimental conditions. Cold-acclimation and repetitive immobilization stress decreased the body weight gain and the epididymal WAT weight. Sucrose overfeeding increased WAT weight but not body weight. These treatments of 4 weeks' duration did not induce any significant difference in WAT cell number from controls, while cold-acclimation increased the tissue cell number as well as the BAT weight.

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    The Japanese Journal of Physiology
    Article . 1994 . Peer-reviewed
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      The Japanese Journal of Physiology
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    Principal component analysis (PCA) is used to reduce the dimensionalities of high dimensional datasets in a variety of research areas. For example, biological macromolecules, such as proteins, exhibit many degrees of freedom, allowing them to adopt intricate structures and exhibit complex functions by undergoing large conformational changes. Therefore, molecular simulations of and experiments on proteins generate a large number of structure variations in high dimensional space. PCA and many PCA-related methods have been developed to extract key features from such structural data, and these approaches have been widely applied for over 30 years to elucidate macromolecular dynamics. This review mainly focuses on the methodological aspects of PCA and related methods, and their applications for investigating protein dynamics.

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    https://doi.org/10.20944/prepr...
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  • Authors: Hideki Yamamura; Yuzuru Iimura; Masayuki Hayakawa; Youji Nakagawa; +2 Authors

    Tolerance of microorganisms to diverse stresses (i.e., multistress tolerance) is a very useful property with industrial applications. We have developed a simple method for isolating multistress-tolerant semidominant mutants of the budding yeast Saccharomyces cerevisiae by one-step selection under lethal hydrogen peroxide (H(2)O(2)) stress condition, which we named the lethal concentration of H(2)O(2) (LCH) method. This method involves simply isolating colonies after plating of mutagenized S. cerevisiae cells, which are cultivated overnight in liquid media, on agar plates containing a lethal concentration of H(2)O(2) for the wild-type strain. Phenotypic and genetic analyses of the ten strains isolated by this method revealed that two strains exhibiting stress tolerance to H(2)O(2), ethanol, heat shock, salt, organic solvent, freeze-thaw, chronological aging, and high concentrations of glucose possess semidominant and distinct single-gene mutations designated as MLT1-1 (multistress tolerance) and MLT2-1, which are responsible for multistress tolerance. From these results, we expect this method to confer multistress tolerance on industrial yeasts.

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    Authors: Tatsunori Suzuki; Kikuko Amagase; Youichiro Hattori; Takashi Ohno; +13 Authors

    The gastrointestinal tract is known to be rich in neural systems, among which afferent neurons are reported to exhibit protective actions. We tested whether an endogenous neuropeptide, calcitonin gene-related peptide (CGRP), can prevent gastric mucosal injury elicited by ethanol and enhance healing of acetic acid-induced ulcer using CGRP knockout mice (CGRP(-/-)).The stomach was perfused with 1.6 mmol/L capsaicin or 1 mol/L NaCl, and gastric mucosal injury elicited by 50% ethanol was estimated. Levels of CGRP in the perfusate were determined by enzyme immunoassay. Gastric ulcers were induced by serosal application of absolute acetic acid.Capsaicin inhibited injured area dose-dependently. Fifty percent ethanol containing capsaicin immediately increased intragastric levels of CGRP in wild-type (WT) mice, although 50% ethanol alone did not. The protective action of capsaicin against ethanol was completely abolished in CGRP(-/-). Preperfusion with 1 mol/L NaCl increased CGRP release and reduced mucosal damage during ethanol perfusion. However, 1 mol/L NaCl was not effective in CGRP(-/-). Healing of ulcer elicited by acetic acid in CGRP(-/-) mice was markedly delayed, compared with that in WT. In WT, granulation tissues were formed at the base of ulcers, and substantial neovascularization was induced, whereas those were poor in CGRP(-/-). Expression of vascular endothelial growth factor was more markedly reduced in CGRP(-/-) than in WT.CGRP has a preventive action on gastric mucosal injury and a proangiogenic activity to enhance ulcer healing. These results indicate that the CGRP-dependent pathway is a good target for regulating gastric mucosal protection and maintaining gastric mucosal integrity.

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    Gastroenterology
    Article . 2008 . Peer-reviewed
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      Gastroenterology
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    Authors: Frédéric Chevallier; Pierre Regnier; Julia Pongratz; Atul K. Jain; +30 Authors

    Abstract. Regional land carbon budgets provide insights on the spatial distribution of the land uptake of atmospheric carbon dioxide, and can be used to evaluate carbon cycle models and to define baselines for land-based additional mitigation efforts. The scientific community has been involved in providing observation-based estimates of regional carbon budgets either by downscaling atmospheric CO2 observations into surface fluxes with atmospheric inversions, by using inventories of carbon stock changes in terrestrial ecosystems, by upscaling local field observations such as flux towers with gridded climate and remote sensing fields or by integrating data-driven or process-oriented terrestrial carbon cycle models. The first coordinated attempt to collect regional carbon budgets for nine regions covering the entire globe in the RECCAP-1 project has delivered estimates for the decade 2000–2009, but these budgets were not comparable between regions, due to different definitions and component fluxes reported or omitted. The recent recognition of lateral fluxes of carbon by human activities and rivers, that connect CO2 uptake in one area with its release in another also requires better definition and protocols to reach harmonized regional budgets that can be summed up to the globe and compared with the atmospheric CO2 growth rate and inversion results. In this study, for the international initiative RECCAP-2 coordinated by the Global Carbon Project, which aims as an update of regional carbon budgets over the last two decades based on observations, for 10 regions covering the globe, with a better harmonization that the precursor project, we provide recommendations for using atmospheric inversions results to match bottom-up carbon accounting and models, and we define the different component fluxes of the net land atmosphere carbon exchange that should be reported by each research group in charge of each region. Special attention is given to lateral fluxes, inland water fluxes and land use fluxes.

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    https://doi.org/10.5194/gmd-20...
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    Geoscientific Model Development (GMD)
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    Wageningen Staff Publications
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    https://dx.doi.org/10.60692/vq...
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      https://doi.org/10.5194/gmd-20...
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  • Authors: Yuichi Nakahara; Tomoo Funayama; Takashi Okuda; Masahiko Watanabe; +7 Authors

    Anhydrobiotic larvae of Polypedilum vanderplanki are known to show an extremely high tolerance against a range of stresses. We have recently reported that this insect withstands exposure to high doses of gamma-rays (linear energy transfer [LET] 0.2 keV/microm). However, its tolerance against high LET radiation remains unknown. The aim of this study is to characterize the tolerance to high-LET radiations of P. vanderplanki.Larval survival and subsequent metamorphoses were compared between anhydrobiotic (dry) and non-anhydrobiotic (wet) samples after exposure to 1 - 7000 Gy of three types of heavy ions delivered from the azimuthally varying field (AVF) cyclotron with LET values ranging from 16.2 - 321 keV/microm. The tolerance against 4He ions was also compared among three chironomid species.At all LET values measured, dry larvae consistently showed greater radiation tolerance than hydrated larvae, perhaps due to the presence of high concentrations of the disaccharide trehalose in anhydrobiotic animals, and the radiation-induced damage became evident at lower doses as development progressed. Relative biological effectiveness (RBE) values based on the median inhibitory doses reached a maximum at 116 keV/microm (12C), and the maximum RBE clearly increased as development progressed. Lower D0 (dose to reduce survival from relative value 1.00 - 0.37 on the exponential part of the survival curve), and higher Dq (quasi-threshold dose) were found in individuals exposed to 4He ions, compared to gamma-rays, and in P. vanderplanki larvae compared to non-anhydrobiotic chironomids.Anhydrobiosis potentiates radiation tolerance in terms of larval survival, pupation and adult emergence of P. vanderplanki exposed to high-LET radiations as well as to low-LET radiation. P. vanderplanki larvae might have more efficient DNA damage repair after radiation than other chironomid species.

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    Authors: Athanasios Ragkos; Kentaro Hayashi; João Serra; Hideaki Shibata; +4 Authors

    Sustainable nitrogen (N) management in agriculture is one of the most important issues affecting the environmental performance of modern agriculture. It is actually well perceived that coordinated efforts and holistic approaches are required to regulate N use by farmers. The purpose of this study was to provide an initial examination of stakeholders’ views in Japan regarding N use in agriculture and challenges to increase its sustainability. The analysis was based on a questionnaire study of five types of stakeholders (farmers, advisors, researchers, suppliers, policy makers). By means of multivariate analysis techniques it was revealed that consensus was lacking either in the acknowledgment of the causes and effects of unsustainable N management or in the challenges that need to be addressed. N losses from farms and the effects of N use were perceived but not conceived equally by all stakeholders. Organic farming and mandatory measures were the most controversial challenges, while those involving awareness, training and advisory were the most popular. This study cannot provide safe conclusions that can be generalized in the Japanese context, but it indicates domains where further research is required and orientations for future policy design towards more sustainable N use.

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    Sustainability
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    Authors: Yasuaki Hijioka; Ronald C. Estoque; Takuya Togawa; Makoto Ooba;

    The conceptualization of the Shared Socioeconomic Pathways (SSPs) framework represented a major leap in scenario development in the context of global environmental change and sustainability, providing significant advances from the previous scenario frameworks-especially the Intergovernmental Panel on Climate Change (IPCC) Special Report on Emissions Scenarios. It is highly likely that the SSP concept, along with its scenario narratives and their respective results, including land-use change projections, will play a substantial role in the forthcoming Sixth Assessment Report by the IPCC. Here, we offer some insights that could make the SSPs' projected future changes in global land use more comprehensive and also help improve the interpretability of such projections. For example, instead of focusing on the quantity of each land-use class at various time points which results only in a net change when change is detected between time points, we recommend that the projected gross gains and gross losses in each land-use class across all scenarios should also be considered. Overall, the insights presented could also help pave the way for stronger collaboration between the SSP-climate science community and the land system science community; such collaboration is much needed in addressing the challenges of global environmental change towards a climate-resilient sustainable development pathway.

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    AMBIO
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  • Authors: Shin-ichi Nagaoka; Keishi Ohara; Yu Kanesaki; Kouichi Abe; +3 Authors

    The reaction rates (ks) of vitamin E (alpha-, beta-, gamma-, delta-tocopherols, TocH), ubiquinol-10, and related antioxidants (tocol, ubiquinol-0, and hydroquinone) with aroxyl (ArO(.-)) radical have been measured in micellar solution by stopped-flow spectrophotometer. The ks values increased in the order of hydroquinone < tocol < delta-TocH < ubiquinol-0 < gamma-TocH approximately beta-TocH < ubiquinol-10 < alpha-TocH at pH 4 approximately 8. The antioxidants which have lower oxidation potentials showed higher reactivities. The ks values of alpha-, beta-, gamma-, delta-tocopherol, and tocol remained constant between pH 4 and 10, and decreased rapidly at pH 11 approximately 12 by increasing pH value. From the pH dependence of ks values, the pKa values (= 13.1 approximately 12.6) have been determined for these tocopherols. The ks values of ubiquinol-10 also remained constant between pH 4 and 9, and increased rapidly at pH 9.5. Ubiquinol-10 is dibasic acid and can exist in three different molecular forms, depending on the pH value. By comparing the ks values with the mole fraction of each molecular form of ubiquinol-10, the reaction rate ks1 (= 1.21 x 10(5) M(-1)s(-1)) for the undissociated form, ks2 (= 1.04 x 10(6) M(-1)s(-1)) for monoanion and ks3 (= 0 M(-1)s(-1)) for dianion, and the pKa1 and pKa2 values (= 11.4 and 12.7) were determined. The ks2 value is 8.6 times as large as the ks1 value. Similar analyses were performed for ubiquinol-0 and hydroquinone. It was found that the relative ratio of ks values (100:21:20:2.9) of alpha-, beta-, gamma-, delta-tocopherols in micellar dispersion has good correlation with the relative biopotency ratios for rat fetal resorption, rat hemeolysis, and chicken muscle dystrophy. The relative antioxidant activities of alpha-tocopherol and ubiquinol-10 have been discussed based on the ks values obtained and their concentrations in serum and several tissues (heart, muscle, liver, kidney, and brain).

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    Authors: Maki Kawai-Yamada; Ichiro Kasajima; Kentaro Takahara; Toshio Yamamoto; +3 Authors

    Nonphotochemical quenching (NPQ) regulates energy conversion in photosystem II and protects plants from photoinhibition. Here we analyze NPQ capacity in a number of rice cultivars. NPQ was strongly induced under medium and high light intensities in rice leaves. Japonica cultivars generally showed higher NPQ capacities than Indica cultivars when we measured a rice core collection. We mapped NPQ regulator and identified a locus ( qNPQ1-2 ) that seems to be responsible for the difference in NPQ capacity between Indica and Japonica. One of the two rice PsbS homologues ( OsPsbS1 ) was found within the qNPQ1-2 region. PsbS protein was not accumulated in the leaf blade of the mutant harboring transferred DNA insertion in OsPsbS1 . NPQ capacity increased as OsPsbS1 expression increased in a series of transgenic lines ectopically expressing OsPsbS1 in an Indica cultivar. Indica cultivars lack a 2.7-kb region at the point 0.4 kb upstream of the OsPsbS1 gene, suggesting evolutionary discrimination of this gene.

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    Proceedings of the National Academy of Sciences
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      Proceedings of the National Academy of Sciences
      Article . 2011 . Peer-reviewed
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    Authors: Akihiro Kuroshima; Hiroshi Ohinata; Shyamal Kumar Saha; Mitsuru Moriya;

    Interference by lipids with fluorometric assay of DNA in adipose tissues using Hoechst 33258 was investigated. Mixed glycerides shifted the emission maximum of standard DNA and induced a dose-dependent increase in fluorescence intensity. Glycerides in the samples containing a known concentration of DNA yielded erroneously higher DNA concentrations. The DNA concentrations obtained from acetone-defatted white and brown adipose tissues (WAT and BAT) were lower than those of non-defatted ones, while DNA content did not differ in low lipid-containing skeletal muscle between defatted and non-defatted samples, indicating that large amounts of lipids interfere with DNA measurement using Hoechst 33258 and that acetone defatting is a simple method to avoid this interference. Using this defatting method, the cellularity of WAT and BAT was estimated in rats under various experimental conditions. Cold-acclimation and repetitive immobilization stress decreased the body weight gain and the epididymal WAT weight. Sucrose overfeeding increased WAT weight but not body weight. These treatments of 4 weeks' duration did not induce any significant difference in WAT cell number from controls, while cold-acclimation increased the tissue cell number as well as the BAT weight.

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    The Japanese Journal of Physiology
    Article . 1994 . Peer-reviewed
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      The Japanese Journal of Physiology
      Article . 1994 . Peer-reviewed
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    Principal component analysis (PCA) is used to reduce the dimensionalities of high dimensional datasets in a variety of research areas. For example, biological macromolecules, such as proteins, exhibit many degrees of freedom, allowing them to adopt intricate structures and exhibit complex functions by undergoing large conformational changes. Therefore, molecular simulations of and experiments on proteins generate a large number of structure variations in high dimensional space. PCA and many PCA-related methods have been developed to extract key features from such structural data, and these approaches have been widely applied for over 30 years to elucidate macromolecular dynamics. This review mainly focuses on the methodological aspects of PCA and related methods, and their applications for investigating protein dynamics.

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    https://doi.org/10.20944/prepr...
    Article . 2022 . Peer-reviewed
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    Article . 2022
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      https://doi.org/10.20944/prepr...
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  • Authors: Hideki Yamamura; Yuzuru Iimura; Masayuki Hayakawa; Youji Nakagawa; +2 Authors

    Tolerance of microorganisms to diverse stresses (i.e., multistress tolerance) is a very useful property with industrial applications. We have developed a simple method for isolating multistress-tolerant semidominant mutants of the budding yeast Saccharomyces cerevisiae by one-step selection under lethal hydrogen peroxide (H(2)O(2)) stress condition, which we named the lethal concentration of H(2)O(2) (LCH) method. This method involves simply isolating colonies after plating of mutagenized S. cerevisiae cells, which are cultivated overnight in liquid media, on agar plates containing a lethal concentration of H(2)O(2) for the wild-type strain. Phenotypic and genetic analyses of the ten strains isolated by this method revealed that two strains exhibiting stress tolerance to H(2)O(2), ethanol, heat shock, salt, organic solvent, freeze-thaw, chronological aging, and high concentrations of glucose possess semidominant and distinct single-gene mutations designated as MLT1-1 (multistress tolerance) and MLT2-1, which are responsible for multistress tolerance. From these results, we expect this method to confer multistress tolerance on industrial yeasts.

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    Authors: Tatsunori Suzuki; Kikuko Amagase; Youichiro Hattori; Takashi Ohno; +13 Authors

    The gastrointestinal tract is known to be rich in neural systems, among which afferent neurons are reported to exhibit protective actions. We tested whether an endogenous neuropeptide, calcitonin gene-related peptide (CGRP), can prevent gastric mucosal injury elicited by ethanol and enhance healing of acetic acid-induced ulcer using CGRP knockout mice (CGRP(-/-)).The stomach was perfused with 1.6 mmol/L capsaicin or 1 mol/L NaCl, and gastric mucosal injury elicited by 50% ethanol was estimated. Levels of CGRP in the perfusate were determined by enzyme immunoassay. Gastric ulcers were induced by serosal application of absolute acetic acid.Capsaicin inhibited injured area dose-dependently. Fifty percent ethanol containing capsaicin immediately increased intragastric levels of CGRP in wild-type (WT) mice, although 50% ethanol alone did not. The protective action of capsaicin against ethanol was completely abolished in CGRP(-/-). Preperfusion with 1 mol/L NaCl increased CGRP release and reduced mucosal damage during ethanol perfusion. However, 1 mol/L NaCl was not effective in CGRP(-/-). Healing of ulcer elicited by acetic acid in CGRP(-/-) mice was markedly delayed, compared with that in WT. In WT, granulation tissues were formed at the base of ulcers, and substantial neovascularization was induced, whereas those were poor in CGRP(-/-). Expression of vascular endothelial growth factor was more markedly reduced in CGRP(-/-) than in WT.CGRP has a preventive action on gastric mucosal injury and a proangiogenic activity to enhance ulcer healing. These results indicate that the CGRP-dependent pathway is a good target for regulating gastric mucosal protection and maintaining gastric mucosal integrity.

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    Gastroenterology
    Article . 2008 . Peer-reviewed
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      Gastroenterology
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