下出 信次 (シモデ シンジ)

SHIMODE Shinji

所属組織

大学院環境情報研究院 自然環境と情報部門

職名

教授

研究分野・キーワード

生物海洋学、プランクトン、カイアシ類

ホームページ

http://www.mmcer.ynu.ac.jp/shimo/my_site/Welcome.html



写真a

プロフィール 【 表示 / 非表示

  • https://www.researchgate.net/profile/Shinji_Shimode

出身学校 【 表示 / 非表示

  •  
    -
    1996年03月

    横浜国立大学   教育学部   中学校教員養成課程   卒業

出身大学院 【 表示 / 非表示

  •  
    -
    2002年03月

    京都大学  理学研究科  生物科学専攻  博士課程  修了

  •  
    -
    1998年03月

    横浜国立大学  教育学研究科  理科教育専攻  修士課程(博士前期課程)  修了

取得学位 【 表示 / 非表示

  • 博士(理学) - 

学内所属歴 【 表示 / 非表示

  • 2020年04月
    -
    継続中

    専任   横浜国立大学   大学院環境情報研究院   自然環境と情報部門   教授  

  • 2012年04月
    -
    2020年03月

    専任   横浜国立大学   大学院環境情報研究院   自然環境と情報部門   准教授  

  • 2020年04月
    -
    継続中

    併任   横浜国立大学   理工学部   建築都市・環境系学科   教授  

  • 2020年04月
    -
    継続中

    併任   横浜国立大学   大学院環境情報研究院附属臨海環境センター   教授  

  • 2020年04月
    -
    継続中

    併任   横浜国立大学   大学院環境情報学府   環境生命学専攻   教授  

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学外略歴 【 表示 / 非表示

  • 2011年04月
    -
    2012年03月

      東京大学   大学院新領域創成科学研究科   特任准教授

  • 2010年04月
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    2011年03月

      東京大学   大気海洋研究所   特任研究員

  • 2008年04月
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    2010年03月

      東京大学   海洋研究所   特任研究員

  • 2007年04月
    -
    2008年03月

      東京大学   海洋研究所   学術研究支援員

  • 2002年10月
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    2003年03月

      京都大学   教務補佐員

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論文 【 表示 / 非表示

  • Photochemical Production and Biological Consumption of CO in the SML of Temperate Coastal Waters and Their Implications for Air-sea CO Exchange.

    Sugai, Y., K. Tsuchiya, S. Shimode and T. Toda

    Journal of Geophysical Research: Oceans   125 ( 4 ) e2019JC015505   2020年03月  [査読有り]

    共著

     概要を見る

    The sea surface microlayer (SML), less than 1,000‐μm uppermost layer of the ocean water column, is located at the air‐sea interface and plays critical roles in global biogeochemical cycles and climate change through air‐sea gas exchange. To clarify the significance of the dynamics of carbon monoxide (CO) in the SML, where active photochemical and biological processes are expected, in air‐sea CO exchange, the production and consumption of CO in the SML and its sea‐air emission were investigated in temperate coastal waters. In the SML, the light‐normalized photochemical CO production rate was relatively high from spring to autumn (median: 2.57 nM [kWh m−2]−1) when relatively high absorbance of chromophoric dissolved organic matter (0.55 m−1) was observed. Biological CO consumption rate constant in the SML showed relatively high values from spring to autumn (mean ± standard deviation: 0.060 ± 0.010 h−1) during the period of relatively high water temperature (22.3 ± 2.7 °C). The calculated sea‐air CO flux (F) varied similarly to CO concentration in the subsurface water. Comparison among the production, consumption, and sea‐air emission of CO in the SML suggests that biological consumption in the SML can be ignored in air‐sea CO exchange throughout the year whereas photochemical production in the SML enhances F during summer under intense light, active biological production, and weak wind conditions. Further, seawater warming experiments found the tendency of the stimulation of biological CO consumption by water temperature increase from spring to autumn, which suggests negative but insignificant feedback on global warming.

    DOI

  • Incorporation characteristics of exogenous 15N-labeled thymidine, deoxyadenosine, deoxyguanosine and deoxycytidine into bacterial DNA

    Tsuchiya, K., T. Sano, T. Tomioka, A. Kohzu, K. Komatsu, R. Shinohara, S. Shimode, T. Toda, A. Imai

    PLoS ONE   15 ( 2 ) e0229740   2020年02月  [査読有り]

    共著

     概要を見る

    Bacterial production has been often estimated from DNA synthesis rates by using tritium-labeled thymidine. Some bacteria species cannot incorporate extracellular thymidine into their DNA, suggesting their biomass production might be overlooked when using the conventional method. In the present study, to evaluate appropriateness of deoxyribonucleosides for evaluating bacterial production of natural bacterial communities from the viewpoint of DNA synthesis, incorporation rates of four deoxyribonucleosides (thymidine, deoxyadenosine, deoxyguanosine and deoxycytidine) labeled by nitrogen stable isotope (15N) into bacterial DNA were examined in both ocean (Sagami Bay) and freshwater (Lake Kasumigaura) ecosystems in July 2015 and January 2016. In most stations in Sagami Bay and Lake Kasumigaura, we found that incorporation rates of deoxyguanosine were the highest among those of the four deoxyribonucleosides, and the incorporation rate of deoxyguanosine was approximately 2.5 times higher than that of thymidine. Whereas, incorporation rates of deoxyadenosine and deoxycytidine were 0.9 and 0.2 times higher than that of thymidine. These results clearly suggest that the numbers of bacterial species which can incorporate exogenous deoxyguanosine into their DNA are relatively greater as compared to the other deoxyribonucleosides, and measurement of bacterial production using deoxyguanosine more likely reflects larger numbers of bacterial species productions.

    DOI

  • Guanine crystals regulated by chitin-based honeycomb frameworks for tunable structural colors of sapphirinid copepod, Sapphirina nigromaculata.

    Kimura, T., M. Takasaki, R. Hatai, Y. Nagai, K. Uematsu, Y. Oaki, M. Osada, H. Tsuda, T. Ishigure, T. Toyofuku, S. Shimode and H. Imai

    Scientific Reports   10   2266   2020年02月  [査読有り]

    共著

     概要を見る

    Sapphirinid copepods, which are marine zooplankton, exhibit tunable structural colors originating from a layered structure of guanine crystal plates. In the present study, the coloring portion of adult male of a sapphirinid copepod, Sapphirina nigromaculata, under the dorsal body surface was characterized to clarify the regulation and actuation mechanism of the layered guanine crystals for spectral control. The coloring portions are separated into small domains 70–100 µm wide consisting of an ordered array of stacked hexagonal plates ~1.5 µm wide and ~80 nm thick. We found the presence of chitin-based honeycomb frameworks that are composed of flat compartments regulating the guanine crystal plates. The structural color is deduced to be tuned from blue to achromatic via yellow and purple by changing the interplate distance according to vital observation and optical simulation using a photonic array model. The framework structures are essential for the organization and actuation of the particular photonic arrays for the exhibition of the tunable structural color.

  • Effects of container size, density, and incubation period on ammonium excretion rate measurements of planktonic copepods: Validation with a highly sensitive analytical method

    Nakamura Ken-ichi, Takahashi Kazutaka, Shimode Shinji, Shimizu Yugo, Furuya Ken

    PLANKTON & BENTHOS RESEARCH ( 日本プランクトン学会、日本ベントス学会 )  14 ( 2 ) 62 - 70   2019年05月  [査読有り]

    共著

     概要を見る

    <p>Ammonium excretion by planktonic copepods is an important process supplying nitrogen to primary producers and other microbial activity in pelagic ecosystems. Because of methodological constraints, conventional analyses using sealed chamber methods have required the adoption of unnatural experimental settings, such as a small container, high density, or a long incubation for ammonium excretion measurements. Therefore, most of the estimated ammonium excretion rates are potentially linked to stresses on the experimental animals during incubation. In this study, the effects of container size, density, and incubation period on the ammonium excretion rates of five copepod species (<i>Calanus sinicus, Eucalanus californicus, Metridia pacifica, Pleuromamma abdominalis, P. gracilis</i>) were examined using a highly sensitive analytical method that has recently been developed to measure ammonium concentration at the nanomolar level. The results indicate that responses to experimental stresses are species-specific, while incubation in a small container was generally the most significant factor causing overestimation (up to 2.6 times) of the excretion rates. This study shows that this highly sensitive analysis method, which allows short incubations with a single individual in a relatively large-sized container is an appropriate method to estimate ammonium excretion of pelagic copepods in the field using the sealed chamber method.</p>

    Web of Science DOI CiNii

  • Identification of molecular markers associated with starvation in female Calanus sinicus (Copepoda: Calanoida)

    Ohnishi Takuya, Hirai Junya, Shimode Shinji, Tsuda Atsushi

    MARINE ECOLOGY PROGRESS SERIES   614   51 - 65   2019年04月  [査読有り]

    共著

    Web of Science DOI

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研究発表 【 表示 / 非表示

  • 相模湾における寄生性渦鞭毛藻類の浮遊性カイアシ類Calanus sinicusの卵生産に与える影響

    下出信次  [招待有り]

    2019年度日本プランクトン学会春季シンポジウム「プランクトン群集における共生・寄生―宿主個体群動態にインパクトを与える重要な一要因―」  2019年03月  

  • 相模湾真鶴港の微生物食物連鎖構造

    名取則明・菅井洋太・山田幸奈・土屋健司・中川恵・松崎慎一郎・本多牧生・藤木徹一・下出信次・菊池知彦・古谷研・戸田龍樹

    日本海洋学会海洋生物研究会 海洋生物シンポジウム2019  2019年03月  

  • Validation of monthly observations of spectral irradiance and bio-optical properties in the coastal waters of Sagami Bay (FY-3)

    Kuwahara, V. S., S. Shimode, K. Tsuchiya and R. Kurita

    Joint PI JAXA Meeting of Global Environmental Observation Mission  2019年01月  

  • Sapphirinaのグアニン結晶集積体の構造解析

    木村翼・高崎美宏・長井裕季子・Chen Chong ・豊福高志・下出信次・緒明佑哉・今井宏明

    第13回バイオミネラリゼーションワークショップ  2018年11月  

  • サフィリナのグアニン結晶集積体の構造解析

    木村翼・高崎美宏・長井裕季子・Chen Chong ・豊福高志・下出信次・緒明佑哉・今井宏明

    第8回CSJ化学フェスタ2018-日本化学会秋季事業−  2018年10月  

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担当授業科目(学内) 【 表示 / 非表示

  • 大学院環境情報学府  沿岸海洋評価学演習

  • 大学院環境情報学府  沿岸海洋評価学

  • 大学院環境情報学府  地球科学特別実験

  • 大学院環境情報学府  地球科学特別講義

  • 大学院環境情報学府  海洋生物環境学Ⅱ

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