Single cell analysis using a glass microchamber for studying movement fluctuations of Navicula pavillardii and Seminavis robusta diatom cells

Umemura, Kazuo; Sadoya, Yusuke; Nagao, Kazuki; Oikawa, Ryota; Hanada, Yasutaka; Sugioka, Koji; Mayama, Shigeki

doi:10.1016/j.micron.2015.05.005

Cited by 6 publications

(4 citation statements)

References 22 publications

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“…Observation movies of floating diatom cells were recorded for 1 h using a HDR-CX590 video camera (SONY, Tokyo, Japan) at a shutter speed of 1/30 s. The movies were recorded as AVCHD files. The resulting observation movies were analyzed using 2D tracking analysis software (Move-tr/2D, Library, Tokyo, Japan) (Umemura et al, 2013, 2015). The movies were processed according to the following procedure.…”

Section: Methodsmentioning

confidence: 99%

Sinking of Four Species of Living Diatom Cells Directly Observed by a “Tumbled” Optical Microscope

et al. 2021

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Section: Methodsmentioning

confidence: 99%

Sinking of Four Species of Living Diatom Cells Directly Observed by a “Tumbled” Optical Microscope

et al. 2021

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“…Nitzschia sp. were collected from Okinoshima Island in the Chiba Prefecture and subcultured several times using Guillard's (F/2) culture medium (G9903; Sigma-Aldrich, Munich, Germany) with Daigo artificial seawater (395-01343; Nihon Pharmaceutical, Tokyo, Japan) for approximately 2 months (Murase et al, 2011(Murase et al, , 2012Umemura et al, 2015;Ide et al, 2020;Shoumura et al, 2020;Hamano et al, 2021).…”

Section: Methodsmentioning

confidence: 99%

An Efficient Method of Observing Diatom Frustules via Digital Holographic Microscopy

Saitô

Kitamura

Ide

et al. 2022

Microscopy and Microanalysis

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Herein, we propose a convenient method to enable pretreatment of target objects using digital holographic microscopy (DHM). As a test sample, we used diatom frustules (Nitzschia sp.) as the target objects. In the generally used sample preparation method, the frustule suspension is added dropwise onto a glass substrate or into a glass chamber. While our work confirms good observation of purified frustules using the typical sample preparation method, we also demonstrate a new procedure to observe unseparated structures of frustules prepared by baking them on a mica surface. The baked frustules on the mica surface were transferred to a glass chamber with 1% sodium dodecyl sulfate solution. In this manner, the unseparated structures of the diatom frustules were clearly observed. Furthermore, metal-coated frustules prepared by sputtering onto them on a mica surface were also clearly observed using the same procedure. Our method can be applied for the observation of any target object that is pretreated on a solid surface. We expect our proposed method to be a basis for establishing DHM techniques for microscopic observations of biomaterials.

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“…In recent years, Seminavis robusta has gained interest as a model species for benthic diatoms and to study raphid pennate life cycle regulation. This relatively large-sized (∼70 µm initial cell size) raphid pennate diatom inhabits shallow marine and brackish zones and has been reported from the North Sea, the Mediterranean and the Pacific ocean [28,29,30]. In culture, S. robusta cells display typical benthic behaviour, including surface attachment, biofilm formation and vigorous gliding motility, which has been exploited to study chemotaxis [31].…”

Section: Introductionmentioning

confidence: 95%

Diurnal transcript profiling of the diatomSeminavis robustareveals adaptations to a benthic lifestyle

Bilcke

Osuna-Cruz

Silva

et al. 2020

Preprint

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Coastal regions contribute an estimated 20% of annual gross primary production in the oceans, despite occupying only 0.03% of their surface area. Diatoms frequently dominate coastal sediments, where they experience large variations in light regime resulting from the interplay of diurnal and tidal cycles. Here, we report on an extensive diurnal transcript profiling experiment of the motile benthic diatom Seminavis robusta. Nearly 90% (23,328) of expressed protein-coding genes and 66.9% (1124) of expressed long intergenic non-coding RNAs (lincRNAs) showed significant expression oscillations and are predominantly phasing at night with a periodicity of 24h. Phylostratigraphic analysis found that rhythmic genes are enriched in deeply conserved genes, while diatom-specific genes are predominantly associated with midnight expression. Integration of genetic and physiological cell cycle markers with silica depletion data revealed potential new silica cell wall associated gene families specific to diatoms. Additionally, we observed 1752 genes with a remarkable semidiurnal (12-h) periodicity, while the expansion of putative circadian transcription factors may reflect adaptations to cope with highly unpredictable external conditions. Taken together, our results provide new insights into the adaptations of diatoms to the benthic environment and serve as a valuable resource for diurnal regulation in photosynthetic eukaryotes.

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Single cell analysis using a glass microchamber for studying movement fluctuations of Navicula pavillardii and Seminavis robusta diatom cells

Cited by 6 publications

References 22 publications

Sinking of Four Species of Living Diatom Cells Directly Observed by a “Tumbled” Optical Microscope

Sinking of Four Species of Living Diatom Cells Directly Observed by a “Tumbled” Optical Microscope

An Efficient Method of Observing Diatom Frustules via Digital Holographic Microscopy

Diurnal transcript profiling of the diatomSeminavis robustareveals adaptations to a benthic lifestyle

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