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Japanese Marine Life : A Practical Training Guide in Marine Biology (2020)

Inaba, Kazuo. [editor.] ; Hall-Spencer, Jason M. [editor.]

Singapore :Springer Nature Singapore :

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Keywords: Freshwater ecology. ; Marine ecology. ; Water. ; Hydrology. ; Animal culture. ; Oceanography. ; Plant ecology. ; Animal migration. ; Freshwater and Marine Ecology. ; Water. ; Animal Science. ; Ocean Sciences. ; Plant Ecology. ; Animal Migration.

Description / Table of Contents: Chapter 1. Introduction to Marine Biology -- Part I Japanese Marine Flora and Fauna -- Chapter 2. Japanese Marine Life -- Chapter 3. Basic Taxonomy of Marine Organisms -- Chapter 4. Marine Plankton -- Chapter 5. Marine Algae and Plants -- Chapter 6. Marine Animals -- Chapter 7. Distribution of marine species on the marine seashore -- Part II Cell and Developmental Biology -- Chapter 8. Marine organisms and life science -- Chapter 9. Gametes and fertilization -- Chapter 10. Development of Marine Invertebrates -- Chapter 11. Development of marine fish: several procedures for the observation of embryonic development -- Chapter 12. Development of Marine Algae -- Chapter 13. Animal Larvae and Evolution -- Part III Marine Zoology -- Chapter 14. Contribution of marine animals in physiology, endocrinology and ethology -- Chapter 15. Physiology -- Chapter 16. Endocrinology -- Chapter 17. Animal Behavior -- Part IV Marine Ecology -- Chapter 18. Marine Ecology Introduction -- Chapter 19. Marine Ecology – Temperate to Tropical -- Chapter 20. Marine Ecology – Intertidal/Littoral Zone -- Chapter 21. Marine Ecology – Sea Shelf to Deep Sea -- Chapter 22. Marine Ecology – Survey Techniques in Marine Ecology -- Chapter 23. Experimental Design in Marine Ecology -- Part V Marine Environmental Science -- Chapter 24. Marine Environmental Science Introduction -- Chapter 25. Elemental Circulation -- Chapter 26. Human Impact -- Chapter 27. Survey Techniques in Marine Environmental Sciences -- Chapter 28. Experimental Design in Marine Environmental Sciences -- Part VI Selected Topics in Marine Biology -- Chapter 29. Marine Data -- Chapter 30. Biologging -- Chapter 31. Marine Microbes. Chapter 32. Marine Conservation. .

Abstract: This book gives an overview of the diverse marine fauna and flora of Japan and includes practical guides for investigating the biology and ecology of marine organisms. Introducing marine training courses offered at a range of Japanese universities, this is the first English textbook intended for marine biology instructors and students in Japan. It provides essential information on experimental procedures for the major areas of marine biology, including cell and developmental biology, physiology, ecology and environmental sciences, and as such is a valuable resource for those in Asian countries that share a similar flora and fauna. It also appeals to visitors interested in attending Japanese marine courses from countries around the world. .

Type of Medium: Online Resource

Pages: XVI, 367 p. 181 illus., 133 illus. in color. , online resource.

Edition: 1st ed. 2020.

ISBN: 9789811513268

URL: https://doi.org/10.1007/978-981-15-1326-8

DOI: 10.1007/978-981-15-1326-8

DDC: 577.6

Language: English

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Seawater carbonate chemistry and fish communities properties off CO2 seeps in Japan (2020)

Cattano, Carlo ; Agostini, Sylvain ; Harvey, Ben P ; [et al.]

PANGAEA

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Publication Date: 2024-03-15

Description: Ocean acidification will likely change the structure and function of coastal marine ecosystems over coming decades. Volcanic carbon dioxide seeps generate dissolved CO2 and pH gradients that provide realistic insights into the direction and magnitude of these changes. Here, we used fish and benthic community surveys to assess the spatio-temporal dynamics of fish community properties off CO2 seeps in Japan. Adding to previous evidence from ocean acidification ecosystem studies conducted elsewhere, our findings documented shifts from calcified to non-calcified habitats with reduced benthic complexity. In addition, we found that such habitat transition led to decreased diversity of associated fish and to selection of those fish species better adapted to simplified ecosystems dominated by algae. Our data suggest that near-future projected ocean acidification levels will oppose the ongoing range expansion of coral reef-associated fish due to global warming.

Keywords: Alkalinity, total; Aragonite saturation state; Benthos; Bicarbonate ion; Biotic Habitat Profile ratio; Biotic Habitat Profile ratio, standard deviation; Calcite saturation state; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Canopy height; Canopy height, standard deviation; Carbon, inorganic, dissolved; Carbonate ion; Carbonate system computation flag; Carbon dioxide; CO2 vent; Coast and continental shelf; Community composition and diversity; Coverage; Coverage, standard deviation; Entire community; EXP; Experiment; Field observation; Fish; Fish, standard deviation; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Location; North Pacific; OA-ICC; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide, standard deviation; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Pelagos; pH; pH, standard deviation; Potentiometric; Potentiometric titration; Replicates; Rocky-shore community; Salinity; Salinity, standard deviation; Season; Shikine; Site; Species richness; Species richness, standard deviation; Temperate; Temperature, water; Temperature, water, standard deviation; Transect; Type

Type: Dataset

Format: text/tab-separated-values, 892 data points

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Seawater carbonate chemistry and motility of flagellated microalgae (2020)

Wang, Yitao ; Fan, Xiao ; Gao, Guang ; [et al.]

PANGAEA

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Publication Date: 2024-03-15

Description: Motility plays a critical role in algal survival and reproduction, with implications for aquatic ecosystem stability. However, the effect of elevated CO2 on marine, brackish and freshwater algal motility is unclear. Here we show, using laboratory microscale and field mesoscale experiments, that three typical phytoplankton species had decreased motility with increased CO2. Polar marine Microglena sp., euryhaline Dunaliella salina and freshwater Chlamydomonas reinhardtii were grown under different CO2 concentrations for 5 years. Long-term acclimated Microglena sp. showed substantially decreased photo-responses in all treatments, with a photophobic reaction affecting intracellular calcium concentration. Genes regulating flagellar movement were significantly downregulated (P 〈 0.05), alongside a significant increase in gene expression for flagellar shedding (P 〈 0.05). D. salina and C. reinhardtii showed similar results, suggesting that motility changes are common across flagellated species. As the flagella structure and bending mechanism are conserved from unicellular organisms to vertebrates, these results suggest that increasing surface water CO2 concentrations may affect flagellated cells from algae to fish.

Keywords: Alkalinity, total; Alkalinity, total, standard error; Aragonite saturation state; Behaviour; Bicarbonate ion; Bicarbonate ion, standard error; Bottles or small containers/Aquaria (〈20 L); Calcite saturation state; Calcium, flux; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbon, inorganic, dissolved, standard error; Carbonate ion; Carbonate ion, standard error; Carbonate system computation flag; Carbon dioxide; Carbon dioxide, standard error; Chlamydomonas reinhardtii; Chlorophyta; Daily vertical migration; Dunaliella salina; Figure; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Gene expression; Gene name; Irradiance; Laboratory experiment; Laboratory strains; Microglena sp.; Move velocity; Not applicable; OA-ICC; Ocean Acidification International Coordination Centre; Oxygen evolution, per chlorophyll a; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Partial pressure of carbon dioxide (water) at sea surface temperature (wet air), standard error; Pelagos; Percentage; pH; pH, standard error; Phytoplankton; Plantae; Potentiometric; Potentiometric titration; Registration number of species; Respiration; Salinity; Single species; Species; Temperature, water; Time in days; Type; Uniform resource locator/link to reference

Type: Dataset

Format: text/tab-separated-values, 124767 data points

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Seawater carbonate chemistry and composition of intertidal and subtidal communities (2018)

Agostini, Sylvain ; Harvey, Ben P ; Wada, Shigeki ; [et al.]

PANGAEA

In: Supplement to: Agostini, Sylvain; Harvey, Ben P; Wada, Shigeki; Kon, Koetsu; Milazzo, Marco; Inaba, Kazuo; Hall-Spencer, Jason M (2018): Ocean acidification drives community shifts towards simplified non-calcified habitats in a subtropical−temperate transition zone. Scientific Reports, 8(1), https://doi.org/10.1038/s41598-018-29251-7

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Publication Date: 2024-03-15

Description: Rising atmospheric concentrations of carbon dioxide are causing surface seawater pH and carbonate ion concentrations to fall in a process known as ocean acidification. To assess the likely ecological effects of ocean acidification we compared intertidal and subtidal marine communities at increasing levels of pCO2 at recently discovered volcanic seeps off the Pacific coast of Japan (34° N). This study region is of particular interest for ocean acidification research as it has naturally low levels of surface seawater pCO2 (280–320 µatm) and is located at a transition zone between temperate and sub-tropical communities. We provide the first assessment of ocean acidification effects at a biogeographic boundary. Marine communities exposed to mean levels of pCO2 predicted by 2050 experienced periods of low aragonite saturation and high dissolved inorganic carbon. These two factors combined to cause marked community shifts and a major decline in biodiversity, including the loss of key habitat-forming species, with even more extreme community changes expected by 2100. Our results provide empirical evidence that near-future levels of pCO2 shift sub-tropical ecosystems from carbonate to fleshy algal dominated systems, accompanied by biodiversity loss and major simplification of the ecosystem.

Keywords: Alkalinity, total; Alkalinity, total, standard deviation; Aragonite saturation state; Aragonite saturation state, standard deviation; Benthos; Bicarbonate ion; Bicarbonate ion, standard deviation; Calcite saturation state; Calcite saturation state, standard deviation; Calculated using seacarb after Nisumaa et al. (2010); Calculated using seacarb after Orr et al. (2018); Carbon, inorganic, dissolved; Carbon, inorganic, dissolved, standard deviation; Carbonate ion; Carbonate ion, standard deviation; Carbonate system computation flag; Carbon dioxide; Carbon dioxide, standard deviation; CO2 vent; Coast and continental shelf; Community composition and diversity; Coverage; Entire community; EXP; Experiment; Field observation; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Fugacity of carbon dioxide in seawater, standard deviation; Individuals; North Pacific; OA-ICC; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide, standard deviation; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); pH; pH, standard deviation; Rocky-shore community; Salinity; Salinity, standard deviation; Shikine; Site; Temperate; Temperature, water; Temperature, water, standard deviation; Type

Type: Dataset

Format: text/tab-separated-values, 21650 data points

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Seawater carbonate chemistry and dissolution of the triton shell (2018)

Harvey, Ben P ; Agostini, Sylvain ; Wada, Shigeki ; [et al.]

PANGAEA

In: Supplement to: Harvey, Ben P; Agostini, Sylvain; Wada, Shigeki; Inaba, Kazuo; Hall-Spencer, Jason M (2018): Dissolution: The Achilles' Heel of the Triton Shell in an Acidifying Ocean. Frontiers in Marine Science, 5, https://doi.org/10.3389/fmars.2018.00371

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Publication Date: 2024-03-15

Description: Ocean acidification is expected to negatively impact many calcifying marine organisms by impairing their ability to build their protective shells and skeletons, and by causing dissolution and erosion. Here we investigated the large predatory “triton shell” gastropod Charonia lampas in acidified conditions near CO2 seeps off Shikine-jima (Japan) and compared them with individuals from an adjacent bay with seawater pH at present-day levels (outside the influence of the CO2 seep). By using computed tomography we show that acidification negatively impacts their thickness, density, and shell structure, causing visible deterioration to the shell surface. Periods of aragonite undersaturation caused the loss of the apex region and exposing body tissues. While gross calcification rates were likely reduced near CO2 seeps, the corrosive effects of acidification were far more pronounced around the oldest parts of the shell. As a result, the capacity of C. lampas to maintain their shells under ocean acidification may be strongly driven by abiotic dissolution and erosion, and not under biological control of the calcification process. Understanding the response of marine calcifying organisms and their ability to build and maintain their protective shells and skeletons will be important for our understanding of future marine ecosystems.

Keywords: Alkalinity, total; Alkalinity, total, standard deviation; Animalia; Aragonite saturation state; Aragonite saturation state, standard deviation; Benthic animals; Benthos; Bicarbonate ion; Bicarbonate ion, standard deviation; Calcification/Dissolution; Calcite saturation state; Calcite saturation state, standard deviation; Calculated using seacarb after Nisumaa et al. (2010); Calculated using seacarb after Orr et al. (2018); Carbon, inorganic, dissolved; Carbon, inorganic, dissolved, standard deviation; Carbonate ion; Carbonate ion, standard deviation; Carbonate system computation flag; Carbon dioxide; Carbon dioxide, standard deviation; Charonia lampas; CO2 vent; Coast and continental shelf; EXP; Experiment; Field observation; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Fugacity of carbon dioxide in seawater, standard deviation; Growth/Morphology; Location; Mollusca; North Pacific; Number; OA-ICC; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide, standard deviation; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); pH; pH, standard deviation; Position; Registration number of species; Salinity; Salinity, standard deviation; Shell density; Shell density, standard error; Shikine; Single species; Species; Temperature, water; Temperature, water, standard deviation; Thickness; Thickness, standard error; Type; Uniform resource locator/link to reference

Type: Dataset

Format: text/tab-separated-values, 1300 data points

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Phosphoinositide phosphatase activity coupled to an intrinsic voltage sensor (2005)

Murata, Yoshimichi ; Iwasaki, Hirohide ; Sasaki, Mari ; [et al.]

[s.l.] : Macmillian Magazines Ltd.

Nature 435 (2005), S. 1239-1243

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ISSN: 1476-4687

Source: Nature Archives 1869 - 2009

Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics

Notes: [Auszug] Changes in membrane potential affect ion channels and transporters, which then alter intracellular chemical conditions. Other signalling pathways coupled to membrane potential have been suggested but their underlying mechanisms are unknown. Here we describe a novel protein from the ascidian ...

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1038/nature03650

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B-band protein in sea urchin sperm flagella (1988)

Inaba, Kazuo ; Mohri, Toshiko ; Mohri, Hideo

New York, NY : Wiley-Blackwell

Cell Motility and the Cytoskeleton 10 (1988), S. 506-517

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ISSN: 0886-1544

Keywords: axoneme ; spokehead ; dynein ; Life and Medical Sciences ; Cell & Developmental Biology

Source: Wiley InterScience Backfile Collection 1832-2000

Topics: Biology , Medicine

Notes: A high-molecular-weight polypeptide, named B-band, was partially purified from sea urchin sperm flagella using selective extraction, hydroxylapatite chromatography, and sucrose density gradient centrifugation. The molecular weight of the B-band was 440,000 by continuous system of sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). Sedimentation coefficient of the B-band protein was 10.5 S, and its Stokes radius was 10 nm. When examined by low-angle rotary shadowing electron microscopy, this molecule appeared to be composed of four globular heads and two curved linkers (“double headphone shape”), which was quite different from the shape of 21 S dynein, the outer arm dynein. Flagellar axonemes were also subjected to several chemical dissections. The B-band was not extracted with treatments that remove both arm structures but was solubilized with treatments that extract other components such as radial spokes and nexin links. The B-band protein in the axoneme was also more susceptible to trypsin digestion than the arm structures. These results suggest that the B-band protein is a “double headphone-shaped” component of the axonemal structures and makes up the elastic structure that might regulate the active sliding between adjacent doublet microtubules.

Additional Material: 10 Ill.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1002/cm.970100407

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Single-cell genomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden by a dinoflagellate host (2019)

Nakayama, Takuro ; Nomura, Mami ; Takano, Yoshihito ; [et al.]

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences of the United States of America. 2019; 116(32): 15973-15978. Published 2019 Jun 24. doi: 10.1073/pnas.1902538116.

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Publication Date: 2019-06-24

Description: Cyanobacteria are one of the most important contributors to oceanic primary production and survive in a wide range of marine habitats. Much effort has been made to understand their ecological features, diversity, and evolution, based mainly on data from free-living cyanobacterial species. In addition, symbiosis has emerged as an important lifestyle of oceanic microbes and increasing knowledge of cyanobacteria in symbiotic relationships with unicellular eukaryotes suggests their significance in understanding the global oceanic ecosystem. However, detailed characteristics of these cyanobacteria remain poorly described. To gain better insight into marine cyanobacteria in symbiosis, we sequenced the genome of cyanobacteria collected from a cell of a pelagic dinoflagellate that is known to host cyanobacterial symbionts within a specialized chamber. Phylogenetic analyses using the genome sequence revealed that the cyanobacterium represents an underdescribed lineage within an extensively studied, ecologically important group of marine cyanobacteria. Metagenomic analyses demonstrated that this cyanobacterial lineage is globally distributed and strictly coexists with its host dinoflagellates, suggesting that the intimate symbiotic association allowed the cyanobacteria to escape from previous metagenomic studies. Furthermore, a comparative analysis of the protein repertoire with related species indicated that the lineage has independently undergone reductive genome evolution to a similar extent as Prochlorococcus, which has the most reduced genomes among free-living cyanobacteria. Discovery of this cyanobacterial lineage, hidden by its symbiotic lifestyle, provides crucial insights into the diversity, ecology, and evolution of marine cyanobacteria and suggests the existence of other undiscovered cryptic cyanobacterial lineages.

Print ISSN: 0027-8424

Electronic ISSN: 1091-6490

Topics: Biology , Medicine , Natural Sciences in General

Published by National Academy of Sciences

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14-3-3εa directs the pulsatile transport of basal factors toward the apical domain for lumen growth in tubulogenesis (2018)

Mizotani, Yuji ; Suzuki, Mayu ; Hotta, Kohji ; [et al.]

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences of the United States of America. 2018; 115(38): E8873-E8881. Published 2018 Aug 29. doi: 10.1073/pnas.1808756115.

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Publication Date: 2018-08-29

Description: The Ciona notochord has emerged as a simple and tractable in vivo model for tubulogenesis. Here, using a chemical genetics approach, we identified UTKO1 as a selective small molecule inhibitor of notochord tubulogenesis. We identified 14-3-3εa protein as a direct binding partner of UTKO1 and showed that 14-3-3εa knockdown leads to failure of notochord tubulogenesis. We found that UTKO1 prevents 14-3-3εa from interacting with ezrin/radixin/moesin (ERM), which is required for notochord tubulogenesis, suggesting that interactions between 14-3-3εa and ERM play a key role in regulating the early steps of tubulogenesis. Using live imaging, we found that, as lumens begin to open between neighboring cells, 14-3-3εa and ERM are highly colocalized at the basal cortex where they undergo cycles of accumulation and disappearance. Interestingly, the disappearance of 14-3-3εa and ERM during each cycle is tightly correlated with a transient flow of 14-3-3εa, ERM, myosin II, and other cytoplasmic elements from the basal surface toward the lumen-facing apical domain, which is often accompanied by visible changes in lumen architecture. Both pulsatile flow and lumen formation are abolished in larvae treated with UTKO1, in larvae depleted of either 14-3-3εa or ERM, or in larvae expressing a truncated form of 14-3-3εa that lacks the ability to interact with ERM. These results suggest that 14-3-3εa and ERM interact at the basal cortex to direct pulsatile basal accumulation and basal–apical transport of factors that are essential for lumen formation. We propose that similar mechanisms may underlie or may contribute to lumen formation in tubulogenesis in other systems.

Print ISSN: 0027-8424

Electronic ISSN: 1091-6490

Topics: Biology , Medicine , Natural Sciences in General