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  • Articles  (131,129)
  • Springer  (86,198)
  • American Chemical Society  (39,825)
  • BioMed Central
  • 2025-2025
  • 2020-2022
  • 2010-2014  (131,129)
  • 2011  (131,129)
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  • 2025-2025
  • 2020-2022
  • 2010-2014  (131,129)
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  • 1
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    Identification and developmental expression of the full complement of Cytochrome P450 genes in Zebrafish (2011)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 11 (2010): 643, doi:10.1186/1471-2164-11-643.
    Description: Increasing use of zebrafish in drug discovery and mechanistic toxicology demands knowledge of cytochrome P450 (CYP) gene regulation and function. CYP enzymes catalyze oxidative transformation leading to activation or inactivation of many endogenous and exogenous chemicals, with consequences for normal physiology and disease processes. Many CYPs potentially have roles in developmental specification, and many chemicals that cause developmental abnormalities are substrates for CYPs. Here we identify and annotate the full suite of CYP genes in zebrafish, compare these to the human CYP gene complement, and determine the expression of CYP genes during normal development. Zebrafish have a total of 94 CYP genes, distributed among 18 gene families found also in mammals. There are 32 genes in CYP families 5 to 51, most of which are direct orthologs of human CYPs that are involved in endogenous functions including synthesis or inactivation of regulatory molecules. The high degree of sequence similarity suggests conservation of enzyme activities for these CYPs, confirmed in reports for some steroidogenic enzymes (e.g. CYP19, aromatase; CYP11A, P450scc; CYP17, steroid 17a-hydroxylase), and the CYP26 retinoic acid hydroxylases. Complexity is much greater in gene families 1, 2, and 3, which include CYPs prominent in metabolism of drugs and pollutants, as well as of endogenous substrates. There are orthologous relationships for some CYP1 s and some CYP3 s between zebrafish and human. In contrast, zebrafish have 47 CYP2 genes, compared to 16 in human, with only two (CYP2R1 and CYP2U1) recognized as orthologous based on sequence. Analysis of shared synteny identified CYP2 gene clusters evolutionarily related to mammalian CYP2 s, as well as unique clusters. Transcript profiling by microarray and quantitative PCR revealed that the majority of zebrafish CYP genes are expressed in embryos, with waves of expression of different sets of genes over the course of development. Transcripts of some CYP occur also in oocytes. The results provide a foundation for the use of zebrafish as a model in toxicological, pharmacological and chemical disease research.
    Description: This work was supported by NIH grants R01ES015912 and P42ES007381 (Superfund Basic Research Program at Boston University) (to JJS). MEJ was a Guest Investigator at the Woods Hole Oceanographic Institution (WHOI) and was supported by grants from the Swedish research council Formas and Carl Trygger's foundation. AK was a Post-doctoral Fellow at WHOI, and was supported by a fellowship from the Japanese Society for Promotion of Science (JSPS). JZ and TP were Guest Students at the WHOI and were supported by a CAPES Ph.D. Fellowship and CNPq Ph.D. Sandwich Fellowship (JZ), and by a CNPq Ph.D. Fellowship (TP), from Brazil.
    Repository Name: Woods Hole Open Access Server
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  • 2
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    Seasonal and hydrologic drivers of dissolved organic matter and nutrients in the upper Kuparuk River, Alaskan Arctic (2011)
    Springer
    Details
    Publication Date: 2022-05-26
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License. The definitive version was published in Biogeochemistry 103 (2011): 109-124, doi:10.1007/s10533-010-9451-4.
    Description: As the planet warms, widespread changes in Arctic hydrology and biogeochemistry have been documented and these changes are expected to accelerate in the future. Improved understanding of the behavior of water-borne constituents in Arctic rivers with varying hydrologic conditions, including seasonal variations in discharge–concentration relationships, will improve our ability to anticipate future changes in biogeochemical budgets due to changing hydrology. We studied the relationship between seasonal water discharge and dissolved organic carbon and nitrogen (DOC and DON) and nutrient concentrations in the upper Kuparuk River, Arctic Alaska. Fluxes of most constituents were highest during initial snowmelt runoff in spring, indicating that this historically under-studied period contributes significantly to total annual export. In particular, the initial snowmelt period (the stream is completely frozen during the winter) accounted for upwards of 35% of total export of DOC and DON estimated for the entire study period. DOC and DON concentrations were positively correlated with discharge whereas nitrate (NO3 −) and silicate were negatively correlated with discharge throughout the study. However, discharge-specific DOC and DON concentrations (i.e. concentrations compared at the same discharge level) decreased over the summer whereas discharge-specific concentrations of NO3 − and silicate increased. Soluble reactive phosphorus (SRP) and ammonium (NH4 +) were negatively correlated with discharge during the spring thaw, but were less predictable with respect to discharge thereafter. These data provide valuable information on how Arctic watershed biogeochemistry will be affected by future changes in temperature, snowfall, and rainfall in the Arctic. In particular, our results add to a growing body of research showing that nutrient export per unit of stream discharge, particularly NO3 −, is increasing in the Arctic.
    Description: Funding provided by the National Science Foundation, NSF-OPP- 0436118.
    Keywords: Arctic ; Stream ; Headwaters ; Carbon ; Nitrogen ; Nutrients
    Repository Name: Woods Hole Open Access Server
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  • 3
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    The use (and misuse) of sediment traps in coral reef environments : theory, observations, and suggested protocols (2011)
    Springer
    Details
    Publication Date: 2022-05-26
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Coral Reefs 30 (2011): 23-38, doi:10.1007/s00338-010-0705-3.
    Description: Sediment traps are commonly used as standard tools for monitoring “sedimentation” in coral reef environments. In much of the literature where sediment traps were used to measure the effects of “sedimentation” on corals, it is clear from deployment descriptions and interpretations of the resulting data that information derived from sediment traps has frequently been misinterpreted or misapplied. Despite their widespread use in this setting, sediment traps do not provide quantitative information about “sedimentation” on coral surfaces. Traps can provide useful information about the relative magnitude of sediment dynamics if trap deployment standards are used. This conclusion is based first on a brief review of the state of knowledge of sediment trap dynamics, which has primarily focused on traps deployed high above the seabed in relatively deep water, followed by our understanding of near-bed sediment dynamics in shallow-water environments that characterize coral reefs. This overview is followed by the first synthesis of near-bed sediment trap data collected with concurrent hydrodynamic information in coral reef environments. This collective information is utilized to develop nine protocols for using sediment traps in coral reef environments, which focus on trap parameters that researchers can control such as trap height (H), trap mouth diameter (D), the height of the trap mouth above the substrate (z o ), and the spacing between traps. The hydrodynamic behavior of sediment traps and the limitations of data derived from these traps should be forefront when interpreting sediment trap data to infer sediment transport processes in coral reef environments.
    Keywords: Sediment trap ; Coral reefs ; Sedimentation ; Waves ; Currents ; Shear stress
    Repository Name: Woods Hole Open Access Server
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  • 4
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    Cytochrome P450 diversity and induction by gorgonian allelochemicals in the marine gastropod Cyphoma gibbosum (2011)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Ecology 10 (2010): 24, doi:10.1186/1472-6785-10-24.
    Description: Intense consumer pressure strongly affects the structural organization and function of marine ecosystems, while also having a profound effect on the phenotype of both predator and prey. Allelochemicals produced by prey often render their tissues unpalatable or toxic to a majority of potential consumers, yet some marine consumers have evolved resistance to host chemical defenses. A key challenge facing marine ecologists seeking to explain the vast differences in consumer tolerance of dietary allelochemicals is understanding the biochemical and molecular mechanisms underlying diet choice. The ability of marine consumers to tolerate toxin-laden prey may involve the cooperative action of biotransformation enzymes, including the inducible cytochrome P450s (CYPs), which have received little attention in marine invertebrates despite the importance of allelochemicals in their evolution. Here, we investigated the diversity, transcriptional response, and enzymatic activity of CYPs possibly involved in allelochemical detoxification in the generalist gastropod Cyphoma gibbosum, which feeds exclusively on chemically defended gorgonians. Twelve new genes in CYP family 4 were identified from the digestive gland of C. gibbosum. Laboratory-based feeding studies demonstrated a 2.7- to 5.1-fold induction of Cyphoma CYP4BK and CYP4BL transcripts following dietary exposure to the gorgonian Plexaura homomalla, which contains high concentrations of anti-predatory prostaglandins. Phylogenetic analysis revealed that C. gibbosum CYP4BK and CYP4BL were most closely related to vertebrate CYP4A and CYP4F, which metabolize pathophysiologically important fatty acids, including prostaglandins. Experiments involving heterologous expression of selected allelochemically-responsive C. gibbosum CYP4s indicated a possible role of one or more CYP4BL forms in eicosanoid metabolism. Sequence analysis further demonstrated that Cyphoma CYP4BK/4BL and vertebrate CYP4A/4F forms share identical amino acid residues at key positions within fatty acid substrate recognition sites. These results demonstrate differential regulation of CYP transcripts in a marine consumer feeding on an allelochemical-rich diet, and significantly advance our understanding of both the adaptive molecular mechanisms that marine consumers use to cope with environmental chemical pressures and the evolutionary history of allelochemical-metabolizing enzymes in the CYP superfamily.
    Description: Financial support for this work was provided by the Ocean Life Institute Tropical Research Initiative Grant (WHOI) to KEW and MEH; the Robert H. Cole Endowed Ocean Ventures Fund (WHOI) to KEW; the National Undersea Research Center - Program Development Proposal (CMRC-03PRMN0103A) to KEW and a National Science Foundation Graduate Research Fellowship to KEW.
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Transcriptomic assessment of resistance to effects of an aryl hydrocarbon receptor (AHR) agonist in embryos of Atlantic killifish (Fundulus heteroclitus) from a marine Superfund site (2011)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 12 (2011): 263, doi:10.1186/1471-2164-12-263.
    Description: Populations of Atlantic killifish (Fundulus heteroclitus) have evolved resistance to the embryotoxic effects of polychlorinated biphenyls (PCBs) and other halogenated and nonhalogenated aromatic hydrocarbons that act through an aryl hydrocarbon receptor (AHR)-dependent signaling pathway. The resistance is accompanied by reduced sensitivity to induction of cytochrome P450 1A (CYP1A), a widely used biomarker of aromatic hydrocarbon exposure and effect, but whether the reduced sensitivity is specific to CYP1A or reflects a genome-wide reduction in responsiveness to all AHR-mediated changes in gene expression is unknown. We compared gene expression profiles and the response to 3,3',4,4',5-pentachlorobiphenyl (PCB-126) exposure in embryos (5 and 10 dpf) and larvae (15 dpf) from F. heteroclitus populations inhabiting the New Bedford Harbor, Massachusetts (NBH) Superfund site (PCB-resistant) and a reference site, Scorton Creek, Massachusetts (SC; PCB-sensitive). Analysis using a 7,000-gene cDNA array revealed striking differences in responsiveness to PCB-126 between the populations; the differences occur at all three stages examined. There was a sizeable set of PCB-responsive genes in the sensitive SC population, a much smaller set of PCB-responsive genes in NBH fish, and few similarities in PCB-responsive genes between the two populations. Most of the array results were confirmed, and additional PCB-regulated genes identified, by RNA-Seq (deep pyrosequencing). The results suggest that NBH fish possess a gene regulatory defect that is not specific to one target gene such as CYP1A but rather lies in a regulatory pathway that controls the transcriptional response of multiple genes to PCB exposure. The results are consistent with genome-wide disruption of AHR-dependent signaling in NBH fish.
    Description: This work was supported in part by National Institutes of Health grants P42ES007381 (Superfund Basic Research Program at Boston University) and by a grant from the WHOI Ocean Life Institute.
    Repository Name: Woods Hole Open Access Server
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  • 6
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    More than a century of bathymetric observations and present-day shallow sediment characterization in Belfast Bay, Maine, USA: implications for pockmark field longevity (2011)
    Springer
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    Publication Date: 2022-05-25
    Description: This paper is not subject to U.S. copyright. The definitive version was published in Geo-Marine Letters 31 (2011): 237-248, doi:10.1007/s00367-011-0228-0.
    Description: Mechanisms and timescales responsible for pockmark formation and maintenance remain uncertain, especially in areas lacking extensive thermogenic fluid deposits (e.g., previously glaciated estuaries). This study characterizes seafloor activity in the Belfast Bay, Maine nearshore pockmark field using (1) three swath bathymetry datasets collected between 1999 and 2008, complemented by analyses of shallow box-core samples for radionuclide activity and undrained shear strength, and (2) historical bathymetric data (report and smooth sheets from 1872, 1947, 1948). In addition, because repeat swath bathymetry surveys are an emerging data source, we present a selected literature review of recent studies using such datasets for seafloor change analysis. This study is the first to apply the method to a pockmark field, and characterizes macro-scale (〉5 m) evolution of tens of square kilometers of highly irregular seafloor. Presence/absence analysis yielded no change in pockmark frequency or distribution over a 9-year period (1999–2008). In that time pockmarks did not detectably enlarge, truncate, elongate, or combine. Historical data indicate that pockmark chains already existed in the 19th century. Despite the lack of macroscopic changes in the field, near-bed undrained shear-strength values of less than 7 kPa and scattered downcore 137Cs signatures indicate a highly disturbed setting. Integrating these findings with independent geophysical and geochemical observations made in the pockmark field, it can be concluded that (1) large-scale sediment resuspension and dispersion related to pockmark formation and failure do not occur frequently within this field, and (2) pockmarks can persevere in a dynamic estuarine setting that exhibits minimal modern fluid venting. Although pockmarks are conventionally thought to be long-lived features maintained by a combination of fluid venting and minimal sediment accumulation, this suggests that other mechanisms may be equally active in maintaining such irregular seafloor morphology. One such mechanism could be upwelling within pockmarks induced by near-bed currents.
    Description: Graduate support for Brothers came from a Maine Economic Improvement Fund Dissertation Fellowship.
    Repository Name: Woods Hole Open Access Server
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  • 7
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    Mineralogical and geochemical features of sulfide chimneys from the 49°39′E hydrothermal field on the Southwest Indian Ridge and their geological inferences (2011)
    Springer
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Chinese Science Bulletin 56 (2011): 2828-2838, doi:10.1007/s11434-011-4619-4.
    Description: During January–May in 2007, the Chinese research cruise DY115-19 discovered an active hydrothermal field at 49°39′E/37°47′S on the ultraslow spreading Southwest Indian Ridge (SWIR). This was also the first active hydrothermal field found along an ultraslow-spreading ridge. We analyzed mineralogical, textural and geochemical compositions of the sulfide chimneys obtained from the 49°39′E field. Chimney samples show a concentric mineral zone around the fluid channel. The mineral assemblages of the interiors consist mainly of chalcopyrite, with pyrite and sphalerite as minor constitunets. In the intermediate portion, pyrite becomes the dominant mineral, with chalcopyrite and sphalerite as minor constitunets. For the outer wall, the majority of minerals are pyrite and sphalerite, with few chalcopyrite. Towards the outer margin of the chimney wall, the mineral grains become small and irregular in shape gradually, while minerals within interstices are abundant. These features are similar to those chimney edifices found on the East Pacific Rise and Mid-Atlantic Ridge. The average contents of Cu, Fe and Zn in our chimney samples were 2.83 wt%, 45.6 wt% and 3.28 wt%, respectively. The average Au and Ag contents were up to 2.0 ppm and 70.2 ppm respectively, higher than the massive sulfides from most hydrothermal fields along mid-ocean ridge. The rare earth elements geochemistry of the sulfide chimneys show a pattern distinctive from the sulfides recovered from typical hydrothermal fields along sediment-starved mid-ocean ridge, with the enrichment of light rare earth elements but the weak, mostly negative, Eu anomaly. This is attributed to the distinct mineralization environment or fluid compositions in this area.
    Description: This work was supported by the China Ocean Mineral Resources Research and Development Association Program (DY115- 02-1-01) and the State Oceanic Administration Youth Science Fund (2010318).
    Keywords: Sulfide chimneys ; 49°39′E hydrothermal field ; Southwest Indian Ridge ; Mid-ocean ridge ; DY115-19 Chinese cruise
    Repository Name: Woods Hole Open Access Server
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  • 8
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    Temperature, recreational fishing and diapause egg connections : dispersal of spiny water fleas (Bythotrephes longimanus) (2011)
    Springer
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License. The definitive version was published in Biological Invasions 13 (2011): 2513-2531, doi:10.1007/s10530-011-0078-8.
    Description: The spiny water flea (Bythotrephes longimanus) is spreading from Great Lakes coastal waters into northern inland lakes within a northern temperature-defined latitudinal band. Colonization of Great Lakes coastal embayments is assisted by winds and seiche surges, yet rapid inland expansion across the northern states comes through an overland process. The lack of invasions at Isle Royale National Park contrasts with rapid expansion on the nearby Keweenaw Peninsula. Both regions have comparable geology, lake density, and fauna, but differ in recreational fishing boat access, visitation, and containment measures. Tail spines protect Bythotrephes against young of the year, but not larger fish, yet the unusual thick-shelled diapausing eggs can pass through fish guts in viable condition. Sediment traps illustrate how fish spread diapausing eggs across lakes in fecal pellets. Trillions of diapausing eggs are produced per year in Lake Michigan and billions per year in Lake Michigamme, a large inland lake. Dispersal by recreational fishing is linked to use of baitfish, diapausing eggs defecated into live wells and bait buckets, and Bythothephes snagged on fishing line, anchor ropes, and minnow seines. Relatively simple measures, such as on-site rinsing of live wells, restricting transfer of certain baitfish species, or holding baitfish for 24 h (defecation period), should greatly reduce dispersal.
    Description: Study of Lakes Superior and Michigan was funded from NSF OCE-9726680 and OCE-9712872 to W.C.K., OCE-9712889 to J. Churchill. Geographic survey sampling and Park studies in the national parks during 2008-2010 were funded by a grant from the National Park Service Natural Resource Preservation Program GLNF CESU Task Agreement No. J6067080012.
    Keywords: Spiny cladoceran ; Dispersal ; Temperature ; Diapausing eggs ; YOY fish
    Repository Name: Woods Hole Open Access Server
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  • 9
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    Site effects “on the rock”: the case of Castelvecchio Subequo (L’Aquila, central Italy) (2011)
    Springer
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    Publication Date: 2022-05-24
    Description: The April 6, 2009 L’Aquila earthquake was responsible for an “anomalous”, relatively high degree of damage (i.e. Is 7 MCS scale) at Castelvecchio Subequo (CS). Indeed, the village is located at source-to-site distance of about 40 km, and it is surrounded by other inhabited centres to which considerably lower intensities, i.e. Is 5-6, have been attributed. Moreover, the damage was irregularly distributed within CS, being mainly concentrated in the uppermost portion of the old village. Geophysical investigations (ambient seismic noise and weak ground motions analyses) revealed that site effects occurred at CS. Amplifications of the ground motion, mainly striking NE-SW, have been detected at the uppermost portion of the carbonate ridge on which the village is built. Geological/structural and geomechanical field surveys defined that the CS ridge is affected by sets of fractures, joints and shear planes – mainly roughly NW-SE and N-S trending – that are related to the deformation zone of the Subequana valley fault system and to transfer faults linking northward the mentioned tectonic feature with the Middle Aterno Valley fault system. In particular, our investigations highlight that seismic amplifications occur where joints set NW-SE trending are open. On the other hand, no amplification is seen in portions of the ridge where the bedrock is densely fractured but no open joints occur. The fracture opening seems related to the toppling tendency of the bedrock slabs, owing to the local geomorphic setting. These investigations suggest that the detected amplification of the ground motion is probably related to the polarization of the seismic waves along the Castelvecchio Subequo ridge, with the consequent oscillation of the rock slabs perpendicularly to the fractures azimuth.
    Description: Published
    Description: 841-868
    Description: 4.1. Metodologie sismologiche per l'ingegneria sismica
    Description: JCR Journal
    Description: open
    Keywords: Site effects ; Rock site ; Ambient seismic noise ; Structural characteristics ; Geomechanical analyses ; Jointing ; Castelvecchio Subequo ; 2009 L'Aquila earthquake ; central Italy ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
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    Geochemistry of volcanic fluids : A special issue of the Bulletin of Volcanology in honour of Yuri A. Taran (2011)
    Springer
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    Publication Date: 2021-05-17
    Description: This special issue is dedicated to Yuri Taran's outstanding contributions to gas geochemistry that began in the early 1980s with his work on deuterium and 18O compositions of geothermal waters in the Mutnovsky (Kamchatka) region and continues to this day with work on the Kamchatka volcanic volatile budget, carbon isotopes of hydrocarbons, and new insights into the geochemistry of El Chichón volcano, Chiapas. Yuri has contributed greatly to the field of volcanic gas geochemistry and was the first to recognize the distinct deuterium and oxygen isotopic composition of fumarole condensates from volcanoes in Kamchatka (Taran et al. 1987a). The shift in δD and δ18O to significantly heavier values compared to local meteoric water led Yuri to introduce the term “andesitic water” (Taran et al. 1989a, b) which has since been recognized at subduction zone volcanoes globally. This distinct isotopic composition is evidence that volcanoes release water that ultimately originates as subducted seawater and is recycled through the mantle wedge back to the earth's surface. Yuri's early work on the gas emissions from Kamchatka and Kurile Islands volcanoes also included the development and testing of gas geothermometers (Taran 1986) and investigating hydrothermal alteration using isotopic data (Taran et al. 1987b). His curiosity remained focused on the isotope systematics of volcanic gases discharging from Kamchatka and the Kuriles through the late 1980s and 1990s with publications on the gas compositions of Klyuchevskoi (Taran et al. 1991), Mutnovsky (Taran et al. 1992), Avachinsky and Koryaksky (Taran et al. 1997). Yuri was involved in the discovery of a pure and unique rhenium mineral on Kudryavy volcano (Korzhinsky et al. 1994) and provided one of the most detailed chemical studies of high temperature (up to 950°C) fumaroles to date of any volcano (Taran et al. 1995). His 1995 paper on Kudryavy remains highly cited and provides the highest quality volcanic gas data which also include trace elements from a subduction zone. Such data are crucial when we attempt to interpret lower temperature volcanic gas compositions or calculate rare metal fluxes from volcanoes worldwide. His most recent publication on Kamchatka-Kurile volcanic emissions provides a detailed analysis of the total gas flux from these volcanoes (Taran 2009).
    Description: Published
    Description: 369-371
    Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive
    Description: 2.4. TTC - Laboratori di geochimica dei fluidi
    Description: JCR Journal
    Description: reserved
    Keywords: Fluids Geochemistry ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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