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  • Articles  (23)
  • Epsilonproteobacteria
  • FT-ICR-MS
  • Lipids
  • Reactive oxygen species
  • Frontiers Media  (11)
  • Singapore  (8)
  • American Chemical Society  (2)
  • Massachusetts Institute of Technology and Woods Hole Oceanographic Institution  (2)
  • 1
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    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Publication Date: 2022-05-25
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution January 1984
    Description: Proximate analysis was carried out on developing Homarus americanus Milne Edwards larvae and eggs. Lipids were further analyzed for class and fatty acid composition. During embryogenesis, triacylglycerol supplied most of the energy and the fatty acid 20:5 was selectively utilized. Absence of prolonged cold incubation temperatures resulted in increased yolk reserves in newly hatched larvae. Weight, ash, protein, carbohydrate and lipid varied in association with the larval molt cycle. Scant metabolic reserves were accumulated in premetamorphic larvae while large triacylglycerol reserves were stored in postmetamorphic (fourth stage) animals. Absolute levels of metabolic reserves limited the extent of their utilization. Triacylglycerol was the preferred (first used) energy substrate but was usually limited in amount; hence protein was the major source of metabolic energy during starvation in premetamorphic larvae. Dietary intake of carbohydrate and possibly protein based gluconeogenesis were responsible for most chitin synthesis as established carbohydrate reserves were not sufficient. Triacylglycerol served mainly as an energy storage form. P. choline appeared to exist in two metabolic pools; one of which could be catabolized without concomitant tissue loss. P. ethanolamine and sterols were primarily associated with cellular membranes. During tissue catabolism (starvation), P. ethanolamine was catabolized but sterol was conserved. On average, P. ethanolamine fatty acids were the most unsaturated, followed by the fatty acids of P. choline and then triacylglycerol. The type of fatty acid may influence food consumption and rates of absorption. Compared to a diet containing 16:0, one containing 20:5 was related to greater consumption and faster lipid absorption. The fatty acid pattern of the larvae was heavily influenced by diet. The fatty acids 16:0, 18:0, 20:4, 20:5, and 22:6 were conserved under starvation. Conservation of the saturated fatty acids was probably related to control of cellular membrane fluidity. 16:0 and 18:0 were probably used to compensate for the increased membrane unsaturation from the conserved, potentially essential 20:4, 20:5, and 22:6 fatty acids.
    Description: This research was supported by the Massachusetts Institute of Technology/ Woods Hole Oceanographic Institution Joint Program in Oceanography, the WHOI Ocean Industry Program, the U.S. Department of Interior, Bureau of Land Management under Contract No. AA551-CT9-5 and the U.S. Department of Commerce, National Oceanic and Atmospheric Administration, Office of Sea Grant under Grant No. NA80-AA-D-00077 (R/P-5 and R/P-11).
    Keywords: American lobster ; Lobsters ; Lipids
    Repository Name: Woods Hole Open Access Server
    Type: Thesis
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  • 2
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 4 (2013): 262, doi:10.3389/fmicb.2013.00262.
    Description: Manganese (Mn) oxides are among the most reactive sorbents and oxidants within the environment, where they play a central role in the cycling of nutrients, metals, and carbon. Recent discoveries have identified superoxide (O−2) both of biogenic and abiogenic origin as an effective oxidant of Mn(II) leading to the formation of Mn oxides. Here we examined the conditions under which abiotically produced superoxide led to oxidative precipitation of Mn and the solid-phases produced. Oxidized Mn, as both aqueous Mn(III) and Mn(III/IV) oxides, was only observed in the presence of active catalase, indicating that hydrogen peroxide (H2O2), a product of the reaction of O−2 with Mn(II), inhibits the oxidation process presumably through the reduction of Mn(III). Citrate and pyrophosphate increased the yield of oxidized Mn but decreased the amount of Mn oxide produced via formation of Mn(III)-ligand complexes. While complexing ligands played a role in stabilizing Mn(III), they did not eliminate the inhibition of net Mn(III) formation by H2O2. The Mn oxides precipitated were highly disordered colloidal hexagonal birnessite, similar to those produced by biotically generated superoxide. Yet, in contrast to the large particulate Mn oxides formed by biogenic superoxide, abiotic Mn oxides did not ripen to larger, more crystalline phases. This suggests that the deposition of crystalline Mn oxides within the environment requires a biological, or at least organic, influence. This work provides the first direct evidence that, under conditions relevant to natural waters, oxidation of Mn(II) by superoxide can occur and lead to formation of Mn oxides. For organisms that oxidize Mn(II) by producing superoxide, these findings may also point to other microbially mediated processes, in particular enzymatic hydrogen peroxide degradation and/or production of organic ligand metabolites, that allow for Mn oxide formation.
    Description: This project was supported by the National Science Foundation, grants EAR-1245919/1025077 (awarded to Colleen M. Hansel and Bettina M. Voelker), and by the Radcliffe Institute for Advanced Study at Harvard University (through a fellowship to Bettina M. Voelker).
    Keywords: Manganese oxidation ; Manganese oxides ; Superoxide ; Reactive oxygen species ; Mn(III) complexes ; Organic ligands
    Repository Name: Woods Hole Open Access Server
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  • 3
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 772, doi:10.3389/fmicb.2018.00772.
    Keywords: Epsilonproteobacteria ; Taxonomy ; Classification ; Genome ; Phylogenomics ; Epsilonbacteraeota ; Epsilonbacterota ; Evolution
    Repository Name: Woods Hole Open Access Server
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  • 4
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 682, doi:10.3389/fmicb.2017.00682.
    Description: The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria. In order to address this issue, we investigated the phylogenetic placement of this class in the bacterial domain using 16S and 23S rRNA genes, as well as 120 single-copy marker proteins. Single- and concatenated-marker trees were created using a data set of 4,170 bacterial representatives, including 98 Epsilonproteobacteria. Phylogenies were inferred under a variety of tree building methods, with sequential jackknifing of outgroup phyla to ensure robustness of phylogenetic affiliations under differing combinations of bacterial genomes. Based on the assessment of nearly 300 phylogenetic tree topologies, we conclude that the continued inclusion of Epsilonproteobacteria within the Proteobacteria is not warranted, and that this group should be reassigned to a novel phylum for which we propose the name Epsilonbacteraeota (phyl. nov.). We further recommend the reclassification of the order Desulfurellales (Deltaproteobacteria) to a novel class within this phylum and a number of subordinate changes to ensure consistency with the genome-based phylogeny. Phylogenomic analysis of 658 genomes belonging to the newly proposed Epsilonbacteraeota suggests that the ancestor of this phylum was an autotrophic, motile, thermophilic chemolithotroph that likely assimilated nitrogen from ammonium taken up from the environment or generated from environmental nitrate and nitrite by employing a variety of functional redox modules. The emergence of chemoorganoheterotrophic lifestyles in several Epsilonbacteraeota families is the result of multiple independent losses of various ancestral chemolithoautotrophic pathways. Our proposed reclassification of this group resolves an important anomaly in bacterial systematics and ensures that the taxonomy of Proteobacteria remains robust, specifically as genome-based taxonomies become more common.
    Description: The study was supported by a Discovery Outstanding Researcher Award (DP120103498) and an Australian Laureate Fellowship (FL150100038) from the Australian Research Council.
    Keywords: Epsilonproteobacteria ; Taxonomy ; Classification ; Genome ; Phylogenomics ; Epsilonbacteraeota ; Evolution
    Repository Name: Woods Hole Open Access Server
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  • 5
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 901, doi:10.3389/fmicb.2015.00901.
    Description: Many deep-sea hydrothermal vent systems are regularly impacted by volcanic eruptions, leaving fresh basalt where abundant animal and microbial communities once thrived. After an eruption, microbial biofilms are often the first visible evidence of biotic re-colonization. The present study is the first to investigate microbial colonization of newly exposed basalt surfaces in the context of vent fluid chemistry over an extended period of time (4–293 days) by deploying basalt blocks within an established diffuse-flow vent at the 9°50′ N vent field on the East Pacific Rise. Additionally, samples obtained after a recent eruption at the same vent field allowed for comparison between experimental results and those from natural microbial re-colonization. Over 9 months, the community changed from being composed almost exclusively of Epsilonproteobacteria to a more diverse assemblage, corresponding with a potential expansion of metabolic capabilities. The process of biofilm formation appears to generate similar surface-associated communities within and across sites by selecting for a subset of fluid-associated microbes, via species sorting. Furthermore, the high incidence of shared operational taxonomic units over time and across different vent sites suggests that the microbial communities colonizing new surfaces at diffuse-flow vent sites might follow a predictable successional pattern.
    Description: This work was partly supported by grants from the US National Science Foundation to SS (OCE-0452333, 1136727), to TS (OCE-0117117, 0525907, 0961186, 1043064, 0327261, 1131620), to WS and KD (1434798), as well as a grant by the WHOI Deep Ocean Exploration Institute to SB, TS, and SS.
    Keywords: Hydrothermal vents ; Colonization ; Species sorting ; Settlement ; Volcanic eruption ; 16S rRNA ; Epsilonproteobacteria ; Disturbance
    Repository Name: Woods Hole Open Access Server
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  • 6
    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Chemistry 4 (2016): 5, doi:10.3389/fchem.2016.00005.
    Description: Biological production and decay of the reactive oxygen species (ROS) hydrogen peroxide (H2O2) and superoxide (O−2) likely have significant effects on the cycling of trace metals and carbon in marine systems. In this study, extracellular production rates of H2O2 and O−2 were determined for five species of marine diatoms in the presence and absence of light. Production of both ROS was measured in parallel by suspending cells on filters and measuring the ROS downstream using chemiluminescence probes. In addition, the ability of these organisms to break down O−2 and H2O2 was examined by measuring recovery of O−2 and H2O2 added to the influent medium. O−2 production rates ranged from undetectable to 7.3 × 10−16 mol cell−1 h−1, while H2O2 production rates ranged from undetectable to 3.4 × 10−16 mol cell−1 h−1. Results suggest that extracellular ROS production occurs through a variety of pathways even amongst organisms of the same genus. Thalassiosira spp. produced more O−2 in light than dark, even when the organisms were killed, indicating that O−2 is produced via a passive photochemical process on the cell surface. The ratio of H2O2 to O−2 production rates was consistent with production of H2O2 solely through dismutation of O−2 for T. oceanica, while T. pseudonana made much more H2O2 than O−2. T. weissflogii only produced H2O2 when stressed or killed. P. tricornutum cells did not make cell-associated ROS, but did secrete H2O2-producing substances into the growth medium. In all organisms, recovery rates for killed cultures (94–100% H2O2; 10–80% O−2) were consistently higher than those for live cultures (65–95% H2O2; 10–50% O−2). While recovery rates for killed cultures in H2O2 indicate that nearly all H2O2 was degraded by active cell processes, O−2 decay appeared to occur via a combination of active and passive processes. Overall, this study shows that the rates and pathways for ROS production and decay vary greatly among diatom species, even between those that are closely related, and as a function of light conditions.
    Description: This research was supported by NSF grant OCE-1131734/1246174 to BV and CH.
    Keywords: Reactive oxygen species ; Superoxide ; Hydrogen peroxide ; Diatoms ; Culture
    Repository Name: Woods Hole Open Access Server
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  • 7
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    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26829 | 23782 | 2019-11-19 01:08:33 | 26829 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
    Publication Date: 2021-07-24
    Description: The paper provides the methodology in lipid extraction from fish using the Modified Folch's Method. Instructions on sample preparation, and the apparatus and reagents needed are presented. Detailed procedures in lipid extraction are provided.
    Keywords: Chemistry ; Fisheries ; Manuals ; Culture media ; Analysis ; Analytical techniques ; Methodology ; Chemical analysis ; Fish inspection ; Fishery industry ; Food technology ; Standards ; Specifications ; Lipids
    Repository Name: AquaDocs
    Type: book_section
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  • 8
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    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26838 | 23782 | 2019-11-19 00:36:53 | 26838 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
    Publication Date: 2021-07-24
    Description: The paper provides the methodology in the preparation of methyl esters by boron trifluoride method in fish. Instructions on sample preparation and the apparatus and reagents needed are presented. Detailed procedures are also provided.
    Keywords: Chemistry ; Fisheries ; Manuals ; Culture media ; Analysis ; Analytical techniques ; Methodology ; Chemical analysis ; Food technology ; Standards ; Specifications ; Fish oils ; Fats ; Fatty acids ; Esters ; Lipids
    Repository Name: AquaDocs
    Type: book_section
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    Format: C-11.1-C-11.2
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  • 9
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    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26837 | 23782 | 2019-11-19 00:39:35 | 26837 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
    Publication Date: 2021-07-24
    Description: The paper provides the methodology in the determination of the degree of lipid oxidation by gas chromatography. Instructions on sample preparation and the detailed procedures and calculation are provided.
    Keywords: Chemistry ; Fisheries ; Manuals ; Culture media ; Analysis ; Analytical techniques ; Methodology ; Chemical analysis ; Food technology ; Standards ; Specifications ; Lipids ; Fats ; Fatty acids ; Oxidation ; Chromatographic techniques
    Repository Name: AquaDocs
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  • 10
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    Marine Fisheries Research Department, Southeast Asian Fisheries Development Center | Singapore
    In:  http://aquaticcommons.org/id/eprint/26827 | 23782 | 2019-11-19 01:11:10 | 26827 | Southeast Asian Fisheries Development Center, Marine Fisheries Research Department
    Publication Date: 2021-07-24
    Description: The paper discusses the significance of lipid analysis in fish. Fish lipids exist as phospholipids and triglycerides which deteriorate during storage due to hydrolysis and oxidation.
    Keywords: Chemistry ; Fisheries ; Manuals ; Culture media ; Analysis ; Analytical techniques ; Methodology ; Chemical analysis ; Lipids ; Organic compounds ; Fats ; Hydrolysis ; Chemical reactions ; Chemical degradation ; Oxidation
    Repository Name: AquaDocs
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    Format: application/pdf
    Format: application/pdf
    Format: C-1.1
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