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  • Articles  (10)
  • Open Access-Papers  (10)
  • Springer Science and Business Media LLC  (6)
  • BioMed Central  (4)
  • Springer Science + Business Media
  • 1
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    Spatial compartmentalization of free radical formation and mitochondrial heterogeneity in bivalve gills revealed by live-imaging techniques (2016)
    BioMed Central
    In:  EPIC3Frontiers in Zoology, BioMed Central, 13(4)
    Details
    Publication Date: 2016-02-05
    Description: Background: Reactive oxygen (ROS) and nitrogen (RNS) species are produced during normal unstressed metabolic activity in aerobic tissues. Most analytical work uses tissue homogenates, and lacks spatial information on the tissue specific sites of actual ROS formation. Live-imaging techniques (LIT) utilize target-specific fluorescent dyes to visualize biochemical processes at cellular level. Results: Together with oxidative stress measurements, here we report application of LIT to bivalve gills for ex-vivo analysis of gill physiology and mapping of ROS and RNS formation in the living tissue. Our results indicate that a) mitochondria located in the basal parts of the epithelial cells close to the blood vessels are hyperpolarized with high Δψm, whereas b) the peripheral mitochondria close to the cilia have low (depolarized) Δψm. These mitochondria are densely packed (mitotracker Deep Red 633 staining), have acidic pH (Ageladine-A) and collocate with high formation of nitric oxide (DAF-2DA staining). NO formation is also observed in the endothelial cells surrounding the filament blood sinus. ROS (namely H2O2, HOO• and ONOO− radicals, assessed through C-H2DFFDA staining) are mainly formed within the blood sinus of the filaments and are likely to be produced by hemocytes as defense against invading pathogens. On the ventral bend of the gills, subepithelial mucus glands contain large mucous vacuoles showing higher fluorescence intensities for O2 •- than the rest of the tissue. Whether this O2 •- production is instrumental to mucus formation or serves antimicrobial protection of the gill surface is unknown. Cells of the ventral bends contain the superoxide forming mucocytes and show significantly higher protein carbonyl formation than the rest of the gill tissue. Conclusions: In summary, ROS and RNS formation is highly compartmentalized in bivalve gills under unstressed conditions. The main mechanisms are the differentiation of mitochondria membrane potential and basal ROS formation in inner and outer filament layers, as well as potentially antimicrobial ROS formation in the central blood vessel. Our results provide new insight into this subject and highlight the fact that studying ROS formation in tissue homogenates may not be adequate to understand the underlying mechanism in complex tissues. Keywords: Bivalve, Gill, Live-imaging, Fluorescence, Mitochondria, ROS, RNS * Correspondence:
    Repository Name: EPIC Alfred Wegener Institut
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  • 2
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    EGenBio : a data management system for evolutionary genomics and biodiversity (2006)
    BioMed Central
    Details
    Publication Date: 2022-05-25
    Description: From The Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society Baton Rouge, Louisiana. 2–4 March, 2006.
    Description: © 2006 Nahum et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
    Description: EGenBio is a system for manipulation and filtering of large numbers of sequences, integrating curated sequence alignments and phylogenetic trees, managing evolutionary analyses, and visualizing their output. EGenBio is organized into three conceptual divisions, Evolution, Genomics, and Biodiversity. The Genomics division includes tools for selecting pre-aligned sequences from different genes and species, and for modifying and filtering these alignments for further analysis. Species searches are handled through queries that can be modified based on a tree-based navigation system and saved. The Biodiversity division contains tools for analyzing individual sequences or sequence alignments, whereas the Evolution division contains tools involving phylogenetic trees. Alignments are annotated with analytical results and modification history using our PRAED format. A miscellaneous Tools section and Help framework are also available. EGenBio was developed around our comparative genomic research and a prototype database of mtDNA genomes. It utilizes MySQL-relational databases and dynamic page generation, and calls numerous custom programs.
    Description: This work was partly funded by the National Institutes of Health (R22/R33 Innovation and Development grant to David Pollock), the National Science Foundation (CBM2/EPSCOR), and the State of Louisiana (Biological Computation and Visualization Center, Governor's iotechnology Initiative, and startup funds to David Pollock).
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 3
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    The ocean sampling day consortium (2015)
    BioMed Central
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    Publication Date: 2022-10-18
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 4 (2015): 27, doi:10.1186/s13742-015-0066-5.
    Description: Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.
    Description: This work was supported by the Micro B3 project, which is funded from the European Union’s Seventh Framework Programme (FP7; Joint Call OCEAN.2011‐2: Marine microbial diversity – new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no 287589.
    Keywords: Ocean sampling day ; OSD ; Biodiversity ; Genomics ; Health index ; Bacteria ; Microorganism ; Metagenomics ; Marine ; Micro B3 ; Standards
    Repository Name: Woods Hole Open Access Server
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  • 4
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    Simulating social-ecological systems : the Island Digital Ecosystem Avatars (IDEA) consortium (2016)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 5 (2016): 14, doi:10.1186/s13742-016-0118-5.
    Description: Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to conduct the basic scientific research needed to build use-oriented simulations (avatars) of entire social-ecological systems. Islands are the most scientifically tractable places for these studies and we begin with one of the best known: Moorea, French Polynesia. The Moorea IDEA will be a sustainability simulator modeling links and feedbacks between climate, environment, biodiversity, and human activities across a coupled marine–terrestrial landscape. As a model system, the resulting knowledge and tools will improve our ability to predict human and natural change on Moorea and elsewhere at scales relevant to management/conservation actions.
    Description: Work was supported in part by: the Institute of Theoretical Physics and the Pauli Center at ETH Zurich; the US National Science Foundation (NSF Moorea Coral Reef Long Term Ecological Research Site, OCE-1236905; Socio-Ecosystem Dynamics of Natural-Human Networks on Model Islands, CNH-1313830; Coastal SEES: Adaptive Capacity, Resilience, and Coral Reef State Shifts in Social-ecological Systems, OCE-1325652, OCE-1325554); the Gordon and Betty Moore Foundation (Berkeley Initiative in Global Change Biology; Genomic Standards Consortium); Courtney Ross and the Ross Institute; UC Berkeley Vice Chancellor for Research; CRIOBE; and the France Berkeley Fund (FBF 2014-0015).
    Keywords: Computational ecology ; Biodiversity ; Genomics ; Biocode ; Earth observations ; Social-ecological system ; Ecosystem dynamics ; Climate change scenarios ; Predictive modeling
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Erratum: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (2018)
    Springer Science and Business Media LLC
    In:  EPIC3Nature Biotechnology, Springer Science and Business Media LLC, 36(2), pp. 196-196, ISSN: 1087-0156
    Details
    Publication Date: 2023-06-21
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 6
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    Erratum: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (2018)
    Springer Science and Business Media LLC
    In:  EPIC3Nature Biotechnology, Springer Science and Business Media LLC, 36(7), pp. 660-660, ISSN: 1087-0156
    Details
    Publication Date: 2023-06-21
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 7
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    Multi-omics for studying and understanding polar life (2023)
    Springer Science and Business Media LLC
    In:  EPIC3Nature Communications, Springer Science and Business Media LLC, 14(1), pp. 7451-, ISSN: 2041-1723
    Details
    Publication Date: 2023-11-23
    Description: Polar ecosystems are experiencing amongst the most rapid rates of regional warming on Earth. Here, we discuss ‘omics’ approaches to investigate polar biodiversity, including the current state of the art, future perspectives and recommendations. We propose a community road map to generate and more fully exploit multi-omics data from polar organisms. These data are needed for the comprehensive evaluation of polar biodiversity and to reveal how life evolved and adapted to permanently cold environments with extreme seasonality. We argue that concerted action is required to mitigate the impact of warming on polar ecosystems via conservation efforts, to sustainably manage these unique habitats and their ecosystem services, and for the sustainable bioprospecting of novel genes and compounds for societal gain.
    Repository Name: EPIC Alfred Wegener Institut
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  • 8
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    Author Correction: The importance of Antarctic krill in biogeochemical cycles (2019)
    Springer Science and Business Media LLC
    In:  EPIC3Nature Communications, Springer Science and Business Media LLC, 10(1), pp. 5340-5340, ISSN: 2041-1723
    Details
    Publication Date: 2023-05-10
    Description: The original version of this Article included an incorrect competing interests statement, which read ‘The authors declare no competing interests’, rather than the correct ‘The authors declare the following competing interest: Steve Nicol has been employed to provide scientific advice to the Association of Responsible Krill harvesting companies.’ This has been corrected in both the PDF and HTML versions of the Article.
    Repository Name: EPIC Alfred Wegener Institut
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  • 9
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    Circadian regulation of diel vertical migration (DVM) and metabolism in Antarctic krill Euphausia superba (2020)
    Springer Science and Business Media LLC
    In:  EPIC3Scientific Reports, Springer Science and Business Media LLC, 10(1), pp. 16796-16796, ISSN: 2045-2322
    Details
    Publication Date: 2023-05-10
    Description: Antarctic krill (Euphausia superba) are high latitude pelagic organisms which play a key ecological role in the ecosystem of the Southern Ocean. To synchronize their daily and seasonal life-traits with their highly rhythmic environment, krill rely on the implementation of rhythmic strategies which might be regulated by a circadian clock. A recent analysis of krill circadian transcriptome revealed that their clock might be characterized by an endogenous free-running period of about 12–15 h. Using krill exposed to simulated light/dark cycles (LD) and constant darkness (DD), we investigated the circadian regulation of krill diel vertical migration (DVM) and oxygen consumption, together with daily patterns of clock gene expression in brain and eyestalk tissue. In LD, we found clear 24 h rhythms of DVM and oxygen consumption, suggesting a synchronization with photoperiod. In DD, the DVM rhythm shifted to a 12 h period, while the peak of oxygen consumption displayed a temporal advance during the subjective light phase. This suggested that in free-running conditions the periodicity of these clock-regulated output functions might reflect the shortening of the endogenous period observed at the transcriptional level. Moreover, differences in the expression patterns of clock gene in brain and eyestalk, in LD and DD, suggested the presence in krill of a multiple oscillator system. Evidence of short periodicities in krill behavior and physiology further supports the hypothesis that a short endogenous period might represent a circadian adaption to cope with extreme seasonal photoperiodic variability at high latitude.
    Repository Name: EPIC Alfred Wegener Institut
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  • 10
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    Climate change impacts on Antarctic krill behaviour and population dynamics (2023)
    Springer Science and Business Media LLC
    In:  EPIC3Nature Reviews Earth & Environment, Springer Science and Business Media LLC, ISSN: 2662-138X
    Details
    Publication Date: 2024-01-08
    Description: Krill habitats in the Southern Ocean are impacted by changing climate conditions, reduced sea ice and rising temperatures. These changes, in turn, affect krill occurrence, physiology and behaviour, which could have ecosystem impacts. In this Review, we examine climate change impacts on Antarctic krill and the potential implications for the Southern Ocean ecosystem. Since the 1970s, there have been apparent reductions in adult population density and the occurrence of very dense swarms in the northern Southwest Atlantic. These changes were associated with latitudinal and longitudinal rearrangement of population distribution — including a poleward contraction in the Southwest Atlantic — and were likely driven by ocean warming, sea-ice reductions and changes in the quality of larval habitats. As swarms are targeted by fishers and predators, this contraction could increase fishery–predator interactions, potentially exacerbating risk to already declining penguin populations and recovering whale populations. These risks require urgent mitigation measures to be developed. A circumpolar monitoring network using emerging technologies is needed to augment existing surveys and better record the shifts in krill distribution.
    Repository Name: EPIC Alfred Wegener Institut
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