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El-Dairi R, Outinen O, Kankaanpää H. Anthropogenic underwater noise: A review on physiological and molecular responses of marine biota. MARINE POLLUTION BULLETIN 2024; 199:115978. [PMID: 38217911 DOI: 10.1016/j.marpolbul.2023.115978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/15/2024]
Abstract
The detrimental effects of anthropogenic underwater noise on marine organisms have garnered significant attention among scientists. This review delves into the research concerning the repercussions of underwater noise on marine species, with specific emphasis on the physiological and molecular responses of marine biota. This review investigates the sensory mechanisms, hearing sensitivity, and reaction thresholds of diverse marine organisms, shedding light on their susceptibility to underwater noise disturbances. The physiological and molecular effects of anthropogenic underwater noise on marine biota include oxidative stress, energy homeostasis, metabolism, immune function, and respiration. Additionally, changes in the gene expression profile associated with oxidative stress, metabolism, and immunological response are among the responses reported for marine biota. These effects pose a threat to animal fitness and potentially affect their survival as individuals and populations.
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Affiliation(s)
- Rami El-Dairi
- Marine and Freshwater Solutions, Finnish Environment Institute, Agnes Sjöbergin katu 2, FI-00790 Helsinki, Finland.
| | - Okko Outinen
- Marine and Freshwater Solutions, Finnish Environment Institute, Agnes Sjöbergin katu 2, FI-00790 Helsinki, Finland
| | - Harri Kankaanpää
- Marine and Freshwater Solutions, Finnish Environment Institute, Agnes Sjöbergin katu 2, FI-00790 Helsinki, Finland
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Chaung K, Baharav TZ, Henderson G, Zheludev IN, Wang PL, Salzman J. SPLASH: A statistical, reference-free genomic algorithm unifies biological discovery. Cell 2023; 186:5440-5456.e26. [PMID: 38065078 PMCID: PMC10861363 DOI: 10.1016/j.cell.2023.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/31/2023] [Accepted: 10/26/2023] [Indexed: 12/18/2023]
Abstract
Today's genomics workflows typically require alignment to a reference sequence, which limits discovery. We introduce a unifying paradigm, SPLASH (Statistically Primary aLignment Agnostic Sequence Homing), which directly analyzes raw sequencing data, using a statistical test to detect a signature of regulation: sample-specific sequence variation. SPLASH detects many types of variation and can be efficiently run at scale. We show that SPLASH identifies complex mutation patterns in SARS-CoV-2, discovers regulated RNA isoforms at the single-cell level, detects the vast sequence diversity of adaptive immune receptors, and uncovers biology in non-model organisms undocumented in their reference genomes: geographic and seasonal variation and diatom association in eelgrass, an oceanic plant impacted by climate change, and tissue-specific transcripts in octopus. SPLASH is a unifying approach to genomic analysis that enables expansive discovery without metadata or references.
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Affiliation(s)
- Kaitlin Chaung
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Tavor Z Baharav
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - George Henderson
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Ivan N Zheludev
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Peter L Wang
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Julia Salzman
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA; Department of Statistics (by courtesy), Stanford University, Stanford, CA 94305, USA; Department of Biology (by courtesy), Stanford University, Stanford, CA 94305, USA.
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Chaung K, Baharav TZ, Henderson G, Zheludev IN, Wang PL, Salzman J. [WITHDRAWN] SPLASH: a statistical, reference-free genomic algorithm unifies biological discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.17.549408. [PMID: 37503014 PMCID: PMC10370119 DOI: 10.1101/2023.07.17.549408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The authors have withdrawn this manuscript due to a duplicate posting of manuscript number BIORXIV/2022/497555. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author. The correct preprint can be found at doi: https://doi.org/10.1101/2022.06.24.497555.
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Duarte CM, Chapuis L, Collin SP, Costa DP, Devassy RP, Eguiluz VM, Erbe C, Gordon TAC, Halpern BS, Harding HR, Havlik MN, Meekan M, Merchant ND, Miksis-Olds JL, Parsons M, Predragovic M, Radford AN, Radford CA, Simpson SD, Slabbekoorn H, Staaterman E, Van Opzeeland IC, Winderen J, Zhang X, Juanes F. The soundscape of the Anthropocene ocean. Science 2021; 371:371/6529/eaba4658. [DOI: 10.1126/science.aba4658] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Carlos M. Duarte
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
- Arctic Research Centre, Department of Biology, Aarhus University, C.F. Møllers Allé 8, DK-8000 Århus C, Denmark
| | - Lucille Chapuis
- Biosciences, University of Exeter, Prince of Wales Road, Exeter EX4 4PS, UK
| | - Shaun P. Collin
- School of Life Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Daniel P. Costa
- Institute of Marine Sciences, University of California, Santa Cruz, CA 95060, USA
| | - Reny P. Devassy
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Victor M. Eguiluz
- Instituto de Física Interdisciplinar y Sistemas Complejos IFISC (CSIC-UIB), E07122 Palma de Mallorca, Spain
| | - Christine Erbe
- Centre for Marine Science & Technology, Curtin University, Perth, WA 6102, Australia
| | - Timothy A. C. Gordon
- Biosciences, University of Exeter, Prince of Wales Road, Exeter EX4 4PS, UK
- Australian Institute of Marine Science, Perth, WA 6009, Australia
| | - Benjamin S. Halpern
- National Center for Ecological Analysis and Synthesis, University of California, Santa Barbara, CA 93101, USA
- Bren School of Environmental Science and Management, University of California, Santa Barbara, CA 93106, USA
| | - Harry R. Harding
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Michelle N. Havlik
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Mark Meekan
- Australian Institute of Marine Science, Perth, WA 6009, Australia
| | - Nathan D. Merchant
- Centre for Environment, Fisheries and Aquaculture Science, Lowestoft NR33 0HT, UK
| | - Jennifer L. Miksis-Olds
- Center for Acoustics Research and Education, University of New Hampshire, Durham, NH 03824, USA
| | - Miles Parsons
- Centre for Marine Science & Technology, Curtin University, Perth, WA 6102, Australia
- Australian Institute of Marine Science, Perth, WA 6009, Australia
| | - Milica Predragovic
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Andrew N. Radford
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Craig A. Radford
- Institute of Marine Science, Leigh Marine Laboratory, University of Auckland, P.O. Box 349, Warkworth 0941, New Zealand
| | - Stephen D. Simpson
- Biosciences, University of Exeter, Prince of Wales Road, Exeter EX4 4PS, UK
| | - Hans Slabbekoorn
- Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA Leiden, Netherlands
| | | | - Ilse C. Van Opzeeland
- Alfred-Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | | | - Xiangliang Zhang
- Computer, Electrical and Mathematical Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Francis Juanes
- Department of Biology, University of Victoria, Victoria, BC, Canada
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