{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T17:33:22Z","timestamp":1773336802267,"version":"3.50.1"},"reference-count":102,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100011711","name":"Department of Agriculture of Guangdong Province","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100011711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002855","name":"Ministry of Science and Technology of the People's Republic of China","doi-asserted-by":"publisher","award":["2023YFD2401705"],"award-info":[{"award-number":["2023YFD2401705"]}],"id":[{"id":"10.13039\/501100002855","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Comparative Biochemistry and Physiology Part D: Genomics and Proteomics"],"published-print":{"date-parts":[[2026,3]]},"DOI":"10.1016\/j.cbd.2025.101667","type":"journal-article","created":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T01:17:22Z","timestamp":1761959842000},"page":"101667","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"special_numbering":"C","title":["Transcriptomic analysis of the hepatopancreas response to low-pH stress in kuruma shrimp (Marsupenaeus japonicus)"],"prefix":"10.1016","volume":"57","author":[{"given":"Yongkang","family":"Hou","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Caifeng","family":"Liang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dekhkonova Dilorakhon Rasuljon","family":"Kizi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianyong","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.cbd.2025.101667_bb0005","doi-asserted-by":"crossref","DOI":"10.1016\/j.ijbiomac.2024.131090","article-title":"Antioxidant potential and protective effect of modified sea cucumber peptides against H2O2-induced oxidative damage in vitro HepG2 cells and in vivo zebrafish model","volume":"266","author":"Abdo","year":"2024","journal-title":"Int. J. Biol. Macromol."},{"issue":"17","key":"10.1016\/j.cbd.2025.101667_bb0010","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cbd.2025.101667_bb0015","series-title":"bioRxiv","article-title":"Interplay of EGFR, JNK and ROS signalling in soma-germline communication in the Drosophila testis","author":"Alvarez","year":"2024"},{"key":"10.1016\/j.cbd.2025.101667_bb0020","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2021.149807","article-title":"Combined effects of ocean warming and acidification on marine fish and shellfish: a molecule to ecosystem perspective","volume":"802","author":"Baag","year":"2022","journal-title":"Sci. Total Environ."},{"issue":"2","key":"10.1016\/j.cbd.2025.101667_bb0025","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1016\/S0147-6513(03)00028-9","article-title":"Cadmium-induced antioxidant defense mechanism in freshwater teleost Oreochromis mossambicus (Tilapia)","volume":"56","author":"Basha","year":"2003","journal-title":"Ecotoxicol. Environ. Saf."},{"key":"10.1016\/j.cbd.2025.101667_bb0030","doi-asserted-by":"crossref","DOI":"10.1016\/j.dci.2025.105332","article-title":"High temperature induces oxidative damage, immune modulation, and atrophy in the gills and skeletal muscle of the teleost fish black cusk-eel (Genypterus maculatus)","volume":"164","author":"Becerra","year":"2025","journal-title":"Dev. Comp. Immunol."},{"issue":"2","key":"10.1016\/j.cbd.2025.101667_bb0035","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1042\/EBC20230082","article-title":"The structural biology and dynamics of malate dehydrogenases","volume":"68","author":"Berndsen","year":"2024","journal-title":"Essays Biochem."},{"key":"10.1016\/j.cbd.2025.101667_bb0040","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1016\/j.marenvres.2018.04.006","article-title":"Transgenerational deleterious effects of ocean acidification on the reproductive success of a keystone crustacean (Gammarus locusta)","volume":"138","author":"Borges","year":"2018","journal-title":"Mar. Environ. Res."},{"key":"10.1016\/j.cbd.2025.101667_bb0045","first-page":"1","article-title":"Water quality management in aquaculture","volume":"22","author":"Boyd","year":"1985","journal-title":"CMFRI Spec. Publ."},{"issue":"1","key":"10.1016\/j.cbd.2025.101667_bb0050","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1210\/endo.137.1.8536636","article-title":"Differential expression of peroxisome proliferator-activated receptors (PPARs): tissue distribution of PPAR-alpha, -beta, and-gamma in the adult rat","volume":"137","author":"Braissant","year":"1996","journal-title":"Endocrinology"},{"issue":"1","key":"10.1016\/j.cbd.2025.101667_bb0055","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. Methods"},{"issue":"1","key":"10.1016\/j.cbd.2025.101667_bb0060","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1038\/s41392-021-00778-y","article-title":"Targeting lysosomes in human disease: from basic research to clinical applications","volume":"6","author":"Cao","year":"2021","journal-title":"Signal Transduct. Target. Ther."},{"key":"10.1016\/j.cbd.2025.101667_bb0065","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1016\/j.fsi.2016.10.008","article-title":"Differential protein expression using proteomics from a crustacean brine shrimp (Artemia sinica) under CO2-driven seawater acidification","volume":"58","author":"Chang","year":"2016","journal-title":"Fish Shellfish Immunol."},{"key":"10.1016\/j.cbd.2025.101667_bb0070","doi-asserted-by":"crossref","DOI":"10.1016\/j.cbd.2025.101618","article-title":"Whole-genome identification of SOD gene family revealed the expansion of SOD in Chinese mitten crab, Eriocheir sinensis","volume":"56","author":"Chen","year":"2025","journal-title":"Comp. Biochem. Physiol. Part D Genomics Proteomics"},{"issue":"2","key":"10.1016\/j.cbd.2025.101667_bb0075","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1016\/j.fsi.2015.05.055","article-title":"Activation of immunity, immune response, antioxidant ability, and resistance against Vibrio alginolyticus in white shrimp Litopenaeus vannamei decrease under long-term culture at low pH","volume":"46","author":"Chen","year":"2015","journal-title":"Fish Shellfish Immunol."},{"key":"10.1016\/j.cbd.2025.101667_bb0080","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/j.aquatox.2015.04.004","article-title":"Effects of ammonia exposure on apoptosis, oxidative stress and immune response in pufferfish (Takifugu obscurus)","volume":"164","author":"Cheng","year":"2015","journal-title":"Aquat. Toxicol."},{"issue":"23","key":"10.1016\/j.cbd.2025.101667_bb0085","doi-asserted-by":"crossref","DOI":"10.3390\/ani12233383","article-title":"The multiple influences of natural farming environment on the cultured population behavior of kuruma prawn, Penaeus japonicus","volume":"12","author":"Cheng","year":"2022","journal-title":"Animals"},{"issue":"3","key":"10.1016\/j.cbd.2025.101667_bb0090","doi-asserted-by":"crossref","DOI":"10.1016\/j.omtm.2024.101313","article-title":"A GLB1 transgene with enhanced therapeutic potential for the preclinical development of ex-vivo gene therapy to treat mucopolysaccharidosis type IVB","volume":"32","author":"Crippa","year":"2024","journal-title":"Mol. Ther. Methods Clin. Dev."},{"issue":"1","key":"10.1016\/j.cbd.2025.101667_bb0095","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.margen.2009.03.001","article-title":"Aspartic proteinases in Antarctic fish","volume":"2","author":"De Luca","year":"2009","journal-title":"Mar. Genomics"},{"issue":"2012","key":"10.1016\/j.cbd.2025.101667_bb0100","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1146\/annurev-marine-041911-111611","article-title":"Climate change impacts on marine ecosystems","volume":"4","author":"Doney","year":"2012","journal-title":"Annu. Rev. Mar. Sci."},{"key":"10.1016\/j.cbd.2025.101667_bb0105","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1016\/j.fsi.2018.04.050","article-title":"Impairment of the intestine barrier function in Litopenaeus vannamei exposed to ammonia and nitrite stress","volume":"78","author":"Duan","year":"2018","journal-title":"Fish Shellfish Immunol."},{"key":"10.1016\/j.cbd.2025.101667_bb0110","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1016\/j.fsi.2019.02.047","article-title":"Changes in the intestine barrier function of Litopenaeus vannamei in response to pH stress","volume":"88","author":"Duan","year":"2019","journal-title":"Fish Shellfish Immunol."},{"issue":"D1","key":"10.1016\/j.cbd.2025.101667_bb0115","doi-asserted-by":"crossref","first-page":"D222","DOI":"10.1093\/nar\/gkt1223","article-title":"Pfam: the protein families database","volume":"42","author":"Finn","year":"2014","journal-title":"Nucleic Acids Res."},{"issue":"8","key":"10.1016\/j.cbd.2025.101667_bb0120","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1111\/j.1365-3040.2005.01327.x","article-title":"Oxidant and antioxidant signalling in plants: a re-evaluation of the concept of oxidative stress in a physiological context","volume":"28","author":"Foyer","year":"2005","journal-title":"Plant Cell Environ."},{"issue":"5","key":"10.1016\/j.cbd.2025.101667_bb0125","first-page":"100","article-title":"Effects of pH on survival of oriental river prawn (Macrobrachium nipponense) and activities of liver function enzymes","volume":"46","author":"Fu","year":"2016","journal-title":"Freshw. Fish."},{"issue":"11","key":"10.1016\/j.cbd.2025.101667_bb0130","doi-asserted-by":"crossref","first-page":"5350","DOI":"10.1111\/are.15405","article-title":"Characterization and functional analysis of MjChi4 from the kuruma shrimp Marsupenaeus japonicus under the environmental stresses low pH and high ammonia","volume":"52","author":"Fu","year":"2021","journal-title":"Aquac. Res."},{"issue":"7","key":"10.1016\/j.cbd.2025.101667_bb0135","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"Grabherr","year":"2011","journal-title":"Nat. Biotechnol."},{"issue":"1","key":"10.1016\/j.cbd.2025.101667_bb0140","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-020-75021-9","article-title":"Ocean acidification disrupts the orientation of postlarval Caribbean spiny lobsters","volume":"10","author":"Gravinese","year":"2020","journal-title":"Sci. Rep."},{"issue":"5","key":"10.1016\/j.cbd.2025.101667_bb0145","doi-asserted-by":"crossref","DOI":"10.1007\/s00227-022-04053-8","article-title":"Caribbean king crab larvae and juveniles show tolerance to ocean acidification and ocean warming","volume":"169","author":"Gravinese","year":"2022","journal-title":"Mar. Biol."},{"issue":"5","key":"10.1016\/j.cbd.2025.101667_bb0150","doi-asserted-by":"crossref","first-page":"809","DOI":"10.3724\/SP.J.1035.2012.00809","article-title":"Effect of dietary copper level on the immunity, Vibrio-resistant ability, lysozyme mRNA and Toll receptor mRNA expressions in the white shrimp Litopenaeus vannamei","volume":"36","author":"Guo","year":"2012","journal-title":"Acta Hydrobiol. Sin."},{"key":"10.1016\/j.cbd.2025.101667_bb0155","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/j.ecoenv.2017.11.052","article-title":"Adaptation of the white shrimp Litopenaeus vannamei to gradual changes to a low-pH environment","volume":"149","author":"Han","year":"2018","journal-title":"Ecotoxicol. Environ. Saf."},{"key":"10.1016\/j.cbd.2025.101667_bb0160","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.fsi.2018.02.001","article-title":"A comparative study on oxidative stress response in the hepatopancreas and midgut of the white shrimp Litopenaeus vannamei under gradual changes to low or high pH environment","volume":"76","author":"Han","year":"2018","journal-title":"Fish Shellfish Immunol."},{"key":"10.1016\/j.cbd.2025.101667_bb0165","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1016\/j.fsi.2021.12.032","article-title":"Comparative proteomic profiling in Chinese shrimp Fenneropenaeus chinensis under low pH stress","volume":"120","author":"He","year":"2022","journal-title":"Fish Shellfish Immunol."},{"key":"10.1016\/j.cbd.2025.101667_bb0170","article-title":"Cloning and functional analysis of Rac1 in Crassostrea hongkongensis reveals its role in immune defense against Vibrio harveyi","volume":"45","author":"Hou","year":"2025","journal-title":"Aquacult. Rep."},{"issue":"12","key":"10.1016\/j.cbd.2025.101667_bb0175","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0207771","article-title":"Analysis of the transcriptome data in Litopenaeus vannamei reveals the immune basis and predicts the hub regulation-genes in response to high-pH stress","volume":"13","author":"Huang","year":"2018","journal-title":"PLoS ONE"},{"issue":"5","key":"10.1016\/j.cbd.2025.101667_bb0180","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1016\/0271-5317(95)00041-G","article-title":"The integrated antioxidant system","volume":"15","author":"Jacob","year":"1995","journal-title":"Nutr. Res."},{"issue":"suppl_1","key":"10.1016\/j.cbd.2025.101667_bb0185","doi-asserted-by":"crossref","first-page":"D480","DOI":"10.1093\/nar\/gkm882","article-title":"KEGG for linking genomes to life and the environment","volume":"36","author":"Kanehisa","year":"2007","journal-title":"Nucleic Acids Res."},{"issue":"12","key":"10.1016\/j.cbd.2025.101667_bb0190","doi-asserted-by":"crossref","first-page":"2775","DOI":"10.1016\/j.bbamcr.2013.06.024","article-title":"A low temperature-inducible protein AtSRC2 enhances the ROS-producing activity of NADPH oxidase AtRbohF","volume":"1833","author":"Kawarazaki","year":"2013","journal-title":"Biochim. Biophys. Acta Mol. Cell Res."},{"issue":"2","key":"10.1016\/j.cbd.2025.101667_bb0195","article-title":"Elevated lactate dehydrogenase in a patient with late-infantile GM1-gangliosidosis","volume":"3","author":"Kobayashi","year":"2025","journal-title":"Brain Dev. Case Rep."},{"issue":"1","key":"10.1016\/j.cbd.2025.101667_bb0200","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1038\/cdd.2008.150","article-title":"Classification of cell death: recommendations of the Nomenclature Committee on Cell Death 2009","volume":"16","author":"Kroemer","year":"2009","journal-title":"Cell Death Differ."},{"issue":"6","key":"10.1016\/j.cbd.2025.101667_bb0205","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1016\/j.jtherbio.2010.06.008","article-title":"Combined effects of temperature and salinity on critical thermal minima of pacific white shrimp Litopenaeus vannamei (Crustacea: Penaeidae)","volume":"35","author":"Kumlu","year":"2010","journal-title":"J. Therm. Biol."},{"key":"10.1016\/j.cbd.2025.101667_bb0210","doi-asserted-by":"crossref","DOI":"10.1016\/j.envres.2023.116600","article-title":"Review of cadmium toxicity effects on fish: oxidative stress and immune responses","volume":"236","author":"Lee","year":"2023","journal-title":"Environ. Res."},{"key":"10.1016\/j.cbd.2025.101667_bb0215","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1016\/j.aquatox.2019.05.007","article-title":"Effects of ocean acidification on life parameters and antioxidant system in the marine copepod Tigriopus japonicus","volume":"212","author":"Lee","year":"2019","journal-title":"Aquat. Toxicol."},{"issue":"1\u20134","key":"10.1016\/j.cbd.2025.101667_bb0220","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1016\/j.aquaculture.2004.07.001","article-title":"Influence of sediment characteristics on shrimp physiology: pH as principal effect","volume":"240","author":"Lemonnier","year":"2004","journal-title":"Aquaculture"},{"issue":"1","key":"10.1016\/j.cbd.2025.101667_bb0225","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1186\/1471-2105-12-323","article-title":"RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome","volume":"12","author":"Li","year":"2011","journal-title":"BMC Bioinf."},{"issue":"6","key":"10.1016\/j.cbd.2025.101667_bb0230","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1016\/j.fsi.2008.01.007","article-title":"The immune response of white shrimp Litopenaeus vannamei and its susceptibility to Vibrio alginolyticus under low and high pH stress","volume":"25","author":"Li","year":"2008","journal-title":"Fish Shellfish Immunol."},{"issue":"1","key":"10.1016\/j.cbd.2025.101667_bb0235","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1111\/are.14362","article-title":"Transcriptomic response to low pH stress in gills of the Pacific white shrimp, Litopenaeus vannamei","volume":"51","author":"Li","year":"2020","journal-title":"Aquac. Res."},{"key":"10.1016\/j.cbd.2025.101667_bb0240","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1016\/j.fsi.2018.09.026","article-title":"Transcriptome reveals involvement of immune defense, oxidative imbalance, and apoptosis in ammonia-stress response of the black tiger shrimp (Penaeus monodon)","volume":"83","author":"Li","year":"2018","journal-title":"Fish Shellfish Immunol."},{"key":"10.1016\/j.cbd.2025.101667_bb0245","doi-asserted-by":"crossref","DOI":"10.1016\/j.aquaculture.2020.735103","article-title":"The function of Apostichopus japonicas catalase in sea cucumber intestinal immunity","volume":"521","author":"Li","year":"2020","journal-title":"Aquaculture"},{"issue":"1","key":"10.1016\/j.cbd.2025.101667_bb0250","first-page":"41","article-title":"Preliminary study on acute toxicity of pH to Marsupenaeus japonicus","volume":"46","author":"Liang","year":"2019","journal-title":"Fish. Mod."},{"key":"10.1016\/j.cbd.2025.101667_bb0255","doi-asserted-by":"crossref","DOI":"10.1016\/j.aquaculture.2019.734328","article-title":"Transcriptomic analyses of the acute ammonia stress response in the hepatopancreas of the kuruma shrimp (Marsupenaeus japonicus)","volume":"513","author":"Liang","year":"2019","journal-title":"Aquaculture"},{"key":"10.1016\/j.cbd.2025.101667_bb0260","doi-asserted-by":"crossref","DOI":"10.1016\/j.fsi.2025.110344","article-title":"Enhancement of reactive oxygen species metabolism by antioxidant enzyme Cu\/Zn-SOD can block betanodavirus-induced necroptosis and suppress viral replication in fish cells","volume":"162","author":"Liao","year":"2025","journal-title":"Fish Shellfish Immunol."},{"issue":"1\u20132","key":"10.1016\/j.cbd.2025.101667_bb0265","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/j.mrgentox.2008.09.015","article-title":"The role of antioxidants and antioxidant-related enzymes in protective responses to environmentally induced oxidative stress","volume":"674","author":"Lim\u00f3n-Pacheco","year":"2009","journal-title":"Mutat. Res. Genet. Toxicol. Environ. Mutagen."},{"issue":"1","key":"10.1016\/j.cbd.2025.101667_bb0270","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/j.fsi.2010.02.018","article-title":"Effects of anthraquinone extract from Rheum officinale Bail on the growth performance and physiological responses of Macrobrachium rosenbergii under high temperature stress","volume":"29","author":"Liu","year":"2010","journal-title":"Fish Shellfish Immunol."},{"key":"10.1016\/j.cbd.2025.101667_bb0275","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1016\/j.fsi.2020.03.034","article-title":"The red swamp crayfish, Procambarus clarkii cathepsin C, participates in the innate immune response to the viral and bacterial pathogens","volume":"100","author":"Liu","year":"2020","journal-title":"Fish Shellfish Immunol."},{"issue":"1","key":"10.1016\/j.cbd.2025.101667_bb0280","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.aquatox.2010.10.006","article-title":"Environmentally induced oxidative stress in aquatic animals","volume":"101","author":"Lushchak","year":"2011","journal-title":"Aquat. Toxicol."},{"key":"10.1016\/j.cbd.2025.101667_bb0285","doi-asserted-by":"crossref","DOI":"10.1016\/j.aquaculture.2023.739351","article-title":"Insight into the genetic basis of ammonia tolerance in razor clam Sinonovacula constricta by genome-wide association study","volume":"569","author":"Lv","year":"2023","journal-title":"Aquaculture"},{"key":"10.1016\/j.cbd.2025.101667_bb0290","doi-asserted-by":"crossref","DOI":"10.1016\/j.marenvres.2022.105580","article-title":"Effects of ocean acidification and warming on the development and biochemical responses of juvenile shrimp Palaemon elegans (Rathke, 1837)","volume":"176","author":"Maia","year":"2022","journal-title":"Mar. Environ. Res."},{"issue":"19","key":"10.1016\/j.cbd.2025.101667_bb0295","doi-asserted-by":"crossref","first-page":"3787","DOI":"10.1093\/bioinformatics\/bti430","article-title":"Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary","volume":"21","author":"Mao","year":"2005","journal-title":"Bioinformatics"},{"issue":"5","key":"10.1016\/j.cbd.2025.101667_bb0300","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0177448","article-title":"Haemocytes collected from experimentally infected Pacific oysters, Crassostrea gigas: detection of ostreid herpesvirus 1 DNA, RNA, and proteins in relation with inhibition of apoptosis","volume":"12","author":"Martenot","year":"2017","journal-title":"PLoS ONE"},{"issue":"10","key":"10.1016\/j.cbd.2025.101667_bb0305","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1038\/nrg3068","article-title":"Next-generation transcriptome assembly","volume":"12","author":"Martin","year":"2011","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.cbd.2025.101667_bb0310","doi-asserted-by":"crossref","first-page":"1875","DOI":"10.1007\/s00227-012-1954-1","article-title":"Future ocean acidification will be amplified by hypoxia in coastal habitats","volume":"160","author":"Melzner","year":"2013","journal-title":"Mar. Biol."},{"issue":"9","key":"10.1016\/j.cbd.2025.101667_bb0315","doi-asserted-by":"crossref","first-page":"1016","DOI":"10.1038\/ncb2329","article-title":"The AMPK signalling pathway coordinates cell growth, autophagy and metabolism","volume":"13","author":"Mihaylova","year":"2011","journal-title":"Nat. Cell Biol."},{"key":"10.1016\/j.cbd.2025.101667_bb0320","doi-asserted-by":"crossref","DOI":"10.1016\/j.cyto.2025.156889","article-title":"Are F2-isoprostanes a better marker of semen lipid peroxidation than MDA in reproductive pathologies with inflammatory basis?","volume":"188","author":"Moretti","year":"2025","journal-title":"Cytokine"},{"issue":"5","key":"10.1016\/j.cbd.2025.101667_bb0325","doi-asserted-by":"crossref","DOI":"10.1016\/j.xplc.2025.101287","article-title":"Integrative transcriptogenomic analyses reveal the regulatory network underlying rice eating and cooking quality and identify a role for alpha-globulin in modulating starch and sucrose metabolism","volume":"6","author":"Nawade","year":"2025","journal-title":"Plant Commun."},{"key":"10.1016\/j.cbd.2025.101667_bb0330","doi-asserted-by":"crossref","DOI":"10.1016\/j.redox.2023.102926","article-title":"Mitochondrial complex I ROS production and redox signaling in hypoxia","volume":"67","author":"Okoye","year":"2023","journal-title":"Redox Biol."},{"issue":"6","key":"10.1016\/j.cbd.2025.101667_bb0335","doi-asserted-by":"crossref","first-page":"2793","DOI":"10.1007\/s10499-022-00941-4","article-title":"Role of Nrf2-Keap1 signaling in the antioxidant defense response induced by low salinity in the kuruma shrimp (Marsupenaeus japonicus)","volume":"30","author":"Ou","year":"2022","journal-title":"Aquac. Int."},{"issue":"4","key":"10.1016\/j.cbd.2025.101667_bb0340","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1016\/j.aquaculture.2007.07.218","article-title":"Effects of salinity and pH on ion-transport enzyme activities, survival and growth of Litopenaeus vannamei postlarvae","volume":"273","author":"Pan","year":"2007","journal-title":"Aquaculture"},{"key":"10.1016\/j.cbd.2025.101667_bb0345","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1007\/s00360-018-1167-0","article-title":"Effects of ocean acidification and salinity variations on the physiology of osmoregulating and osmoconforming crustaceans","volume":"188","author":"Ramaglia","year":"2018","journal-title":"J. Comp. Physiol. B."},{"key":"10.1016\/j.cbd.2025.101667_bb0350","first-page":"541","article-title":"Ocean acidification","author":"Riebesell","year":"2016","journal-title":"Enc. Mar. Geosci."},{"issue":"1","key":"10.1016\/j.cbd.2025.101667_bb0355","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/10641262.2012.753404","article-title":"Toxic effects of ammonia, nitrite, and nitrate to decapod crustaceans: a review on factors influencing their toxicity, physiological consequences, and coping mechanisms","volume":"21","author":"Romano","year":"2013","journal-title":"Rev. Fish. Sci."},{"key":"10.1016\/j.cbd.2025.101667_bb0360","doi-asserted-by":"crossref","DOI":"10.1016\/j.cbd.2024.101404","article-title":"Ocean warming and acidification alter calcification and innate immune system gene expression in juvenile American lobsters, Homarus americanus","volume":"54","author":"San Antonio","year":"2025","journal-title":"Comp. Biochem. Physiol. Part D Genomics Proteomics"},{"key":"10.1016\/j.cbd.2025.101667_bb0365","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1016\/j.biopha.2016.11.092","article-title":"Oleuropein protects L-02 cells against H2O2-induced oxidative stress by increasing SOD1, GPx1 and CAT expression","volume":"85","author":"Shi","year":"2017","journal-title":"Biomed. Pharmacother."},{"issue":"19","key":"10.1016\/j.cbd.2025.101667_bb0370","doi-asserted-by":"crossref","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs","volume":"31","author":"Sim\u00e3o","year":"2015","journal-title":"Bioinformatics"},{"issue":"4","key":"10.1016\/j.cbd.2025.101667_bb0375","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1093\/icb\/ict028","article-title":"Energy-limited tolerance to stress as a conceptual framework to integrate the effects of multiple stressors","volume":"53","author":"Sokolova","year":"2013","journal-title":"Integr. Comp. Biol."},{"key":"10.1016\/j.cbd.2025.101667_bb0380","doi-asserted-by":"crossref","DOI":"10.1016\/j.fsi.2024.109925","article-title":"Prophenoloxidase-activating system plays a crucial role in innate immune responses to Enterocytozoon hepatopenaei infection in shrimp Litopenaeus vannamei","volume":"154","author":"Sukonthamarn","year":"2024","journal-title":"Fish Shellfish Immunol."},{"issue":"6","key":"10.1016\/j.cbd.2025.101667_bb0385","first-page":"1279","article-title":"Acute toxicity of low-pH stress and its effect on enzyme activity and histological structure of gill and hepatopancreas in Procambarus clarkii","volume":"23","author":"Tao","year":"2016","journal-title":"J. Fish. Sci. China"},{"issue":"4","key":"10.1016\/j.cbd.2025.101667_bb0390","doi-asserted-by":"crossref","first-page":"954","DOI":"10.1016\/j.fsi.2012.09.021","article-title":"Discovery of immune molecules and their crucial functions in shrimp immunity","volume":"34","author":"Tassanakajon","year":"2013","journal-title":"Fish Shellfish Immunol."},{"key":"10.1016\/j.cbd.2025.101667_bb0395","doi-asserted-by":"crossref","DOI":"10.1016\/j.envpol.2024.123956","article-title":"Mechanisms of neurocentral-eyestalk-intestinal immunotoxicity in whiteleg shrimp Litopenaeus vannamei under ammonia nitrogen exposure","volume":"349","author":"Tong","year":"2024","journal-title":"Environ. Pollut."},{"key":"10.1016\/j.cbd.2025.101667_bb0400","doi-asserted-by":"crossref","DOI":"10.1016\/j.pbi.2024.102670","article-title":"Evolving best practices for transcriptome-wide association studies accelerate discovery of gene-phenotype links","volume":"83","author":"Torres-Rodr\u00edguez","year":"2025","journal-title":"Curr. Opin. Plant Biol."},{"issue":"5","key":"10.1016\/j.cbd.2025.101667_bb0405","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nbt.1621","article-title":"Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation","volume":"28","author":"Trapnell","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.cbd.2025.101667_bb0410","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.8191","article-title":"Effects of salinity on photosynthetic traits, ion homeostasis and nitrogen metabolism in wild and cultivated soybean","volume":"7","author":"Ullah","year":"2019","journal-title":"PeerJ"},{"key":"10.1016\/j.cbd.2025.101667_bb0415","doi-asserted-by":"crossref","DOI":"10.1016\/j.aquaculture.2024.742088","article-title":"Effects of hypoxic stress on liver metabolism, oxidative stress, and immunity in yellow catfish (Pelteobagrus fulvidraco) at different water temperatures","volume":"598","author":"Wang","year":"2025","journal-title":"Aquaculture"},{"issue":"1","key":"10.1016\/j.cbd.2025.101667_bb0420","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1093\/bioinformatics\/btp612","article-title":"DEGseq: an R package for identifying differentially expressed genes from RNA-seq data","volume":"26","author":"Wang","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cbd.2025.101667_bb0425","doi-asserted-by":"crossref","DOI":"10.1016\/j.fsi.2024.109419","article-title":"Grass carp peroxiredoxin 5 and 6-mediated autophagy inhibit grass carp reovirus replication and mitigate oxidative stress","volume":"146","author":"Wang","year":"2024","journal-title":"Fish Shellfish Immunol."},{"issue":"4","key":"10.1016\/j.cbd.2025.101667_bb0430","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1016\/j.cbpc.2009.06.010","article-title":"Oxidative stress, DNA damage and antioxidant enzyme gene expression in the Pacific white shrimp, Litopenaeus vannamei when exposed to acute pH stress","volume":"150","author":"Wang","year":"2009","journal-title":"Comp. Biochem. Physiol. Part C Toxicol. Pharmacol."},{"issue":"8","key":"10.1016\/j.cbd.2025.101667_bb0435","doi-asserted-by":"crossref","first-page":"1214","DOI":"10.1111\/j.1365-2109.2011.02887.x","article-title":"The responsive expression of a caspase gene in Chinese shrimp Fenneropenaeus chinensis against pH stress","volume":"42","author":"Wang","year":"2011","journal-title":"Aquac. Res."},{"issue":"6","key":"10.1016\/j.cbd.2025.101667_bb0440","doi-asserted-by":"crossref","first-page":"1915","DOI":"10.1083\/jcb.201708007","article-title":"Superoxide dismutases: dual roles in controlling ROS damage and regulating ROS signaling","volume":"217","author":"Wang","year":"2018","journal-title":"J. Cell Biol."},{"key":"10.1016\/j.cbd.2025.101667_bb0445","doi-asserted-by":"crossref","DOI":"10.1016\/j.fsi.2023.108864","article-title":"The lysosome-phagosome pathway mediates immune regulatory mechanisms in Mesocentrotus nudus against Vibrio coralliilyticus infection","volume":"139","author":"Wang","year":"2023","journal-title":"Fish Shellfish Immunol."},{"key":"10.1016\/j.cbd.2025.101667_bb0450","doi-asserted-by":"crossref","DOI":"10.1016\/j.marpolbul.2023.115050","article-title":"Ocean acidification increases inorganic carbon over organic carbon in shrimp\u2019s exoskeleton","volume":"192","author":"Weerathunga","year":"2023","journal-title":"Mar. Pollut. Bull."},{"key":"10.1016\/j.cbd.2025.101667_bb0455","doi-asserted-by":"crossref","DOI":"10.1016\/j.aquaculture.2025.742571","article-title":"Nitrite and sulfide stress induces hepatopancreatic oxidative stress, lipid metabolism disorders, ferroptosis and apoptosis in the Chinese mitten crab, Eriocheir sinensis","author":"Xing","year":"2025","journal-title":"Aquaculture"},{"key":"10.1016\/j.cbd.2025.101667_bb0460","article-title":"Characterization, expression profiling, and immunological role of Cathepsin D in Sebastes schlegelii during bacterial infection","volume":"2025","author":"Xu","year":"2025","journal-title":"Dev. Comp. Immunol."},{"issue":"2","key":"10.1016\/j.cbd.2025.101667_bb0465","doi-asserted-by":"crossref","first-page":"R14","DOI":"10.1186\/gb-2010-11-2-r14","article-title":"Gene ontology analysis for RNA-seq: accounting for selection bias","volume":"11","author":"Young","year":"2010","journal-title":"Genome Biol."},{"issue":"3","key":"10.1016\/j.cbd.2025.101667_bb0470","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1016\/j.cbpa.2010.07.013","article-title":"Immune responses and expression of immune-related genes in swimming crab Portunus trituberculatus exposed to elevated ambient ammonia-N stress","volume":"157","author":"Yue","year":"2010","journal-title":"Comp. Biochem. Physiol. A Mol. Integr. Physiol."},{"key":"10.1016\/j.cbd.2025.101667_bb0475","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1016\/j.fsi.2018.05.036","article-title":"Effects of acute ammonia toxicity on oxidative stress, immune response and apoptosis of juvenile yellow catfish Pelteobagrus fulvidraco and the mitigation of exogenous taurine","volume":"79","author":"Zhang","year":"2018","journal-title":"Fish Shellfish Immunol."},{"key":"10.1016\/j.cbd.2025.101667_bb0480","series-title":"Effects of pH Stress on Physiological and Biochemical Indexes in Three Species of Shrimps","author":"Zhao","year":"2011"},{"key":"10.1016\/j.cbd.2025.101667_bb0485","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1016\/j.aquaculture.2018.11.023","article-title":"Comparative transcriptome analysis provides comprehensive insights into the heat stress response of Marsupenaeus japonicus","volume":"502","author":"Zheng","year":"2019","journal-title":"Aquaculture"},{"key":"10.1016\/j.cbd.2025.101667_bb0490","doi-asserted-by":"crossref","first-page":"710","DOI":"10.1016\/j.fsi.2017.09.054","article-title":"Transcriptome analysis of Kuruma shrimp (Marsupenaeus japonicus) hepatopancreas in response to white spot syndrome virus (WSSV) under experimental infection","volume":"70","author":"Zhong","year":"2017","journal-title":"Fish Shellfish Immunol."},{"issue":"2","key":"10.1016\/j.cbd.2025.101667_bb0495","first-page":"224","article-title":"Glutathione S-transferase in the white shrimp Litopenaeus vannamei: characterization and regulation under pH stress","volume":"150","author":"Zhou","year":"2009","journal-title":"Comp. Biochem. Physiol. C: Toxicol. Pharmacol."},{"issue":"6","key":"10.1016\/j.cbd.2025.101667_bb0500","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1016\/j.jtherbio.2010.06.004","article-title":"Effect of temperature on antioxidant enzyme gene expression and stress protein response in white shrimp, Litopenaeus vannamei","volume":"35","author":"Zhou","year":"2010","journal-title":"J. Therm. Biol."},{"key":"10.1016\/j.cbd.2025.101667_bb0505","doi-asserted-by":"crossref","DOI":"10.1016\/j.dci.2024.105306","article-title":"CgmiR307 involved in the regulation of Nrf2-dependent oxidative response in the Pacific oyster Crassostrea gigas under high-temperature stress","volume":"162","author":"Zhou","year":"2025","journal-title":"Dev. Comp. Immunol."},{"key":"10.1016\/j.cbd.2025.101667_bb0510","doi-asserted-by":"crossref","DOI":"10.1016\/j.ijbiomac.2024.133305","article-title":"miR-8-3p regulates the antioxidant response and apoptosis in white shrimp, Litopenaeus vannamei under ammonia-N stress","volume":"274","author":"Zhuo","year":"2024","journal-title":"Int. J. Biol. Macromol."}],"container-title":["Comparative Biochemistry and Physiology Part D: Genomics and Proteomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1744117X25002564?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1744117X25002564?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T06:30:51Z","timestamp":1773297051000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1744117X25002564"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3]]},"references-count":102,"alternative-id":["S1744117X25002564"],"URL":"https:\/\/doi.org\/10.1016\/j.cbd.2025.101667","relation":{},"ISSN":["1744-117X"],"issn-type":[{"value":"1744-117X","type":"print"}],"subject":[],"published":{"date-parts":[[2026,3]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Transcriptomic analysis of the hepatopancreas response to low-pH stress in kuruma shrimp (Marsupenaeus japonicus)","name":"articletitle","label":"Article Title"},{"value":"Comparative Biochemistry and Physiology Part D: Genomics and Proteomics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.cbd.2025.101667","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}],"article-number":"101667"}}