{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T20:41:11Z","timestamp":1740170471962,"version":"3.37.3"},"reference-count":61,"publisher":"PeerJ","license":[{"start":{"date-parts":[[2024,1,16]],"date-time":"2024-01-16T00:00:00Z","timestamp":1705363200000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["32370436"],"award-info":[{"award-number":["32370436"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Education and Teaching Reform Program of Yancheng Teachers University","award":["2021YCTCJGZ002"],"award-info":[{"award-number":["2021YCTCJGZ002"]}]},{"DOI":"10.13039\/501100012670","name":"Open Foundation of Jiangsu Key Laboratory for Bioresources of Saline Soils","doi-asserted-by":"crossref","award":["JKLBS2019006"],"award-info":[{"award-number":["JKLBS2019006"]}],"id":[{"id":"10.13039\/501100012670","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>The Chinese mitten crab (<jats:italic>Eriocheir sinensis<\/jats:italic>) is an important commercial species in China. <jats:italic>E. sinensis<\/jats:italic> is typically farmed in rice-crab symbiosis, as an important ecological farming model. However, <jats:italic>E. sinensis<\/jats:italic> is often exposed to a high ammonia environment due to the application of nitrogen fertilizers essential for rice growth. We investigated the molecular mechanisms in the gills of <jats:italic>E. sinensis<\/jats:italic> exposed to high ammonia at transcriptional and histological levels. We randomly assigned <jats:italic>E. sinensis<\/jats:italic> to two groups (control group, CG; ammonia stress group, AG), and gill samples were excised from the CG and AG groups for histopathological and transcriptome analyses. The histopathological evaluation revealed that ammonia stress damaged the gills of <jats:italic>E. sinensis<\/jats:italic>. The transcriptome analysis showed that some essential genes, including <jats:italic>Xanthine dehydrogenase<\/jats:italic> (<jats:italic>XDH<\/jats:italic>), <jats:italic>Ubiquitin C-terminal hydrolase-L3<\/jats:italic> (<jats:italic>UCHL3<\/jats:italic>), <jats:italic>O-linked N-acetylglucosamine transferase<\/jats:italic> (<jats:italic>OGT<\/jats:italic>), <jats:italic>Cathepsin B<\/jats:italic> (<jats:italic>CTSB<\/jats:italic>), and <jats:italic>Ubiquitin-conjugating enzyme E2 W<\/jats:italic> (<jats:italic>UBE2W<\/jats:italic>) changed significantly during ammonia exposure. These genes are related to ammonia detoxification, the immune response, and apoptosis. This study demonstrated the molecular response mechanism of <jats:italic>E. sinensis<\/jats:italic> gills to ammonia stress at the transcriptional and histological levels. This study provides insight for further study on the molecular mechanism of ammonia stress in crustaceans and supplies technical support for rice crab symbiosis.<\/jats:p>","DOI":"10.7717\/peerj.16786","type":"journal-article","created":{"date-parts":[[2024,1,16]],"date-time":"2024-01-16T09:10:54Z","timestamp":1705396254000},"page":"e16786","source":"Crossref","is-referenced-by-count":0,"title":["Transcriptome analysis of Chinese mitten crabs (<i>Eriocheir sinensis<\/i>) gills in response to ammonia stress"],"prefix":"10.7717","volume":"12","author":[{"given":"Zhengfei","family":"Wang","sequence":"first","affiliation":[{"name":"Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers Universtiy, Yancheng, Jiangsu Province, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yue","family":"Wang","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers Universtiy, Yancheng, Jiangsu Province, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yayun","family":"Guan","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers Universtiy, Yancheng, Jiangsu Province, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhuofan","family":"Chen","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers Universtiy, Yancheng, Jiangsu Province, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yaotong","family":"Zhai","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers Universtiy, Yancheng, Jiangsu Province, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ya","family":"Wu","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ying","family":"Zhou","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers Universtiy, Yancheng, Jiangsu Province, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinghao","family":"Hu","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers Universtiy, Yancheng, Jiangsu Province, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4452-045X","authenticated-orcid":true,"given":"Lulu","family":"Chen","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers Universtiy, Yancheng, Jiangsu Province, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"4443","published-online":{"date-parts":[[2024,1,16]]},"reference":[{"issue":"9","key":"10.7717\/peerj.16786\/ref-1","doi-asserted-by":"publisher","first-page":"1355","DOI":"10.1016\/j.chemosphere.2008.04.037","article-title":"Sublethal ammonia exposure of Nile tilapia (Oreochromis niloticus L.): effects on gill, liver and kidney histology","volume":"72","author":"Benli","year":"2008","journal-title":"Chemosphere"},{"issue":"3\u20134","key":"10.7717\/peerj.16786\/ref-2","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/0166-445X(93)90059-A","article-title":"Hemolymph PCO2, hemocyanin, protein levels and urea excretions of Penaeus monodon exposed to ambient ammonia","volume":"27","author":"Chen","year":"1993","journal-title":"Aquatic Toxicology"},{"issue":"4","key":"10.7717\/peerj.16786\/ref-3","doi-asserted-by":"publisher","first-page":"1343","DOI":"10.1016\/j.foodchem.2006.10.047","article-title":"Compositional characteristics and nutritional quality of Chinese mitten crab (Eriocheir sinensis)","volume":"103","author":"Chen","year":"2006","journal-title":"Food Chemistry"},{"issue":"3","key":"10.7717\/peerj.16786\/ref-4","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1016\/j.cbpc.2004.03.013","article-title":"Increase of uricogenesis in the kuruma shrimp Marsupenaeus japonicus reared under hyper-osmotic conditions","volume":"138","author":"Cheng","year":"2004","journal-title":"Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology"},{"issue":"3","key":"10.7717\/peerj.16786\/ref-5","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/j.ecoenv.2019.04.033","article-title":"Ammonia toxicity in the mud crab (Scylla paramamosain): the mechanistic insight from physiology to transcriptome analysis","volume":"179","author":"Cheng","year":"2019","journal-title":"Ecotoxicology and Environmental Safety"},{"key":"10.7717\/peerj.16786\/ref-6","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1016\/j.fsi.2021.10.017","article-title":"Effects of chitin from Daphnia similis and its derivative, chitosan on the immune response and disease resistance of white shrimp, Litopenaeus vannamei","volume":"119","author":"Cheng","year":"2021","journal-title":"Fish and Shellfish Immunology"},{"key":"10.7717\/peerj.16786\/ref-7","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1016\/j.fsi.2020.01.014","article-title":"Probiotic, Bacillus subtilis E20 alters the immunity of white shrimp, Litopenaeus vannamei via glutamine metabolism and hexosamine biosynthetic pathway","volume":"98","author":"Chien","year":"2020","journal-title":"Fish and Shellfish Immunology"},{"issue":"11","key":"10.7717\/peerj.16786\/ref-8","doi-asserted-by":"publisher","first-page":"1684","DOI":"10.1261\/rna.046011.114","article-title":"Power analysis and sample size estimation for RNA-seq differential expression","volume":"20","author":"Ching","year":"2014","journal-title":"RNA"},{"issue":"3","key":"10.7717\/peerj.16786\/ref-9","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1007\/s40071-019-0232-y","article-title":"Ammonia toxicity in Southern King Crab (Lithodes santolla, Molina 1742) larvae","volume":"11","author":"Diodato","year":"2019","journal-title":"International Aquatic Research"},{"issue":"1","key":"10.7717\/peerj.16786\/ref-10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/gcc.2870040102","article-title":"TP53 tumor suppressor gene: a model for investigating human mutagenesis","volume":"4","author":"Fromentel","year":"1992","journal-title":"Genes, Chromosomes and Cancer"},{"issue":"11","key":"10.7717\/peerj.16786\/ref-11","doi-asserted-by":"publisher","first-page":"3640","DOI":"10.1021\/es052537o","article-title":"Cathepsin B and glutathione peroxidase show differing transcriptional responses in the grass shrimp, Palaemonetes pugio following exposure to three xenobiotics","volume":"40","author":"Griffitt","year":"2006","journal-title":"Environmental Science & Technology"},{"issue":"4","key":"10.7717\/peerj.16786\/ref-12","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1016\/j.cbpc.2013.03.001","article-title":"Gene expression of apoptosis-related genes, stress protein and antioxidant enzymes in hemocytes of white shrimp Litopenaeus vannamei under nitrite stress","volume":"157","author":"Guo","year":"2013","journal-title":"Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology"},{"key":"10.7717\/peerj.16786\/ref-13","doi-asserted-by":"publisher","first-page":"1494","DOI":"10.1038\/nprot.2013.084","article-title":"D. novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis","volume":"8","author":"Haas","year":"2013","journal-title":"Nature Protocols"},{"issue":"8","key":"10.7717\/peerj.16786\/ref-14","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1007\/s003600100219","article-title":"Ammonia uptake and its effects on ionoregulation in the freshwater crayfish Pacifastacus leniusculus (Dana)","volume":"171","author":"Harris","year":"2001","journal-title":"Journal of Comparative Physiology B"},{"key":"10.7717\/peerj.16786\/ref-15","doi-asserted-by":"publisher","first-page":"431","DOI":"10.3389\/fphys.2012.00431","article-title":"Multiple functions of the crustacean gill: osmotic\/ionic regulation, acid-base balance, ammonia excretion, and bioaccumulation of toxic metals","volume":"3","author":"Henry","year":"2012","journal-title":"Frontiers in Physiology"},{"issue":"3","key":"10.7717\/peerj.16786\/ref-16","first-page":"412","article-title":"Effects of ammonia nitrogen stress on immune indices and hepatopancreas structure of Eriocheir sinensis","volume":"14","author":"Hong","year":"2007a","journal-title":"Journal of Fishery Sciences of China"},{"issue":"3","key":"10.7717\/peerj.16786\/ref-17","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1016\/j.cbpc.2007.01.003","article-title":"Metabolic and immune responses in Chinese mitten-handed crab (Eriocheir sinensis) juveniles exposed to elevated ambient ammonia","volume":"145","author":"Hong","year":"2007b","journal-title":"Comparative Biochemistry and Physiology, Part C"},{"key":"10.7717\/peerj.16786\/ref-18","doi-asserted-by":"publisher","first-page":"105903","DOI":"10.1016\/j.aquatox.2021.105903","article-title":"Ammonia exposure induces endoplasmic reticulum stress and apoptosis in Chinese striped-necked turtles (Mauremys sinensis)","volume":"237","author":"Huang","year":"2021","journal-title":"Aquatic Toxicology"},{"key":"10.7717\/peerj.16786\/ref-19","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/S1546-5098(01)20005-3","article-title":"Ammonia toxicity, tolerance, and excretion","volume":"20","author":"Ip","year":"2001","journal-title":"Fish Physiology"},{"issue":"1","key":"10.7717\/peerj.16786\/ref-20","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1111\/are.12872","article-title":"Immune responses of Litopenaeus vannamei to non-ionic ammonia stress: a comparative study on shrimps in freshwater and seawater conditions","volume":"48","author":"Jia","year":"2017","journal-title":"Aquaculture Research"},{"issue":"1\u20134","key":"10.7717\/peerj.16786\/ref-21","doi-asserted-by":"publisher","first-page":"479","DOI":"10.1016\/j.aquaculture.2004.05.003","article-title":"Effects of temperature on acute toxicity of ammonia to Penaeus semisulcatus juveniles","volume":"241","author":"K\u0131r","year":"2004","journal-title":"Aquaculture"},{"issue":"1","key":"10.7717\/peerj.16786\/ref-22","doi-asserted-by":"publisher","first-page":"567183","DOI":"10.1111\/and.13474","article-title":"UBE2W down-regulation promotes cell apoptosis and correlates with hypospermatogenesis","volume":"52","author":"Lei","year":"2020","journal-title":"Andrologia"},{"issue":"1\u20132","key":"10.7717\/peerj.16786\/ref-23","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/j.dci.2012.03.016","article-title":"Recent advances in researches on the innate immunity of shrimp in China","volume":"39","author":"Li","year":"2013","journal-title":"Developmental & Comparative Immunology"},{"issue":"1","key":"10.7717\/peerj.16786\/ref-24","doi-asserted-by":"publisher","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 and Shellfish Immunology"},{"issue":"17","key":"10.7717\/peerj.16786\/ref-25","doi-asserted-by":"publisher","first-page":"734328","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"},{"issue":"9","key":"10.7717\/peerj.16786\/ref-26","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1242\/jeb.204.9.1605","article-title":"Reduction in the rates of protein and amino acid catabolism to slow down the accumulation of endogenous ammonia: a strategy potentially adopted by mudskippers (Periophthalmodon schlosseri and Boleophthalmus boddaerti) during aerial exposure in constant darkness","volume":"204","author":"Lim","year":"2001","journal-title":"Journal of Experimental Biology"},{"key":"10.7717\/peerj.16786\/ref-27","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1016\/j.aquaculture.2014.05.029","article-title":"Effects of ammonia exposure on nitrogen metabolism in gills and hemolymph of the swimming crab Portunus trituberculatus","volume":"432","author":"Liu","year":"2014","journal-title":"Aquaculture"},{"issue":"4","key":"10.7717\/peerj.16786\/ref-28","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of relative gene expression data using real-time quantitative pcr and the 2\u2212\u0394\u0394CT method","volume":"25","author":"Livak","year":"2001","journal-title":"Methods"},{"issue":"3","key":"10.7717\/peerj.16786\/ref-29","doi-asserted-by":"publisher","first-page":"e0173835","DOI":"10.1371\/journal.pone.0173835","article-title":"Estimation of genetic parameters and genotype-by-environment interactions related to acute ammonia stress in Pacific white shrimp (Litopenaeus vannamei) juveniles at two different salinity levels","volume":"12","author":"Lu","year":"2017","journal-title":"PLOS ONE"},{"key":"10.7717\/peerj.16786\/ref-30","doi-asserted-by":"publisher","first-page":"757602","DOI":"10.3389\/fmars.2021.757602","article-title":"Long-term ammonia toxicity in the hepatopancreas of swimming crab Portunus trituberculatus: cellular stress response and tissue damage","volume":"8","author":"Lu","year":"2022","journal-title":"Frontiers in Marine Science"},{"issue":"9","key":"10.7717\/peerj.16786\/ref-31","doi-asserted-by":"publisher","first-page":"927","DOI":"10.1016\/j.aquatox.2021.105903","article-title":"Effects of acute and chronic toxicity of unionized ammonia on mud crab, Scylla serrata (Forssk\u00e5l, 1755) larvae","volume":"36","author":"Luke","year":"2005","journal-title":"Aquaculture Research"},{"issue":"2","key":"10.7717\/peerj.16786\/ref-32","doi-asserted-by":"publisher","first-page":"533","DOI":"10.1007\/s10499-021-00828-w","article-title":"The effects of ammonia exposure on immune response, oxidative stress, and apoptosis in Procambarus clarkii","volume":"30","author":"Luo","year":"2022","journal-title":"Aquaculture International"},{"issue":"8","key":"10.7717\/peerj.16786\/ref-33","doi-asserted-by":"publisher","first-page":"622","DOI":"10.1038\/nrm2217","article-title":"Lysosomes: fusion and function","volume":"8","author":"Luzio","year":"2007","journal-title":"Nature Reviews Molecular Cell Biology"},{"issue":"2","key":"10.7717\/peerj.16786\/ref-34","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1016\/j.cbpa.2011.06.012","article-title":"Effects of high environmental ammonia on branchial ammonia excretion rates and tissue Rh-protein mRNA expression levels in seawater acclimated Dungeness crab Metacarcinus magister","volume":"160","author":"Martin","year":"2011","journal-title":"Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology"},{"issue":"1","key":"10.7717\/peerj.16786\/ref-35","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1146\/annurev-biochem-061516-044916","article-title":"Mechanisms of deubiquitinase specificity and regulation","volume":"86","author":"Mevissen","year":"2017","journal-title":"Annual Review of Biochemistry"},{"issue":"7","key":"10.7717\/peerj.16786\/ref-36","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1038\/nmeth.1226","article-title":"Mapping and quantifying mammalian transcriptomes by RNA-Seq","volume":"5","author":"Mortazavi","year":"2008","journal-title":"Nature Methods"},{"issue":"9","key":"10.7717\/peerj.16786\/ref-37","doi-asserted-by":"publisher","first-page":"1511","DOI":"10.1242\/jeb.00283","article-title":"Evolution of glutamine synthetase in vertebrates: multiple glutamine synthetase genes expressed in rainbow trout (Oncorhynchus mykiss)","volume":"206","author":"Murray","year":"2003","journal-title":"Journal of Experimental Biology"},{"issue":"4","key":"10.7717\/peerj.16786\/ref-38","doi-asserted-by":"publisher","first-page":"957","DOI":"10.1007\/s11802-018-3574-y","article-title":"Levels of metabolic enzymes and nitrogenous compounds in the swimming crab Portunus trituberculatus exposed to elevated ambient ammonia-N","volume":"17","author":"Pan","year":"2018","journal-title":"Journal of Ocean University of China"},{"issue":"6","key":"10.7717\/peerj.16786\/ref-39","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1016\/j.aquaculture.2014.08.008","article-title":"Digital gene expression analysis in the gills of the swimming crab (Portunus trituberculatus) exposed to elevated ambient ammonia-N","volume":"434","author":"Ren","year":"2014","journal-title":"Aquaculture"},{"issue":"6","key":"10.7717\/peerj.16786\/ref-40","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1016\/j.cbpa.2015.04.013","article-title":"Ammonia and urea excretion in the swimming crab Portunus trituberculatus exposed to elevated ambient ammonia-N","volume":"187","author":"Ren","year":"2015","journal-title":"Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology"},{"issue":"1\u20134","key":"10.7717\/peerj.16786\/ref-41","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1016\/j.aquaculture.2007.01.035","article-title":"Ontogenetic changes in tolerance to acute ammonia exposure and associated gill histological alterations during early juvenile development of the blue swimmer crab, Portunus pelagicus","volume":"266","author":"Romano","year":"2007","journal-title":"Aquaculture"},{"issue":"1","key":"10.7717\/peerj.16786\/ref-42","doi-asserted-by":"publisher","first-page":"2013","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":"Reviews in Fisheries Science"},{"article-title":"Rice-fish culture in the Mekong Delta, Vietnam: constraint analysis and adaptive research","year":"1998","author":"Rothuis","key":"10.7717\/peerj.16786\/ref-43"},{"issue":"2","key":"10.7717\/peerj.16786\/ref-44","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1016\/S1096-4959(02)00145-8","article-title":"Role of amino acid metabolism in an air-breathing catfish, Clarias batrachus in response to exposure to a high concentration of exogenous ammonia","volume":"133","author":"Saha","year":"2002","journal-title":"Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology"},{"issue":"8","key":"10.7717\/peerj.16786\/ref-45","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1016\/j.fsi.2019.11.060","article-title":"Comparative transcriptome analysis of the gills of Procambarus clarkii provide novel insights into the response mechanism of ammonia stress tolerance","volume":"96","author":"Shen","year":"2021","journal-title":"Fish and Shellfish Immunology"},{"issue":"4","key":"10.7717\/peerj.16786\/ref-46","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1016\/j.aquatox.2014.06.018","article-title":"Gill remodeling in three freshwater teleosts in response to high environmental ammonia","volume":"155","author":"Sinha","year":"2014","journal-title":"Aquatic Toxicology"},{"key":"10.7717\/peerj.16786\/ref-47","doi-asserted-by":"publisher","first-page":"6053","DOI":"10.21203\/rs.3.rs-985862\/v1","article-title":"The effects of ammonia stress exposure on protein degradation, immune response, degradation of nitrogen-containing compounds and energy metabolism of Chinese mitten crab","volume":"49","author":"Tang","year":"2022","journal-title":"Molecular Biology Reports"},{"issue":"5","key":"10.7717\/peerj.16786\/ref-48","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1016\/j.foodchem.2018.10.137","article-title":"Nitrogen fertilizer at heading stage effectively compensates for the deterioration of rice quality by affecting the starch-related properties under elevated temperatures","volume":"277","author":"Tang","year":"2019","journal-title":"Food Chemistry"},{"issue":"5","key":"10.7717\/peerj.16786\/ref-49","doi-asserted-by":"publisher","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":"Nature Biotechnology"},{"issue":"19","key":"10.7717\/peerj.16786\/ref-50","doi-asserted-by":"publisher","first-page":"105989","DOI":"10.1016\/j.aquatox.2021.105989","article-title":"Immune defense, detoxification, and metabolic changes in juvenile Eriocheir sinensis exposed to acute ammonia","volume":"240","author":"Wang","year":"2021","journal-title":"Aquatic Toxicology"},{"issue":"1","key":"10.7717\/peerj.16786\/ref-51","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1007\/s003600050190","article-title":"Potential of active excretion of ammonia in three different haline species of crabs","volume":"169","author":"Weihrauch","year":"1999","journal-title":"Journal of Comparative Physiology B"},{"issue":"18","key":"10.7717\/peerj.16786\/ref-52","doi-asserted-by":"publisher","first-page":"2765","DOI":"10.1242\/jeb.205.18.2765","article-title":"Active ammonia excretion across the gills of the green shore crab Carcinus maenas: participation of Na(+)\/K(+)-ATPase, V-type H(+)-ATPase and functional microtubules","volume":"205","author":"Weihrauch","year":"2002","journal-title":"Journal of Experimental Biology"},{"issue":"7","key":"10.7717\/peerj.16786\/ref-53","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1016\/j.ecoenv.2019.05.029","article-title":"Stress response and tolerance mechanisms of ammonia exposure based on transcriptomics and metabolomics in Litopenaeus vannamei","volume":"180","author":"Xiao","year":"2019","journal-title":"Ecotoxicology and Environmental Safety"},{"issue":"9","key":"10.7717\/peerj.16786\/ref-54","doi-asserted-by":"publisher","first-page":"1441","DOI":"10.1007\/s10646-020-02279-0","article-title":"Hemocytes transcriptomes reveal metabolism changes and detoxification mechanisms in response to ammonia stress in Octopus minor","volume":"29","author":"Xu","year":"2020","journal-title":"Ecotoxicology"},{"issue":"3","key":"10.7717\/peerj.16786\/ref-55","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1016\/S2095-3119(13)60722-4","article-title":"Effect of different rice-crab coculture modes on soil carbohydrates","volume":"13","author":"Yan","year":"2013","journal-title":"Journal of Integrative Agriculture"},{"issue":"6","key":"10.7717\/peerj.16786\/ref-56","doi-asserted-by":"publisher","first-page":"404","DOI":"10.1016\/j.ygeno.2018.09.001","article-title":"Transcriptomic evidence of adaptive tolerance to high environmental ammonia in mudskippers","volume":"110","author":"You","year":"2018","journal-title":"Genomics"},{"issue":"2","key":"10.7717\/peerj.16786\/ref-57","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1007\/BF01313716","article-title":"Effect of ammonia on survival and osmoregulation in different life stages of the lobster Homarus americanus","volume":"110","author":"Young-Lai","year":"1991","journal-title":"Marine Biology"},{"issue":"3","key":"10.7717\/peerj.16786\/ref-58","doi-asserted-by":"publisher","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":"Comparative Biochemistry and Physiology, Part A"},{"issue":"1","key":"10.7717\/peerj.16786\/ref-59","doi-asserted-by":"publisher","first-page":"25","DOI":"10.4137\/BCBCR.S32783","article-title":"A review of systemic treatment in metastatic triple-negative breast cancer","volume":"10","author":"Zeichner","year":"2016","journal-title":"Breast Cancer (Auckl)"},{"key":"10.7717\/peerj.16786\/ref-60","doi-asserted-by":"publisher","first-page":"797241","DOI":"10.3389\/fmars.2021.797241","article-title":"Physiological and molecular responses in the gill of the swimming crab Portunus trituberculatus during long-term ammonia stress","volume":"8","author":"Zhang","year":"2021","journal-title":"Frontiers in Marine Science"},{"key":"10.7717\/peerj.16786\/ref-61","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1016\/j.fsi.2022.01.009","article-title":"Molecular characteristics and immune function of ubiquitin C-terminal hydrolase-L3 in Macrobrachium nipponense","volume":"121","author":"Zhu","year":"2022","journal-title":"Fish and Shellfish Immunology"}],"container-title":["PeerJ"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/peerj.com\/articles\/16786.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/16786.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/16786.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/16786.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,16]],"date-time":"2024-01-16T09:11:08Z","timestamp":1705396268000},"score":1,"resource":{"primary":{"URL":"https:\/\/peerj.com\/articles\/16786"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1,16]]},"references-count":61,"alternative-id":["10.7717\/peerj.16786"],"URL":"https:\/\/doi.org\/10.7717\/peerj.16786","archive":["CLOCKSS","LOCKSS","Portico"],"relation":{},"ISSN":["2167-8359"],"issn-type":[{"type":"electronic","value":"2167-8359"}],"subject":[],"published":{"date-parts":[[2024,1,16]]},"article-number":"e16786"}}