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Characterization of gill transcriptome, SSR/SNP markers and expression analysis of lysozyme LysC gene from Carassius auratus upon Aeromonas hydrophila infection 嗜水气单胞菌感染鲫鱼鳃转录组、SSR/SNP标记及溶菌酶LysC基因表达分析
Q1 Agricultural and Biological Sciences Pub Date : 2023-09-01 DOI: 10.1016/j.aaf.2023.08.011
Meijuan Shi, Xiucai Hu, Rongrong Liu, Yanjing Yang, Aijun Lv
The gills are large mucosal surfaces and play primary roles in respiration and immune defences. However, the molecular mechanism for gills of fish needs still to be explored. In the present study, transcriptomic analysis and identification of SSR and SNP markers were performed in the gills of crucian carp Carassius auratus. The results showed a total of 84,259 unigenes were annotated to NCBI NR, KEGG and GO databases for 55,283, 39,303, 33,388, respectively. Enriched KEGG pathway analyses for the identified genes showed the mainly functional modules such as metabolism, cellular processes, environmental adaptation, genetic processing, organismal and immune systems. Moreover, 22,102 SSRs (simple sequence repeats) were potentially identified and 9776 (44.2%) were accounted for the most dinucleotides. Transition and transversion sites of SNPs (single nucleotide polymorphisms) were also observed. Tissue distribution showed that the expression level of lysozyme LysC gene was relatively high in intestine, liver, spleen and kidney tissues and up-regulated in gills, skin and brain after the A. hydrophila infection. We discovered the immune-related pathways through the transcriptome analysis in the gills of crucian carp, some potential SSR/SNP markers were identified, and lysozyme gene predominantly expressed in mucosal immune organs (eg., gills, skin, intestine) responded to A. hydrophila infection. To the best of our knowledge, this was the detailed report on the molecular characteristics in crucian carp gills with transcriptome analysis, which will not only provide a scientific reference for further understanding the local defense mechanism, but also lay a foundation for molecular marker-assisted breeding in fish.
鳃是大的粘膜表面,在呼吸和免疫防御中起主要作用。然而,鱼鳃的分子机制仍有待进一步研究。本研究对鲫鱼鳃进行了转录组学分析及SSR和SNP标记的鉴定。结果显示,共有84259个unigenes被注释到NCBI NR、KEGG和GO数据库中,分别为55,283、39,303和33,388个。富集的KEGG通路分析显示,所鉴定基因的主要功能模块包括代谢、细胞过程、环境适应、遗传加工、机体和免疫系统。此外,潜在鉴定的简单序列重复序列为22102个,其中二核苷酸最多的为9776个(44.2%)。单核苷酸多态性(snp)的过渡位点和翻转位点也被观察到。组织分布表明,溶菌酶LysC基因在嗜水单胞菌感染后,在肠、肝、脾和肾组织中表达量较高,在鳃、皮肤和脑组织中表达量上调。我们通过对鲫鱼鳃的转录组分析,发现了与免疫相关的途径,鉴定出了一些潜在的SSR/SNP标记,溶菌酶基因主要表达于粘膜免疫器官(如;(鳃、皮肤、肠道)对嗜水单胞杆菌感染有反应。据我们所知,这是利用转录组分析对鲫鱼鳃的分子特征进行的详细报道,这不仅将为进一步了解鲫鱼鳃的局部防御机制提供科学参考,也将为鱼类分子标记辅助育种奠定基础。
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引用次数: 0
Impact assessment of biofouling resistant nano copper oxide–polyaniline coating on aquaculture cage nets 耐生物污纳米氧化铜聚苯胺涂层对养殖笼网的影响评价
Q1 Agricultural and Biological Sciences Pub Date : 2023-09-01 DOI: 10.1016/j.aaf.2022.01.002
Pachareentavita Muhamed Ashraf , Nalini Manju Lekshmi , Shunmugavel Chinnadurai , Sajeevan Anjitha , Mathath Archana , Chirayil Meethalepurayil Vineeth Kumar , Kavitha Mandhiram Sandhya , Ambarish Purackattu Gop

Biofouling is a major issue in aquaculture cages and nano materials based antifouling strategies became more prominent in recent years. Polyethylene aquaculture cage net surface which is modified with polyaniline and nano-copper oxide (CuO), reported to have biofouling resistance. Leaching of nano CuO from the net to the aquatic environment and its bioaccumulation in fish is the major concern against the technology adoption. The present study aimed to understand the accumulation of copper in fishes grown in a nano CuO treated aquaculture cage net. Studied the leaching pattern of nano CuO, biofouling inhibition and changes in strength of the cage net due to the nano CuO treatments. Fishes grown in the treated cages exhibited normal growth characteristics with no signs of abnormalities and also copper in their organs were within the prescribed standard limit. The CuO treated cage net exhibited excellent biofouling resistance and the percentage of occlusion of mesh by foulers were 56.77% more efficient than untreated cage net. Rate of nano CuO leached to the aquatic system was less than 8 μg/g·d. The fouling organism assemblage on untreated and treated net was 18 and 11 species, respectively. Major calcareous shelled foulers were absent on treated nets. The study highlighted the potential application of nano CuO treatment to control biofouling in aquaculture cages.

生物污垢是水产养殖网箱中的一个主要问题,近年来基于纳米材料的防污策略变得更加突出。用聚苯胺和纳米氧化铜(CuO)对聚乙烯养殖网箱网表面进行改性,研究表明其具有生物防污性能。纳米CuO从网中浸出到水生环境中及其在鱼类中的生物累积是阻碍该技术采用的主要问题。本研究旨在了解在纳米CuO处理的水产养殖网箱中生长的鱼类体内铜的积累。研究了纳米CuO的浸出模式、生物结垢抑制以及纳米CuO处理对网箱网强度的影响。在处理过的网箱中生长的鱼类表现出正常的生长特征,没有异常迹象,其器官中的铜也在规定的标准限度内。CuO处理的笼网表现出优异的生物污垢抗性,污垢对网眼的堵塞率比未处理的笼网高56.77%。纳米CuO对水体的浸出率小于8μg/g·d。未处理网和处理网的污染生物群落分别为18种和11种。经过处理的渔网上没有主要的钙质外壳污垢。该研究强调了纳米CuO处理在控制水产养殖网箱生物淤积方面的潜在应用。
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引用次数: 2
Assessing methods for multiple imputation of systematic missing data in marine fisheries time series with a new validation algorithm 用一种新的验证算法评估海洋渔业时间序列中系统缺失数据的多重插补方法
Q1 Agricultural and Biological Sciences Pub Date : 2023-09-01 DOI: 10.1016/j.aaf.2021.12.013
Iván F. Benavides , Marlon Santacruz , Jhoana P. Romero-Leiton , Carlos Barreto , John Josephraj Selvaraj

Time series from fisheries often contain multiple missing data. This is a severe limitation that prevents using the data for research on population dynamics, stock assessment, forecasting, and, hence, decision-making around marine resources. Several methods have been proposed to impute missing data in univariate time series. Still, their performances depend not only on the amount of missing data but also on the data structure. This study compares the performance of twelve imputation methods on the time series of marine fishery landings for six species in the Colombian Pacific Ocean. Unlike other studies, we validate the precision of the imputations in the same target time series that include missing data, using the Known Sub-Sequence Algorithm (KSSA), a novelty validation approach that simulates missing data in known sub-sequences of the target time series. The results showed that the best methods for imputation are Seasonal Decomposition with Kalman filters and Structural Models with Kalman filters fitted by maximum likelihood. Results also show that validating the imputation methods with other time series different to the target time series, leads to wrong imputation methods choices. It is noteworthy that these methods and also the validation framework are mainly suited to time series with non-random distribution of missing data, this is, missing data produced systematically in chunks or clusters with predictable frequency, which are common in marine sciences.

渔业的时间序列通常包含多个缺失的数据。这是一个严重的限制,阻碍了将数据用于种群动态研究、种群评估、预测,从而阻碍了围绕海洋资源的决策。已经提出了几种方法来估算单变量时间序列中的缺失数据。尽管如此,它们的性能不仅取决于丢失数据的数量,还取决于数据结构。本研究比较了12种插补方法对哥伦比亚太平洋六个物种海洋渔业登陆时间序列的表现。与其他研究不同,我们使用已知子序列算法(KSSA)验证了包括缺失数据的同一目标时间序列中的输入精度,该算法是一种新颖的验证方法,模拟了目标时间序列的已知子序列中的缺失数据。结果表明,最佳的插补方法是使用卡尔曼滤波器的季节分解和使用最大似然拟合的卡尔曼滤波器的结构模型。结果还表明,用不同于目标时间序列的其他时间序列验证插补方法,会导致插补方法的选择错误。值得注意的是,这些方法和验证框架主要适用于缺失数据非随机分布的时间序列,也就是说,以可预测频率系统生成的大块或集群中的缺失数据,这在海洋科学中很常见。
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引用次数: 5
Germ cell development in teleost gonads 远洋性腺中生殖细胞的发育
Q1 Agricultural and Biological Sciences Pub Date : 2023-08-18 DOI: 10.1016/j.aaf.2023.07.002
Partigya Sharma, Shriya Purohit, Sachin Kothiyal, Indrashis Bhattacharya

Among vertebrate species, fishes are considered to be the most developmentally diverse taxa exhibiting remarkable gonadal plasticity with capacity of sex reversal. Sex determination in teleost fishes is governed via a complex regulatory network involving multiple genetic, environmental (temperature, population density, pH), social interaction/stress factors. Piscine germ-line originates as Primordial germ cells (PGC) from cleavage blastomeres/endoderm and gets specified by maternal inheritance of Vasa, Nanos, Tdrds, Dnd, Dazl etc and subsequently migrates to reach the embryonic gonadal primordium. Post-hatching, mitotically active germ cells (Gc) continue to proliferate via two distinct pathways-firstly, stem cell-like mode followed by meiosis-committed cystic division. In Japanese rice fish medaka, Oryzias latipes sex gets determined on the chromosomal basis, where XY becomes a male because of testicular Dmy transcription and XX develops as female owing to Gc restricted Foxl3 expression. Sex specific germ-line stem cell systems also have been found in adult O. latipes. Intriguingly in teleost fishes, the developmental fate of transplanted Gc do not depend on the sex of the donor rather solely relies upon the sex of the recipient. Furthermore, sexually mature piscine gonads remain developmentally plastic showing extensive responsiveness towards sex steroids. The critical regulation of gonadal differentiation is directed by female specific 17β-estradiol (E2) and bio-active male androgen 11-keto-testosretone (11-kT). Various transcription factors (TFs) e.g.- Dmrt1, DAX1, Ad4BP/SF-1, Foxl2 regulate the bio-conversion rate of testosterone (T) to either E2 or 11-kT. Similarly, multiple endocrine factors (EFs) e.g.- LH, FSH, E2, 11-kT and growth factors (GFs) e.g- AMH, GSDF, IGF-1/3, GDF-9/BMP-15 critically induce Gc differentiation to regulate the gametogenic output. In this article we have precisely discussed the endocrine regulation of Gc development during gonadal maturation of teleosts.

在脊椎动物中,鱼类被认为是发育最多样化的类群,具有显著的性腺可塑性和性别逆转能力。远志鱼类的性别决定受复杂的调控网络控制,涉及多种遗传、环境(温度、种群密度、酸碱度)、社会互动/压力因素。鱼类的生殖细胞系(PGC)起源于卵裂胚泡/内胚层的原始生殖细胞(Primordial germ cells),由母体遗传的 Vasa、Nanos、Tdrds、Dnd、Dazl 等指定,随后迁移到胚胎性腺原基。孵化后,有丝分裂活跃的生殖细胞(Gc)继续通过两种不同的途径增殖--首先是干细胞模式,然后是减数分裂承诺的囊状分裂。在日本稻鱼青鳉(Oryzias latipes)中,性别是由染色体决定的,其中 XY 因睾丸 Dmy 转录而成为雄性,XX 则因 Gc 受限的 Foxl3 表达而发育为雌性。在长尾鳕成体中也发现了性别特异性生殖系干细胞系统。有趣的是,在远洋鱼类中,移植的 Gc 的发育命运并不取决于供体的性别,而完全取决于受体的性别。此外,性成熟的鱼类性腺在发育过程中仍具有可塑性,对性类固醇具有广泛的反应性。性腺分化的关键调控因素是雌性特异性 17β-雌二醇(E2)和具有生物活性的雄性雄激素 11-酮-雌酮(11-kT)。各种转录因子(TFs),如 Dmrt1、DAX1、Ad4BP/SF-1 和 Foxl2 可调节睾酮(T)向 E2 或 11-kT 的生物转换率。同样,多种内分泌因子(EFs),如 LH、FSH、E2、11-kT 和生长因子(GFs),如 AMH、GSDF、IGF-1/3、GDF-9/BMP-15,也能关键性地诱导 Gc 分化,从而调节配子的产生。在这篇文章中,我们精确地讨论了在远洋鱼类性腺成熟过程中 Gc 发育的内分泌调控。
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引用次数: 0
Effects of dietary lipid levels on lipid accumulation and health status of adult Onychostoma macrolepis 膳食脂质水平对成年大鲤鱼脂质积累和健康状况的影响
Q1 Agricultural and Biological Sciences Pub Date : 2023-08-18 DOI: 10.1016/j.aaf.2023.07.008

The effects of different dietary lipid levels on lipid accumulation, inflammatory response, serum bio-chemical index and histological features of intestine and hepatopancreas of O. macrolepis was experimentally evaluated in an eight-weeks study. Fish (initial weight 50.11 ± 2.86 g) were fed with five iso-nitrogenous diets (around 390 g/kg protein) varying with lipid level (5%, 7%, 9%, 11%, 13%, being LL5, LL7, LL9, LL11, and LL13 respectively) in triplicates. Results showed that the content of crude lipid in carcass and hepatopancreas were not affected by dietary lipid levels (P > 0.05). Serum ALT, TP, HDL-c and MDA, etc., were not significantly affected by diets (P > 0.05), while serum total antioxidant capacity in LL9 and LL11 groups were significantly higher than the other groups (P < 0.05). Histological features of hepatopancreas and intestine showed no significant difference among the five diets (P > 0.05), while the height of intestine villus showed the higher trend in LL9 compared with other groups. The relative expression of lipid metabolism related genes (ppar α, cpt-1α, fas, and hsl) and immune response related genes (tlr 22, nrf 2, tnfα, and il-γ) in the hepatopancreas of fish fed diets differing in their crude lipid levels were not significantly different (P > 0.05). The results suggested that a proper dietary lipid level of 9%–11% could maintain higher antioxidant and health status of adult O.macrolepis.

在一项为期八周的研究中,实验评估了不同日粮脂质水平对大黄鱼脂质积累、炎症反应、血清生化指标以及肠道和肝胰脏组织学特征的影响。鱼(初始体重为 50.11 ± 2.86 克)被喂食五种等氮饲料(约 390 克/千克蛋白质),这些饲料的脂质含量各不相同(5%、7%、9%、11%、13%,分别为 LL5、LL7、LL9、LL11 和 LL13),每种饲料喂食三份。结果表明,胴体和肝胰脏中的粗脂含量不受日粮脂质水平的影响(P > 0.05)。血清 ALT、TP、HDL-c 和 MDA 等受日粮影响不明显(P > 0.05),而 LL9 和 LL11 组血清总抗氧化能力明显高于其他组(P < 0.05)。肝胰腺和肠道组织学特征在五种日粮中无显著差异(P > 0.05),而肠绒毛高度在 LL9 组较其他组有升高趋势。粗脂肪含量不同的日粮在鱼类肝胰脏中脂代谢相关基因(ppar α、cpt-1α、fas和hsl)和免疫反应相关基因(tlr 22、nrf 2、tnfα和il-γ)的相对表达量无显著差异(P > 0.05)。结果表明,9%-11%的适当膳食脂质水平可维持大菱鲆成鱼较高的抗氧化能力和健康状况。
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引用次数: 0
Efficacy of garlic and cinnamon as an alternative to chemotherapeutic agents in controlling Saprolegnia infection in Nile tilapia 大蒜和肉桂替代化疗药物控制尼罗罗非鱼腐殖菌感染的疗效
Q1 Agricultural and Biological Sciences Pub Date : 2023-08-01 DOI: 10.1016/j.aaf.2023.07.010
S. Aly, M. Elatta, Asmaa Nasr, M. Fathi
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引用次数: 1
High trophic similarity between non-native common carp and gibel carp in Turkish freshwaters: Implications for management 土耳其淡水中非本地鲤鱼和白鲢的高营养相似性:对管理的影响
Q1 Agricultural and Biological Sciences Pub Date : 2023-08-01 DOI: 10.1016/j.aaf.2023.08.003
S. Aksu, Ö. Emiroğlu, P. Balzani, J. Britton, E. Köse, I. Kurtul, S. Başkurt, Oğuzcan Mol, Emre Çınar, P. Haubrock, Pinar Oztopcu-Vatan, A. Tarkan
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引用次数: 1
The effect of variable light intensity in luminescent-netting pots on the catch of snow crab (Chionoecetes opilio) 不同光强对雪蟹捕获量的影响
Q1 Agricultural and Biological Sciences Pub Date : 2023-08-01 DOI: 10.1016/j.aaf.2023.08.001
Colin H. Frank, S. M. Bayse
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引用次数: 0
Bioeconomic analysis of the commercial production of Nile tilapia with biofloc and green water technologies 利用生物絮团和绿水技术进行尼罗罗非鱼商业化生产的生物经济分析
Q1 Agricultural and Biological Sciences Pub Date : 2023-08-01 DOI: 10.1016/j.aaf.2023.07.004
Berenice Suárez-Puerto, M. Araneda, M. Gullian-Klanian
{"title":"Bioeconomic analysis of the commercial production of Nile tilapia with biofloc and green water technologies","authors":"Berenice Suárez-Puerto, M. Araneda, M. Gullian-Klanian","doi":"10.1016/j.aaf.2023.07.004","DOIUrl":"https://doi.org/10.1016/j.aaf.2023.07.004","url":null,"abstract":"","PeriodicalId":36894,"journal":{"name":"Aquaculture and Fisheries","volume":"13 3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79469833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Transcriptomic and behavioral studies reveal that glutamate receptors are involved in depressive-like behavior in adult olive flounder Paralichthys olivaceus 转录组学和行为学研究表明,谷氨酸受体参与了成年橄榄比目鱼的抑郁样行为
Q1 Agricultural and Biological Sciences Pub Date : 2023-08-01 DOI: 10.1016/j.aaf.2023.08.002
Liangfang Liu, Tangsong Feng, Mengmeng Shi, Huafeng Zou, Weiqun Lu
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引用次数: 0
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Aquaculture and Fisheries
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