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Transcriptome analysis reveals immune-related genes in tissues of Vibrio anguillarum-infected turbot Scophthalmus maximus

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Journal of Oceanology and Limnology 2024年第1期42卷 332-344页

作者： Yuting SONG Maqsood Ahmed SOOMRO Xianzhi DONG Guobin HU college of marine life sciences Ocean University of ChinaQingdao 266003China institute of evolution&marine biodiversity Ocean University of ChinaQingdao 266003China institute of Biophysis Chinese Academy of SciencesBeijing 100101China

Turbot Scophthalmus maximus is an important mariculture fish species with high economic ***,the bacterial diseases caused by Vibrio anguillarum infection bring huge economic losses to the turbot aquaculture *** understand the immune response of the turbot against *** infection and to explore novel immune-related genes,the transcriptome analysis of turbot spleen and gills were conducted after *** *** expressed genes(DEGs)were identified in spleen and gill of the turbot amounted to 17261 and 16436,respectively.A large number of immunerelated DEGs were enriched in cytokine-cytokine receptor interaction signaling pathway,and the others by the kyoto encyclopedia of genes and genomes(KEGG)*** gene ontology(GO)classification analysis revealed that *** infection had the greatest effect on biological processes and cellular *** immune-related DEGs were identified in the spleen(cstl.1,egfl6,lamb21,v2rx4,calcr,and gpr78a)and gills(ghra,sh3gl2a,cst12,inhbaa,cxcl8,and il-1b)by heat *** proteinprotein interaction(PPI)networks were constructed to analyze the immune *** results demonstrate that the maturation and antigen processing of major histocompatibility complex(MHC)class II molecule,and calcitonin-or adrenomedullin-regulated physiological activity were important events in the immunity of turbot against *** *** the gills,the protein interactions in TGF-βsignaling pathway,production of inflammatory factors,and endocytosis regulation were most *** research laid a foundation for discovering novel immune-related genes and enriching the knowledge of immune mechanisms of turbot against *** infection.

关键词： Scophthalmus maximus Vibrio anguillarum transcriptome differentially expressed genes immune mechanism

Findings on three endocommensal scuticociliates(Protista,Ciliophora)from freshwater mollusks,including their morphology and molecular phylogeny with descriptions of two new species

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marine life Science & Technology 2024年第2期6卷 212-235页

作者： Tao Li Tengyue Zhang Mingjian Liu Zhe Zhang Jiachen Zhang Junhua Niu Xiangrui Chen Saleh A.Al‑Farraj Weibo Song institute of evolution and marine biodiversity Ocean University of China and Key Laboratory of Evolution and Marine Biodiversity(Ministry of Education)Qingdao 266003China The Key Laboratory of Zoological Systematics and Application College of Life SciencesHebei UniversityBaoding 071002China college of marine life sciences Ocean University of ChinaQingdao 266003China School of marine sciences Ningbo UniversityNingbo 315800China Zoology Department College of ScienceKing Saud University11451 RiyadhSaudi Arabia Laboratory for marine Biology and Biotechnology Laoshan LaboratoryQingdao 266237China

Species of the ciliate genera Myxophyllum and Conchophthirus are found as endocommensals of terrestrial and freshwater mollusks,*** far,there have been few studies of these genera and morphological data for most members are often *** the present work,two new species,Myxophyllum weishanense *** Conchophthirus paracurtus ***.,and a known species,Conchophthirus lamellidens,were isolated from hosts in Lake Weishan Wetland,*** studies indicate that *** *** be recognized mainly by the combination of about 60 somatic kineties on both ventral and dorsal sides and the presence of caudal *** paracurtus *** from congeners in its body shape and size,having a glabrous area on the posterior right side,and having fewer somatic *** addition,differences in their ITS2(Internally Transcribed Spacer 2)secondary structures support the discrimination of the two new species from their highly similar *** improved diagnosis for the poorly known species,***-lidens is also *** analyses reveal that members of the genus Myxophyllum belong to a fully supported clade that is sister to a large,poorly supported clade consisting of Hemispeiridae,Ancistridae,and several lineages of the nonmonophyletic *** Myxophyllum clade also includes Protophyra ovicola JQ956552,a possible *** of the two new Conchophthirus species cluster with other congeners in a fully supported clade that is unrelated to either the‘typical’thigmotrichs or to pleuronematids,thus conflicting with the traditional classification,and may represent an orphan scuticociliate lineage.

关键词： Ciliates Endocommensal ITS2 secondary structure Mollusks New taxa Wetland

RpL 38 modulates germ cell differentiation by controlling Bam expression in Drosophila testis

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Science China life sciences 2024年

作者： Yang Fang Fengchao Zhang Fangzhen Zhao Jiajia Wang Xinkai Cheng Fei Ye Jiayu He Long Zhao Ying Su Key Laboratory of evolution & marine biodiversity (Ministry of Education) and institute of evolution & marine biodiversity Ocean University of China college of marine life sciences Ocean University of China Fisheries college Ocean University of China

Switching from mitotic spermatogonia to meiotic spermatocytes is critical to producing haploid sperms during male germ cell differentiation. However, the underlying mechanisms of this switch remain largely unexplored. In Drosophila melanogaster, the gene RpL38encodes the ribosomal protein L38, one component of the 60S subunit of ribosomes. We found that its depletion in spermatogonia severely diminished the production of mature sperms and thus led to the infertility of male flies. By examining the germ cell differentiation in testes,we found that RpL38-knockdown blocked the transition from spermatogonia to spermatocytes and accumulated spermatogonia in the testis. To understand the intrinsic reason for this blockage, we conducted proteomic analysis for these spermatogonia populations. Differing from the control spermatogonia, the accumulated spermatogonia in RpL38-knockdown testes already expressed many spermatocyte markers but lacked many meiosis-related proteins, suggesting that spermatogonia need to prepare some important proteins for meiosis to complete their switch into spermatocytes. Mechanistically, we found that the expression of bag of marbles (bam), a crucial determinant in the transition from spermatogonia to spermatocytes, was inhibited at both the mRNA and protein levels upon RpL38 depletion. We also confirmed that the bam loss phenocopied RpL38 RNAi in the testis phenotype and transcriptomic profiling. Strikingly, overexpressing bam was able to fully rescue the testis abnormality and infertility of RpL38-knockdown flies, indicating that bam is the key effector downstream of RpL38 to regulate spermatogonia differentiation. Overall, our data suggested that germ cells start to prepare meiosis-related proteins as early as the spermatogonial stage, and RpL38 in spermatogonia is required to regulate their transition toward spermatocytes in a bamdependent manner, providing new knowledge for our understanding of the transition process from spermatogonia to spe

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Integrative analysis of transcriptomic profile reveals potential roles of miRNAs in regulating development of Marsupenaeus japonicas

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Journal of Oceanology and Limnology 2024年第1期42卷 201-215页

作者： Jing WANG Longjun PU Xiaojuan ZHANG Cuicui LIANG Dandan DONG Jiantao GUAN Huarong GUO Ministry of Education Key Laboratory of marine Genetics and Breeding College of Marine Life SciencesOcean University of ChinaQingdao 266003China institute of evolution&marine biodiversity Ocean University of ChinaQingdao 266003China Yellow Sea Fisheries Research institute Chinese Academy of Fishery SciencesQingdao 266071China

Regulation of microRNAs(miRNAs)on various biological processes has been a surprising and exciting *** of miRNAs is the first step to comprehensively understand their ***,attempts on global identification and functional verification of miRNAs are very limited in penaeid shrimp Marsupenaeus japonicus,an economically important aquatic *** performing an integrated analysis of transcriptomic profile from gastrula embryos of ***,21conserved miRNAs in ***(mja-miRNAs),belonging to 19 miRNA families,were identified and *** the 21 mja-miRNAs,15 miRNAs were successfully verified to be predominantly expressed in gastrula stage,where they displayed dynamic expression patterns compared with those in naupliuin *** on perfect or near-perfect match to target region,120 target genes were predicted at transcriptome-wide ***,gene ontology(GO)classification and metabolic pathway annotation revealed eight targets that were actively involved in developmental *** the predicted miRNA-mRNA pairs,six targets were then randomly selected and experimentally validated by dual luciferase reporter assay,where three pairs were proved with potential targeting ***,to search for conserved miRNAs potentially involved in early development of ***,we combined in silico and experimental methods,which can be applied in other organisms as *** data implied important roles of miRNAs in the early embryonic development and also suggested the presence of complex miRNA-mRNA functional networks in ***.

关键词： microRNAs(miRNAs) identification Marsupenaeus japonicus embryo transcriptome

An efficient method for constructing a random insertional mutant library for forward genetics in Nannochloropsis oceanica

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Journal of Oceanology and Limnology 2024年第1期42卷 216-225页

作者： Zhongyi ZHANG Hang LIU Xiaohui PAN Yanan ZONG Leili FENG Lixian LIU Li GUO Guanpin YANG college of marine life sciences Ocean University of ChinaQingdao 266003China institutes of evolution and marine biodiversity Ocean University of ChinaQingdao 266003China Key Laboratory of marine Genetics and Breeding of Ministry of Education Ocean University of ChinaQingdao 266003China

Insertional mutation,phenotypic evaluation,and mutated gene cloning are widely used to clone genes from *** genes can be integrated into the genome during non-homologous end joining(NHEJ)of the double-strand breaks of DNA,causing insertional *** random insertional mutant library constructed using this method has become a method of forward genetics for gene ***,the establishment of a random insertional mutant library requires a high transformation efficiency of exogenous *** microalgal species show a low transformation efficiency,making constructing random insertional mutant libraries *** this study,we established a highly efficient transformation method for constructing a random insertional mutant library of Nannochloropsis oceanica,and tentatively tried to isolate its genes to prove the feasibility of the method.A gene that may control the growth rate and cell size was *** method will facilitate the genetic studies of ***,which should also be a reference for other microalgal species.

关键词： Nannochloropsis oceanica genetic transformation random insertional mutant library zeocin pretreatment forward genetics

Temperate Stutzerimonas Phage Encoding Toxin-Antitoxin System Genes Represents a Novel Genus

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Journal of Ocean University of China 2024年第4期23卷 1087-1101页

作者： ZHANG Hong GUO Ruizhe GAO Chen ZHENG Kaiyang XIONG Yao DONG Yue LIU Yundan WANG Ziyue CHEN Ying WANG Hongmin SHAO Hongbing SUNG Yeong Yik MOK Wen Jye WONG Li Lian MCMINN Andrew WANG Min LIANG Yantao college of marine life sciences Institute of Evolution and Marine BiodiversityMOE Laboratory of Evolution and Marine BiodiversityFrontiers Science Center for Deep Ocean Multispheres and Earth SystemCenter for Ocean Carbon NeutralityOcean University of ChinaQingdao 266003China UMT-OUC Joint Center for marine Studies Qingdao 266003China institute of marine Biotechnology Universiti Malaysia Terengganu21030 Kuala TerengganuMalaysia institute for marine and Antarctic Studies University of TasmaniaHobartTAS 7001Australia Haide college Ocean University of ChinaQingdao 266100China The Affiliated Hospital of Qingdao University Qingdao 266001China

Stutzerimonas have been extensively studied due to their remarkable metabolic and physiological ***,research on its phages is currently *** this study,we isolated a novel double-stranded DNA(dsDNA)phage,vB_SstM-PG1,from the marine environment that infects Stutzerimonas stutzeri *** dsDNA genome is 37204 bp long with a G/C content of 64.14%and encodes 54 open reading *** phage possesses a tail packaging structure that is different from known Stutzerimonas stutzeri phages and exhibits structural protein characteristics similar to those of temperate *** addition,two genes of toxin-antitoxin system,including YdaS_antitoxin and HEPN_SAV_6107,were found in the vB_SstM-PG1 genome and play important roles in regulating host growth and *** phylogenetic tree and comparative genomic analysis,it has been determined that vB_SstM-PG1 is not closely related to any phages previously identified in the GenBank ***,it has a connection with enigmatic,uncultured ***,the vB_SstM-PG1 virus exhibits an average nucleotide identity of over 70%with six uncultivated viruses identified in the IMG/VR v4 *** significant finding has resulted in the identification of a novel viral genus known as Metabovirus.

关键词： Stutzerimonas vB_SstM-PG1 Metabovirus temperate phage genomic and phylogenetic analysis

Characterization of a Novel Esterase Belonging to Family V from Marinobacter flavimaris

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Journal of Ocean University of China 2024年第1期23卷 221-232页

作者： HE Jingjing ZHANG Yunhui WU Leilei WANG Yaru ZHANG He LIU Zhengang SHI Xiaochong Frontiers Science Center for Deep Ocean Multispheres and Earth System and College of Marine Life SciencesOcean University of ChinaQingdao 266003China Laboratory for marine Ecology and Environmental Science Laoshan LaboratoryQingdao 266237China institute of evolution&marine biodiversity Ocean University of ChinaQingdao 266003China

Lipolytic enzymes have attracted enormous attentions because of their ability in ester hydrolysis,ester synthesis,transesterification and other biochemical *** are important sources of lipolytic enzymes applied in ***,a novel lipolytic enzyme encoded by esterase gene est1347 was identified in Marinobacter flavimaris WLL162,and was purified and *** lipolytic enzyme Est1347 consisted of 312 amino acid residues and a 21-amino-acids N-terminal signal peptide with a predicted molecular weight of 34.2 *** belongs to family V of bacterial lipolytic enzymes based on the amino acid sequence homology ***1347 is a mesophilic and alkali-resistant enzyme with the highest activity at 45℃and pH 8.5;it is stable at temperatures below 50℃and pH 7.5–***1347 showed a preference for middle-length chain substrate p-NPC10 and a wide range of other *** Km,Vmax,Kcat and Kcat/Km values of Est1347 for p-NPC10 in pH 8.5 at 45℃were 0.9411 mmol L^(−1),1285μmol min^(−1)mg^(−1),698.91 s^(−1)and 743.65 s^(−1)(mmol L^(−1))^(−1),*** is also tolerant to the metal ions,organic solvents and *** conclusion,the esterase Est1347 laid a foundation for further study of bacterial lipolytic enzyme family V.

关键词： esterase Marinobacter flavimaris enzymatic properties lipolytic enzyme family V

Adenine nucleotide translocase 2(Ant2)is required for individualization of spermatogenesis of Drosophila melanogaster

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Insect Science 2024年第4期31卷 1055-1072页

作者： Zhen He Yang Fang Fengchao Zhang Yang Liu Xinkai Cheng Jiajia Wang Dechen Li Dengsong Chen Fan Wu Industrial Crops institute Hubei Academy of Agriculture SciencesWuhanChina institute of evolution&marine biodiversity Ocean University of ChinaQingdaoShandong ProvinceChina

Successful completion of spermatogenesis is crucial for the perpetuation of the *** Drosophila,spermatid individualization,a process involving changes in mitochondrial structure and function is critical to produce functional mature ***2,encoding a mitochondrial adenine nucleotide translocase,is highly expressed in male testes and plays a role in energy metabolism in the ***,its molecular function remains ***,we identified an important role of Ant2 in spermatid *** Ant2 knockdown testes,spermatid individualization complexes composed of F-actin cones exhibited a diffuse distribution,and mature sperms were absent in the seminal vesicle,thus leading to male *** most striking effects in Ant2-knockdown spermatids were decrease in tubulin polyglycylation and disruption of proper mitochondria derivatives *** apoptotic cells were also observed in Ant2-knockdown *** further investigate the phenotype of Ant2 knockdown in testes at the molecular level,complementary transcriptome and proteome analyses were *** the mRNA level,868 differentially expressed genes were identified,of which 229 genes were upregulated and 639 were downregulated induced via Ant2 ***-labeling proteome analysis revealed 350 differentially expressed proteins,of which 117 proteins were upregulated and 233 were *** expression of glutathione transferase(GstD5,GstE5,GstE8,and GstD3),proteins involved in reproduction were significantly regulated at both the mRNA and protein *** results indicate that Ant2 is crucial for spermatid maturation by affecting mitochondrial morphogenesis.

关键词： adenine nucleotide translocase Drosophila melanogaster individualization complexes mitochondria spermatogenesis tubulin polyglycylation

Genes and proteins expressed at different life cycle stages in the model protist Euplotes vannus revealed by both transcriptomic and proteomic approaches

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Science China life sciences 2024年

作者： Yaohan Jiang Xiao Chen Chundi Wang Liping Lyu Saleh A.Al-Farraj Naomi A.Stover Feng Gao Key Laboratory of evolution & marine biodiversity (Ministry of Education) and institute of evolution & marine biodiversity Ocean University of China marine college Shandong University Zoology Department College of Science King Saud University Department of Biology Bradley University Laboratory for marine Biology and Biotechnology Qingdao Marine Science and Technology Center

Sexual reproduction first appeared in unicellular protists and has continued to be an essential biological process in almost all *** protists, which contain both germline and somatic genomes within a single cell, have evolved a special form of sexual reproduction called conjugation that involves mitosis, meiosis, fertilization, nuclear differentiation, genome rearrangement, and the development of unique cellular structures. The molecular basis and mechanisms of conjugation vary dramatically among ciliates, and many details of the process and its regulation are still largely unknown. In order to better comprehend these processes and mechanisms from an evolutionary perspective, this study provides the first comprehensive overview of the transcriptome and proteome profiles during the entire life cycle of the newly-established marine model ciliate Euplotes vannus. Transcriptome analyses from 14 life cycle stages(three vegetative stages and 11sexual stages) revealed over 26,000 genes that are specifically expressed at different stages, many of which are related to DNA replication,transcription, translation, mitosis, meiosis, nuclear differentiation, and/or genome rearrangement. Quantitative proteomic analyses identified 338 proteins with homologs associated with conjugation and/or somatic nuclear development in other ciliates, including dicer-like proteins, Hsp90 proteins, RNA polymerase II and transcription elongation factors, ribosomal-associated proteins, and ubiquitin-related proteins. Four of these homologs belong to the PIWI family, each with different expression patterns identified and confirmed by RT-qPCR,which may function in small RNA-mediated genome rearrangement. Proteins involved in the nonhomologous end-joining pathway are induced early during meiosis and accumulate in the developing new somatic nucleus, where more than 80% of the germline sequences are eliminated from the somatic genome. A number of new candidate genes and proteins likely t

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