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1. Identification and comparative analysis of the Eriocheir sinensis microRNA transcriptome response to Spiroplasma eriocheiris infection using a deep sequencing approach

Author:
Ou, Jiangtao; Meng, Qingguo; Li, Yue; Xiu, Yunji; Du, Jie; Gu, Wei; Wu, Ting; Li, Wenjie; Ding, Zhengfeng; Wang, Wen
Source:
Fish & shellfish immunology 2012 v.32 no.2 pp. 345-352
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; Eriocheir sinensis; RNA libraries; Spiroplasma; arthropods; bioinformatics; crabs; crustacean culture; freshwater aquaculture; gene expression regulation; hemocytes; high-throughput nucleotide sequencing; host-pathogen relationships; innate immunity; microRNA; non-coding RNA; pathogens; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; China;     Show all 20 Subjects
Abstract:
... The Chinese mitten crab Eriocheir sinensis is one of the most important freshwater aquaculture crustacean species in China. MicroRNAs (miRNAs) are small non-coding RNAs that are important effectors in the intricate host–pathogen interaction network. To increase the repertoire of miRNAs characterized in crustaceans and to examine the relationship between host miRNA expression and pathogen infection ...
DOI:
10.1016/j.fsi.2011.11.027

2. Early response of gene expression in the distal intestine of Atlantic salmon (Salmo salar L.) during the development of soybean meal induced enteritis

Author:
Sahlmann, Christian; Sutherland, Ben J.G.; Kortner, Trond M.; Koop, Ben F.; Krogdahl, Åshild; Bakke, Anne Marie
Source:
Fish & shellfish immunology 2013 v.34 no.2 pp. 599-609
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; Salmo salar; T-lymphocytes; collagenase; diet; endocytosis; enteritis; exocytosis; extracellular matrix; fish meal; gene expression; gene expression regulation; genes; guanosinetriphosphatase; histology; immune response; inflammation; ingredients; intestines; lipid metabolism; microarray technology; oligonucleotides; oral exposure; proteolysis; quantitative polymerase chain reaction; soybean meal; soybeans; transcriptomics; transporters;     Show all 29 Subjects
Abstract:
... Plant products in general and soybeans in particular can challenge the function and health of the intestinal tract. Salmonids develop an intestinal inflammation when fed diets containing soybean meal (SBM) and certain other legume ingredients. In the present study a 44K oligonucleotide salmonid microarray, qPCR and histology were used to investigate early response mechanisms in the distal intestin ...
DOI:
10.1016/j.fsi.2012.11.031

3. Validation of housekeeping genes as internal controls for studying gene expression during Pacific oyster (Crassostrea gigas) development by quantitative real-time PCR

Author:
Du, Yishuai; Zhang, Linlin; Xu, Fei; Huang, Baoyu; Zhang, Guofan; Li, Li
Source:
Fish & shellfish immunology 2013 v.34 no.3 pp. 939-945
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; Crassostrea gigas; Ostreid herpesvirus 1; actin; data collection; essential genes; gene expression; gene expression regulation; glyceraldehyde-3-phosphate dehydrogenase; immune response; mortality; oyster larvae; quantitative polymerase chain reaction; ribosomal RNA; translation (genetics); ubiquitin-protein ligase;     Show all 16 Subjects
Abstract:
... Hatchery-reared larvae of the Pacific oyster (Crassostrea gigas) often suffer from massive mortality induced by Ostreid herpesvirus 1 (OsHV-1) infection, indicating the importance of better understanding of oyster immune defense systems. The accuracy of measurements of gene expression levels based on quantitative real-time PCR assays relies on the use of housekeeping genes as internal controls; ho ...
DOI:
10.1016/j.fsi.2012.12.007

4. Trascriptome analysis of the Pacific white shrimp Litopenaeus vannamei exposed to nitrite by RNA-seq

Author:
Guo, Hui; Ye, Chao-Xia; Wang, An-Li; Xian, Jian-An; Liao, Shao-An; Miao, Yu-Tao; Zhang, Sheng-Peng
Source:
Fish & shellfish immunology 2013 v.35 no.6 pp. 2008-2016
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; Litopenaeus vannamei; apoptosis; databases; gene expression regulation; high-throughput nucleotide sequencing; immune response; nitrites; quantitative polymerase chain reaction; shrimp; transcriptomics; unigenes;     Show all 12 Subjects
Abstract:
... In the present study, transcriptome of nitrite-exposed Litopenaeus vannamei was performed using a newly developed high-throughput sequencing technology (Illumina RNA-seq). As many as 42,336 unigenes were generated with 561 bp of average length and 736 bp of unigene N50 after filtering and assembly. These unigenes from the de novo assembly were further annotated using BLAST and BLAST2GO softwares. ...
DOI:
10.1016/j.fsi.2013.09.019

5. Immune gene discovery in the crucian carp Carassius auratus

Author:
Rhee, Jae-Sung; Jeong, Chang-Bum; Kim, Duck-Hyun; Kim, Il-Chan; Lee, Yong Sung; Lee, Chulwoo; Lee, Jae-Seong
Source:
Fish & shellfish immunology 2014 v.36 no.1 pp. 240-251
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; Carassius auratus; RNA; antimicrobial proteins; fish; fish culture; immune system; immunity; monitoring; proteinase inhibitors; proteinases; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; sequence analysis; transcriptomics; unigenes;     Show all 16 Subjects
Abstract:
... The crucian carp Carassius auratus (Cyprinidae) is one of the important fish species in aquaculture. Although the crucian carp has several economic benefits, their immune system and gene information have not been investigated in depth as yet. Here, we performed the transcriptome analysis of C. auratus using the pyrosequencing method and selected several immune-related genes. Of unigenes obtained i ...
DOI:
10.1016/j.fsi.2013.11.009

6. Identification and comparative analysis of the Pseudosciaena crocea microRNA transcriptome response to poly(I:C) infection using a deep sequencing approach

Author:
Qi, Pengzhi; Guo, Baoying; Zhu, Aiyi; Wu, Changwen; Liu, Changlin
Source:
Fish & shellfish immunology 2014 v.39 no.2 pp. 483-491
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; Larimichthys crocea; gene expression regulation; high-throughput nucleotide sequencing; immune response; immune system; microRNA; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction;     Show all 9 Subjects
Abstract:
... Two sRNA libraries with or without poly(I:C) infection of large yellow croaker Pseudosciaena crocea were constructed and sequenced using the high-throughput Illumina/Solexa deep sequencing technology. The high-throughput sequencing pipeline yielded 163,79,272 and 217,07,070 raw reads corresponding to 132,27,594 and 206,86,409 clean reads for the normal and infected libraries, respectively. Bioinfr ...
DOI:
10.1016/j.fsi.2014.06.009

7. Molecular aspects, genomic arrangement and immune responsive mRNA expression profiles of two CXC chemokine receptor homologs (CXCR1 and CXCR2) from rock bream, Oplegnathus fasciatus

Author:
Umasuthan, Navaneethaiyer; Wan, Qiang; Revathy, Kasthuri Saranya; Whang, Ilson; Noh, Jae Koo; Kim, Seokryel; Park, Myoung-Ae; Lee, Jehee
Source:
Fish & shellfish immunology 2014 v.40 no.1 pp. 304-318
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; phylogeny; signal transduction; mammals; CXCR2 receptor; Streptococcus iniae; concanavalin A; bream; leukocytes; gene expression; amino acids; spleen; viruses; pathogenesis; Edwardsiella tarda; introns; tissues; interleukin-8; transcription factors; messenger RNA; complementary DNA; models; Oplegnathus fasciatus; CXCR1 receptor; immune response; kidneys; exons; quantitative polymerase chain reaction; bacterial artificial chromosomes; innate immunity; inflammation; binding sites;     Show all 32 Subjects
Abstract:
... The CXCR1 and CXCR2 are the prototypical receptors and are the only known receptors for mammalian ELR+ (Glu-Leu-Arg) CXC chemokines, including CXCL8 (interleukin 8). These receptors transduce the ELR+ chemokine signals and operate the downstream signaling pathways in inflammation and innate immunity. In this study, we report the identification and characterization of CXCR1 and CXCR2 genes from roc ...
DOI:
10.1016/j.fsi.2014.06.006

8. Transcriptome analysis and microsatellite discovery in the blunt snout bream (Megalobrama amblycephala) after challenge with Aeromonas hydrophila

Author:
Tran, Ngoc Tuan; Gao, Ze-Xia; Zhao, Hong-Hao; Yi, Shao-Kui; Chen, Bo-Xiang; Zhao, Yu-Hua; Lin, Li; Liu, Xue-Qin; Wang, Wei-Min
Source:
Fish & shellfish immunology 2015 v.45 no.1 pp. 72-82
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; Aeromonas hydrophila; Danio rerio; Megalobrama amblycephala; National Center for Biotechnology Information; aquaculture; bacteria; bacterial infections; cDNA libraries; complementary DNA; databases; defense mechanisms; farmed fish; freshwater; freshwater fish; gene expression; gene expression regulation; herbivores; immune response; immunogenetics; indigenous species; microsatellite repeats; pathogens; proteins; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; sequence homology; signal transduction; tissues; transcriptomics; unigenes; China;     Show all 32 Subjects
Abstract:
... The blunt snout bream, Megalobrama amblycephala, is a herbivorous freshwater fish species native to China and a major aquaculture species in Chinese freshwater polyculture systems. In recent years, the bacterium Aeromonas hydrophila has been reported to be its pathogen causing great losses of farmed fish. To understand the immune response of the blunt snout bream to A. hydrophila infection, we use ...
DOI:
10.1016/j.fsi.2015.01.034

9. Proteomic analysis of hemolymph from poly(I:C)-stimulated Crassostrea gigas

Author:
Green, Timothy J.; Chataway, Timothy; Melwani, Aroon R.; Raftos, David A.
Source:
Fish & shellfish immunology 2016 v.48 pp. 39-42
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; Crassostrea gigas; RNA; cytokines; gene expression regulation; genes; heat shock proteins; hemocytes; mammals; microarray technology; mortality; oysters; proteomics; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; tandem mass spectrometry; two-dimensional gel electrophoresis;     Show all 17 Subjects
Abstract:
... Synthetic double stranded RNA (Poly(I:C)) injection of Crassostrea gigas results in a systemic antiviral response involving many evolutionary conserved antiviral effectors (ISGs). Compared to mammals, the timing of C. gigas ISG expression to viral or poly(I:C) injection is delayed (>12 h p.i.). It could be interpreted that a cytokine is responsible for the systemic, but delayed expression of C. gi ...
DOI:
10.1016/j.fsi.2015.11.018

10. Transcriptomic analysis of koi (Cyprinus carpio) spleen tissue upon cyprinid herpesvirus 3 (CyHV3) infection using next generation sequencing

Author:
Lee, Xuezhu; Yi, Yang; Weng, Shaoping; Zeng, Jie; Zhang, Hetong; He, Jianguo; Dong, Chuanfu
Source:
Fish & shellfish immunology 2016 v.49 pp. 213-224
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; Cyprinid herpesvirus 3; Cyprinus carpio; computer software; databases; financial economics; gene expression; gene expression regulation; high-throughput nucleotide sequencing; innate immunity; koi; proteins; quantitative polymerase chain reaction; spleen; tissues; transcriptomics; unigenes;     Show all 17 Subjects
Abstract:
... Cyprinid Herpesvirus 3 (CyHV-3) can infect and specifically cause a huge economic loss in both common carp (Cyprinus carpio) and its ornamental koi variety. The molecular mechanisms underlying CyHV-3 infection are not well understood. In this study, koi spleen tissues of both mock and CyHV-3 infection groups were collected, and high-throughput sequencing technology was used to analyze the differen ...
DOI:
10.1016/j.fsi.2015.12.007

11. Identification and functional characterization of three TLR signaling pathway genes in Cyclina sinensis

Author:
Ren, Yipeng; Pan, Heting; Pan, Baoping; Bu, Wenjun
Source:
Fish & shellfish immunology 2016 v.50 pp. 150-159
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; Micrococcus luteus; RNA interference; Toll-like receptors; Vibrio anguillarum; clams; gene expression; genes; hemocytes; host-pathogen relationships; immune response; innate immunity; messenger RNA; quantitative polymerase chain reaction; signal transduction; tissues;     Show all 16 Subjects
Abstract:
... Toll-like receptors (TLRs) are an ancient family of pattern recognition receptors that play a critical role in initiating and activating the innate immune system. In this study, we identified two TLR genes (CsTLR4 and CsTLR13) and the MyD88 (CsMyD88) gene using a transcriptome library from Cyclina sinensis. The sequence features and mRNA expression profiles of the genes were characterized, and the ...
DOI:
10.1016/j.fsi.2016.01.025

12. Identification and characterization of miR-31 potential targets by RNA-seq

Author:
Xueping, Sun; Zhimeng, Lv; Chenghua, Li; Meng, Lu; Pengjuan, Zhang; Weiwei, Zhang
Source:
Fish & shellfish immunology 2016 v.51 pp. 26-32
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; Apostichopus japonicus; amino acid sequences; cucumbers; gene expression regulation; quantitative polymerase chain reaction; sequence analysis; transcriptomics; unigenes;     Show all 9 Subjects
Abstract:
... In our previous work, miR-31 displayed differential significant expression in Apostichopus japonicus sea cucumber with skin ulcer syndrome and modulated coelomocytes ROS production by targeting p105. To identify other promising targets ofmiR-31, 4 transcriptome libraries of coelomocytes, as well as 2 control libraries, were constructed frommiR-31 mimics (31 M) or AMO-miR-31 (31I) and injected into ...
DOI:
10.1016/j.fsi.2016.02.014

13. Comparative analysis of the small RNA transcriptomes of miiuy croaker revealed microRNA-mediated regulation of TLR signaling pathway response to Vibrio anguillarum infection

Author:
Xu, Guoliang; Han, Jingjing; Xu, Tianjun
Source:
Fish & shellfish immunology 2016 v.52 pp. 248-257
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; Miichthys miiuy; Vibrio anguillarum; aquaculture; bacterial infections; bioinformatics; financial economics; fish; genes; high-throughput nucleotide sequencing; immune response; messenger RNA; microRNA; nucleotide sequences; pathogens; prediction; quantitative polymerase chain reaction; signal transduction; transcription factor NF-kappa B; translation (genetics);     Show all 20 Subjects
Abstract:
... MicroRNAs (miRNAs) are an abundant class of endogenous noncoding small RNAs (sRNAs) that are partially complementary to their target messenger RNA (mRNA), which post-transcriptionally regulate various biological processes by repressing mRNA translation or inducing mRNA degradation. MiRNAs have been demonstrated to play crucial roles in the host response to infection by diverse pathogens. As an imp ...
DOI:
10.1016/j.fsi.2016.03.011

14. Differentially proteomic analysis of the Chinese shrimp at WSSV latent and acute infection stages by iTRAQ approach

Author:
Li, Shihao; Li, Fuhua; Sun, Zheng; Zhang, Xiaojun; Xiang, Jianhai
Source:
Fish & shellfish immunology 2016 v.54 pp. 629-638
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; Western blotting; actin; acute course; adenine; apoptosis; clathrin; cytoskeleton; gene expression regulation; infectious diseases; myosin; peptides; peroxiredoxin; phagocytosis; protein synthesis; proteomics; quantitative polymerase chain reaction; shrimp; tropomyosins; tubulin;     Show all 20 Subjects
Abstract:
... As the direct executors of biological function, the expression level of proteins will reveal the molecular mechanisms regulating WSSV acute infection more directly. In the present study, the iTRAQ approach was applied to identifying differentially expressed proteins in Chinese shrimp during WSSV latent infection and acute infection. A total of 4051 unique peptides corresponding to 1286 proteins we ...
DOI:
10.1016/j.fsi.2016.05.016

15. The miiuy croaker microRNA transcriptome and microRNA regulation of RIG-I like receptor signaling pathway after poly(I:C) stimulation

Author:
Han, Jingjing; Xu, Guoliang; Xu, Tianjun
Source:
Fish & shellfish immunology 2016 v.54 pp. 419-426
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; Miichthys miiuy; RNA libraries; apoptosis; cytokines; fish; genes; interferons; messenger RNA; microRNA; non-coding RNA; quantitative polymerase chain reaction; researchers; reverse transcriptase polymerase chain reaction; signal transduction; spleen; translation (genetics);     Show all 17 Subjects
Abstract:
... MicroRNAs (miRNAs) as endogenous small non-coding RNAs play key regulatory roles in diverse biological processes via degrading the target mRNAs or inhibiting protein translation. Previously many researchers have reported the identification, characteristic of miRNAs and the interaction with its target gene. But, the study on the regulation of miRNAs to biological processes via regulatory the key si ...
DOI:
10.1016/j.fsi.2016.04.126

16. Identification and expression analysis of IκB and NF-κB genes from Cyclina sinensis

Author:
Gao, Shan; Ren, Yipeng; Zhang, Haijing; Pan, Baoping; Gao, Hong
Source:
Fish & shellfish immunology 2016 v.56 pp. 427-435
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; Micrococcus luteus; RNA interference; Vibrio anguillarum; adults; aquaculture; clams; defense mechanisms; gene expression; genes; hemocytes; innate immunity; messenger RNA; quantitative polymerase chain reaction; signal transduction; tissues; transcription factor NF-kappa B;     Show all 17 Subjects
Abstract:
... With the increasing economic importance of Cyclina sinensis aquaculture, interest in its defense mechanisms against pathogenic infection has grown in recent years. Inhibitor of nuclear factor-kappaB (IκB) and nuclear factor-kappaB (NF-κB) are proteins with central roles in many important physiological and pathological processes, such as innate immune responses. In this study, we identified CsIκB a ...
DOI:
10.1016/j.fsi.2016.07.035

17. Three novel C1q domain containing proteins from the disk abalone Haliotis discus discus: Genomic organization and analysis of the transcriptional changes in response to bacterial pathogens

Author:
Bathige, S.D.N.K.; Umasuthan, Navaneethaiyer; Jayasinghe, J.D.H.E.; Godahewa, G.I.; Park, Hae-Chul; Lee, Jehee
Source:
Fish & shellfish immunology 2016 v.56 pp. 181-187
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; abalone; lipopolysaccharides; phylogeny; Gram-positive bacteria; open reading frames; hepatopancreas; amino acids; reverse transcription; Vibrio parahaemolyticus; Haliotis discus; Listeria monocytogenes; signal peptide; databases; pathogens; tissues; sequence analysis; complementary DNA; muscles; immune response; exons; quantitative polymerase chain reaction; proteins; bacterial artificial chromosomes; innate immunity; gills;     Show all 26 Subjects
Abstract:
... The globular C1q (gC1q) domain containing proteins, commonly referred as C1q domain containing (C1qDC) proteins, are an essential family of proteins involved in various innate immune responses. In this study, three novel C1qDC proteins were identified from the disk abalone (Haliotis discus discus) transcriptome database and designated as AbC1qDC1, AbC1qDC2, and AbC1qDC3. The cDNA sequences of AbC1 ...
DOI:
10.1016/j.fsi.2016.07.010

18. RNA-seq analysis revealed ROS-mediated related genes involved in cadmium detoxification in the razor clam Sinonovacula constricta

Author:
Wang, Zhenhui; Shao, Yina; Li, Chenghua; Zhang, Weiwei; Duan, Xuemei; Zhao, Xuelin; Qiu, Qiongfen; Jin, Chunhua
Source:
Fish & shellfish immunology 2016 v.57 pp. 350-361
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; Veneroida; cadmium; catalytic activity; gene expression regulation; glutathione; heat shock proteins; heavy metals; hepatopancreas; littoral zone; metallothionein; quantitative polymerase chain reaction; sequence analysis; toxicology; unigenes;     Show all 15 Subjects
Abstract:
... The razor clam Sinonovacula constricta is a eukaryotic benthic intertidal bivalve species that is tolerant to different heavy metals, such as cadmium ion (Cd2+). However, the mechanism by which S. constricta responds to Cd2+-induced stress remains unclear. In this study, eight transcriptome libraries were constructed and sequenced using razor clams exposed to Cd2+ for 12 and 48 h. A total of 18,33 ...
DOI:
10.1016/j.fsi.2016.08.051

19. Transcriptome analysis of grey mullet (Mugil cephalus) after challenge with Lactococcus garvieae

Author:
Byadgi, Omkar; Chen, Yao-Chung; Barnes, Andrew C.; Tsai, Ming-An; Wang, Pei-Chyi; Chen, Shih-Chu
Source:
Fish & shellfish immunology 2016 v.58 pp. 593-603
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; Lactococcus garvieae; Mugil cephalus; Toll-like receptors; antigens; bacterial infections; coagulation; complement; fish; gene expression regulation; hosts; immune response; industry; kidneys; mariculture; quantitative polymerase chain reaction; spleen; transcriptomics; unigenes; Taiwan;     Show all 20 Subjects
Abstract:
... Grey mullet (Mugil cephalus) is an economically important fish species in Taiwan mariculture industry. Moreover, grey mullet are common hosts of a bacterial infection by Lactococcus garvieae. However, until now the information related to the immune system of grey mullet is unclear. Therefore, to understand the molecular basis underlying the host immune response to L. garvieae infection, Illumina H ...
DOI:
10.1016/j.fsi.2016.10.006

20. Characterization of microRNAs by deep sequencing in red claw crayfish Cherax quadricarinatus haematopoietic tissue cells after white spot syndrome virus infection

Author:
Zhao, Meng-ru; Meng, Chuang; Xie, Xiao-lu; Li, Cheng-hua; Liu, Hai-peng
Source:
Fish & shellfish immunology 2016 v.59 pp. 469-483
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; Cherax quadricarinatus; White spot syndrome virus; apoptosis; autophagy; cell culture; cell differentiation; computer software; crayfish culture; energy metabolism; gene expression regulation; genes; high-throughput nucleotide sequencing; immune response; microRNA; prediction; quantitative analysis; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; shrimp; signal transduction; transcription (genetics); viruses;     Show all 23 Subjects
Abstract:
... White spot syndrome virus (WSSV) is one of the most prevalent and widespread viruses in both shrimp and crayfish aquaculture. MicroRNAs (miRNAs) are crucial post-transcriptional regulators and play critical roles in cell differentiation and proliferation, apoptosis, signal transduction and immunity. In this study, miRNA expression profiles were identified via deep sequencing in red claw crayfish C ...
DOI:
10.1016/j.fsi.2016.11.012