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  1. Article ; Online: Comprehensive Atlas of Alternative Splicing Reveals NSRP1 Promoting Adipogenesis through

    Liu, Lei / Wang, Wei / Liu, Weiwei / Li, Xingzheng / Yi, Guoqiang / Adetula, Adeyinka Abiola / Huang, Haibo / Tang, Zhonglin

    International journal of molecular sciences

    2024  Volume 25, Issue 5

    Abstract: Alternative splicing (AS) plays a crucial role in regulating gene expression, function, and diversity. However, limited reports exist on the identification and comparison of AS in Eastern and Western pigs. Here, we analyzed 243 transcriptome data from ... ...

    Abstract Alternative splicing (AS) plays a crucial role in regulating gene expression, function, and diversity. However, limited reports exist on the identification and comparison of AS in Eastern and Western pigs. Here, we analyzed 243 transcriptome data from eight tissues, integrating information on transcription factors (TFs), selection signals, splicing factors (SFs), and quantitative trait loci (QTL) to comprehensively study alternative splicing events (ASEs) in pigs. Five ASE types were identified, with Mutually Exclusive Exon (MXE) and Skipped Exon (SE) ASEs being the most prevalent. A significant portion of genes with ASEs (ASGs) showed conservation across all eight tissues (63.21-76.13% per tissue). Differentially alternative splicing genes (DASGs) and differentially expressed genes (DEGs) exhibited tissue specificity, with blood and adipose tissues having more DASGs. Functional enrichment analysis revealed coDASG_DEGs in adipose were enriched in pathways associated with adipose deposition and immune inflammation, while coDASG_DEGs in blood were enriched in pathways related to immune inflammation and metabolism. Adipose deposition in Eastern pigs might be linked to the down-regulation of immune-inflammation-related pathways and reduced insulin resistance. The TFs, selection signals, and SFs appeared to regulate ASEs. Notably, ARID4A (TF), NSRP1 (SF),
    MeSH term(s) Swine ; Animals ; Alternative Splicing ; Adipogenesis/genetics ; Plant Breeding ; Transcriptome ; Inflammation ; Gene Expression Profiling
    Language English
    Publishing date 2024-03-01
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms25052874
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: miR-378a-3p responds to physical activity by modulating insulin-mediated glucose uptake and tricarboxylic acid cycle in skeletal muscle.

    Wang, Zishuai / Yao, Yilong / Hou, Xinhua / Fan, Danyang / Liu, Yanwen / Adetula, Adeyinka Abiola / Yang, Yalan / Li, Kui / Tang, Zhonglin

    Genes & diseases

    2023  Volume 11, Issue 3, Page(s) 101052

    Language English
    Publishing date 2023-07-28
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2821806-1
    ISSN 2352-3042 ; 2352-3042
    ISSN (online) 2352-3042
    ISSN 2352-3042
    DOI 10.1016/j.gendis.2023.06.021
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Long-lasting effects of lipopolysaccharide on the reproduction and splenic transcriptome of hens and their offspring.

    Liu, Lei / Wang, Di / Li, Xingzheng / Adetula, Adeyinka Abiola / Khan, Adnan / Zhang, Bing / Liu, Huagui / Yu, Ying / Chu, Qin

    Ecotoxicology and environmental safety

    2022  Volume 237, Page(s) 113527

    Abstract: Lipopolysaccharide (LPS) is ubiquitous in the environment and is released after the death of gram-negative bacteria, which may be related to inflammation and immunosuppression. However, its impact on the reproduction of animals and their offspring, ... ...

    Abstract Lipopolysaccharide (LPS) is ubiquitous in the environment and is released after the death of gram-negative bacteria, which may be related to inflammation and immunosuppression. However, its impact on the reproduction of animals and their offspring, especially the underlying mechanism need further elucidation. Here, we used laying hens as a model organism to investigate the effects of maternal exposure to LPS (LPS maternal stimulation) on animal and their offspring's immunity and reproductive performance, as well as the regulatory role of the transcriptome. We found that the LPS maternal stimulation could reduce the egg-laying rate of hens and their offspring, especially during the early and late laying stages. The transcriptome study of the spleen in F0, F1 and F2 generations showed that the maternal stimulation of the LPS affects the patterns of gene expression in laying hens, and this change has a long-lasting effect. Further analysis of DEGs and their enrichment pathways found that the LPS maternal stimulation mainly affects the reproduction and immunity of laying hens and their offspring. The DEGs such as AVD, HPS5, CATHL2, S100A12, EXFABP, RSFR, LY86, PKD4, XCL1, FOS, TREM2 and MST1 may play an essential role in the regulation of the immunity and egg-laying rate of hens. Furthermore, the MMR1L3, C3, F13A1, LY86 and GDPD2 genes with heritable effects are highly correlated with the egg-laying rate, may have an important reference value for further research. Our study reveals the profound implications of LPS exposure on immunity and reproduction of offspring, elaborating the impact of immune alteration on the egg-laying rate, emphasizing the regulatory role of intergenerational transmission of the transcriptome, implying that the environment parents being exposed to has an important impact on offspring.
    MeSH term(s) Animal Feed ; Animals ; Chickens ; Female ; Lipopolysaccharides/metabolism ; Reproduction ; Spleen ; Transcriptome
    Chemical Substances Lipopolysaccharides
    Language English
    Publishing date 2022-04-19
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 436536-7
    ISSN 1090-2414 ; 0147-6513
    ISSN (online) 1090-2414
    ISSN 0147-6513
    DOI 10.1016/j.ecoenv.2022.113527
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Transcriptional analyses provide novel insights into the transgenerational effects of Poly (I:C) on chickens.

    Liu, Lei / Wang, Di / Fu, Yang / Duan, Zhongyi / Adetula, Adeyinka Abiola / Liu, Huagui / Yu, Ying / Chu, Qin

    Ecotoxicology and environmental safety

    2022  Volume 247, Page(s) 114216

    Abstract: Pathogenic microorganisms that are ubiquitous in the environment threaten human health and food safety. Polyinosinic:polycytidylic acid (Poly (I:C)) is a macromolecule with a double-stranded RNA structure, which is often used to simulate viruses. Our ... ...

    Abstract Pathogenic microorganisms that are ubiquitous in the environment threaten human health and food safety. Polyinosinic:polycytidylic acid (Poly (I:C)) is a macromolecule with a double-stranded RNA structure, which is often used to simulate viruses. Our previous study found that Poly (I:C) maternal stimulation could affect the reproduction of laying hens and their offspring, but the underlying mechanism needed to be explored. In the present study, splenic transcriptomes were sequenced and analyzed from two groups (Poly (I:C) treatment as the challenged group and saline treatment as the control) and in three generations (maternal stimulated F0 hens, unchallenged F1 and F2 generations). The results showed that Poly (I:C) maternal stimulation affected gene expression patterns in laying hens and their offspring. A total of 27 differentially expressed genes (DEGs) with the same regulating trend were discovered in the F0 and F1 generations, indicating an influence of the intergenerational transmission effect. Functional enrichment analysis of Gene Ontology (GO) showed that lymphocyte differentiation, positive regulation of leukocyte differentiation, positive regulation of MAPK cascade, and T cell differentiation were the common biological processes between F0 and F1 generations, revealing Poly (I:C) could affect the immunity of the treated F0 hens and the unchallenged subsequent generations. Further study showed that pathways associated with growth, development, biosynthesis, and metabolism of F2 chicks were also affected by Poly (I:C) maternal stimulation. Correlation analysis between DEGs and reproductive traits revealed that PHLDA2 (pleckstrin homology-like domain family A member 2) and PODN (podocan) with inheritable effect were highly correlated with egg-laying rate and egg weight in F1 hens, suggesting their potential long-term role in regulating reproductive traits. ARHGAP40, FGB, HRH4, PHLDA2, PODN, NTSR1, and NMU were supposed to play important roles in regulating chickens' immunity and reproductive traits. This study reveals the far-reaching effect on transcriptome induced by Poly (I:C), reflecting the influence of the mother's living environment on the offspring. It is an important reference for future research into the multi-generational transmission of maternal stimulation and harmful environmental factors.
    MeSH term(s) Humans ; Animals ; Female ; Chickens/genetics ; Poly I-C/toxicity ; Reproduction ; Oviposition ; Transcriptome
    Chemical Substances Poly I-C (O84C90HH2L)
    Language English
    Publishing date 2022-10-23
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 436536-7
    ISSN 1090-2414 ; 0147-6513
    ISSN (online) 1090-2414
    ISSN 0147-6513
    DOI 10.1016/j.ecoenv.2022.114216
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Association of single nucleotide polymorphism at long non-coding RNA 8138.1 with duration of fertility in egg-laying hens.

    Adetula, Adeyinka Abiola / Azmal, Syed Ali / Sun, Chenghao / Elokil, Abdelmotaleb / Li, Shijun

    PeerJ

    2019  Volume 7, Page(s) e7282

    Abstract: A previous genome-wide transcriptional analysis identified long non-coding RNA 8138.1 ( ...

    Abstract A previous genome-wide transcriptional analysis identified long non-coding RNA 8138.1 (
    Language English
    Publishing date 2019-07-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2703241-3
    ISSN 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.7282
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: RAI14

    Adetula, Adeyinka Abiola / Liu, Xiaolei / Yang, Liubin / Fang, Chengchi / Yu, Hui / Li, Hua / Li, Shijun

    Archives animal breeding

    2020  Volume 63, Issue 2, Page(s) 231–239

    Abstract: A genome-wide association study (GWAS) was performed on a resource family consisting of white and colored chickens for identification of genes related to plumage coloration using the Fixed and random model Circulating Probability Unification (FarmCPU) ... ...

    Abstract A genome-wide association study (GWAS) was performed on a resource family consisting of white and colored chickens for identification of genes related to plumage coloration using the Fixed and random model Circulating Probability Unification (FarmCPU) package. GWAS identified three chromosomal single-nucleotide polymorphisms (SNPs), demonstrating the polygenic basis of plumage phenotypes. Herein, retinoic acid-induced protein 14 (
    Language English
    Publishing date 2020-07-14
    Publishing country Germany
    Document type Journal Article
    ISSN 2363-9822
    ISSN (online) 2363-9822
    DOI 10.5194/aab-63-231-2020
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Transcriptome sequencing reveals key potential long non-coding RNAs related to duration of fertility trait in the uterovaginal junction of egg-laying hens.

    Adetula, Adeyinka Abiola / Gu, Lantao / Nwafor, Chinedu Charles / Du, Xiaoyong / Zhao, Shuhong / Li, Shijun

    Scientific reports

    2018  Volume 8, Issue 1, Page(s) 13185

    Abstract: Duration of fertility, (DF) is an important functional trait in poultry production and lncRNAs have emerged as important regulators of various process including fertility. In this study we applied a genome-guided strategy to reconstruct the uterovaginal ... ...

    Abstract Duration of fertility, (DF) is an important functional trait in poultry production and lncRNAs have emerged as important regulators of various process including fertility. In this study we applied a genome-guided strategy to reconstruct the uterovaginal junction (UVJ) transcriptome of 14 egg-laying birds with long- and short-DF (n = 7); and sought to uncover key lncRNAs related to duration of fertility traits by RNA-sequencing technology. Examination of RNA-seq data revealed a total of 9977 lncRNAs including 2576 novel lncRNAs. Differential expression (DE) analysis of lncRNA identified 223 lncRNAs differentially expressed between the two groups. DE-lncRNA target genes prediction uncovered over 200 lncRNA target genes and functional enrichment tests predict a potential function of DE-lncRNAs. Gene ontology classification and pathway analysis revealed 8 DE-lncRNAs, with the majority of their target genes enriched in biological functions such as reproductive structure development, developmental process involved in reproduction, response to cytokine, carbohydrate binding, chromatin organization, and immune pathways. Differential expression of lncRNAs and target genes were confirmed by qPCR. Together, these results significantly expand the utility of the UVJ transcriptome and our analysis identification of key lncRNAs and their target genes regulating DF will form the baseline for understanding the molecular functions of lncRNAs regulating DF.
    MeSH term(s) Animals ; Chickens/genetics ; Female ; Fertility ; Gene Ontology ; RNA, Long Noncoding/genetics ; Sequence Analysis, RNA ; Transcriptome
    Chemical Substances RNA, Long Noncoding
    Language English
    Publishing date 2018-09-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-018-31301-z
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  8. Article ; Online: Research Note: Association of single nucleotide polymorphism of AKT3 with egg production traits in White Muscovy ducks (Cairina moschata).

    Bello, Semiu Folaniyi / Xu, Haiping / Li, Kan / Guo, Lijin / Zhang, Siyu / Ahmed, Ridwan Olawale / Bekele, Endashaw Jebessa / Zheng, Ming / Xian, Mingjian / Abdalla, Bahareldin Ali / Adeola, Adeniyi Charles / Adetula, Adeyinka Abiola / Lawal, Raman Akinyanju / Zhu, Weijian / Zhang, Dexiang / Zhang, Xiquan / Ji, Congliang / Nie, Qinghua

    Poultry science

    2022  Volume 101, Issue 12, Page(s) 102211

    Abstract: Prior studies on transcriptomes of hypothalamus and ovary revealed that AKT3 is one of the candidate genes that might affect egg production in White Muscovy ducks. The role of AKT3 in the uterus during reproductive processes cannot be overemphasized. ... ...

    Abstract Prior studies on transcriptomes of hypothalamus and ovary revealed that AKT3 is one of the candidate genes that might affect egg production in White Muscovy ducks. The role of AKT3 in the uterus during reproductive processes cannot be overemphasized. However, functional role of this gene in the tissues and on egg production traits of Muscovy ducks remains unknown. To identify the relationship between AKT3 and egg production traits in ducks, relative expression profile was first examined prior to identifying the variants within AKT3 that may underscore egg production traits [age at first egg (AFE), number of eggs at 300 d (N300D), and number of eggs at 59 wk (N59W)] in 549 ducks. The mRNA expression of AKT3 gene in high producing (HP) ducks was significantly higher than low producing (LP) ducks in the ovary, oviduct, and hypothalamus (P < 0.05 or 0.001). Three variants in AKT3 (C-3631A, C-3766T, and C-3953T) and high linkage block between C-3766T and C-3953T which are significantly (P < 0.05) associated with N300D and N59W were discovered. This study elucidates novel knowledge on the molecular mechanism of AKT3 that might be regulating egg production traits in Muscovy ducks.
    MeSH term(s) Female ; Animals ; Ducks/genetics ; Polymorphism, Single Nucleotide ; Reproduction/genetics ; Chickens ; Ovum
    Language English
    Publishing date 2022-09-28
    Publishing country England
    Document type Journal Article
    ZDB-ID 242586-5
    ISSN 1525-3171 ; 0032-5791
    ISSN (online) 1525-3171
    ISSN 0032-5791
    DOI 10.1016/j.psj.2022.102211
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  9. Article ; Online: circRNAome profiling reveals circFgfr2 regulates myogenesis and muscle regeneration via a feedback loop.

    Yan, Junyu / Yang, Yalan / Fan, Xinhao / Liang, Guoming / Wang, Zishuai / Li, Jiju / Wang, Liyuan / Chen, Yun / Adetula, Adeyinka Abiola / Tang, Yijie / Li, Kui / Wang, Dazhi / Tang, Zhonglin

    Journal of cachexia, sarcopenia and muscle

    2021  Volume 13, Issue 1, Page(s) 696–712

    Abstract: Background: Circular RNAs (circRNAs) represent a novel class of non-coding RNAs formed by a covalently closed loop and play crucial roles in many biological processes. Several circRNAs associated with myogenesis have been reported. However, the dynamic ... ...

    Abstract Background: Circular RNAs (circRNAs) represent a novel class of non-coding RNAs formed by a covalently closed loop and play crucial roles in many biological processes. Several circRNAs associated with myogenesis have been reported. However, the dynamic expression, function, and mechanism of circRNAs during myogenesis and skeletal muscle development are largely unknown.
    Methods: Strand-specific RNA-sequencing (RNA-seq) and microarray datasets were used to profile the dynamic circRNAome landscape during skeletal muscle development and myogenic differentiation. Bioinformatics analyses were used to characterize the circRNAome and identify candidate circRNAs associated with myogenesis. Bulk and single-cell RNA-seq were performed to identify the downstream genes and pathways of circFgfr2. The primary myoblast cells, C2C12 cells, and animal model were used to assess the function and mechanism of circFgfr2 in myogenesis and muscle regeneration in vitro or in vivo by RT-qPCR, western blotting, dual-luciferase activity assay, RNA immunoprecipitation, RNA fluorescence in situ hybridization, and chromatin immunoprecipitation.
    Results: We profiled the dynamic circRNAome in pig skeletal muscle across 27 developmental stages and detected 52 918 high-confidence circRNAs. A total of 2916 of these circRNAs are conserved across human, mouse, and pig, including four circRNAs (circFgfr2, circQrich1, circMettl9, and circCamta1) that were differentially expressed (|log
    Conclusions: The present study provides a comprehensive circRNA resource for skeletal muscle study. The functional and mechanistic analysis of circFgfr2 uncovered a circRNA-mediated auto-regulatory feedback loop regulating myogenesis and muscle regeneration, which provides new insight to further understand the regulatory mechanism of circRNAs.
    MeSH term(s) Animals ; DNA Helicases/metabolism ; Feedback ; In Situ Hybridization, Fluorescence ; Mice ; Muscle Development/genetics ; Muscle, Skeletal/metabolism ; Poly-ADP-Ribose Binding Proteins/metabolism ; RNA Helicases/metabolism ; RNA Recognition Motif Proteins/metabolism ; Regeneration/genetics ; Swine
    Chemical Substances Poly-ADP-Ribose Binding Proteins ; RNA Recognition Motif Proteins ; DNA Helicases (EC 3.6.4.-) ; RNA Helicases (EC 3.6.4.13)
    Language English
    Publishing date 2021-11-22
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2586864-0
    ISSN 2190-6009 ; 2190-5991
    ISSN (online) 2190-6009
    ISSN 2190-5991
    DOI 10.1002/jcsm.12859
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  10. Article ; Online: Gene expression profiling of porcine skeletal muscle satellite cells after poly(I:C) stimulation.

    Tran-Thi, Thuy-Nhien / Wang, Sheng / Adetula, Adeyinka Abiola / Zou, Cheng / Omar, Abdullah Ibne / Han, Jian-Lin / Zhang, Ding-Xiao / Zhao, Shu-Hong

    Gene

    2019  Volume 695, Page(s) 113–121

    Abstract: Porcine satellite cells (PSCs) play a vital role in the construction, development and self-renewal of skeletal muscle. In this study, PSCs were exposed to poly(I:C) stimulation to mimic viral infection during the proliferation and differentiation phases ... ...

    Abstract Porcine satellite cells (PSCs) play a vital role in the construction, development and self-renewal of skeletal muscle. In this study, PSCs were exposed to poly(I:C) stimulation to mimic viral infection during the proliferation and differentiation phases at 0, 12, 24 and 48 hours (h) of the stimulation. The untreated and treated PSCs were analyzed by the RNA-Seq technology. There were 88, 119, 104 and 95 genes being differentially expressed in 0 h vs 12 h treated, 12 h vs 24 h treated, 0 h vs 24 h treated and 24 h vs 48 h untreated comparison libraries, respectively. The GO terms analysis results showed that during the proliferation phase of treated PSCs, the up-regulated genes related to the immune system were highly expressed. In addition, the gene expressions associated with muscle structure development in response to growth factor emerged during the differentiation phase of untreated PSCs. The biological pathways associated with Influenza A, Toll-like receptor and chemokine signaling were revealed in PSCs following poly(I:C) stimulation. The differentially expressed genes were confirmed by quantitative real-time PCR. These findings expanded our understanding of gene expressions and signaling pathways about the infiltrated mechanism of the virus into PSCs.
    MeSH term(s) Animals ; Cell Differentiation/drug effects ; Cell Differentiation/genetics ; Cell Proliferation/drug effects ; Cell Proliferation/genetics ; Gene Expression Profiling ; Gene Expression Regulation/drug effects ; Gene Expression Regulation/genetics ; Gene Ontology ; MicroRNAs/genetics ; Microarray Analysis ; Muscle, Skeletal/drug effects ; Muscle, Skeletal/metabolism ; Poly I-C/pharmacology ; Satellite Cells, Skeletal Muscle/metabolism ; Swine ; Toll-Like Receptors/genetics
    Chemical Substances MicroRNAs ; Toll-Like Receptors ; Poly I-C (O84C90HH2L)
    Language English
    Publishing date 2019-01-08
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2018.12.059
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