scholarly journals Discovery and identification of candidate sex-related genes based on transcriptome sequencing of Russian sturgeon (Acipenser gueldenstaedtii) gonads

2016 ◽  
Vol 48 (7) ◽  
pp. 464-476 ◽  
Author(s):  
Yadong Chen ◽  
Yongtao Xia ◽  
Changwei Shao ◽  
Lei Han ◽  
Xuejie Chen ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Ribosomal Proteins ◽  
Differentially Expressed Gene ◽  
Gonadal Development ◽  
Differentially Expressed ◽  
Russian Sturgeon ◽  
Female Gonad ◽  
Accurate Identification ◽  
Acipenser Gueldenstaedtii ◽  
Transduction Mechanisms

As the Russian sturgeon ( Acipenser gueldenstaedtii) is an important food and is the main source of caviar, it is necessary to discover the genes associated with its sex differentiation. However, the complicated life and maturity cycles of the Russian sturgeon restrict the accurate identification of sex in early development. To generate a first look at specific sex-related genes, we sequenced the transcriptome of gonads in different development stages (1, 2, and 5 yr old stages) with next-generation RNA sequencing. We generated >60 million raw reads, and the filtered reads were assembled into 263,341 contigs, which produced 38,505 unigenes. Genes involved in signal transduction mechanisms were the most abundant, suggesting that development of sturgeon gonads is under control of signal transduction mechanisms. Differentially expressed gene analysis suggests that more genes for protein synthesis, cytochrome c oxidase subunits, and ribosomal proteins were expressed in female gonads than in male. Meanwhile, male gonads expressed more transposable element transposase, reverse transcriptase, and transposase-related genes than female. In total, 342, 782, and 7,845 genes were detected in intersex, male, and female transcriptomes, respectively. The female gonad expressed more genes than the male gonad, and more genes were involved in female gonadal development. Genes (sox9, foxl2) are differentially expressed in different sexes and may be important sex-related genes in Russian sturgeon. S ox9 genes are responsible for the development of male gonads and foxl2 for female gonads.

scholarly journals Transcriptomic Analysis Following Artificial Selection for Grasshopper Size

Insects ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 176
Author(s):  
Shuang Li ◽  
Dong-Nan Cui ◽  
Hidayat Ullah ◽  
Jun Chen ◽  
Shao-Fang Liu ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Differentially Expressed Genes ◽  
Artificial Selection ◽  
Metabolic Process ◽  
Transcriptomic Analysis ◽  
Differentially Expressed ◽  
General Function ◽  
Selection Experiment ◽  
Transduction Mechanisms ◽  
Selection For

We analyzed the transcriptomes of Romalea microptera grasshoppers after 8 years of artificial selection for either long or short thoraces. Evolution proceeded rapidly during the experiment, with a 13.3% increase and a 32.2% decrease in mean pronotum lengths (sexes combined) in the up- and down-selected colonies, respectively, after only 11 generations. At least 16 additional traits also diverged between the two colonies during the selection experiment. Transcriptomic analysis identified 693 differentially expressed genes, with 386 upregulated and 307 downregulated (55.7% vs. 44.3%), including cellular process, metabolic process, binding, general function prediction only, and signal transduction mechanisms. Many of the differentially expressed genes (DEGs) are known to influence animal body size.

149: The Effect of Denervation on Signal Transduction Mechanisms of M2 and M3 Mediated Bladder Contractile Response

2005 ◽  
Vol 173 (4S) ◽  
pp. 40-40
Author(s):  
Leo R. Doumanian ◽  
Alan S. Braverman ◽  
Amitt S. Tibb ◽  
Michael R. Ruggieri
Keyword(s):  
Signal Transduction ◽  
Contractile Response ◽  
Transduction Mechanisms

Decoding Psoriasis: Integrated Bioinformatics Approach to Understand Hub Genes and Involved Pathways

2020 ◽  
Vol 26 (29) ◽  
pp. 3619-3630
Author(s):  
Saumya Choudhary ◽  
Dibyabhaba Pradhan ◽  
Noor S. Khan ◽  
Harpreet Singh ◽  
George Thomas ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Gene ◽  
Therapeutic Targets ◽  
Interaction Network ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
Keratinocyte Differentiation ◽  
Hub Genes ◽  
Lesional Skin ◽  
Ncbi Gene Expression Omnibus

Background: Psoriasis is a chronic immune mediated skin disorder with global prevalence of 0.2- 11.4%. Despite rare mortality, the severity of the disease could be understood by the accompanying comorbidities, that has even led to psychological problems among several patients. The cause and the disease mechanism still remain elusive. Objective: To identify potential therapeutic targets and affecting pathways for better insight of the disease pathogenesis. Method: The gene expression profile GSE13355 and GSE14905 were retrieved from NCBI, Gene Expression Omnibus database. The GEO profiles were integrated and the DEGs of lesional and non-lesional psoriasis skin were identified using the affy package in R software. The Kyoto Encyclopaedia of Genes and Genomes pathways of the DEGs were analyzed using clusterProfiler. Cytoscape, V3.7.1 was utilized to construct protein interaction network and analyze the interactome map of candidate proteins encoded in DEGs. Functionally relevant clusters were detected through Cytohubba and MCODE. Results: A total of 1013 genes were differentially expressed in lesional skin of which 557 were upregulated and 456 were downregulated. Seven dysregulated genes were extracted in non-lesional skin. The disease gene network of these DEGs revealed 75 newly identified differentially expressed gene that might have a role in development and progression of the disease. GO analysis revealed keratinocyte differentiation and positive regulation of cytokine production to be the most enriched biological process and molecular function. Cytokines -cytokine receptor was the most enriched pathways. Among 1013 identified DEGs in lesional group, 36 DEGs were found to have altered genetic signature including IL1B and STAT3 which are also reported as hub genes. CCNB1, CCNA2, CDK1, IL1B, CXCL8, MKI 67, ESR1, UBE2C, STAT1 and STAT3 were top 10 hub gene. Conclusion: The hub genes, genomic altered DEGs and other newly identified differentially dysregulated genes would improve our understanding of psoriasis pathogenesis, moreover, the hub genes could be explored as potential therapeutic targets for psoriasis.

Identification of the Differentially Expressed Genes Involved in the Synergistic Neurotoxicity of an HIV Protease Inhibitor and Methamphetamine

2019 ◽  
Vol 17 (4) ◽  
pp. 290-303
Author(s):  
Sangsang Li ◽  
Yanfei Li ◽  
Bingpeng Deng ◽  
Jie Yan ◽  
Yong Wang
Keyword(s):  
Protease Inhibitor ◽  
Growth Inhibition ◽  
Quantitative Polymerase Chain Reaction ◽  
Differentially Expressed Gene ◽  
Antiretroviral Drugs ◽  
Differentially Expressed ◽  
Hiv Protease ◽  
Hiv Protease Inhibitor ◽  
Dopaminergic Cells ◽  
Immunodeficiency Syndrome

Background: The abuse of psychostimulants such as methamphetamine (METH) is common in human immunodeficiency virus (HIV)-infected individuals. Acquired immunodeficiency syndrome (AIDS) patients taking METH and antiretroviral drugs could suffer severe neurologic damage and cognitive impairment. Objective: To reveal the underlying neuropathologic mechanisms of an HIV protease inhibitor (PI) combined with METH, growth-inhibition tests of dopaminergic cells and RNA sequencing were performed. Methods: A combination of METH and PI caused more growth inhibition of dopaminergic cells than METH alone or a PI alone. Furthermore, we identified differentially expressed gene (DEG) patterns in the METH vs. untreated cells (1161 genes), PI vs. untreated cells (16 genes), METH-PI vs. PI (3959 genes), and METH-PI vs. METH groups (14 genes). Results: The DEGs in the METH-PI co-treatment group were verified in the brains of a mouse model using quantitative polymerase chain reaction and were involved mostly in the regulatory functions of cell proliferation and inflammation. Conclusion: Such identification of key regulatory genes could facilitate the study of their neuroprotective potential in the users of METH and PIs.

Gene Set Correlation Analysis and Visualization Using Gene Expression Data

2020 ◽  
Vol 15 ◽  
Author(s):  
Chen-An Tsai ◽  
James J. Chen
Keyword(s):  
Gene Expression ◽  
Correlation Analysis ◽  
Gene Expression Data ◽  
Differentially Expressed Gene ◽  
Differentially Expressed ◽  
Superior Performance ◽  
Expression Data ◽  
Gene Set ◽  
Gene Sets ◽  
Set Correlation

Background: Gene set enrichment analyses (GSEA) provide a useful and powerful approach to identify differentially expressed gene sets with prior biological knowledge. Several GSEA algorithms have been proposed to perform enrichment analyses on groups of genes. However, many of these algorithms have focused on identification of differentially expressed gene sets in a given phenotype. Objective: In this paper, we propose a gene set analytic framework, Gene Set Correlation Analysis (GSCoA), that simultaneously measures within and between gene sets variation to identify sets of genes enriched for differential expression and highly co-related pathways. Methods: We apply co-inertia analysis to the comparisons of cross-gene sets in gene expression data to measure the costructure of expression profiles in pairs of gene sets. Co-inertia analysis (CIA) is one multivariate method to identify trends or co-relationships in multiple datasets, which contain the same samples. The objective of CIA is to seek ordinations (dimension reduction diagrams) of two gene sets such that the square covariance between the projections of the gene sets on successive axes is maximized. Simulation studies illustrate that CIA offers superior performance in identifying corelationships between gene sets in all simulation settings when compared to correlation-based gene set methods. Result and Conclusion: We also combine between-gene set CIA and GSEA to discover the relationships between gene sets significantly associated with phenotypes. In addition, we provide a graphical technique for visualizing and simultaneously exploring the associations of between and within gene sets and their interaction and network. We then demonstrate integration of within and between gene sets variation using CIA and GSEA, applied to the p53 gene expression data using the c2 curated gene sets. Ultimately, the GSCoA approach provides an attractive tool for identification and visualization of novel associations between pairs of gene sets by integrating co-relationships between gene sets into gene set analysis.

PD-L1 Signal Transduction Mechanisms in Cancer Cells

2018 ◽  
Vol 17 (2) ◽  
pp. 72-86
Author(s):  
Miren Zuazo-Ibarra ◽  
Maria Gato-Canas ◽  
Hugo Arasanz-Esteban ◽  
Gonzalo Fernandez-Hinojal ◽  
Maria Ibanez-Vea ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Cancer Cells ◽  
Transduction Mechanisms

scholarly journals Angiotensin II biosynthesis and its receptor signal transduction mechanisms in dog cardiac sympathetic ganglia.

1996 ◽  
Vol 71 ◽  
pp. 330
Author(s):  
Kazushi Kushiku ◽  
Ryoko Tokunaga ◽  
Hiromi Yamada ◽  
Kazuhiko Shibata ◽  
Katsuhiro Yamada ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Angiotensin Ii ◽  
Sympathetic Ganglia ◽  
Receptor Signal ◽  
Transduction Mechanisms

scholarly journals Transcriptional Response in the Digestive Gland of the King Scallop (Pecten maximus) after the Injection of Domoic Acid

Toxins ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 339
Author(s):  
Pablo Ventoso ◽  
Antonio J. Pazos ◽  
Juan Blanco ◽  
M. Luz Pérez-Parallé ◽  
Juan C. Triviño ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Gene Ontology ◽  
Immune System ◽  
Digestive Gland ◽  
Domoic Acid ◽  
Differentially Expressed ◽  
Pecten Maximus ◽  
System Process ◽  
Immune System Process ◽  
Response To Stress

Some diatom species of the genus Pseudo-nitzschia produce the toxin domoic acid. The depuration rate of domoic acid in Pecten maximus is very low; for this reason, king scallops generally contain high levels of domoic acid in their tissues. A transcriptomic approach was used to identify the genes differentially expressed in the P. maximus digestive gland after the injection of domoic acid. The differential expression analysis found 535 differentially expressed genes (226 up-regulated and 309 down-regulated). Protein–protein interaction networks obtained with the up-regulated genes were enriched in gene ontology terms, such as vesicle-mediated transport, response to stress, signal transduction, immune system process, RNA metabolic process, and autophagy, while networks obtained with the down-regulated genes were enriched in gene ontology terms, such as response to stress, immune system process, ribosome biogenesis, signal transduction, and mRNA processing. Genes that code for cytochrome P450 enzymes, glutathione S-transferase theta-1, glutamine synthase, pyrroline-5-carboxylate reductase 2, and sodium- and chloride-dependent glycine transporter 1 were among the up-regulated genes. Therefore, a stress response at the level of gene expression, that could be caused by the domoic acid injection, was evidenced by the alteration of several biological, cellular, and molecular processes.

scholarly journals Transcriptomic and epigenomic remodeling occurs during vascular cambium periodicity in Populus tomentosa

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Bo Chen ◽  
Huimin Xu ◽  
Yayu Guo ◽  
Paul Grünhofer ◽  
Lukas Schreiber ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Plant Hormone ◽  
Target Genes ◽  
Populus Tomentosa ◽  
Differentially Expressed ◽  
Vascular Cambium ◽  
Differentially Methylated Region ◽  
Gene Body Methylation ◽  
Transcription Analysis ◽  
Global Methylation

AbstractTrees in temperate regions exhibit evident seasonal patterns, which play vital roles in their growth and development. The activity of cambial stem cells is the basis for regulating the quantity and quality of wood, which has received considerable attention. However, the underlying mechanisms of these processes have not been fully elucidated. Here we performed a comprehensive analysis of morphological observations, transcriptome profiles, the DNA methylome, and miRNAs of the cambium in Populus tomentosa during the transition from dormancy to activation. Anatomical analysis showed that the active cambial zone exhibited a significant increase in the width and number of cell layers compared with those of the dormant and reactivating cambium. Furthermore, we found that differentially expressed genes associated with vascular development were mainly involved in plant hormone signal transduction, cell division and expansion, and cell wall biosynthesis. In addition, we identified 235 known miRNAs and 125 novel miRNAs. Differentially expressed miRNAs and target genes showed stronger negative correlations than other miRNA/target pairs. Moreover, global methylation and transcription analysis revealed that CG gene body methylation was positively correlated with gene expression, whereas CHG exhibited the opposite trend in the downstream region. Most importantly, we observed that the number of CHH differentially methylated region (DMR) changes was the greatest during cambium periodicity. Intriguingly, the genes with hypomethylated CHH DMRs in the promoter were involved in plant hormone signal transduction, phenylpropanoid biosynthesis, and plant–pathogen interactions during vascular cambium development. These findings improve our systems-level understanding of the epigenomic diversity that exists in the annual growth cycle of trees.

scholarly journals Comprehensive high-throughput meta-analysis of differentially expressed microRNAs in transcriptomic datasets reveals significant disruption of MAPK/JNK signal transduction pathway in Adult T-cell leukemia/lymphoma

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Shahrzad Shadabi ◽  
Nargess Delrish ◽  
Mehdi Norouzi ◽  
Maryam Ehteshami ◽  
Fariba Habibian-Sezavar ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signal Transduction ◽  
T Cell ◽  
Network Analysis ◽  
High Throughput ◽  
Target Gene ◽  
Differentially Expressed ◽  
Cell Leukemia ◽  
Adult T Cell Leukemia ◽  
Healthy Donors

Abstract Background Human T-lymphotropic virus 1 (HTLV-1) infection may lead to the development of Adult T-cell leukemia/lymphoma (ATLL). To further elucidate the pathophysiology of this aggressive CD4+ T-cell malignancy, we have performed an integrated systems biology approach to analyze previous transcriptome datasets focusing on differentially expressed miRNAs (DEMs) in peripheral blood of ATLL patients. Methods Datasets GSE28626, GSE31629, GSE11577 were used to identify ATLL-specific DEM signatures. The target genes of each identified miRNA were obtained to construct a protein-protein interactions network using STRING database. The target gene hubs were subjected to further analysis to demonstrate significantly enriched gene ontology terms and signaling pathways. Quantitative reverse transcription Polymerase Chain Reaction (RTqPCR) was performed on major genes in certain pathways identified by network analysis to highlight gene expression alterations. Results High-throughput in silico analysis revealed 9 DEMs hsa-let-7a, hsa-let-7g, hsa-mir-181b, hsa-mir-26b, hsa-mir-30c, hsa-mir-186, hsa-mir-10a, hsa-mir-30b, and hsa-let-7f between ATLL patients and healthy donors. Further analysis revealed the first 5 of DEMs were directly associated with previously identified pathways in the pathogenesis of HTLV-1. Network analysis demonstrated the involvement of target gene hubs in several signaling cascades, mainly in the MAPK pathway. RT-qPCR on human ATLL samples showed significant upregulation of EVI1, MKP1, PTPRR, and JNK gene vs healthy donors in MAPK/JNK pathway. Discussion The results highlighted the functional impact of a subset dysregulated microRNAs in ATLL on cellular gene expression and signal transduction pathways. Further studies are needed to identify novel biomarkers to obtain a comprehensive mapping of deregulated biological pathways in ATLL.

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