scholarly journals Ontogeny of ornithine-urea cycle gene expression in zebrafish (Danio rerio)

2013 ◽  
Vol 304 (11) ◽  
pp. R991-R1000 ◽  
Author(s):  
Christophe M. R. LeMoine ◽  
Patrick J. Walsh
Keyword(s):  
Gene Expression ◽  
Urea Cycle ◽  
Methylation Status ◽  
Zebrafish Embryos ◽  
Carbamoyl Phosphate ◽  
Differential Gene Regulation ◽  
Urea Production ◽  
Differential Gene ◽  
Waste Handling

Although the majority of adult teleosts excrete most of their nitrogenous wastes as ammonia, several fish species are capable of producing urea early in development. In zebrafish, it is unclear whether this results from a functional ornithine-urea cycle (O-UC) and, if so, how it might be regulated. This study examined the spatiotemporal patterns of gene expression of four major O-UC enzymes: carbamoyl phosphate synthase III (CPSIII), ornithine transcarboxylase, arginosuccinate synthetase, and arginosuccinate lyase, using real-time PCR and whole mount in situ hybridization. In addition, we hypothesized that CPSIII gene expression was epigenetically regulated through methylation of its promoter, a widespread mode of differential gene regulation between tissues and life stages in vertebrates. Furthermore, to assess CPSIII functionality, we used morpholinos to silence CPSIII in zebrafish embryos and assessed their nitrogenous waste handling during development, and in response to ammonia injections. Our results suggest that mRNAs of O-UC enzymes are expressed early in zebrafish development and colocalize to the embryonic endoderm. In addition, the methylation status of CPSIII promoter is not consistent with the patterns of expression observed in developing larvae or adult tissues, suggesting other means of transcriptional regulation of this enzyme. Finally, CPSIII morphants exhibited a transient reduction in CPSIII enzyme activity 24 h postfertilization, which was paralleled by reduced urea production during development and in response to an ammonia challenge. Overall, we conclude that the O-UC is functional in zebrafish embryos, providing further evidence that the capacity to produce urea via the O-UC is widespread in developing teleosts.

Differential gene expression as a toxicant-sensitive endpoint in zebrafish embryos and larvae

2007 ◽  
Vol 81 (4) ◽  
pp. 355-364 ◽  
Author(s):  
Doris Voelker ◽  
Christoph Vess ◽  
Michaela Tillmann ◽  
Roland Nagel ◽  
Georg W. Otto ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Zebrafish Embryos ◽  
Differential Gene

Heterogeneity of gene expression in human atheroma unmasked using cDNA representational difference analysis

2002 ◽  
Vol 9 (2) ◽  
pp. 121-130 ◽  
Author(s):  
Kerry L. Tyson ◽  
Peter L. Weissberg ◽  
Catherine M. Shanahan
Keyword(s):  
Gene Expression ◽  
Representational Difference Analysis ◽  
Pcr Analysis ◽  
Cdna Clones ◽  
Difference Analysis ◽  
Complex Interactions ◽  
Atherosclerotic Lesions ◽  
Differential Gene ◽  
Disease Associated Genes

The rupture of an atherosclerotic plaque can have profound consequences, such as myocardial or cerebrovascular infarction. The complex interactions of vascular smooth muscle cells (VSMCs) with inflammatory and immune cells are thought to contribute to both plaque genesis and stability. Key to our understanding of these processes is the identification of genes expressed in human atheromatous lesions. We have employed cDNA representational difference analysis (RDA) to investigate the differences in gene expression between normal and atherosclerotic human vessels. Thirty-one cDNA clones representing sequences expressed in atheroma were isolated, many of which encoded components of inflammatory and immune pathways. The reciprocal experiment, to identify genes expressed in the healthy vasculature, identified two genes associated with the contractile functions of VSMCs. Semiquantitative RT-PCR analysis of expression of these genes in forty samples, derived from healthy and atheromatous vessels, demonstrated marked heterogeneity of gene expression between lesions, although several of the genes were preferentially expressed in atherosclerotic lesions. In situ hybridization identified subsets of macrophages at sites of neovascularization within the lesion and intimal VSMCs as expressing the disease-associated genes. In conclusion, cDNA RDA is a useful, fast, and efficient technique for studying differential gene expression particularly when clinical material is limiting.

scholarly journals DUCTAL CARCINOMA IN SITU AND INVASIVE BREAST CANCER-BASED DIFFERENTIAL GENE EXPRESSION STUDY FOR THERAPEUTIC DEVELOPMENT

2016 ◽  
Vol 9 (9) ◽  
pp. 48
Author(s):  
Harshitha Gopisetty Ramachandra ◽  
Seethalakshmi Sakthivel ◽  
Inamul Hasan Madar ◽  
Iftikhar Aslam Tayubi ◽  
Skm Habeeb
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Gene Expression Profiling ◽  
Ductal Carcinoma In Situ ◽  
Invasive Breast Cancer ◽  
Expression Profiling ◽  
Carcinoma In Situ ◽  
Ductal Carcinoma ◽  
Differential Gene

ABSTRACTObjective: Breast cancer is the second most common cancer in women globally. Multiple inherited mutations in genes are predominantly associatedwith breast cancer. The gene expression profiling of breast tumors generated by DNA microarray analysis provides molecular phenotyping thatdetermines and characterizes the classifications of these tumors.Methods: In this work, we used gene expression profiling of breast cancer samples from Gene Expression Omnibus (GEO) database. The datasetGSE41194, retrieved from GEO, was used to investigate differential gene expression in ductal carcinoma in situ (DCIS) and invasive breast cancer (IBC).The dataset contains 26 DCIS and 24 IBC samples. The data were analyzed in R and Bioconductor. To normalize the data Robust Multiarray Average(RMA) method was applied, limma software was used to identify the differentially expressed genes (DEGs) in DCIS and IBC; an adjusted p value ≤0.05was used to filter differentially expressed probe sets, and a fold change (FC) ≥ 2 to identify upregulated and ≤−2 for downregulated genes. The DEGsretrieved were clustered and annotated using Database for Annotation, Visualization and Integrated Discovery (DAVID) Bioinformatics Resourceswith an EASE score ≤0.1 and count 2.Results: The analysis obtained 72 DEGs with a p≤0.05. The FC≥2 identified 38 upregulated probesets and FC≤−2 identified 34 downregulated probesets. The up and downregulated genes obtained in various comparisons were characterized based on gene ontology (GO) and pathway analyses inDAVID, which retrieved six genes that had principal pathways targeting breast cancer.Conclusion: Identification of these genes and pathways enhances the knowledge and progression of DCIS to IBC; paving a novel way for developingnew therapies for treating patients with breast cancer.Keywords: Molecular phenotyping, Gene Expression, Ductal carcinoma in situ, Invasive breast cancer.

scholarly journals Upregulated Ribosomal Pathway Impairs Follicle Development in a Polycystic Ovary Syndrome Mouse Model: Findings of Differential Gene Expression Analysis of Oocytes

2021 ◽  
Author(s):  
Natsuki Nakanishi ◽  
Satoko Osuka ◽  
Tomohiro Kono ◽  
Hisato Kobayashi ◽  
Shinya Ikeda ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Mouse Model ◽  
Differential Gene Expression ◽  
Polycystic Ovary ◽  
Methylation Status ◽  
Rna Seq ◽  
Ovary Syndrome ◽  
Pcos Group ◽  
Differential Gene

Abstract Background: Polycystic ovary syndrome (PCOS), a common endocrinal disorder, is associated with impaired oocyte development, which leads to infertility. However, the pathogenesis of PCOS has not been completely elucidated. Limited studies have analyzed the pathological characteristics of oocytes in PCOS. This study aimed to analyze the differentially expressed genes (DEGs) and epigenetic changes in the oocytes of the PCOS mouse model to identify the etiological factors.Methods: C57BL/6J female mice were subcutaneously injected with vehicle or 5α-dihydrotestosterone (250 µg/day) on days 16–18 of pregnancy. Female offspring were used as the control or PCOS group. The oocytes were collected from mice aged 7–9 weeks. The DEGs between the control and PCOS groups were analyzed using RNA sequencing (RNA-Seq). Additionally, the DNA methylation status was analyzed using the post-bisulfite adaptor tagging method. The ovarian tissue sections were stained with hematoxylin and eosin to examine the morphological changes. The proteins, Rps21 and Rpl36, were measured using immunostaining.Results: Compared with the control group, the PCOS group exhibited impaired estrous cycle and polycystic ovary-like morphology. RNA-Seq analysis revealed that 90 DEGs were upregulated and 27 DEGs were downregulated in the PCOS mouse model. DNA methylation analysis revealed 30 hypomethylated and 10 hypermethylated regions in the PCOS group. However, the DNA methylation status was not correlated with differential gene expression. The Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that five DEGs (Rps21, Rpl36, Rpl36a, Rpl37a, and Rpl22l1) were enriched in ribosome-related pathways. The immunohistochemical analysis revealed that the expression levels of Rps21 and Rpl36 were significantly upregulated in the PCOS mouse model.Conclusions: These results suggest that differential gene expression in the oocytes of the PCOS mouse model is related to impaired folliculogenesis. These findings improved our understanding of the pathogenesis of PCOS.

scholarly journals Irisin directly stimulates osteoclastogenesis and bone resorption in vitro and in vivo

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Eben G Estell ◽  
Phuong T Le ◽  
Yosta Vegting ◽  
Hyeonwoo Kim ◽  
Christiane Wrann ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bone Marrow ◽  
Bone Resorption ◽  
Osteoclast Differentiation ◽  
Neutralizing Antibody ◽  
Mouse Bone Marrow ◽  
Differential Gene

Irisin, a skeletal-muscle secreted myokine, facilitates muscle-bone crosstalk and skeletal remodeling in part by its action on osteoblasts and osteocytes. In this study, we investigated whether irisin directly regulates osteoclasts. In vitro, irisin (2–10 ng/mL) increased osteoclast differentiation in C57BL/6J mouse bone marrow progenitors; however, this increase was blocked by a neutralizing antibody to integrin αVβ5. Irisin also increased bone resorption on several substrates in situ. RNAseq revealed differential gene expression induced by irisin including upregulation of markers for osteoclast differentiation and resorption, as well as osteoblast-stimulating ‘clastokines’. Forced expression of the irisin precursor Fndc5 in transgenic C57BL/6J mice resulted in lower bone mass at three ages and greater in vitro osteoclastogenesis from Fndc5-transgenic bone marrow progenitors. This study demonstrates that irisin acts directly on osteoclast progenitors to increase differentiation and promote bone resorption, supporting the tenet that irisin not only stimulates bone remodeling but may also be an important counter-regulatory hormone.

scholarly journals Differential Gene Expression in Ductal Carcinoma in Situ of the Breast Based on ERBB2 Status

2017 ◽  
Vol 24 (1) ◽  
pp. 102-110 ◽  
Author(s):  
Emmanuel Agosto-Arroyo ◽  
Tatyana Isayeva ◽  
Shi Wei ◽  
Jonas S. Almeida ◽  
Shuko Harada
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Ductal Carcinoma In Situ ◽  
Carcinoma In Situ ◽  
Ductal Carcinoma ◽  
Differential Gene

scholarly journals Observation of miRNA Gene Expression in Zebrafish Embryos by In Situ Hybridization to MicroRNA Primary Transcripts

Zebrafish ◽  
2011 ◽  
Vol 8 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Xinjun He ◽  
Yi-Lin Yan ◽  
April DeLaurier ◽  
John H. Postlethwait
Keyword(s):  
Gene Expression ◽  
In Situ Hybridization ◽  
Mirna Gene ◽  
Zebrafish Embryos

scholarly journals Single-nucleus RNA-sequencing in pre-cellularization Drosophila melanogaster embryos

2021 ◽  
Author(s):  
Ashley R Albright ◽  
Michael R Stadler ◽  
Michael Eisen
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Rna Sequencing ◽  
Regulation Of Gene Expression ◽  
Single Nucleus ◽  
Differential Gene ◽  
The Difference ◽  
In Situ Hybridizations ◽  
Genome Activation

Our current understanding of the regulation of gene expression in the early Drosophila melanogaster embryo comes from observations of a few genes at a time, as with in situ hybridizations, or observation of gene expression levels without regards to patterning, as with RNA-sequencing. Single-nucleus RNA-sequencing however, has the potential to provide new insights into the regulation of gene expression for many genes at once while simultaneously retaining information regarding the position of each nucleus prior to dissociation based on patterned gene expression. In order to establish the practicality of single-nucleus RNA sequencing in the context of a real biological question, here we look at the difference in gene expression between control and an insulator protein, dCTCF, maternal null embryos during zygotic genome activation at nuclear cycle 14. We find that early embryonic nuclei can be grouped into distinct clusters according to gene expression. From both virtual and published in situ hybridizations, we also find that these clusters correspond to spatial regions of the embryo. Lastly, we present multiple examples of differential gene expression between control and maternal CTCF null nuclei in one or more clusters, but not in bulk when grouping expression across all nuclei. These results highlight the potential for single-nucleus RNA-sequencing to reveal new insights into the regulation of gene expression in the early Drosophila melanogaster embryo.

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