scholarly journals Differentially expressed genes in cotyledon of ewes fed mycotoxins

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
J. L. Britt ◽  
R. E. Noorai ◽  
S. K. Duckett
Keyword(s):  
Wound Healing ◽  
Differentially Expressed Genes ◽  
Ergot Alkaloid ◽  
Ergot Alkaloids ◽  
Late Gestation ◽  
Fetal Weight ◽  
Differentially Expressed ◽  
Coagulation Cascade ◽  
Peroxisome Proliferator ◽  
Metabolism Regulation

Abstract Background Ergot alkaloids (E+) are mycotoxins produced by the endophytic fungus, Epichloë coenophiala, in tall fescue that are associated with ergotism in animals. Exposure to ergot alkaloids during gestation reduces fetal weight and placental mass in sheep. These reductions are related to vasoconstrictive effects of ergot alkaloids and potential alterations in nutrient transport to the fetus. Cotyledon samples were obtained from eight ewes that were fed E+ (n = 4; E+/E+) or E- (endophyte-free without ergot alkaloids; n = 4; E−/E-) seed during both mid (d 35 to 85) and late (d 85–133) gestation to assess differentially expressed genes associated with ergot alkaloid induced reductions in placental mass and fetal weight, and discover potential adaptive mechanisms to alter nutrient supply to fetus. Results Ewes fed E+/E+ fescue seed during both mid and late gestation had 20% reduction in fetal body weight and 33% reduction in cotyledon mass compared to controls (E−/E-). Over 13,000 genes were identified with 110 upregulated and 33 downregulated. Four genes had a |log2FC| > 5 for ewes consuming E+/E+ treatment compared to controls: LECT2, SLC22A9, APOC3, and MBL2. REViGO revealed clusters of upregulated genes associated glucose, carbohydrates, lipid, protein, macromolecular and cellular metabolism, regulation of wound healing and response to starvation. For downregulated genes, no clusters were present, but all enriched GO terms were associated with anion and monocarboxylic acid transport. The complement and coagulation cascade and the peroxisome proliferator-activated receptor signaling pathway were found to be enriched for ewes consuming E+/E+ treatment. Conclusions Consumption of ergot alkaloids during gestation altered the cotyledonary transcriptome specifically related to macronutrient metabolism, wound healing and starvation. These results show that ergot alkaloid exposure upregulates genes involved in nutrient metabolism to supply the fetus with additional substrates in attempts to rescue fetal growth.

scholarly journals Differentially expressed genes in cotyledon of ewes fed mycotoxins

2020 ◽  
Author(s):  
Jessica L Britt ◽  
Rooksana Noorai ◽  
Susan Duckett
Keyword(s):  
Wound Healing ◽  
Differentially Expressed Genes ◽  
Ergot Alkaloid ◽  
Ergot Alkaloids ◽  
Late Gestation ◽  
Fetal Weight ◽  
Differentially Expressed ◽  
Coagulation Cascade ◽  
Peroxisome Proliferator ◽  
Metabolism Regulation

Abstract Background: Ergot alkaloids (E+) are mycotoxins produced by the endophytic fungus, Epichloë coenophiala, in tall fescue that are associated with ergotism in animals. Exposure to ergot alkaloids during gestation reduces fetal weight and placental mass in sheep. These reductions are related to vasoconstrictive effects of ergot alkaloids and potential alterations in nutrient transport to the fetus. Cotyledon samples were obtained from eight ewes that were fed E+ (n = 4; E+/E+) or E- (endophyte-free without ergot alkaloids; n = 4; E-/E-) seed during both mid (d 35 to 85) and late (d 85-133) gestation to assess differentially expressed genes associated with ergot alkaloid induced reductions in placental mass and fetal weight, and discover potential adaptive mechanisms to alter nutrient supply to fetus. Results: Ewes fed E+/E+ fescue seed during both mid and late gestation had 20% reduction in fetal body weight and 33% reduction in cotyledon mass compared to controls (E-/E-). Over 13,000 genes were identified with 110 upregulated and 33 downregulated. Four genes had a |log2FC|>5 for ewes consuming E+/E+ treatment compared to controls: LECT2, SLC22A9, APOC3, and MBL2. REViGO revealed clusters of upregulated genes associated glucose, carbohydrates, lipid, protein, macromolecular and cellular metabolism, regulation of wound healing and response to starvation. For downregulated genes, no clusters were present, but all enriched GO terms were associated with anion and monocarboxylic acid transport. The complement and coagulation cascade and the peroxisome proliferator-activated receptor signaling pathway were found to be enriched for ewes consuming E+/E+ treatment. Conclusions: Consumption of ergot alkaloids during gestation altered the cotyledonary transcriptome specifically related to macronutrient metabolism, wound healing and starvation. These results show that ergot alkaloid exposure upregulates genes involved in nutrient metabolism to supply the fetus with additional substrates in attempts to rescue fetal growth.

scholarly journals Differentially expressed genes in cotyledon of ewes fed mycotoxins

2020 ◽  
Author(s):  
Jessica L Britt ◽  
Rooksana Noorai ◽  
Susan Duckett
Keyword(s):  
Wound Healing ◽  
Differentially Expressed Genes ◽  
Ergot Alkaloid ◽  
Ergot Alkaloids ◽  
Late Gestation ◽  
Fetal Weight ◽  
Differentially Expressed ◽  
Coagulation Cascade ◽  
Peroxisome Proliferator ◽  
Metabolism Regulation

Abstract Background Ergot alkaloids (E+) are mycotoxins produced by the endophytic fungus, Epichloë coenophiala, in tall fescue that are associated with ergotism in animals. Exposure to ergot alkaloids during gestation reduces fetal weight and placental mass in sheep. These reductions are related to vasoconstrictive effects of ergot alkaloids and potential alterations in nutrient transport to the fetus. Cotyledon samples were obtained from eight ewes that were fed E+ (n = 4; E+/E+) or E- (endophyte-free without ergot alkaloids; n = 4; E-/E-) seed during both mid (d 35 to 85) and late (d 85-133) gestation to assess differentially expressed genes associated with ergot alkaloid induced reductions in placental mass and fetal weight, and discover potential adaptive mechanisms to alter nutrient supply to fetus. Results Ewes fed E+/E+ fescue seed during both mid and late gestation had 20% reduction in fetal body weight and 33% reduction in cotyledon mass compared to controls (E-/E-). Over 13,000 genes were identified with 110 upregulated and 33 downregulated. Four genes had a |log2FC|>5 for ewes consuming E+/E+ treatment compared to controls: LECT2, SLC22A9, APOC3, and MBL2. REViGO revealed clusters of upregulated genes associated glucose, carbohydrates, lipid, protein, macromolecular and cellular metabolism, regulation of wound healing and response to starvation. For downregulated genes, no clusters were present, but all enriched GO terms were associated with anion and monocarboxylic acid transport. The complement and coagulation cascade and the peroxisome proliferator-activated receptor signaling pathway were found to be enriched for ewes consuming E+/E+ treatment. Conclusions Consumption of ergot alkaloids during gestation altered the cotyledonary transcriptome specifically related to macronutrient metabolism, wound healing and starvation. These results show that ergot alkaloid exposure upregulates genes involved in nutrient metabolism to supply the fetus with additional substrates in attempts to rescue fetal growth.

scholarly journals Differentially expressed genes in cotyledon of ewes fed mycotoxins

2020 ◽  
Author(s):  
Jessica L Britt ◽  
Rooksana Noorai ◽  
Susan Duckett
Keyword(s):  
Wound Healing ◽  
Differentially Expressed Genes ◽  
Ergot Alkaloid ◽  
Ergot Alkaloids ◽  
Late Gestation ◽  
Fetal Weight ◽  
Differentially Expressed ◽  
Coagulation Cascade ◽  
Peroxisome Proliferator ◽  
Metabolism Regulation

Abstract Background Ergot alkaloids (E+) are mycotoxins produced by the endophytic fungus, Epichloë coenophiala, in tall fescue that are associated with ergotism in animals. Exposure to ergot alkaloids during gestation reduces fetal weight and placental mass in sheep. These reductions are related to vasoconstrictive effects of ergot alkaloids and potential alterations in nutrient transport to the fetus. Cotyledon samples were obtained from eight ewes that were fed E+ (n = 4; E+/E+) or E- (endophyte-free without ergot alkaloids; n = 4; E-/E-) seed during both mid (d 35 to 85) and late (d 85–133) gestation to assess differentially expressed genes associated with ergot alkaloid induced reductions in placental mass and fetal weight, and discover potential adaptive mechanisms to alter nutrient supply to fetus. Results Ewes fed E+/E + fescue seed during both mid and late gestation had 20% reduction in fetal body weight and 33% reduction in cotyledon mass compared to controls (E-/E-). Over 13,000 genes were identified with 110 upregulated and 33 downregulated. Four genes had a |log2FC|>5 for ewes consuming E+/E + treatment compared to controls: LECT2, SLC22A9, APOC3, and MBL2. REViGO revealed clusters of upregulated genes associated glucose, carbohydrates, lipid, protein, macromolecular and cellular metabolism, regulation of wound healing and response to starvation. For downregulated genes, no clusters were present, but all enriched GO terms were associated with anion and monocarboxylic acid transport. The complement and coagulation cascade and the peroxisome proliferator-activated receptor signaling pathway were found to be enriched for ewes consuming E+/E + treatment. Conclusions Consumption of ergot alkaloids during gestation altered the cotyledonary transcriptome specifically related to macronutrient metabolism, wound healing and starvation. These results show that ergot alkaloid exposure upregulates genes involved in nutrient metabolism to supply the fetus with additional substrates in attempts to rescue fetal growth.

scholarly journals Screening of Prognostic Factors in Early-Onset Breast Cancer

2020 ◽  
Vol 19 ◽  
pp. 153303381989367 ◽  
Author(s):  
Zhun Yu ◽  
Qi He ◽  
Guoping Xu
Keyword(s):  
Breast Cancer ◽  
Transcription Factor ◽  
Differentially Expressed Genes ◽  
Early Onset ◽  
Differentially Expressed ◽  
Peroxisome Proliferator ◽  
Early Onset Breast Cancer ◽  
Microrna Target ◽  
Peroxisome Proliferator Activated Receptor ◽  
Protein Protein Interaction

Background: Gene expression profiles from early-onset breast cancer and normal tissues were analyzed to explore the genes and prognostic factors associated with breast cancer. Methods: GSE109169 and GSE89116 were obtained from the database of Gene Expression Omnibus. We firstly screened the differentially expressed genes between tumor samples and normal samples from patients with early-onset breast cancer. Based on database for annotation, visualization and intergrated discovery (DAVID) tool, functional analysis was calculated. Transcription factor-target regulation and microRNA-target gene network were constructed using the tool of transcriptional regulatory relatitionships unraveled by sentence-based text mining (TRRUST) and miRWalk2.0, respectively. The prognosis-related survival information was compiled based on The Cancer Genome Atlas breast cancer clinical data. Results: A total of 708 differentially expressed genes from GSE109169 data sets and 358 differentially expressed genes from GSE89116 data sets were obtained, of which 122 common differentially expressed genes including 102 uniformly downregulated genes and 20 uniformly upregulated genes were screened. Protein–protein interaction network with a total of 83 nodes and 157 relationship pairs was obtained, and genes in protein–protein interaction, such as peroxisome proliferator-activated receptor γ, FGF2, adiponectin, and PCK1, were recognized as key nodes in protein–protein interaction. In total, 66 transcription factor–target relationship pairs were obtained, and peroxisome proliferator-activated receptor γ was the only one downregulated transcription factor. MicroRNA-target gene network contained 368 microRNA-target relationship pairs. Moreover, 16 differentially expressed genes, including 2 upregulations and 14 downregulations, were related to a significant correlation with the prognosis, including SQLE and peroxisome proliferator-activated receptor γ. Conclusions: SQLE and peroxisome proliferator-activated receptor γ might be important prognostic factors in breast cancers, and adiponectin might be important in breast cancer pathogenesis regulated by peroxisome proliferator-activated receptor γ.

scholarly journals Identification of regulatory networks and hub genes controlling mammary gland development and lactation in dairy goats during the late lactation, dry period, and late gestation stages

2020 ◽  
Author(s):  
Rong Xuan ◽  
Tianle Chao ◽  
Xiaodong Zhao ◽  
Aili Wang ◽  
Yunpeng Chu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Mammary Gland ◽  
Differentially Expressed Genes ◽  
Mammary Gland Development ◽  
Late Gestation ◽  
Differentially Expressed ◽  
Dry Period ◽  
Mammary Gland Tissue ◽  
Three Stages ◽  
Gland Development

Abstract Background From the late lactation to late gestation stages, the mammary gland tissue of goats undergoes a process from involution to remodeling and then to high differentiation of mammary gland tissue. From the perspective of lactation, this is a continuous development process of the goat mammary gland from the termination of lactation to the restoration of lactation. We performed transcriptome sequencing on goat mammary gland tissues at three mammary gland developmental stages to screen for differentially expressed genes that affect mammary gland development and the physiological process of lactation and mapped their expression profiles in three stages. The objective of this study is to reveal the expression characteristics of these genes and their potential function during mammary gland development and lactation. Results We identified 1,381 differentially expressed genes in the mammary gland during three stages and found that the expression level of genes encoding casein, such as alpha-s1-casein (CSN1S1), alpha-s2-casein (CSN1S2), beta-casein (CSN2), and kappa-casein (CSN3), and alpha-lactalbumin (LALBA) were higher in mammary gland tissues during the late lactation stage and late gestation stage than those during the dry period. In addition, we constructed six functional networks related to differentially expressed genes and found that these genes are closely related to mammary gland growth and development, apoptosis, immunity, substance transport, biosynthesis, and metabolism. Finally, we identified 35 differentially expressed transcription factors, which were classified into 16 families, and predicted that transcription factors of the basic leucine zipper domain (bZIP) family and basic helix-loop-helix (bHLH) family regulated the expression levels of genes related to mammary gland development and lactation. Conclusions Among the late lactation, dry period, and late gestation stages, there are differences in the expression levels of genes related to mammary gland growth and development, apoptosis, immunity, basic substance transport, biosynthesis, and metabolism in mammary gland tissues. Some genes in the same family or with similar functions have similar expression patterns. These differentially expressed genes or transcription factors work synergistically to participate in the regulation of mammary gland development and the physiological process of lactation.

Mining the Bioinformation of Differentially Expressed Genes in Obese Mice Treated with Chronic Intermittent Hypoxia Based on the Bioinformatics Methods

2012 ◽  
Vol 195-196 ◽  
pp. 429-434
Author(s):  
De Bi ◽  
Hua Jun Xiao ◽  
Cui Hong Zhou ◽  
Jun Zhou
Keyword(s):  
Differentially Expressed Genes ◽  
Intermittent Hypoxia ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
Chronic Intermittent Hypoxia ◽  
Molecular Characteristics ◽  
Peroxisome Proliferator ◽  
Obese Mice ◽  
Hybridization Data ◽  
Peroxisome Proliferator Activated Receptors

Objective: To analyze the differentially expressed genes expressed genes in obese mice that treated with chronic intermittent hypoxia (CIH) for getting better understanding of the molecular characteristics in the obese mice caused by CIH. Methods: Got the microarray hybridization data from the Gene Expression Omnibus (GEO) database. Identified the differentially expressed genes expressed genes in CIH obese mice and the patterns of their regulation using public bioinformatics software and database, such as BRB-Arraytools, Genecodis and DAVID, KEGG. Results and Conclusion: We found the Peroxisome proliferator activated receptors (PPARs) pathway involved in the down-regulated genes. These data mining findings between room air and CIH mice by bioinformatics methods could provide better understanding of the molecular activity change in obese caused by CIH.

scholarly journals Source of Dietary Fat in Pig Diet Affects Adipose Expression of Genes Related to Cancer, Cardiovascular, and Neurodegenerative Diseases

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 948
Author(s):  
Maria Oczkowicz ◽  
Tomasz Szmatoła ◽  
Małgorzata Świątkiewicz
Keyword(s):  
Differentially Expressed Genes ◽  
Beef Tallow ◽  
Rapeseed Oil ◽  
Fluid Shear Stress ◽  
Coconut Oil ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
Coagulation Cascade ◽  
P Value

It has been known for many years that excessive consumption of saturated fats has proatherogenic properties, contrary to unsaturated fats. However, the molecular mechanism covering these effects is not fully understood. In this paper, we aimed to identify differentially expressed genes (DEGs) using RNA-sequencing, following feeding pigs with different sources of fat. After comparison of adipose samples from three dietary groups (rapeseed oil (n = 6), beef tallow (n = 5), coconut oil (n = 5)), we identified 29 DEGs (adjusted p-value < 0.05, fold change > 1.3) between beef tallow and rapeseed oil and 2 genes between coconut oil and rapeseed oil groups. No differentially expressed genes were observed between coconut oil and beef tallow groups. Almost all 29 DEGs between rapeseed oil and beef tallow groups are connected to neurodegenerative, cardiovascular diseases, or cancer (e.g., PLAU, CYBB, NCF2, ZNF217, CHAC1, CTCFL). Functional analysis of these genes revealed that they are associated with fluid shear stress response, complement and coagulation cascade, ROS signaling, neurogenesis, and regulation of protein binding and protein catabolic processes. Furthermore, gene set enrichment analysis (GSEA) of the whole datasets from all three comparisons suggests that both beef tallow and coconut oil may trigger changes in the expression level of genes crucial in the pathogenesis of civilization diseases.

scholarly journals A comparison of transcriptomic profiles in endometrium during window of implantation between women with unexplained recurrent implantation failure and recurrent miscarriage

Reproduction ◽  
2017 ◽  
Vol 153 (6) ◽  
pp. 749-758 ◽  
Author(s):  
Jin Huang ◽  
Hao Qin ◽  
Yihua Yang ◽  
Xiaoyan Chen ◽  
Jiamiao Zhang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Recurrent Miscarriage ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Coagulation Cascade ◽  
Support Vector ◽  
Implantation Failure ◽  
Rna Seq ◽  
Recurrent Implantation Failure ◽  
Altered Expression

The endometrium becomes receptive to the embryo only in the mid-luteal phase, but not in the other stages of the menstrual cycle. Endometrial factors play an important role in implantation. Women with recurrent miscarriage and recurrent implantation failure have both been reported to have altered expression of receptivity markers during the window of implantation. We aimed to compare the gene expression profiles of the endometrium in the window of implantation among women with unexplained recurrent implantation failures (RIF) and unexplained recurrent miscarriages (RM) by RNA sequencing (RNA-Seq). In total 20 patients (9 RIF and 11 RM) were recruited. In addition 4 fertile subjects were included as reference. Endometrium samples were precisely timed on the 7th day after luteal hormone surge (LH + 7). All the 24 endometrium samples were extracted for total RNA. The transcriptome was determined by RNA-Seq in the first 14 RNA samples (5 RIF, 6 RM and 3 fertile). Differentially expressed genes between RM and RIF were validated by quantitative real-time PCR (qPCR) in all 24 RNA samples (9 RIF, 11 RM and 4 fertile). Transcriptomic profiles of RM and RIF, but not control samples, were separated from each other by principle component analysis (PCA) and support vector machine (SVM). Complementary and coagulation cascades pathway was significantly up-regulated in RIF while down-regulated in RM. Differentially expressed genes C3, C4, C4BP, DAF, DF and SERPING1 in complement and coagulation cascade pathway between RM and RIF were further validated by qPCR. This study compared endometrial transcriptome among patients with RIF and RM in the window of implantation; it identified differential molecular pathways in endometrium between RIF and RM, which potentially affect the implantation process.

scholarly journals The Type 3 Deiodinase Is a Critical Modulator of Thyroid Hormone Sensitivity in the Fetal Brain

2021 ◽  
Vol 15 ◽  
Author(s):  
Maria Elena Martinez ◽  
Arturo Hernandez
Keyword(s):  
Differential Expression ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Fetal Brain ◽  
Axonal Guidance ◽  
Late Gestation ◽  
Differentially Expressed ◽  
Pathway Analyses ◽  
Type 3 ◽  
The Brain

Thyroid hormones (TH) are critical for the development and function of the central nervous system (CNS). Although their effects on the rodent brain peak within 2–3 weeks postnatally, the fetal brain has been found largely insensitive to exogenously administrated TH. To address this issue, here we examined gene expression in brains from mouse fetuses deficient in the type 3 deiodinase (DIO3), the selenoenzyme responsible for clearing TH. At embryonic day E18.5 qPCR determinations indicated a marked increase in the mRNA expression of T3-responsive genes Klf9 and Nrgn. The increased expression of these genes was confirmed by in situ hydridization in multiple areas of the cortex and in the striatum. RNA sequencing revealed 246 genes differentially expressed (70% up-regulated) in the brain of E18.5 Dio3−/− male fetuses. Differential expression of 13 of these genes was confirmed in an extended set of samples that included females. Pathway analyses of differentially expressed genes indicated enrichment in glycolysis and signaling related to axonal guidance, synaptogenesis and hypoxia inducible factor alpha. Additional RNA sequencing identified 588 genes differentially expressed (35% up-regulated) in the brain of E13.5 Dio3−/− male fetuses. Differential expression of 13 of these genes, including Klf9, Hr, and Mgp, was confirmed in an extended set of samples including females. Although pathway analyses of differentially expressed genes at E13.5 also revealed significant enrichment in axonal guidance and synaptogenesis signaling, top enrichment was found for functions related to the cell cycle, aryl hydrocarbon receptor signaling, PCP and kinetochore metaphase signaling pathways and mitotic roles of polo-like kinase. Differential expression at E13.5 was confirmed by qPCR for additional genes related to collagen and extracellular matrix and for selected transcription factors. Overall, our results demonstrate that the rodent fetal brain is sensitive to TH as early as E13.5 of gestational age, and suggest that TH distinctly affects brain developmental programs in early and late gestation. We conclude that DIO3 function is critical to ensure an adequate timing for TH action in the developing brain and is probably the main factor underlying the lack of effects on the fetal brain observed in previous studies after TH administration.

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