scholarly journals Arginine Alters miRNA Expression Involved in Development and Proliferation of Rat Mammary Tissue

Animals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 535
Author(s):  
Gang Zhou ◽  
Qiaoyun Xu ◽  
Feifan Wu ◽  
Mengzhi Wang ◽  
Lianmin Chen ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Control Diet ◽  
Rna Extraction ◽  
Experimental Period ◽  
Differentially Expressed ◽  
Mammary Tissue ◽  
Control Group ◽  
Sequencing Analysis ◽  
Significant Difference

This study was designed to determine the effects of dietary arginine on development and proliferation in rat mammary tissue through changes in miRNA profiles. Twelve pregnant Wistar rats were allocated randomly to two groups. A basal diet containing arginine or the control diet containing glutamate on an equal nitrogen basis as the arginine supplemented diet were used. The experiment included a pre-experimental period of four days before parturition and an experimental period of 17 days after parturition. Mammary tissue was collected for histology, RNA extraction and high-throughput sequencing analysis. The greater mammary acinar area indicated that arginine supplementation enhanced mammary tissue development (p < 0.01). MicroRNA profiling indicated that seven miRNA (miR-206-3p, miR-133a-5p, miR-133b-3p, miR-1-3p, miR-133a-3p, miR-1b and miR-486) were differentially expressed in response to Arginine when compared with the glutamate-based control group. In silico gene ontology enrichment and KEGG pathway analysis revealed between 240 and 535 putative target genes among the miRNA. Further verification by qPCR revealed concordance with the differential expression from the sequencing results: 17 of 28 target genes were differentially expressed (15 were highly expressed in arginine and 2 in control) and 11 target genes did not have significant difference in expression. In conclusion, our study suggests that arginine may potentially regulate the development of rat mammary glands through regulating miRNAs.

scholarly journals Identification and characterization of heat-responsive microRNAs at the booting stage in two rice varieties 9311 and Nagina 22

Genome ◽  
2021 ◽  
Author(s):  
Ying Luo ◽  
Tao Wang ◽  
Dan Yang ◽  
Biao Luo ◽  
Weiping Wang ◽  
...  
Keyword(s):  
Stress Responses ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Elevated Temperatures ◽  
Differentially Expressed ◽  
Control Group ◽  
Microrna Target ◽  
Rice Varieties ◽  
Booting Stage ◽  
Differentially Expressed Mirnas

Abstract: MicroRNAs (miRNAs) are small, non-coding, regulatory RNAs that play important roles in abiotic stress responses in plants. but their regulatory roles in the adaptive response to heat stress at the booting stage in two rice varieties 9311 and Nagina 22, remain largely unknown. In this study, 464 known miRNAs and 123 potential novel miRNAs were identified. Of these miRNAs, a total of 90 differential expressed miRNAs were obtained with 9311 libraries as control group, of which 54 upregulated and 36 downregulated miRNAs. To gain insight into functional significance, 2773 potential target genes of these 90 differentially expressed miRNAs were predicted. GO enrichment showed that the predicted target genes of differentially expressed miRNAs including NACs, LACs, CSD, and Hsp40. KEGG pathway analysis showed that target genes of these differentially expressed miRNAs were significantly enriched in plant hormone signal transduction pathway. The expression levels of ten differentially expressed miRNAs and their target genes obtained by qRT-PCR were largely consistent with the sequencing results. This study lays a foundation for the elucidation of the miRNA-mediated regulatory mechanism in rice at elevated temperatures. Key words: rice, heat-responsive, microRNA, target gene, booting stage, high-throughput sequencing

Genome-wide analysis of microRNAs expression profiling in patients with primary IgA nephropathy

Genome ◽  
2013 ◽  
Vol 56 (3) ◽  
pp. 161-169 ◽  
Author(s):  
Kuibi Tan ◽  
Jing Chen ◽  
Wuxian Li ◽  
Yuyu Chen ◽  
Weiguo Sui ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Immunoglobulin A ◽  
Differentially Expressed ◽  
Control Group ◽  
Pathological Changes ◽  
Genome Wide ◽  
Differentially Expressed Mirnas ◽  
Specific Tissue ◽  
Mirnas Expression

The aim of this study was to investigate the differential expression characteristics and the roles of the genome-wide microRNAs (miRNAs) in immunoglobulin A nephropathy (IgAN) kidney tissues. We used Illumina high-throughput sequencing technology to evaluate the miRNAs expression of six biopsy tissues from IgAN and six normal renal cortex specimens from patients with renal cell carcinoma. We observed a total of 85 miRNAs that were differentially expressed in the six IgAN patients, of which 11 miRNAs were up-regulated and 74 miRNAs were down-regulated in patients' tissues compared with control tissues. Additionally, we identified 55 candidate novel miRNAs in our study, which comprised seven candidates who were detected in the IgAN group and 49 candidates who were detected in the control group. Only one candidate (miR-n-9) was expressed in both groups. The bioinformatics showed that the regulated target genes of differentially expressed miRNAs were associated with immune and renal pathological changes. The identification of specific tissue miRNAs in our study not only helped clarify the genetics or immunology mechanisms involved in the pathogenesis of IgAN but also helped explain the pathological changes in the kidney tissues. We hypothesize that some significant miRNAs might potentially serve as novel diagnostic biomarkers in IgAN patients.

scholarly journals Diagnostic Biomarker Hsa_circ_0126218 and Functioning Prediction in Peripheral Blood Monocular Cells of Female Patients With Major Depressive Disorder

2021 ◽  
Vol 9 ◽  
Author(s):  
Tianyi Bu ◽  
Zhengxue Qiao ◽  
Wenbo Wang ◽  
Xiuxian Yang ◽  
Jiawei Zhou ◽  
...  
Keyword(s):  
Peripheral Blood ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Characteristic Curve ◽  
Pathological Process ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Diagnostic Biomarker ◽  
Major Depressive ◽  
Female Patients

IntroductionAlthough major depressive diroder (MDD) has brought huge burden and challenges to society globally, effective and accurate diagnoses and treatments remain inadequate. The pathogenesis that for women are more likely to suffer from depression than men needs to be excavated as well. The function of circRNAs in pathological process of depression has not been widely investigated. This study aims to explore potential diagnostic biomarker circRNA of female patients with MDD and to investigate its role in pathogenesis.MethodsFirst, an expression profile of circRNAs in the peripheral blood monocular cells of MDD patients and healthy peripherals were established based on high-throughput sequencing analysis. In addition, the top 10 differentially expressed circRNAs were quantified by quantitative real-time PCR to explore diagnostic biomarkers. To further investigate the function of biomarkers in the pathogenesis of MDD, bioinformatics analysis on downstream target genes of the biomarkers was carried out.ResultsThere is a mass of dysregulated circRNAs in PBMCs between female MDD patients and healthy controls. Among the top 10 differentially expressed circRNAs, hsa_circ_0126218 is more feasible as a diagnostic biomarker. The expression level of hsa_circ_0126218 displayed upregulation in patients with MDD and the area under the operating characteristic curve of hsa_circ_0126218 was 0.801 (95% CI 0.7226–0.8791, p &lt; 0.0001). To explain the competing endogenous RNA role of hsa_circ_0126218 in the pathogenesis of female MDD, a hsa_circ_0126218-miRNA-mRNA network was established. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses stated that some of the enriched pathways downstream of hsa_circ_0126218 are closely related to MDD. Moreover, we established a protein-protein network to further screen out the hub genes (PIK3CA, PTEN, MAPK1, CDC42, Lyn, YES1, EPHB2, SMAD2, STAT1, and ILK). The function of hsa_circ_0126218 was refined by constructing a verified circRNA-predicted miRNA-hub gene subnetwork.Conclusionhsa_circ_0126218 can be considered as a new female MDD biomarker, and the pathogenesis of female MDD by the downstream regulation of hsa_circ_0126218 has been predicted. These findings may help further improve the early detection, effective diagnosis, convenient monitoring of complications, precise treatment, and timely recurrence prevention of depression.

scholarly journals Identification of microRNAs regulated by tobacco curly shoot virus co-infection with its betasatellite in Nicotiana benthamiana

2019 ◽  
Vol 16 (1) ◽  
Author(s):  
Jiang Du ◽  
Gentu Wu ◽  
Zhongpiao Zhou ◽  
Jiayuan Zhang ◽  
Mingjun Li ◽  
...  
Keyword(s):  
Nicotiana Benthamiana ◽  
Defense Mechanisms ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Defense Responses ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Sequencing Analysis ◽  
Virus Infections ◽  
Tobacco Curly Shoot Virus

Abstract Background MicroRNAs (miRNAs) are a class of 21–24 nucleotide endogenous non-coding small RNAs that play important roles in plant development and defense responses to biotic and abiotic stresses. Tobacco curly shoot virus (TbCSV) is a monopartite begomovirus, cause leaf curling and plant stunting symptoms in many Solanaceae plants. The betasatellite of TbCSV (TbCSB) induces more severe symptoms and enhances virus accumulation when co-infect the plants with TbCSV. Methods In this study, miRNAs regulated by TbCSV and TbCSB co-infection in Nicotiana benthamiana were characterized using high-throughput sequencing technology. Results Small RNA sequencing analysis revealed that a total of 13 known miRNAs and 42 novel miRNAs were differentially expressed in TbCSV and TbCSB co-infected N. benthamiana plants. Several potential miRNA-targeted genes were identified through data mining and were involved in both catalytic and metabolic processes, in addition to plant defense mechanisms against virus infections according to Gene Ontology (GO) analyses. In addition, the expressions of several differentially expressed miRNAs and their miRNA-targeted gene were validated through quantitative real time polymerase chain reaction (qRT-PCR) approach. Conclusions A large number of miRNAs are identified, and their target genes, functional annotations also have been explored. Our results provide the information on N. benthamiana miRNAs and would be useful to further understand miRNA regulatory mechanisms after TbCSV and TbCSB co-infection.

scholarly journals Effects of keratinocyte-derived and fibroblast-derived exosomes on human epidermal melanocytes

2021 ◽  
Vol 0 ◽  
pp. 1-10
Author(s):  
Hai-Xia Shi ◽  
Ru-Zhi Zhang ◽  
Li Xiao ◽  
Li Wang
Keyword(s):  
Signaling Pathway ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Tyrosinase Activity ◽  
The Other ◽  
Differentially Expressed ◽  
Ras Signaling ◽  
Sequencing Analysis ◽  
Melanin Synthesis

Background: Exosomes have been demonstrated to carry proteins, membrane lipids, mRNAs and microRNAs which can be transferred to surrounding cells and regulate the functions of those recipient cells. Objectives: The objective of the study was to investigate the effects of exosomes released by keratinocytes and fibroblasts on the proliferation, tyrosinase activity and melanogenesis of melanocytes. Methods: Melanocytes, keratinocytes and fibroblasts obtained from human foreskin were cultured and exosomes secreted by keratinocytes and fibroblasts were harvested from the culture supernatants by ultracentrifugation. Each exosome fraction was divided into two parts; one part was subjected to high-throughput sequencing using an Illumina HiSeq sequencer to characterize the microRNA expression profiles, while the other part was labeled with the fluorescent dye PKH67 and was then co-cultivated with epidermal melanocytes. Results: High-throughput sequencing analysis showed 168 differentially expressed microRNA within exosomes derived from keratinocytes and from fibroblasts, 97 of those being up-regulated with the other 71 down-regulated. Gene ontology analysis showed that the target genes responsible for these differentially expressed microRNAs were mainly enriched in the protein-binding region of molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that target genes regulated by differentially expressed microRNA were mainly involved in mitogen-activated protein kinase (MAPK) signaling pathway, Ras signaling pathway, cAMP signaling pathway and Wnt signaling pathway. Keratinocyte-derived exosomes were taken up by melanocytes co-cultured with them and promoted the proliferation, tyrosinase activity and melanin synthesis of those melanocytes. However, fibroblast-derived exosomes had no similar effects on melanocytes. Conclusion: Keratinocyte-derived exosomes but not fibroblast-derived exosomes were taken up by melanocytes in co-culture and significantly stimulated their proliferation, tyrosinase activity and melanin synthesis. Those different effects may be mainly due to the differential expression of microRNAs in exosomes derived from the different types of cells. Limitations: Electron microscopy of the obtained exosomes and in-depth study of apparently differentially expressed microRNAs were not performed.

scholarly journals Comprehensive circular RNA expression profiles in intermuscular fat from lean and obese pigs

2019 ◽  
Author(s):  
Zhiguo Miao ◽  
Jinzhou Zhang ◽  
Shan Wang ◽  
Paneng Wei
Keyword(s):  
Expression Profile ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Circular Rna ◽  
Differentially Expressed ◽  
Real Time Quantitative Pcr ◽  
Significant Difference ◽  
Intermuscular Fat ◽  
Fattening Period

AbstractCircular RNA (circRNA) plays an important regulatory role in development and differentiation. Intermuscular fat in pork affects the tenderness and juiciness of the meat. In this study, we investigated the performances of Landrace (lean) and Jinhua (obese) pigs at the fattening period and explored the expression profile of circRNAs in intermuscular fat from the two breeds by Illumina high-throughput sequencing. we identified 5 548 circRNAs, specifically 2 651 (47.78%) in the Jinhua pigs, and 2 897 (52.22%) in the Landrace pigs. A totale of 809 differentially expressed circRNAs were observed between the the Jinhua and Landrace pigs, but only 29 of these circRNAs showed significant difference (19 upregulated and 10 downregulated). All 1 306 unigenes and 27 differentially expressed unigenesinvolved in lipid transport and metabolism; replication, recombination and repair; and signaling pathway were annotated. A total of 550 target miRNAs were perfect seed matches and 20 522 target genes were foundBy RNAhybrid and miRanda software prediction. Results from real-time quantitative PCR also confirmed the differential expression of 13 mRNAs between the two pig breeds. This study provides comprehensive expression profiles of circRNAs in Sus scrofa adipose metabolism and development, which can be used to clarify their functions.Summary statementThe paper explored the expression profile of circRNAs in intermuscular fat from Landrace and Jinhua pigs at the fattening period, to provide insights into circRNAregulation in animal adipose metabolism.

Effect of dietary probiotic, antibiotic or combination on broiler performance, cecum microbial population and ileal development

2020 ◽  
Vol 21 (3) ◽  
pp. 74-79
Author(s):  
Ahmed Elbaz ◽  
Said El-sheikh
Keyword(s):  
Control Diet ◽  
Low Density Lipoprotein ◽  
Density Lipoprotein ◽  
Experimental Period ◽  
Nutrient Digestibility ◽  
Lipoprotein Cholesterol ◽  
Control Group ◽  
Gut Health ◽  
Feed Conversion ◽  
Broiler Performance

Objective: To investigate the effect of antibiotics and/or probiotics on broiler performance, some serum metabolites, cecum microflora composition, and ileum histomorphology under the Egyptian conditions. Design: Randomized controlled experimental study. Animals: Two hundred forty 1-day-old Ross (308) chicks were reared till 35 days of age. Procedures: The birds were randomly allocated into four main groups: a control diet without additives (CON); probiotic (Lactobacillus acidophilus) supplemented diet (PRO); antibiotic (Avilamycin) supplemented diet (ANT) and a mix group (AP) that received antibiotic in the diet form 1 to 4 days of age and treated during the rest of the experimental period with probiotics. Results: Chickens fed on probiotic or antibiotic diets had linear improvement in live body weight (LBW) and feed conversion ratio (FCR) compared with the control group, while the best LBW and FCR were in the AP group. An improvement in the nutrient digestibility was observed in the probiotic added groups (PRO and AP). Serum cholesterol and low-density lipoprotein cholesterol contents decreased when antimicrobial (probiotic or antibiotic) supplementations were used, while there was an increase in high-density lipoprotein cholesterol contents, serum total protein, and albumin levels. Among all groups, cecum Clostridium perfringens and Escherichia coli counts decreased; however, there was an increase in Lactobacillus count compared to the control group. In probiotic supplemented groups (PRO and AP), a significant (P<0.05) improvement in ilea architecture. Conclusion and clinical relevance: Using probiotic after initial treatment with an antibiotic in broiler diets had a positive effect on broiler growth performance, gut health (improved cecum microbial populations and ileum histomorphology), and nutrient digestibility.

Bioinformatics Analysis and Validation of Differentially Expressed MicroRNAs with Their Target Genes Involved in GLP-1RA Facilitated Osteogenesis

2020 ◽  
Vol 15 ◽  
Author(s):  
Na Wang ◽  
Yukun Li ◽  
Sijing Liu ◽  
Liu Gao ◽  
Chang Liu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Bioinformatics Analysis ◽  
Differentially Expressed ◽  
Functional Study ◽  
Regulation Network ◽  
Glucagon Like Peptide 1 ◽  
G Protein Coupled ◽  
Lower Expression

Background: Recent studies revealed that the hypoglycemic hormone, glucagon-like peptide-1 (GLP-1), acted as an important modulator in osteogenesis of bone marrow derived mesenchymal stem cells (BMSCs). Objectives: The aim of this study was to identify the specific microRNA (miRNA) using bioinformatics analysis and validate the presence of differentially expressed microRNAs with their target genes after GLP-1 receptor agonist (GLP-1RA) administration involved in ostogenesis of BMSCs. Methods: MiRNAs were extracted from BMSCs after 5 days’ treatment and sent for high-throughput sequencing for differentially expressed (DE) miRNAs analyses. Then the expression of the DE miRNAs verified by the real-time RT-PCR analyses. Target genes were predicted, and highly enriched GOs and KEGG pathway analysis were conducted using bioinformatics analysis. For the functional study, two of the target genes, SRY (sex determining region Y)-box 5 (SOX5) and G protein-coupled receptor 84 (GPR84), were identified. Results: A total of 5 miRNAs (miRNA-509-5p, miRNA-547-3p, miRNA-201-3p, miRNA-201-5p, and miRNA-novel-272-mature) were identified differentially expressed among groups. The expression of miRNA-novel-272-mature were decreased during the osteogenic differentiation of BMSCs, and GLP-1RA further decreased its expression. MiRNA-novel-272-mature might interact with its target mRNAs to enhance osteogenesis. The lower expression of miRNA-novel-272-mature led to an increase in SOX5 and a decrease in GPR84 mRNA expression, respectively. Conclusions: Taken together, these results provide further insights to the pharmacological properties of GLP-1RA and expand our knowledge on the role of miRNAs-mRNAs regulation network in BMSCs’ differentiation.

Screening candidate microR-15a- IRAK2 regulatory pairs for predicting the response to Staphylococcus aureus-induced mastitis in dairy cows

2019 ◽  
Vol 86 (4) ◽  
pp. 425-431 ◽  
Author(s):  
Zhi Chen ◽  
Jingpeng Zhou ◽  
Xiaolong Wang ◽  
Yang Zhang ◽  
Xubin Lu ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Differential Expression ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Interleukin 1 ◽  
Differentially Expressed ◽  
Luciferase Reporter ◽  
Expression Of Genes ◽  
Chinese Holstein Cows ◽  
Reporter Assays

AbstractWe established a mastitis model using exogenous infection of the mammary gland of Chinese Holstein cows with Staphylococcus aureus and extracted total RNA from S. aureus-infected and healthy mammary quarters. Differential expression of genes due to mastitis was evaluated using Affymetrix technology and results revealed a total of 1230 differentially expressed mRNAs. A subset of affected genes was verified via Q-PCR and pathway analysis. In addition, Solexa high-throughput sequencing technology was used to analyze profiles of miRNA in infected and healthy quarters. These analyses revealed a total of 52 differentially expressed miRNAs. A subset of those results was verified via Q-PCR. Bioinformatics techniques were used to predict and analyze the correlations among differentially expressed miRNA and mRNA. Results revealed a total of 329 pairs of negatively associated miRNA/mRNA, with 31 upregulated pairs of mRNA and 298 downregulated pairs of mRNA. Differential expression of miR-15a and interleukin-1 receptor-associated kinase-like 2 (IRAK2), were evaluated by western blot and luciferase reporter assays. We conclude that miR-15a and miR-15a target genes (IRAK2) constitute potential miRNA–mRNA regulatory pairs for use as biomarkers to predict a mastitis response.

Sign in / Sign up

Export Citation Format

Share Document