scholarly journals Identification and Bioinformatics Analysis of Differentially Expressed Milk Exosomal Micrornas in Milk Exosomes of Heat-Stressed Holstein Cows

2021 ◽  
Author(s):  
Yue Wang ◽  
Jian Fang ◽  
Han-Fang Zeng ◽  
Hui-Xia Li ◽  
Kun-Lin Chen
Keyword(s):  
Heat Stress ◽  
Dairy Cows ◽  
Mapk Pathway ◽  
Genetic Material ◽  
Tissue Growth ◽  
Differentially Expressed ◽  
Holstein Cows ◽  
Small Rna Sequencing ◽  
Exosomal Mirnas ◽  
Differentially Expressed Mirnas

Abstract Background In summer, heat stress is one of the primary reasons for the compromised health and low milk productivity of dairy cows. Hyperthermia affects milk synthesis and secretion in the mammary glands of dairy cows. As molecules for intercellular communication, milk-derived exosomes carry genetic material, proteins and, lipids, playing a crucial role in mammary tissue growth and milk synthesis in dairy cows. The aim of this study was to explore the milk exosomal miRNAs profile of heat-stressed and normal Holstein cows. Results We isolated and identified milk exosomes to screening for differentially expressed miRNAs using small RNA sequencing. Then, TargetScan and miRanda algorithms were used to predict the putative targets of the differentially expressed miRNAs, whereas GO and KEGG pathway enrichment analyses were performed for the differentially expressed miRNA-target genes. Our results showed that 215 miRNAs were significantly differentially expressed in heat-stressed milk exosomes, of which one was up-regulated and 214 were significantly downregulated. GO and KEGG enrichment analyses indicated that differentially expressed miRNAs might play a role in apoptosis, autophagy, and the p38 MAPK pathway. qRT-PCR assay verified that the expression of miRNAs was consistent with the sequencing results, warranting further verification of their specific targets of action. Conclusions In conclusion, changes in the miRNA expression profile of milk exosomes indicated the role of exosomal miRNAs in regulating heat stress resistance and apoptosis in dairy cows. Our results suggested that milk-derived exosomal miRNAs could increase mammary gland resistance to heat stress, thereby enhancing milk synthesis in dairy cows.

scholarly journals Analysis of circulating-microRNA expression in lactating Holstein cows under summer heat stress

2020 ◽  
Author(s):  
Jihwan Lee ◽  
Suhyun Lee ◽  
Junkyu Son ◽  
Hyeonju Lim ◽  
Euntae Kim ◽  
...  
Keyword(s):  
Heat Stress ◽  
South Korea ◽  
Expression Profiles ◽  
Stress Conditions ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
Holstein Cows ◽  
Small Rna Sequencing ◽  
Circulating Microrna ◽  
Differentially Expressed Mirnas

AbstractKorean peninsular weather is rapidly becoming subtropical due to global warming. In summer 2018, South Korea experienced the highest temperatures since the meteorological observations recorded in 1907. Heat stress has a negative effect on Holstein cows, the most popular breed of dairy cattle in South Korea, which is susceptible to heat. To examine physiological changes in dairy cows under heat stress conditions, we analyzed the profiles circulating microRNAs isolated from whole blood samples collected under heat stress and non-heat stress conditions using small RNA sequencing. We compared the expression profiles in lactating cows under heat stress and non-heat stress conditions to understand the regulation of biological processes in heat-stressed cows. Moreover, we measured several heat stress indicators, such as rectal temperature, milk yield, average daily gain, and progesterone concentration. All these assessments showed that pregnant cows were more susceptible to heat stress than non-pregnant cows. Particularly, progesterone concentrations known to have maternal warming effects were at similar levels in non-pregnant cows but significantly increased in pregnant cows under heat stress conditions. The differentially expressed miRNAs and their putative target genes were analyzed in pregnant cows. Interestingly, we found that differentially expressed miRNAs (bta-miR-146b, bta-miR-20b, bta-miR-29d-3p, bta-miR-1246) specifically targeted progesterone biosynthesis (StAR) and the function of corpus luteum-related genes (CCL11, XCL), suggesting that pregnant cows with elevated progesterone concentrations are more susceptible to heat stress. In addition, we found the differential expression of 11 miRNAs (bta-miR-19a, bta-miR-19b, bta-miR-30a-5p, and several from the bta-miR-2284 family) in both pregnant and non-pregnant cows under heat stress conditions. In target gene prediction and gene set enrichment analysis, these miRNAs were found to be associated with the cytoskeleton, cell junction, vasculogenesis, cell proliferation, ATP synthesis, oxidative stress, and immune responses involved in heat response. These miRNAs can be used as potential biomarkers for heat stress.

scholarly journals Pancreatic Acinar Cells Employ miRNAs as Mediators of Intercellular Communication to Participate in the Regulation of Pancreatitis-Associated Macrophage Activation

2016 ◽  
Vol 2016 ◽  
pp. 1-11 ◽  
Author(s):  
Yong Zhao ◽  
Hao Wang ◽  
Ming Lu ◽  
Xin Qiao ◽  
Bei Sun ◽  
...  
Keyword(s):  
Macrophage Activation ◽  
Target Genes ◽  
Culture Media ◽  
Mapk Pathway ◽  
Acinar Cells ◽  
Differentially Expressed ◽  
Pancreatic Acinar Cells ◽  
Supernatant Fraction ◽  
Exosomal Mirnas ◽  
Differentially Expressed Mirnas

Macrophage activation plays an important role in the inflammatory response in acute pancreatitis. In the present study, the activation of AR42J pancreatic acinar cells was induced by taurolithocholate treatment. The results showed that the culture medium from the activated AR42J cells significantly enhanced NFκB activation in the macrophages compared to that without taurolithocholate treatment. Additionally, the precipitates obtained from ultracentrifugation of the culture media that were rich in exosomes were markedly more potent in activating macrophages compared with the supernatant fraction lacking exosomes. The results indicated that the mediators carried by the exosomes played important roles in macrophage activation. Exosomal miRNAs were extracted and examined using microarrays. A total of 115 differentially expressed miRNAs were identified, and 30 showed upregulated expression, while 85 displayed downregulated expression. Target genes of the differentially expressed miRNAs were predicted using TargetScan, MiRanda, and PicTar software programs. The putative target genes were subjected to KEGG functional analysis. The functions of the target genes were primarily enriched in MAPK pathways. Specifically, the target genes regulated macrophage activation through the TRAF6-TAB2-TAK1-NIK/IKK-NFκB pathway. As the mediators of signal transduction, miRNAs and their predicted target mRNAs regulate every step in the MAPK pathway.

scholarly journals Plasma-Derived Exosomal hsa-miR-4488 and hsa-miR-1228-5p: Novel Biomarkers for Dermatomyositis-Associated Interstitial Lung Disease with Anti-Melanoma Differentiation-Associated Protein 5 Antibody-Positive Subset

2021 ◽  
Vol 2021 ◽  
pp. 1-16
Author(s):  
Danli Zhong ◽  
Chanyuan Wu ◽  
Dong Xu ◽  
Jingjing Bai ◽  
Qian Wang ◽  
...  
Keyword(s):  
Interstitial Lung Disease ◽  
Lung Disease ◽  
Target Genes ◽  
Homo Sapiens ◽  
Differentially Expressed ◽  
Transmission Electron ◽  
Exosomal Mirnas ◽  
Differentially Expressed Mirnas ◽  
Novel Biomarkers ◽  
And Gender

The present study is aimed at profiling circulating exosome-derived microRNAs (miRNAs/miRs) from patients with dermatomyositis (DM), in particular those complicated with interstitial lung disease (ILD) with anti-melanoma differentiation-associated protein 5 (MDA5) antibody-positive. Fifteen participants were enrolled, including five patients with DM complicated with ILDs prior to treatment with circulating anti-MDA5 antibody-positive status [DM-ILD-MDA5 Ab(+)], five DM patients without ILDs who were negative for 16 detectable myositis-specific antibodies [DM-nonILD-MSA16(-)], and five age- and gender-matched healthy donor controls (HCs). The characteristics of the exosomes extracted by Ribo™ Exosome Isolation Reagent were identified using transmission electron microscopy (TEM), nanoparticle tracking analysis (NTA), and flow cytometry. Differentially expressed miRNAs, determined by next-generation deep sequencing, were identified through the criteria of ∣ log 2   fold   change ∣ ≥ 1 and P < 0.01 . A total of 38 miRNAs were significantly upregulated in exosomes from patients with DM-ILD-MDA5 Ab(+) compared to those from HC, while 21 miRNAs were significantly downregulated. Compared to exosomes derived from patients with DM-nonILD-MSA16(-), 51 miRNAs were significantly upregulated and 33 miRNAs were significantly downregulated from patients with DM-ILD-MDA5 Ab(+). A total of 73 exosomal miRNAs were significantly differentially expressed between DM-nonILD-MSA16(-) and HC. In particular, two miRNAs, Homo sapiens- (hsa-) miR-4488 and hsa-miR-1228-5p, were common differentially expressed miRNAs among three comparisons. GO and KEGG analyses suggested that several pathways may contribute the pathogenesis of DM-ILD-MDA5 Ab(+) and DM-nonILD-MSA16(-), while PPI network analysis of hsa-miR-4488 and hsa-miR-1228-5p indicated that their predicted target genes, DExD-box helicase 39B and MDM2, may be involved in the mechanisms of DM-ILD-MDA5 Ab(+).

scholarly journals Small RNA sequencing evaluation of renal microRNA biomarkers in dogs with X-linked hereditary nephropathy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Candice P. Chu ◽  
Shiguang Liu ◽  
Wenping Song ◽  
Ethan Y. Xu ◽  
Mary B. Nabity
Keyword(s):  
Small Rna ◽  
Target Genes ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Rna Seq ◽  
Ckd Progression ◽  
Critical Pathways ◽  
Qrt Pcr ◽  
Hereditary Nephropathy ◽  
Differentially Expressed Mirnas

AbstractDogs with X-linked hereditary nephropathy (XLHN) are an animal model for Alport syndrome in humans and progressive chronic kidney disease (CKD). Using mRNA sequencing (mRNA-seq), we have characterized the gene expression profile affecting the progression of XLHN; however, the microRNA (miRNA, miR) expression remains unknown. With small RNA-seq and quantitative RT-PCR (qRT-PCR), we used 3 small RNA-seq analysis tools (QIAGEN OmicSoft Studio, miRDeep2, and CPSS 2.0) to profile differentially expressed renal miRNAs, top-ranked miRNA target genes, and enriched biological processes and pathways in CKD progression. Twenty-three kidney biopsies were collected from 5 dogs with XLHN and 4 age-matched, unaffected littermates at 3 clinical time points (T1: onset of proteinuria, T2: onset of azotemia, and T3: advanced azotemia). We identified up to 23 differentially expressed miRNAs at each clinical time point. Five miRNAs (miR-21, miR-146b, miR-802, miR-142, miR-147) were consistently upregulated in affected dogs. We identified miR-186 and miR-26b as effective reference miRNAs for qRT-PCR. This study applied small RNA-seq to identify differentially expressed miRNAs that might regulate critical pathways contributing to CKD progression in dogs with XLHN.

scholarly journals Characteristic Dissection of Xanthomonas oryzae pv. oryzae Responsive MicroRNAs in Rice

2020 ◽  
Vol 21 (3) ◽  
pp. 785
Author(s):  
Yanfeng Jia ◽  
Chunrong Li ◽  
Quanlin Li ◽  
Pengcheng Liu ◽  
Dongfeng Liu ◽  
...  
Keyword(s):  
Rice Variety ◽  
Bioinformatic Analysis ◽  
Infection Process ◽  
Xanthomonas Oryzae ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Stem Loop ◽  
Differentially Expressed Mirnas ◽  
Plant Pathogen Interaction

MicroRNAs (miRNAs) are crucial player in plant-pathogen interaction. While the evidence has demonstrated that rice miRNAs mediate immune response to pathogens invasion, the roles of miRNAs on Xanthomonas oryzae pv. oryzae (Xoo) attack remain be in place. Herein, we monitored the responsive changes of rice miRNAs at 0, 8, 24 h across Xoo strain PXO86 infection in its compatible rice variety IR24 and incompatible variety IRBB5 by small RNA sequencing, and the genes targeted by miRNAs were also detected via degradome technology. The faithfulness of sequencing data was validated through quantitative real-time stem-loop reverse transcription-polymerase chain reaction assay. Bioinformatic analysis showed that the differentially expressed miRNAs could be divided into three immunity-related clusters, and 80 regulatory units were emerged in infection process, which comprises 29 differentially expressed known miRNAs and 38 cleaved targets. Furthermore, the miRNA presumptive function of separate immunity cluster in rice-Xoo interplay was confirmed through overexpressing osa-miR164a, osa-miR167d and osa-miR159b, and the disruption of regulatory units, osa-miR164a/OsNAC60, osa-miR167d-5p/OsWD40-174 and osa-miR159b/OsMYBGA, OsLRR-RLK2, OsMPK20-4, may reset rice defense response to Xoo infestation in a controllable manner. These findings provide new insights into the complex roles of characteristic miRNAs and their targets in rice-Xoo interactions.

scholarly journals PSXI-1 Effects of mineral supplementation during summer on physiological variables and milk production in Holstein dairy cows

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 389-389
Author(s):  
Andrea Dahnae del Rio-Aviles ◽  
Abelardo Correa-Calderon ◽  
Leonel Avendaño-Reyes ◽  
Milton G Thomas ◽  
R Mark Enns ◽  
...  
Keyword(s):  
Heat Stress ◽  
Dairy Cows ◽  
Milk Production ◽  
Treatment Time ◽  
Holstein Cows ◽  
Productive Performance ◽  
Negative Effects ◽  
Physiological Variables ◽  
Northwest Mexico ◽  
Mineral Supplementation

Abstract Summer season in northwest Mexico is characterized by hot-humid weather conditions that lead to heat stress and affect physiological and productive performance of lactating Holstein cows. Mineral supplementation has been proposed as strategy to alleviate negative effects of heat stress in dairy cattle. Thus, the objective of this study was to evaluate the effect of an injectable mineral supplement on physiological variables and milk production in Holstein cows managed during summer. Sixteen cows were randomly assigned to 1 of 2 experimental groups: Mineral-treated (TRT; n = 8) or control (CON; n = 8). The TRT group received 3 injections of Fosfosan® (10 ml, i.m., Virbac, Uruguay), on days 0, 7 and 17, considering summer onset as day 0 (June 21st), whereas group CON was untreated. Physiological variables such as respiratory rate (RR), vaginal temperature (VT) and skin-surface temperature (SST), were registered twice a week (0500-1700 h) during 6 weeks. Ambient temperature and humidity were collected to calculate the daily temperature and humidity index (THI). Data were analyzed using a mixed model with repeated measures, which included fixed effects of treatment, time and treatment*time, and sire as random effect. According to the THI, Holstein cows were exposed to heat stress during the experiment (&gt;72 units). Cows in the TRT group showed higher (P &lt; 0.05) milk production than CON cows (17.93±0.47 vs 17.02±0.51 kg/day) and lower (P &lt; 0.01) VT (39.14±0.11 vs 39.46±0.15 °C). Relative to CON cows, treated cows also had lower RR (63.16±0.65 vs 64.47±0.76 breaths/min) and lower SST (33.75±0.15 vs 34.02±0.16 °C). All physiological variables showed a significant effect of time (P &lt; 0.01). In conclusion, mineral supplementation during summer appears to improve physiological and productive performance in heat-stressed milking dairy cows; therefore, we suggest to consider this management as strategy to reduce negative effects of summer and heat stress on the dairy industry in northwest Mexico.

scholarly journals Early Response of Radish to Heat Stress by Strand-Specific Transcriptome and miRNA Analysis

2019 ◽  
Vol 20 (13) ◽  
pp. 3321 ◽  
Author(s):  
Zhuang Yang ◽  
Wen Li ◽  
Xiao Su ◽  
Pingfei Ge ◽  
Yan Zhou ◽  
...  
Keyword(s):  
Heat Stress ◽  
Heat Shock ◽  
Rna Sequencing ◽  
Carbon Fixation ◽  
Enrichment Analysis ◽  
Early Response ◽  
Differentially Expressed ◽  
Physiological Parameter ◽  
Small Rna Sequencing ◽  
Sequencing Technology

Radish is a crucial vegetable crop of the Brassicaceae family with many varieties and large cultivated area in China. Radish is a cool season crop, and there are only a few heat tolerant radish varieties in practical production with little information concerning the related genes in response to heat stress. In this work, some physiological parameter changes of young leaves under short-term heat stress were detected. Furthermore, we acquired 1802 differentially expressed mRNAs (including encoding some heat shock proteins, heat shock factor and heat shock-related transcription factors), 169 differentially expressed lncRNAs and three differentially expressed circRNAs (novel_circ_0000265, novel_circ_0000325 and novel_circ_0000315) through strand-specific RNA sequencing technology. We also found 10 differentially expressed miRNAs (ath-miR159b-3p, athmiR159c, ath-miR398a-3p, athmiR398b-3p, ath-miR165a-5p, ath-miR169g-3p, novel_86, novel_107, novel_21 and ath-miR171b-3p) by small RNA sequencing technology. Through function prediction and enrichment analysis, our results suggested that the significantly possible pathways/complexes related to heat stress in radish leaves were circadian rhythm-plant, photosynthesis—antenna proteins, photosynthesis, carbon fixation in photosynthetic organisms, arginine and proline metabolism, oxidative phosphorylation, peroxisome and plant hormone signal transduction. Besides, we identified one lncRNA–miRNA–mRNAs combination responsive to heat stress. These results will be helpful for further illustration of molecular regulation networks of how radish responds to heat stress.

scholarly journals The Encystment-Related MicroRNAs and Its Regulation Molecular Mechanism in Pseudourostyla cristata Revealed by High Throughput Small RNA Sequencing

2020 ◽  
Vol 21 (7) ◽  
pp. 2309
Author(s):  
Nan Pan ◽  
Muhammad Zeeshan Bhatti ◽  
Haiyang Zhang ◽  
Bing Ni ◽  
Xinpeng Fan ◽  
...  
Keyword(s):  
Target Genes ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Ciliated Protozoa ◽  
Two Component System ◽  
Vegetative Cells ◽  
Cellular Processes ◽  
Physiological Processes ◽  
Differentially Expressed Mirnas ◽  
Pseudourostyla Cristata

MicroRNAs (miRNAs) regulate the expression of target genes in diverse cellular processes and play important roles in different physiological processes. However, little is known about the microRNAome (miRNAome) during encystment of ciliated protozoa. In the current study, we first investigated the differentially expressed miRNAs and relative signaling pathways participating in the transformation of vegetative cells into dormant cysts of Pseudourostyla cristata (P. cristata). A total of 1608 known miRNAs were found in the two libraries. There were 165 miRNAs with 1217 target miRNAs. The total number of differential miRNAs screened between vegetative cells and dormant cysts databases were 449 with p < 0.05 and |log2 fold changes| > 1. Among them, the upregulated and downregulated miRNAs were 243 and 206, respectively. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that some of the differentially expressed miRNAs were mainly associated with oxidative phosphorylation, two-component system, and biosynthesis of amino acids. Combining with our bioinformatics analyzes, some differentially expressed miRNAs including miR-143, miR-23b-3p, miR-28, and miR-744-5p participates in the encystment of P. cristata. Based on these findings, we propose a hypothetical signaling network of miRNAs regulating or promoting P. cristata encystment. This study shed new lights on the regulatory mechanisms of miRNAs in encystment of ciliated protozoa.

scholarly journals Determination of the MiRNAs Related to Bean Pyralid Larvae Resistance in Soybean Using Small RNA and Transcriptome Sequencing

2019 ◽  
Vol 20 (12) ◽  
pp. 2966 ◽  
Author(s):  
Weiying Zeng ◽  
Zudong Sun ◽  
Zhenguang Lai ◽  
Shouzhen Yang ◽  
Huaizhu Chen ◽  
...  
Keyword(s):  
Small Rna ◽  
Transcriptome Sequencing ◽  
Target Genes ◽  
Isoquinoline Alkaloid ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Small Rna Sequencing ◽  
Regulatory Pathways ◽  
Oil Crops ◽  
Differentially Expressed Mirnas

Soybean is one of the most important oil crops in the world. Bean pyralid is a major leaf-feeding insect of soybean. In order to screen out the functional genes and regulatory pathways related to the resistance for bean pyralid larvae, the small RNA and transcriptome sequencing were performed based on the highly resistant material (Gantai-2-2) and highly susceptible material (Wan 82-178) of soybean. The results showed that, when comparing 48 h feeding with 0 h feeding, 55 differentially expressed miRNAs were identified in Gantai-2-2 and 58 differentially expressed miRNAs were identified in Wan82-178. When comparing Gantai-2-2 with Wan82-178, 77 differentially expressed miRNAs were identified at 0 h feeding, and 70 differentially expressed miRNAs were identified at 48 h feeding. The pathway analysis of the predicted target genes revealed that the plant hormone signal transduction, RNA transport, protein processing in the endoplasmic reticulum, zeatin biosynthesis, ubiquinone and other terpenoid-quinone biosynthesis, and isoquinoline alkaloid biosynthesis may play important roles in soybean’s defense against the stress caused by bean pyralid larvae. According to conjoint analysis of the miRNA/mRNA, a total of 20 differentially expressed miRNAs were negatively correlated with 26 differentially expressed target genes. The qRT-PCR analysis verified that the small RNA sequencing results were credible. According to the analyses of the differentially expressed miRNAs, we speculated that miRNAs are more likely to play key roles in the resistance to insects. Gma-miR156q, Gma-miR166u, Gma-miR166b, Gma-miR166j-3p, Gma-miR319d, Gma-miR394a-3p, Gma-miR396e, and so on—as well as their negatively regulated differentially expressed target genes—may be involved in the regulation of soybean resistance to bean pyralid larvae. These results laid a foundation for further in-depth research regarding the action mechanisms of insect resistance.

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