Identification and characterization of differentially expressed exosomal microRNAs in bovine milk infected with Staphylococcus aureus

BMC Genomics ◽

10.1186/s12864-019-6338-1 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 6

Author(s):

Shaoyang Ma ◽

Chao Tong ◽

Eveline M. Ibeagha-Awemu ◽

Xin Zhao

Keyword(s):

Staphylococcus Aureus ◽

Target Gene ◽

Protein Transport ◽

Target Genes ◽

Bovine Milk ◽

Differentially Expressed ◽

Control Group ◽

Mastitic Milk ◽

Identification And Characterization

Abstract Background MicroRNAs (miRNAs) in milk-derived exosomes may reflect pathophysiological changes caused by mastitis. This study profiled miRNAs in exosomes from both normal milk and mastitic milk infected by Staphylococcus aureus (S. aureus). The potential targets for differentially expressed (DE) miRNAs were predicted and the target genes for bta-miR-378 and bta-miR-185 were also validated. Results Total RNA from milk exosomes was collected from healthy cows (n = 3, the control group) and S. aureus infected cows (n = 6, the SA group). Two hundred ninety miRNAs (221 known and 69 novel ones) were identified. Among them, 22 known and 15 novel miRNAs were differentially expressed. Target genes of DE miRNAs were significantly enriched in intracellular protein transport, endoplasmic reticulum and identical protein binding. The expression of two miRNAs (bta-miR-378 and bta-miR-185) with high read counts and log2 fold changes (> 3.5) was significantly higher in mastitic milk infected with S. aureus. One target gene (VAT1L) of bta-miR-378 and five target genes (DYRK1B, MLLT3, HP1BP3, NPR2 and PGM1) of bta-miR-185 were validated. Conclusion DE miRNAs in exosomes from normal and S. aureus infected milk were identified. The predicted targets for two DE miRNAs (bta-miR-378 and bta-miR-185) were further validated. The linkage between the validated target genes and diseases suggested that we should pay particular attention to exosome miRNAs from mastitic milk in terms of milk safety.

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Identification and characterization of differentially expressed exosomal microRNAs in bovine milk infected with Staphylococcus aureus

10.21203/rs.2.12751/v4 ◽

2019 ◽

Author(s):

Shaoyang Ma ◽

Chao Tong ◽

Eveline M. Ibeagha-Awemu ◽

Xin Zhao

Keyword(s):

Staphylococcus Aureus ◽

Target Gene ◽

Protein Transport ◽

Target Genes ◽

Bovine Milk ◽

Differentially Expressed ◽

Control Group ◽

Mastitic Milk ◽

Identification And Characterization

Abstract Background: MicroRNAs (miRNA) in milk-derived exosomes may reflect pathophysiological changes caused by mastitis. This study profiled miRNAs in exosomes from both normal milk and mastitic milk infected by Staphylococcus aureus (S. aureus). The potential targets for differentially expressed (DE) miRNAs were predicted and the target genes for bta-miR-378 and bta-miR-185 were also validated. Results: Total RNA from milk exosomes was collected from healthy cows (n=3, the control group) and S. aureus infected cows (n=6, the SA group). Two hundred ninety miRNAs (221 known and 69 novel ones) were identified. Among them, 22 known and 15 novel miRNAs were differentially expressed. Target genes of DE miRNAs were significantly enriched in intracellular protein transport, endoplasmic reticulum and identical protein binding. Two miRNAs (bta-miR-378 and bta-miR-185) with high read counts and log 2 fold changes (>3.5) were significantly higher in mastitic milk infected with S. aureus. One target gene (V AT1L) of bta-miR-378 and five target genes (DYRK1B , MLLT3 , HP1BP3 , NPR2 and PGM1) of bta-miR-185 were validated. Conclusion: DE miRNAs in exosomes from normal and S. aureus infected milk were identified. The predicted targets for two DE miRNAs (bta-miR-378 and bta-miR-185) were further validated. The linkage between the validated target genes and diseases suggested that we should pay particular attention to exosome miRNAs from mastitic milk in terms of milk safety.

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Exosomal Bta-miR-185 and Bta-miR-378 Are Potential Markers for Quality Control of Milk Infected by Staphylococcus aureus

10.21203/rs.2.12751/v1 ◽

2019 ◽

Author(s):

Shaoyang Ma ◽

Chao Tong ◽

Eveline M. Ibeagha-Awemu ◽

Xin Zhao

Keyword(s):

Staphylococcus Aureus ◽

Quality Control ◽

Endoplasmic Reticulum ◽

Target Gene ◽

Protein Transport ◽

Target Genes ◽

Intracellular Protein ◽

Intracellular Protein Transport ◽

Mastitic Milk ◽

Potential Biomarkers

Abstract MicroRNAs (miRNA) in milk-derived exosomes may reflect pathophysiological changes caused by mastitis. This study profiled miRNAs in milk exosomes and potential markers for quality control of milk infected by Staphylococcus aureus (S. aureus). Total RNA from milk exosomes was collected from healthy cows (n=3) and S. aureus infected cows (n=6). Two hundred ninety miRNAs (221 known and 69 novel ones) were identified. Among them, 22 known and 15 novel miRNAs were differentially expressed (DE). Target genes of DE miRNAs were significantly enriched in intracellular protein transport, endoplasmic reticulum and identical protein binding. Two miRNAs (bta-miR-378 and bta-miR-185) with high read counts and log2 fold changes (>3.5) were considered as potential milk exosome biomarker miRNAs for S. aureus mastitis and milk quality. One target gene (VAT1L) of bta-miR-378 and five target genes (DYRK1B, MLLT3, HP1BP3, NPR2 and PGM1) of bta-miR-185 were validated. DE miRNAs in exosomes from normal and S. aureus infected milk were identified. Two DE miRNAs could be used as potential biomarkers for the infection. The linkage between the validated target genes and diseases suggest that we should pay particular attention to exosome miRNAs from mastitic milk in terms of milk safety.

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Exosomal Bta-miR-185 and Bta-miR-378 Are Potential Markers for Quality Control of Milk Infected by Staphylococcus aureus

10.21203/rs.2.12751/v2 ◽

2019 ◽

Author(s):

Shaoyang Ma ◽

Chao Tong ◽

Eveline M. Ibeagha-Awemu ◽

Xin Zhao

Keyword(s):

Staphylococcus Aureus ◽

Quality Control ◽

Endoplasmic Reticulum ◽

Target Gene ◽

Protein Transport ◽

Target Genes ◽

Intracellular Protein ◽

Intracellular Protein Transport ◽

Mastitic Milk ◽

Potential Biomarkers

Abstract MicroRNAs (miRNA) in milk-derived exosomes may reflect pathophysiological changes caused by mastitis. This study profiled miRNAs in milk exosomes and potential markers for quality control of milk infected by Staphylococcus aureus (S. aureus). Total RNA from milk exosomes was collected from healthy cows (n=3) and S. aureus infected cows (n=6). Two hundred ninety miRNAs (221 known and 69 novel ones) were identified. Among them, 22 known and 15 novel miRNAs were differentially expressed (DE). Target genes of DE miRNAs were significantly enriched in intracellular protein transport, endoplasmic reticulum and identical protein binding. Two miRNAs (bta-miR-378 and bta-miR-185) with high read counts and log2 fold changes (>3.5) were considered as potential milk exosome biomarker miRNAs for S. aureus mastitis and milk quality. One target gene (VAT1L) of bta-miR-378 and five target genes (DYRK1B, MLLT3, HP1BP3, NPR2 and PGM1) of bta-miR-185 were validated. DE miRNAs in exosomes from normal and S. aureus infected milk were identified. Two DE miRNAs could be used as potential biomarkers for the infection. The linkage between the validated target genes and diseases suggest that we should pay particular attention to exosome miRNAs from mastitic milk in terms of milk safety.

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MyDGR: a server for identification and characterization of diversity-generating retroelements

Nucleic Acids Research ◽

10.1093/nar/gkz329 ◽

2019 ◽

Vol 47 (W1) ◽

pp. W289-W294 ◽

Cited By ~ 5

Author(s):

Fatemeh Sharifi ◽

Yuzhen Ye

Keyword(s):

Target Gene ◽

Target Genes ◽

Web Server ◽

Nucleotide Sequences ◽

Bacterial Genomes ◽

Fasta Format ◽

Reverse Transcriptases ◽

Identification And Characterization ◽

The Web

Abstract MyDGR is a web server providing integrated prediction and visualization of Diversity-Generating Retroelements (DGR) systems in query nucleotide sequences. It is built upon an enhanced version of DGRscan, a tool we previously developed for identification of DGR systems. DGR systems are remarkable genetic elements that use error-prone reverse transcriptases to generate vast sequence variants in specific target genes, which have been shown to benefit their hosts (bacteria, archaea or phages). As the first web server for annotation of DGR systems, myDGR is freely available on the web at http://omics.informatics.indiana.edu/myDGR with all major browsers supported. MyDGR accepts query nucleotide sequences in FASTA format, and outputs all the important features of a predicted DGR system, including a reverse transcriptase, a template repeat and one (or more) variable repeats and their alignment featuring A-to-N (N can be C, T or G) substitutions, and VR-containing target gene(s). In addition to providing the results as text files for download, myDGR generates a visual summary of the results for users to explore the predicted DGR systems. Users can also directly access pre-calculated, putative DGR systems identified in currently available reference bacterial genomes and a few other collections of sequences (including human microbiomes).

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Identification and Characterization of Differentially Expressed microRNAs and Target Gene Related to Flax Stem Development

Journal of Natural Fibers ◽

10.1080/15440478.2021.1902902 ◽

2021 ◽

pp. 1-17

Author(s):

Ying Yu ◽

Hongyu Chen ◽

Yiying Yang ◽

Didong Lou ◽

Chunbo Liang ◽

...

Keyword(s):

Target Gene ◽

Differentially Expressed ◽

Stem Development ◽

Identification And Characterization

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Genome-wide identification and characterization of long non-coding RNAs related to grain yield in foxtail millet [Setaria italica (L.) P. Beauv.]

BMC Genomics ◽

10.1186/s12864-020-07272-9 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Zilong Zhao ◽

Dan Liu ◽

Yanjiao Cui ◽

Suying Li ◽

Dan Liang ◽

...

Keyword(s):

Grain Yield ◽

Molecular Mechanisms ◽

High Throughput Sequencing ◽

Target Genes ◽

Foxtail Millet ◽

Differentially Expressed ◽

High Yield ◽

Yield Formation ◽

Identification And Characterization

Abstract Background Long noncoding RNAs (lncRNAs) have been reported to play critical roles in diverse growth and development processes in plants. However, the systematic identification and characterization of lncRNAs in foxtail millet is nearly blank. Results In this study, we performed high-throughput sequencing of young spikelets from four foxtail millet varieties in different yield levels at booting stage. As a result, a total of 12,378 novel lncRNAs were identified, and 70 were commonly significantly differentially expressed in comparisons between high-yield varieties and conventional varieties, suggesting that they involved in yield formation and regulation in foxtail millet. Functional analysis revealed that among the 70 significantly differentially expressed lncRNAs, 67 could transcriptionally modulate target genes in cis and in trans. Moreover, 18 lncRNAs related to grain yield in foxtail millet were predicted to function as miRNA target mimics and regulate gene expression by competing for the interaction between miRNAs and their target mRNAs. Conclusion Our results will provide materials for elucidation of the molecular mechanisms of lncRNAs participate in yield regulation, and will contribute to high yield foxtail millet breeding.

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Identification and Characterization of a Shuttle Plasmid with Antibiotic Resistance Gene from Staphylococcus aureus

Current Microbiology ◽

10.1007/s00284-002-3841-3 ◽

2003 ◽

Vol 46 (6) ◽

pp. 413-417 ◽

Cited By ~ 2

Author(s):

Mausumi Bhakta ◽

Manjusri Bal

Keyword(s):

Staphylococcus Aureus ◽

Antibiotic Resistance ◽

Resistance Gene ◽

Antibiotic Resistance Gene ◽

Shuttle Plasmid ◽

Identification And Characterization

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Proteomic Characterization of Bacteriophage Peptides from the Mastitis Producer Staphylococcus aureus by LC-ESI-MS/MS and the Bacteriophage Phylogenomic Analysis

Foods ◽

10.3390/foods10040799 ◽

2021 ◽

Vol 10 (4) ◽

pp. 799

Author(s):

Ana G. Abril ◽

Mónica Carrera ◽

Karola Böhme ◽

Jorge Barros-Velázquez ◽

Benito Cañas ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Dairy Products ◽

Phylogenomic Analysis ◽

Esi Ms ◽

Complement Inhibitors ◽

Staphylococcus Spp ◽

The Relationship ◽

Phage Proteins ◽

Identification And Characterization

The present work describes LC-ESI-MS/MS MS (liquid chromatography-electrospray ionization-tandem mass spectrometry) analyses of tryptic digestion peptides from phages that infect mastitis-causing Staphylococcus aureus isolated from dairy products. A total of 1933 nonredundant peptides belonging to 1282 proteins were identified and analyzed. Among them, 79 staphylococcal peptides from phages were confirmed. These peptides belong to proteins such as phage repressors, structural phage proteins, uncharacterized phage proteins and complement inhibitors. Moreover, eighteen of the phage origin peptides found were specific to S. aureus strains. These diagnostic peptides could be useful for the identification and characterization of S. aureus strains that cause mastitis. Furthermore, a study of bacteriophage phylogeny and the relationship among the identified phage peptides and the bacteria they infect was also performed. The results show the specific peptides that are present in closely related phages and the existing links between bacteriophage phylogeny and the respective Staphylococcus spp. infected.

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