scholarly journals Pathophysiological Significance of Neutrophilic Transfer RNA-Derived Small RNAs in Asymptomatic Moyamoya Disease

Cells ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1086
Author(s):  
Lingzhi Li ◽  
Ping Liu ◽  
Rongliang Wang ◽  
Yuyou Huang ◽  
Jichang Luo ◽  
...  
Keyword(s):  
Moyamoya Disease ◽  
Small Rnas ◽  
Treatment Options ◽  
Transfer Rna ◽  
Polymerase Chain ◽  
Functional Pathway ◽  
Pathway Analyses ◽  
Log Linear ◽  
Regulatory Functions ◽  
Pathological Manifestation

Understanding asymptomatic moyamoya disease (aMMD), for which treatment options are currently limited, is key to the development of therapeutic strategies that will slow down the progression of this disease, as well as facilitate the discovery of therapeutic targets for symptomatic MMD. Newly found transfer RNA-derived small RNAs (tsRNAs) perform potential regulatory functions in neovascularization, which is a well-known pathological manifestation of MMD. In this study, the neutrophilic tsRNA transcriptome in aMMD was profiled using next-generation RNA sequencing in five patients and five matched healthy subjects. A negative binominal generalized log-linear regression was used to identify differentially expressed (DE)-tsRNAs in aMMD. Gene Ontology and functional pathway analyses were used to identify biological pathways involved with the targeted genes of the DE-tsRNAs. Four tsRNAs were selected and validated using quantitative reverse transcription polymerase chain reaction. In total, 186 tsRNAs were DE between the two groups. Pathophysiological events, including immune response, angiogenesis, axon guidance, and metabolism adjustment, were enriched for the DE-tsRNAs. The expression levels of the four DE-tsRNAs were consistent with those in the neutrophilic transcriptome. These aberrantly expressed tsRNAs and their targeted pathophysiological processes provide a basis for potential future interventions for aMMD.

scholarly journals Expression profiles and potential roles of transfer RNA‐derived small RNAs in atherosclerosis

2021 ◽  
Author(s):  
Xiangqin He ◽  
Yanyan Yang ◽  
Qi Wang ◽  
Jueru Wang ◽  
Shifang Li ◽  
...  
Keyword(s):  
Small Rnas ◽  
Expression Profiles ◽  
Transfer Rna

scholarly journals Transfer RNA demethylase ALKBH3 promotes cancer progression via induction of tRNA-derived small RNAs

2018 ◽  
Vol 47 (5) ◽  
pp. 2533-2545 ◽  
Author(s):  
Zhuojia Chen ◽  
Meijie Qi ◽  
Bin Shen ◽  
Guanzheng Luo ◽  
Yingmin Wu ◽  
...  
Keyword(s):  
Cancer Progression ◽  
Small Rnas ◽  
Transfer Rna

scholarly journals Investigation of Carbapenemase Genes in Carbapenem Resistant Enterobacterales Isolates: First KPC Report From Dokuz Eylul University Hospital

2021 ◽  
Author(s):  
Şeyda Şilan Okalin ◽  
Ayşe Nur Sarı Kaygısız ◽  
Mahmut Cem Ergon ◽  
İbrahim Mehmet Ali Öktem
Keyword(s):  
Treatment Options ◽  
Carbapenem Resistance ◽  
Tracheal Aspirate ◽  
University Hospital ◽  
Chain Reaction ◽  
Specific Primers ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Carbapenemase Gene ◽  
Polymerase Chain

Objective: In recent years, increasing carbapenem resistance of Enterobacterales bacteria limits treatment options, considerably. The main mechanism of this resistance is the production of carbapenemase enzymes. The aim of this study is to determine carbapenemase gene types in Enterobacterales isolates from our hospitalized patients and assess the clonal associations of the isolates with KPC gene. Method: A total of 48 clinical Enterobacterales isolates resistant to at least one carbapeneme and received between January 2019 and March 2019 were included in the study. Sample types were consisted of urine, blood, tracheal aspirate, wound and sputum. Of these isolates, three were Escherichia coli while 45 were Klebsiella pneumoniae. Types of carbapenemases were investigated by polymerase chain reaction, using specific primers for VIM, IMP, NDM, KPC and OXA-48 genes. PFGE was performed to determine the clonal associations between blaKPC positive K. pnemoniae isolates. Results: According to the results, blaOXA-48 (n=2) and blaKPC (n=1) were found to be present among E. coli isolates. Regarding 45 K. pneumoniae isolates; only blaOXA-48 and only blaNDM were present in 30 and two isolates, respectively. Seven K. pneumoniae isolates were found positive for both blaOXA-48 and blaNDM. Remaining K. pneumoniae isolates (n=6) harboured only blaKPC. None of the isolates were positive for blaIMP and blaVIM. PFGE analysis showed four isolates had the same pulsotype (A), while two had different pulsotypes (B-C). Conclusion: To our knowledge, this is the first report of KPC gene isolated in Dokuz Eylul University Hospital.

scholarly journals Equine Adipose-Derived Mesenchymal Stromal Cells Release Extracellular Vesicles Enclosing Different Subsets of Small RNAs

2019 ◽  
Vol 2019 ◽  
pp. 1-12 ◽  
Author(s):  
Stefano Capomaccio ◽  
Katia Cappelli ◽  
Cinzia Bazzucchi ◽  
Mauro Coletti ◽  
Rodolfo Gialletti ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Extracellular Vesicles ◽  
Mesenchymal Stromal Cells ◽  
Stromal Cells ◽  
Small Rnas ◽  
Rna Binding ◽  
Bioinformatic Analysis ◽  
Protein Coding ◽  
Significant Enrichment ◽  
Pathway Analyses

Background. Equine adipose-derived mesenchymal stromal cells (e-AdMSC) exhibit attractive proregenerative properties strongly related to the delivery of extracellular vesicles (EVs) that enclose different kinds of molecules including RNAs. In this study, we investigated small RNA content of EVs produced by e-AdMSC with the aim of speculating on their possible biological role. Methods. EVs were obtained by ultracentrifugation of the conditioned medium of e-AdMSC of 4 subjects. Transmission electron microscopy and scanning electron microscopy were performed to assess their size and nanostructure. RNA was isolated, enriched for small RNAs (<200 nt), and sequenced by Illumina technology. After bioinformatic analysis with state-of-the-art pipelines for short sequences, mapped reads were used to describe EV RNA cargo, reporting classes, and abundances. Enrichment analyses were performed to infer involved pathways and functional categories. Results. Electron microscopy showed the presence of vesicles ranging in size from 30 to 300 nm and expressing typical markers. RNA analysis revealed that ribosomal RNA was the most abundant fraction, followed by small nucleolar RNAs (snoRNAs, 13.67%). Miscellaneous RNA (misc_RNA) reached 4.57% of the total where Y RNA, RNaseP, and vault RNA represented the main categories. miRNAs were sequenced at a lower level (3.51%) as well as protein-coding genes (1.33%). Pathway analyses on the protein-coding fraction revealed a significant enrichment for the “ribosome” pathway followed by “oxidative phosphorylation.” Gene Ontology analysis showed enrichment for terms like “extracellular exosome,” “organelle envelope,” “RNA binding,” and “small molecule metabolic process.” The miRNA target pathway analysis revealed the presence of “signaling pathways regulating pluripotency of stem cells” coherent with the source of the samples. Conclusion. We herein demonstrated that e-AdMSC release EVs enclosing different subsets of small RNAs that potentially regulate a number of biological processes. These findings shed light on the role of EVs in the context of MSC biology.

Transfer RNA-derived small RNAs in plants

2017 ◽  
Vol 61 (2) ◽  
pp. 155-161 ◽  
Author(s):  
Lei Zhu ◽  
David W. Ow ◽  
Zhicheng Dong
Keyword(s):  
Small Rnas ◽  
Transfer Rna

scholarly journals MicroRNAs of Equine Amniotic Mesenchymal Cell-derived Microvesicles and Their Involvement in Anti-inflammatory Processes

2018 ◽  
Vol 27 (1) ◽  
pp. 45-54 ◽  
Author(s):  
Anna Lange-Consiglio ◽  
Barbara Lazzari ◽  
Claudia Perrini ◽  
Flavia Pizzi ◽  
Alessandra Stella ◽  
...  
Keyword(s):  
Small Rnas ◽  
Cell Communication ◽  
Mesenchymal Cell ◽  
Chain Reaction ◽  
Endometrial Cells ◽  
Inflammatory Processes ◽  
Immune System Regulation ◽  
Polymerase Chain ◽  
Amniotic Membranes

Cell-derived microvesicles (MVs) are a recently discovered mechanism of cell-to-cell communication. Our previous data show that MVs secreted by equine amniotic mesenchymal-derived cells (AMCs) are involved in downregulation of proinflammatory genes in lipopolysaccharide-stressed equine tendon and endometrial cells. The aim of the present study was to evaluate whether AMC-MVs contain selected microRNAs (miRNAs) involved in inflammation. Two pools of cells, derived from 3 amniotic membranes each, and their respective MVs were collected. Small RNAs were extracted and deep sequenced, followed by miRNA in silico detection. The analysis identified 1,285 miRNAs, which were quantified both in AMCs and MVs. Among these miRNAs, 401 were classified as Equus caballus miRNAs, 257 were predicted by homology with other species (cow, sheep, and goat), and 627 were novel candidate miRNAs. Moreover, 146 miRNAs differentially expressed (DE) in AMCs and MVs were identified, 36 of which were known and the remaining were novel. Among the known DE miRNAs, 17 showed higher expression in MVs. Three of these were validated by real time polymerase chain reaction: eca-miR-26, eca-miR-146a, and eca-miR-223. Gene ontology analysis of validated targets showed that the DE miRNAs in cells and MVs could be involved both in immune system regulation by modulating interleukin signaling and in the inflammatory process. In conclusion, this study suggests a significant role of AMCs in modulating immune response through cell–cell communication via MV-shuttling miRNAs.

scholarly journals Dose–response algorithms for water-bornePseudomonas aeruginosafolliculitis

2014 ◽  
Vol 143 (7) ◽  
pp. 1524-1537 ◽  
Author(s):  
D. J. ROSER ◽  
B. VAN DEN AKKER ◽  
S. BOASE ◽  
C. N. HAAS ◽  
N. J. ASHBOLT ◽  
...  
Keyword(s):  
Water Quality ◽  
Polymerase Chain Reaction ◽  
Organic Carbon ◽  
Dose Response ◽  
Quantitative Polymerase Chain Reaction ◽  
Exponential Model ◽  
Chain Reaction ◽  
Density Estimates ◽  
Polymerase Chain ◽  
Log Linear

SUMMARYWe developed two dose–response algorithms forP. aeruginosapool folliculitis using bacterial and lesion density estimates, associated with undetectable, significant, and almost certain folliculitis. Literature data were fitted to Furumoto & Mickey's equations, developed for plant epidermis-invading pathogens:Nl = Aln(1 + BC) (log-linear model);Pinf = 1−e(−rcC)(exponential model), whereAandBare 2.51644 × 107lesions/m2and 2.28011 × 10−11 c.f.u./mlP. aeruginosa, respectively;C = pathogen density (c.f.u./ml),Nl = folliculitis lesions/m2,Pinf = probability of infection, andrC = 4·3 × 10−7 c.f.u./mlP. aeruginosa. Outbreak data indicates these algorithms apply to exposure durations of 41 ± 25 min. Typical water quality benchmarks (≈10−2 c.f.u./ml) appear conservative but still useful as the literature indicated repeated detection likely implies unstable control barriers and bacterial bloom potential. In future, culture-based outbreak testing should be supplemented with quantitative polymerase chain reaction and organic carbon assays, and quantification of folliculitis aetiology to better understandP. aeruginosarisks.

scholarly journals tRFtarget: a database for transfer RNA-derived fragment targets

2020 ◽  
Vol 49 (D1) ◽  
pp. D254-D260 ◽  
Author(s):  
Ningshan Li ◽  
Nayang Shan ◽  
Lingeng Lu ◽  
Zuoheng Wang
Keyword(s):  
Binding Sites ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Target Prediction ◽  
Transfer Rna ◽  
Web Based ◽  
New Class ◽  
Physiological Processes ◽  
Graphic Illustration ◽  
Functional Pathway

Abstract Transfer RNA-derived fragments (tRFs) are a new class of small non-coding RNAs and play important roles in biological and physiological processes. Prediction of tRF target genes and binding sites is crucial in understanding the biological functions of tRFs in the molecular mechanisms of human diseases. We developed a publicly accessible web-based database, tRFtarget (http://trftarget.net), for tRF target prediction. It contains the computationally predicted interactions between tRFs and mRNA transcripts using the two state-of-the-art prediction tools RNAhybrid and IntaRNA, including location of the binding sites on the target, the binding region, and free energy of the binding stability with graphic illustration. tRFtarget covers 936 tRFs and 135 thousand predicted targets in eight species. It allows researchers to search either target genes by tRF IDs or tRFs by gene symbols/transcript names. We also integrated the manually curated experimental evidence of the predicted interactions into the database. Furthermore, we provided a convenient link to the DAVID® web server to perform downstream functional pathway analysis and gene ontology annotation on the predicted target genes. This database provides useful information for the scientific community to experimentally validate tRF target genes and facilitate the investigation of the molecular functions and mechanisms of tRFs.

Expression profiles of tRNA-derived fragments and their potential roles in ovarian endometriosis

Epigenomics ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 183-197
Author(s):  
Licong Shen ◽  
Xiaxia Hong ◽  
Wenjun Zhou ◽  
Yi Zhang
Keyword(s):  
Expression Profiles ◽  
Bioinformatic Analysis ◽  
Vital Role ◽  
Small Rna Sequencing ◽  
Chain Reaction ◽  
Ovarian Endometriosis ◽  
Paired Samples ◽  
Polymerase Chain ◽  
Pathway Analyses ◽  
Ovarian Endometriomas

Aim: Transfer RNA-derived fragments have been reported to play a vital role in disease progression, but their role in the pathogenesis of endometriosis remains unknown. Materials & methods: Small RNA sequencing was conducted in three paired ovarian endometriomas and eutopic endometria. The data from 22 paired samples were validated by quantitative real-time polymerase chain reaction (qPCR) and bioinformatic analysis was performed to establish the roles of these fragments in endometriosis pathogenesis. Results: We identified 19 upregulated and five downregulated tRNA-derived fragments, of which tiRNA-5 was the most common. Gene Ontology and pathway analyses revealed that these molecules could have roles in the pathogenesis of endometriosis. Conclusion: tRNA-derived fragments are dysregulated and could be involved in the pathogenesis and progression of ovarian endometriosis.

Sign in / Sign up

Export Citation Format

Share Document