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exosome and RNA sequence

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https://www.readbyqxmd.com/read/28423032/complete-study-demonstrating-the-absence-of-rhabdovirus-in-a-distinct-sf9-cell-line
#1
Yoshifumi Hashimoto, Daniel Macri, Indresh Srivastava, Clifton McPherson, Rachael Felberbaum, Penny Post, Manon Cox
A putative novel rhabdovirus (SfRV) was previously identified in a Spodoptera frugiperda cell line (Sf9 cells [ATCC CRL-1711 lot 58078522]) by next generation sequencing and extensive bioinformatic analysis. We performed an extensive analysis of our Sf9 cell bank (ATCC CRL-1711 lot 5814 [Sf9L5814]) to determine whether this virus was already present in cells obtained from ATCC in 1987. Inverse PCR of DNA isolated from Sf9 L5814 cellular DNA revealed integration of SfRV sequences in the cellular genome. RT-PCR of total RNA showed a deletion of 320 nucleotides in the SfRV RNA that includes the transcriptional motifs for genes X and L...
2017: PloS One
https://www.readbyqxmd.com/read/28411393/global-exosome-transcriptome-profiling-reveals-biomarkers-for-multiple-sclerosis
#2
Igor Selmaj, Maria Cichalewska, Magdalena Namiecinska, Grazyna Galazka, Wojciech Horzelski, Krzysztof W Selmaj, Marcin P Mycko
OBJECTIVE: Accumulating evidence supports a role for exosomes in immune regulation. In this study, we investigated the total circulating exosome transcriptome in relapsing-remitting multiple sclerosis patients (RRMS) and healthy controls (HC). METHODS: Next generation sequencing (NGS) was used to define the global RNA profile of serum exosomes in 19 RRMS patients (9 in relapse, 10 in remission) and 10 HC. We analyzed 5 million reads and over 50,000 transcripts per sample, including a detailed analysis of microRNA (miRNA) differentially expressed in RRMS...
April 15, 2017: Annals of Neurology
https://www.readbyqxmd.com/read/28411247/exosomal-microrna-transfer-into-macrophages-mediates-cellular-postconditioning
#3
Geoffrey de Couto, Romain Gallet, Linda Cambier, Ervin Jaghatspanyan, Nupur Makkar, James Frederick Dawkins, Benjamin P Berman, Eduardo Marbán
BACKGROUND: Cardiosphere-derived cells (CDCs) confer cardioprotection in acute myocardial infarction (MI) via distinctive macrophage (MΦ) polarization. Here we demonstrate that CDC-secreted exosomes (CDCexo) recapitulate the cardioprotective effects of CDC therapy known as cellular postconditioning. METHODS: Rats and pigs underwent MI induced by ischemia-reperfusion prior to intracoronary infusion of CDCexo, inert fibroblast exosomes (Fbexo; control), or vehicle. Two days later, infarct size was quantified...
April 14, 2017: Circulation
https://www.readbyqxmd.com/read/28407805/revelation-of-mrnas-and-proteins-in-porcine-milk-exosomes-by-transcriptomic-and-proteomic-analysis
#4
Ting Chen, Qian-Yun Xi, Jia-Jie Sun, Rui-Song Ye, Xiao Cheng, Rui-Ping Sun, Song-Bo Wang, Gang Shu, Li-Na Wang, Xiao-Tong Zhu, Qing-Yan Jiang, Yong-Liang Zhang
BACKGROUND: Milk is a complex liquid that provides nutrition to newborns. Recent reports demonstrated that milk is enriched in maternal-derived exosomes that are involved in fetal physiological and pathological conditions by transmission of exosomal mRNAs, miRNAs and proteins. Until now, there is no such research relevant to exosomal mRNAs and proteins in porcine milk, therefore, we have attempted to investigate porcine milk exosomal mRNAs and proteins using RNA-sequencing and proteomic analysis...
April 13, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28381156/characterization-of-exosomal-rnas-derived-from-human-gastric-cancer-cells-by-deep-sequencing
#5
Jia Ren, Quan Zhou, Hao Li, Jianfang Li, Li Pang, Liping Su, Qinlong Gu, Zhenggang Zhu, Bingya Liu
Exosomes secreted from the cell to the extracellular environment play an important role in intercellular communication. Next-generation sequencing technology, which has achieved great development recently, allows us to detect more complete data and gain even deeper analyses of RNA transcriptomes. In our research, we extracted exosomes from different gastric cancer cell lines and immortalized normal gastric mucosal epithelial cell line and examined the amounts of exosomal proteins and RNAs. Our data showed that the secreted amount of cancer cell-derived exosomes, which contain proteins and RNAs, was much higher than that of normal cell-derived exosomes...
April 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28350318/overexpression-of-exosomal-cardioprotective-mirnas-mitigates-hypoxia-induced-h9c2-cells-apoptosis
#6
Jinwei Zhang, Jideng Ma, Keren Long, Wanling Qiu, Yujie Wang, Zihui Hu, Can Liu, Yi Luo, Anan Jiang, Long Jin, Qianzi Tang, Xun Wang, Xuewei Li, Mingzhou Li
Recent evidence suggests that hypoxia caused by acute myocardial infarction can induce cardiomyocyte apoptosis. Exosomes are signalling mediators that contribute to intercellular communication by transporting cytosolic components including miRNAs, mRNAs, and proteins. However, the systemic regulation and function of exosomal miRNAs in hypoxic cardiomyocytes are currently not well understood. Here, we used small RNA sequencing to investigate the effects of hypoxia stress on miRNAome of rat cardiomyoblast cells (H9c2) and corresponding exosomes...
March 28, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28341602/cytosolic-yb-1-and-nsun2-are-the-only-proteins-recognizing-specific-motifs-present-in-mrnas-enriched-in-exosomes
#7
Olga A Kossinova, Alexander V Gopanenko, Svetlana N Tamkovich, Olga A Krasheninina, Alexey E Tupikin, Elena Kiseleva, Darya D Yanshina, Alexey A Malygin, Alia G Ven'yaminova, Marsel R Kabilov, Galina G Karpova
Exosomes, membranous vesicles secreted by various cells, are involved in intercellular communication and carry vast repertoires of RNAs and proteins. Processes mediating RNA sorting into exosomes are currently poorly understood. Using bioinformatics approaches, three structural motifs ACCAGCCU, CAGUGAGC and UAAUCCCA have been discovered as enriched in exosomal mRNAs and long noncoding RNAs. Here, utilizing short RNA hairpins, each containing one of the motifs, in a pull-down assay of cytosolic extract of human embryonic kidney 293 (HEK293) cells, we prove that multifunctional RNA-binding protein YB-1 specifically interacts with all three motifs, whereas methyltransferase NSUN2 recognizes only the motif CAGUGAGC...
March 21, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28213378/prognostic-role-of-circulating-exosomal-mirnas-in-multiple-myeloma
#8
Salomon Manier, Chia-Jen Liu, Hervé Avet-Loiseau, Jihye Park, Jiantao Shi, Federico Campigotto, Karma Z Salem, Daisy Huynh, Siobhan V Glavey, Bradley Rivotto, Antonio Sacco, Aldo M Roccaro, Juliette Bouyssou, Stéphane Minvielle, Philippe Moreau, Thierry Facon, Xavier Leleu, Edie Weller, Lorenzo Trippa, Irene M Ghobrial
Exosomes, secreted by several cell types, including cancer cells, can be isolated from the peripheral blood and have been shown to be powerful markers of disease progression in cancer. In this study, we examined the prognostic significance of circulating exosomal microRNAs (miRNAs) in multiple myeloma (MM). A cohort of 156 patients with newly diagnosed MM, uniformly treated and followed, was studied. Circulating exosomal miRNAs were isolated and used to perform small RNA sequencing analysis on 10 samples and a qRT-PCR array on 156 samples...
February 17, 2017: Blood
https://www.readbyqxmd.com/read/28195143/aging-and-serum-exomir-content-in-women-effects-of-estrogenic-hormone-replacement-therapy
#9
Reeta Kangas, Timo Törmäkangas, Vidal Fey, Juha Pursiheimo, Ilkka Miinalainen, Markku Alen, Jaakko Kaprio, Sarianna Sipilä, Anna-Marja Säämänen, Vuokko Kovanen, Eija K Laakkonen
Exosomes participate in intercellular messaging by transporting bioactive lipid-, protein- and RNA-molecules and -complexes. The contents of the exosomes reflect the physiological status of an individual making exosomes promising targets for biomarker analyses. In the present study we extracted exosome microRNAs (exomiRs) from serum samples of premenopausal women (n = 8) and monozygotic postmenopausal twins (n = 10 female pairs), discordant for the use of estrogenic hormone replacement therapy (HRT), in order to see whether the age or/and the use of HRT associates with exomiR content...
February 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28167212/recruitment-of-rna-molecules-by-connexin-rna-binding-motifs-implication-in-rna-and-dna-transport-through-microvesicles-and-exosomes
#10
REVIEW
Marta Varela-Eirin, Adrian Varela-Vazquez, Marina Rodríguez-Candela Mateos, Anton Vila-Sanjurjo, Eduardo Fonseca, José L Mascareñas, M Eugenio Vázquez, Maria D Mayan
Connexins (Cxs) are integral membrane proteins that form high-conductance plasma membrane channels, allowing communication from cell to cell (via gap junctions) and from cells to the extracellular environment (via hemichannels). Initially described for their role in joining excitable cells (nerve and muscle), gap junctions (GJs) are found between virtually all cells in solid tissues and are essential for functional coordination by enabling the direct transfer of small signalling molecules, metabolites, ions, and electrical signals from cell to cell...
April 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28148795/hepatitis-b-virus-encoded-mirna-controls-viral-replication
#11
Xi Yang, Hongfeng Li, Huahui Sun, Hongxia Fan, Yaqi Hu, Min Liu, Xin Li, Hua Tang
microRNAs (miRNAs) are a class of small single-stranded non-coding functional RNAs. Hepatitis B virus (HBV) is an enveloped DNA virus with virions and subviral forms of particles that lack a core. It was not known whether HBV encodes miRNAs. Here, we identified an HBV-encoded miRNA (called HBV-miR-3) by deep sequencing and northern blot. HBV-miR-3 is located at nts 373-393 of the HBV genome and was generated from 3.5Kb, 2,4Kb and 2.1Kb HBV in classic miRNA biogenesis (Drosha-Dicer dependent) manner. HBV-miR-3 was highly expressed in hepatoma cell lines with an integrated HBV genome and HBV (+) hepatoma tumors...
February 1, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28127559/variety-of-rnas-in-peripheral-blood-cells-plasma-and-plasma-fractions
#12
Anna V Savelyeva, Elena V Kuligina, Dmitry N Bariakin, Vadim V Kozlov, Elena I Ryabchikova, Vladimir A Richter, Dmitry V Semenov
Human peripheral blood contains RNA in cells and in extracellular membrane vesicles, microvesicles and exosomes, as well as in cell-free ribonucleoproteins. Circulating mRNAs and noncoding RNAs, being internalized, possess the ability to modulate vital processes in recipient cells. In this study, with SOLiD sequencing technology, we performed identification, classification, and quantification of RNAs from blood fractions: cells, plasma, plasma vesicles pelleted at 16,000g and 160,000g, and vesicle-depleted plasma supernatant of healthy donors and non-small cell lung cancer (NSCLC) patients...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28096131/nutrition-micrornas-and-human-health
#13
REVIEW
Juan Cui, Beiyan Zhou, Sharon A Ross, Janos Zempleni
MicroRNAs (miRs) hybridize with complementary sequences in mRNA and silence genes by destabilizing mRNA or preventing translation of mRNA. Over 60% of human protein-coding genes are regulated by miRs, and 1881 high-confidence miRs are encoded in the human genome. Evidence suggests that miRs not only are synthesized endogenously, but also might be obtained from dietary sources, and that food compounds alter the expression of endogenous miR genes. The main food matrices for studies of biological activity of dietary miRs include plant foods and cow milk...
January 2017: Advances in Nutrition
https://www.readbyqxmd.com/read/28069372/rna-exosome-and-non-coding-rna-coupled-mechanisms-in-aid-mediated-genomic-alterations
#14
REVIEW
Brice Laffleur, Uttiya Basu, Junghyun Lim
The eukaryotic RNA exosome is a well-conserved protein complex with ribonuclease activity implicated in RNA metabolism. Various families of non-coding RNAs have been identified as substrates of the complex, underscoring its role as a non-coding RNA processing/degradation unit. However, the role of RNA exosome and its RNA processing activity on DNA mutagenesis/alteration events have not been investigated until recently. B lymphocytes use two DNA alteration mechanisms, class switch recombination (CSR) and somatic hypermutation (SHM), to re-engineer their antibody gene expressing loci until a tailored antibody gene for a specific antigen is satisfactorily generated...
January 7, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28051166/identification-of-small-rnas-in-extracellular-vesicles-from-the-commensal-yeast-malassezia-sympodialis
#15
Simon Rayner, Sören Bruhn, Helen Vallhov, Anna Andersson, R Blake Billmyre, Annika Scheynius
Malassezia is the dominant fungus in the human skin mycobiome and is associated with common skin disorders including atopic eczema (AE)/dermatitis. Recently, it was found that Malassezia sympodialis secretes nanosized exosome-like vesicles, designated MalaEx, that carry allergens and can induce inflammatory cytokine responses. Extracellular vesicles from different cell-types including fungi have been found to deliver functional RNAs to recipient cells. In this study we assessed the presence of small RNAs in MalaEx and addressed if the levels of these RNAs differ when M...
January 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28043542/the-analysis-of-exosomal-micro-rnas-in-peripheral-blood-mononuclear-cell-derived-macrophages-after-infection-with-bacillus-calmette-gu%C3%A3-rin-by-rna-sequencing
#16
Esmaeil Mortaz, Shamila D Alipoor, Payam Tabarsi, Ian M Adcock, Johan Garssen, Ali Akbar Velayati
OBJECTIVE/BACKGROUND: Tuberculosis (TB) is a major global threat to human health, especially in low-income countries. The diagnosis of TB is challenging because of the limitations of specificity and sensitivity with the current diagnostics. Novel, selective biomarkers for TB would be of great practical value. Exosomes are bioactive vesicles with 30-100nm in diameter, which are secreted from almost all cell types and are found in virtually every human body fluid. Exosomes transport micro-RNAs (miRNAs), which are post-transcriptional regulators of gene expression, around the body and allow miRNAs to modulate biological pathways in target cells...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28017589/distinctive-patterns-of-transcription-and-rna-processing-for-human-lincrnas
#17
Margarita Schlackow, Takayuki Nojima, Tomas Gomes, Ashish Dhir, Maria Carmo-Fonseca, Nick J Proudfoot
Numerous long intervening noncoding RNAs (lincRNAs) are generated from the mammalian genome by RNA polymerase II (Pol II) transcription. Although multiple functions have been ascribed to lincRNAs, their synthesis and turnover remain poorly characterized. Here, we define systematic differences in transcription and RNA processing between protein-coding and lincRNA genes in human HeLa cells. This is based on a range of nascent transcriptomic approaches applied to different nuclear fractions, including mammalian native elongating transcript sequencing (mNET-seq)...
January 5, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28005467/defining-the-purity-of-exosomes-required-for-diagnostic-profiling-of-small-rna-suitable-for-biomarker-discovery
#18
Camelia Quek, Shayne A Bellingham, Chol-Hee Jung, Benjamin J Scicluna, Mitch C Shambrook, Robyn A Sharples, Lesley Cheng, Andrew F Hill
Small non-coding RNAs (ncRNA), including microRNAs (miRNA), enclosed in exosomes are being utilised for biomarker discovery in disease. Two common exosome isolation methods involve differential ultracentrifugation or differential ultracentrifugation coupled with Optiprep gradient fractionation. Generally, the incorporation of an Optiprep gradient provides better separation and increased purity of exosomes. The question of whether increased purity of exosomes is required for small ncRNA profiling, particularly in diagnostic and biomarker purposes, has not been addressed and highly debated...
February 2017: RNA Biology
https://www.readbyqxmd.com/read/28000095/exosomes-from-ipscs-delivering-sirna-attenuate-intracellular-adhesion-molecule-1-expression-and-neutrophils-adhesion-in-pulmonary-microvascular-endothelial-cells
#19
Zhihai Ju, Jinhui Ma, Chen Wang, Jie Yu, Yeru Qiao, Feilong Hei
The pro-inflammatory activation of pulmonary microvascular endothelial cells resulting in continuous expression of cellular adhesion molecules, and subsequently recruiting primed neutrophils to form a firm neutrophils-endothelium (PMN-EC) adhesion, has been examined and found to play a vital role in acute lung injury (ALI). RNA interference (RNAi) is a cellular process through harnessing a natural pathway silencing target gene based on recognition and subsequent degradation of specific mRNA sequences. It opens a promising approach for precision medicine...
April 2017: Inflammation
https://www.readbyqxmd.com/read/27943208/small-rna-library-construction-for-exosomal-rna-from-biological-samples-for-the-ion-torrent-pgm%C3%A2-and-ion-s5%C3%A2-system
#20
Lesley Cheng, Andrew F Hill
Next-generation deep sequencing (NGS) technology represents a powerful and innovative approach to profile small RNA. Currently, there are a number of large-scale and benchtop sequencing platforms available on the market. Although each platform is relatively straightforward to operate, constructing cDNA libraries can be the most difficult part of the NGS workflow. Constructing quality libraries is essential to obtaining a successful sequencing run of high-quality reads and coverage. The quality and yield of RNA affect hybridization and ligation of sequencing adapters...
2017: Methods in Molecular Biology
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