Wyniki wyszukiwania - Biblioteka Nauki

1

An approach for the identification of microRNA with an application to Anopheles gambiae

100%

Chatterjee R. , Chaudhuri K.

Acta Biochimica Polonica

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2006

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tom 53

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nr 2

303-309

EN

MicroRNAs (miRNAs) are an abundant class of 20-27 nt long noncoding RNAs, involved in post-transcriptional regulation of genes in eukaryotes. These miRNAs are usually highly conserved between the genomes of related organisms and their pre-miRNA transcript, about 60-120 nt long, forms extended stem-loop structure. Keeping these facts in mind miRsearch is developed which relies on searching the homologues of all known miRNAs of one organism in the genome of a related organism allowing few mismatches depending on the phylogenetic distance between them, followed by assessing for the capability of formation of stem-loop structure. The precursor sequences so obtained were then screened through the RNA folding program MFOLD selecting the cut-off values on the basis of known Drosophila melanogaster pre-miRNAs. With this approach, about 91 probable candidate miRNAs along with pre-miRNAs were identified in Anopheles gambiae using known D. melanogaster miRNAs. Out of these, 41 probable miRNAs have 100% similarity with already known D. melanogaster miRNAs and others were found to be at least 85% similar to the miRNAs of various other organisms.

2

Diet-Derived MicroRNAs: Separating the Dream from Reality

100%

Cottrill K. A. , Chan S. Y.

microRNA Diagnostics and Therapeutics

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2014

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tom 1

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nr 1

EN

Background: Both pleiotropic and ubiquitous, microRNAs (miRNAs) exert control over a wide range of cellular functions. They have been detected in virtually every extracellular fluid in the mammalian body, and many circulate substantial anatomical distances in plasma. Thus, secreted miRNAs are valuable not only as diagnostic tools but also may serve as novel biological effectors that can be transmitted between source and recipient tissue. Design: This review will discuss the possibility of delivering functional miRNAs from exogenously derived dietary sources. We will examine prior research interrogating the existence and relevance of such a mechanism. Findings: Recent findings have reported cross-kingdom transfer of specific plant-derived miRNAs to mammalian tissue following consumption of plant-based foods. These exogenous miRNAs were reported to be active in the recipient organisms, directing changes in gene expression at distant organ sites. In spite of this, subsequent studies have been unable to find evidence of substantial exogenous diet-derived miRNAs in mammalian circulation or tissues, regardless of diet. Conclusion: Further examination of diet-derived miRNA uptake is ongoing, but it does not appear that horizontal delivery of miRNAs via normal dietary intake is a generalizable or frequent process to maintain robust expression of these miRNAs in most higher-order animal organisms.

3

In situ hybridization-based detection of microRNAs in human diseases

100%

Zhang X. , Lu X. , Lopez-Berestein G. , Sood A. K. , Calin G.

microRNA Diagnostics and Therapeutics

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2014

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tom 1

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nr 1

EN

MicroRNAs (miRNAs) are small non-coding RNAs that regulate various aspects of gene expression in physiology and development. Links between miRNAs and the initiation and progression of human diseases are becoming increasingly apparent. The development of methods to detect the subcellular and tissue localization of miRNAs is essential for understanding their biological role in homeostasis. In this review, we discuss how in situ hybridization can complement tissuelevel miRNA expression profiling and its role as an investigational tool to better understand the etiology of human diseases. Furthermore, in situ hybridization of miRNAs represents a potent diagnostic assay that could be further refined and utilized for clinical applications.

4

Reprogramming immune responses via microRNA modulation

100%

Cubillos-Ruiz J. R. , Rutkowski M. R. , Tchou J. , Conejo-Garcia J. R.

microRNA Diagnostics and Therapeutics

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2014

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tom 1

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nr 1

EN

It is becoming increasingly clear that there are unique sets of miRNAs that have distinct governing roles in several aspects of both innate and adaptive immune responses. In addition, new tools allow selective modulation of the expression of individual miRNAs, both in vitro and in vivo. Here, we summarize recent advances in our understanding of how miRNAs drive the activity of immune cells, and how their modulation in vivo opens new avenues for diagnostic and therapeutic interventions in multiple diseases, from immunodeficiency to cancer. Recent contributions from our laboratory and other groups to novel formulations for miRNA mimetics are further discussed

5

MicroRNA biogenesis: Epigenetic modifications as another layer of complexity in the microRNA expression regulation

100%

Bhat S. , Jarmolowski A. , Szweykowska-Kulińska Z.

Acta Biochimica Polonica

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2016

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tom 63

|

nr 4

717-723

EN

Since their discovery, microRNAs have led to a huge shift in our understanding of the regulation of key biological processes. The discovery of epigenetic modifications that affect microRNA expression has added another layer of complexity to the already tightly controlled regulatory machinery. Modifications like uridylation, adenylation and RNA editing have been shown to have variable effects on miRNA biogenesis and action. Methylation of the N6 adenosine has been studied extensively in mRNA. Presence of the N6-methyl-adenosine (m6A) mark and its critical importance in miRNA biogenesis in animals adds to our understanding of the regulatory mechanisms, while its effect on miRNA biogenesis in plants is yet to be understood.

6

Developmental changes in barley microRNA expression profiles coupled with miRNA target analysis

100%

Pacak A. , Kruszka K. , Swida-Barteczka A. , Nuc P. , Karlowski W. , Jarmolowski A. , Szweykowska-Kulinska Z.

Acta Biochimica Polonica

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2016

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tom 63

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nr 4

799-809

EN

MicroRNAs are 19- to 24-nt-long single-stranded RNAs that are crucial regulators of gene expression which control plant development and response to environmental cues. We have analyzed microtranscriptomes of five barley developmental stages. Generally, during the barley development, miR168-3p and miR1432-5p levels increase while the 5'U-miR156-5p level decreases (with exception for the 2-week-old barley). We have identified two miR156-5p izomiRs (called 5'U-miR156-5p [20 nt] and 5'UU-miR156-5p [21 nt]), which were expressed differently during barley development. The 5' U-miR156-5p level decreased in 3-week-, 6-week-, and 68-day-old barley, when compared to the 1-week-old plants. Meanwhile, the 5' UU-miR156-5p level increased significantly in the 68-day-old barley plants. Moreover, only the 5' U-miR156 isomiR recognizes and guides unique transcription factor mRNAs from the Squamosa Promoter Binding Protein-Like (SPL) family. We identified many non-canonical microRNAs with changed expression levels during the barley development. Here, we present the profiles of microRNA expression characteristics for particular barley developmental stages. These analyses are accompanied by the experimental degradome analysis of miRNA targets.

7

MicroRNA in the pathogenesis of glaucoma

100%

Gasińska K. , Kosior-Jarecka E. , Żarnowski T.

OphthaTherapy

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2020

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tom 7

|

nr 4

277-286

EN

MicroRNAs are short ribonucleic acid molecules that regulate gene expression. The involvement of various types of microRNAs in the pathogenesis of glaucoma has been proved. Most of them affect trabecular meshwork in the anterior chamber angle, causing excessive deposition of extracellular matrix and blockage of the aqueous humor outflow. MicroRNAs affect the contractility of the trabecular meshwork cells, decreasing its permeability and increasing intraocular pressure. They participate in the regulation of apoptosis of trabecular meshwork cells and retinal ganglion cells. MicroRNAs may be potential biomarkers for glaucoma and, in the future, a target for gene therapy.

PL

MikroRNA to krótkie cząsteczki kwasu rybonukleinowego regulujące ekspresję genów. Wykazano udział różnych rodzajów mikroRNA w patogenezie jaskry. Większość z nich wpływa na beleczkowanie w kącie przesączania, powodując nadmierne odkładanie się macierzy zewnątrzkomórkowej i blokowanie drogi odpływu cieczy wodnistej. Cząsteczki mikroRNA zmieniają kurczliwość komórek beleczkowania, powodują spadek jego przepuszczalności i wzrost ciśnienia wewnątrzgałkowego. Uczestniczą w regulacji apoptozy komórek beleczkowania i komórek zwojowych siatkówki. Cząsteczki mikroRNA mogą być biomarkerami jaskry, a w przyszłości stać się celem terapii genowej.

8

Exploring Baltic Sea cyanobacteria for small-molecule inhibitors of microRNA function: a project description

89%

Brzuzan P. , Mazur-Marzec H. , Stefaniak F. , Woźny M. , Florczyk M.

Environmental Biotechnology

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2018

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tom Vol. 14, No. 1

1--4

EN

Cyanobacteria constitute a rich source of biologically active and structurally diverse compounds. The pharmacological potential of these compounds resides among others in their ability to control the proliferation and growth of cancer cell lines and potent disease-causing microbial agents. Despite recent scientific advances, the way these compounds interact with the body’s molecular structure are still unclear and science still has to discover how the cyanobacterial metabolites interact with cell structures and how cells react to them. In this project, we will study yet unexamined cyanobacterial metabolites, especially the compounds which act as chemical ligands for microRNA (miRNA) -binding sites, making them promising regulators (inhibitors) of gene networks that are involved in various diseases. We will first develop a stable cell line that constitutively expresses a unique miRNA reporter system. Then, we will conduct a screen on chemical compounds discovered in Baltic cyanobacteria to identify small molecules with inhibitory activity and specificity to MIR92b-3p, which has a significant impact on liver cell behavior in humans. We assume that a successful MIR92b-3p inhibitor will bind to the precursors of MIR92b-3p miRNA, disabling the action of either of the two processing enzymes involved in the biogenesis of any miRNA in a cell (Drosha or Dicer), thus affecting the MIR92b function. The discoveries made with these inhibitory chemical molecules could provide insight into the role of the MIR92 pathway in liver diseases and cancer, and possibly, if promising results appear, they may facilitate a strategy for treating some human diseases in the future.

9

MicroRNA and Immune Response to Viral, Bacterial and Fungal Infections

88%

Agosile O. O. , Benson U. , Oduwe U. , Okei N. C. , Fajobi S. J. , Akachukwu S. O. , Oyetayo B. O. , Faniyi A. J. , Njoku P. C. , Olagunju A. S.

World News of Natural Sciences

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2022

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tom 44

24-42

EN

Several kinds of microRNA have been studied as prospective biomarkers in the pursuit of better diagnostics tests for infectious diseases. miRNA which is processed mostly from introns plays a significant role in gene expression involving cell differentiation, proliferation, apoptosis, metabolism, and immune response. Many miRNA mimics or inhibitors are in their clinical phases and advancement in RNA interference will make miRNA become effective tools in the treatment of human infectious diseases. miRNA has been discovered to be largely involved in viral gene regulation as well as the change of host cellular genes during viral infections. The role of miRNA in most bacterial infections has not been thoroughly explored compared to viral infections. Recent studies have highlighted the vital role of host immunity against bacterial infections. miRNA that is sequenced due to fungal infections bear a close similarity to those produced in response to allergy or inflammation. Host-derived miRNA plays a vital role in immune regulation; inflammatory responses may be enhanced or inhibited by its upregulation or downregulation. Here, we outlined the involvement of microRNA in viral, fungal, and bacterial infections and the immune response associated. Further studies on these, will provide advanced diagnostic and treatment protocols for infectious diseases.

10

Molecular biology of sporadic vestibular schwannomas including genetic and epigenetic alterations

88%

Makuszewska M. , Litwiniuk-Kosmala M. , Bartoszewicz R. , Niemczyk K.

Polski Przegląd Otorynolaryngologiczny

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2020

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tom 9(3)

23-29

EN

Introduction: Vestibular schwannomas (VS) are benign tumors developing from the myelin-producing Schwann cells, which surround the vestibular branches of the auditory nerve. The vast majority occur sporadically and a small proportion are associated with neurofibromatosis type 2 (NF2). Most sVS are slow-growing neoplasms; however some have a cystic structure, show more rapid growth, cause more frequently paralysis of the facial nerve, and brainstem compression. The molecular hallmark of both sporadic and NF-2 associated VS is the inactivation of the tumor-suppressor gene NF2, also called merlin gene. Purpose: The paper presents the current knowledge on the molecular biology of VS, including: information on genetic and epigenetic aberrations, changes in gene expression and specific microRNA expression profiles.

11

How the RNA isolation method can affect microRNA microarray results

88%

Podolska A. , Kaczkowski B. , Litman T. , Fredholm M. , Cirera S.

Acta Biochimica Polonica

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2011

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tom 58

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nr 4

535-540

EN

The quality of RNA is crucial in gene expression experiments. RNA degradation interferes in the measurement of gene expression, and in this context, microRNA quantification can lead to an incorrect estimation. In the present study, two different RNA isolation methods were used to perform microRNA microarray analysis on porcine brain tissue. One method is a phenol-guanidine isothiocyanate-based procedure that permits isolation of total RNA. The second method, miRVana™ microRNA isolation, is column based and recovers the small RNA fraction alone. We found that microarray analyses give different results that depend on the RNA fraction used, in particular because some microRNAs appear very sensitive to the RNA isolation method. We conclude that precautions need to be taken when comparing microarray studies based on RNA isolated with different methods.

12

MicroRNAs as new immunity regulators in viral and bacterial infections

88%

Szumna M. , Hukowska-Szematowicz B.

Acta Biologica

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2020

|

tom 27

13

From mysterious supernatant entity to miRNA-150 in antigen- specific exosomes: a history of hapten-specific T suppressor factor

88%

Ptak W. , Nazimek K. , Askenase P. W. , Bryniarski K.

Archivum Immunologiae et Therapiae Experimentalis

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2015

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tom 63

|

nr 5

14

Modified S-transform as a tool to identify secondary structure elements in RNA

88%

Singh N. , Sharma S. D. , Yennamalli R. M.

Bio-Algorithms and Med-Systems

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2017

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tom Vol. 13, no. 4

182--193

EN

In this article, we describe the applicability of a signal processing method, specifically the modified S-transform (MST) method, on RNA sequences to identify periodicities between 2 and 11. MicroRNAs (miRNA) are associated with gene regulation and gene silencing and thus have wide applications in biological sciences. Also, the functionality of miRNA is highly associated with its secondary structures (stem, bulge and loop). Signal processing methods have been previously applied on genomic data to reveal the periodicities that determine a wide variety of biological functions, ranging from exon detection to microsatellite identification in DNA sequences. However, there has been less focus on RNA-based signal processing. Here, we show that the signal processing method can be successfully applied to miRNA sequences. We observed that these periodicities are highly correlated with the secondary structure of miRNA and such methods could possibly be used as indicators of secondary and tertiary structure formation.

15

The correlation of structural features of mature miRNAs with their biological function

75%

Belter A. , Naskret-Barciszewska M. Z.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2014

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tom 95

|

nr 3

16

Identification of miRNAs and their potential targets in halophyte plant Thellungiella halophila

75%

Panahi B. , Mohammadi S. A. , Ebrahimie E.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2013

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tom 94

|

nr 3

17

The role of microRNA (miRNA) as a biomarker in HPV and EBV-related cancers

75%

Kolesnik M. , Stepien E. , Polz-Dacewicz M.

Journal of Pre-Clinical and Clinical Research

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2021

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tom 15

|

nr 2

18

The microRNA-guided regulation of tillering in barley

75%

Pacak A. , Kruszka K. , Swida-Barteczka A. , Karlowski W. , Jarmolowski A. , Szweykowska-Kulinska Z.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2015

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tom 96

|

nr 1

19

Identification of putative miRNAs from expressed sequence tags of Gnetum gnemon L. and their cross-kingdom targets

75%

Krishnatreya D. B. , Ray D. , Baruah P. M. , Dowarah B. , Bardoloi K. S. , Agarwal H. , Agarwala N.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2021

|

tom 102

|

nr 2

20

MicroRNA expression prediction: Regression from regulatory elements

75%

Oğul H. , Tuncer M. E.

Biocybernetics and Biomedical Engineering

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2016

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tom Vol. 36, no. 1

89--94

EN

MicroRNAs are known as important actors in post-transcriptional regulation and relevant biological processes. Their expression levels do not only provide information about their own activities but also implicitly explain the behaviors of their targets, thus, in turn, the circuitry of underlying gene regulatory network. In this study, we consider the problem of estimating the expression of a newly discovered microRNA with known promoter sequence in a certain condition where the expression values of some known microRNAs are available. To this end, we offer a regression model to be learnt from the expression levels of other microRNAs obtained through a microarray experiment. To our knowledge, this is the first study that evaluates the predictability of microRNA expression from the regulatory elements found in its promoter sequence. The results obtained through the experiments on real microarray data justify the applicability of the framework in practice.