Academic literature on the topic 'Regulatory ncRNAs'
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Journal articles on the topic "Regulatory ncRNAs"
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Lee, Yong Sun. "Are We Studying Non-Coding RNAs Correctly? Lessons from nc886." International Journal of Molecular Sciences 23, no. 8 (April 12, 2022): 4251. http://dx.doi.org/10.3390/ijms23084251.
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Non-coding RNAs (ncRNAs), such as microRNAs or long ncRNAs, have brought about a new paradigm in the regulation of gene expression. Sequencing technologies have detected transcripts with tremendous sensitivity and throughput and revealed that the majority of them lack protein-coding potential. Myriad articles have investigated numerous ncRNAs and many of them claim that ncRNAs play gene-regulatory roles. However, it is questionable whether all these articles draw conclusions through cautious gain- and loss-of function experiments whose design was reasonably based on an ncRNA’s correct identity and features. In this review, these issues are discussed with a regulatory ncRNA, nc886, as an example case to represent cautions and guidelines when studying ncRNAs.
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Chao, Haoyu, Yueming Hu, Liang Zhao, Saige Xin, Qingyang Ni, Peijing Zhang, and Ming Chen. "Biogenesis, Functions, Interactions, and Resources of Non-Coding RNAs in Plants." International Journal of Molecular Sciences 23, no. 7 (March 28, 2022): 3695. http://dx.doi.org/10.3390/ijms23073695.
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Plant transcriptomes encompass a large number of functional non-coding RNAs (ncRNAs), only some of which have protein-coding capacity. Since their initial discovery, ncRNAs have been classified into two broad categories based on their biogenesis and mechanisms of action, housekeeping ncRNAs and regulatory ncRNAs. With advances in RNA sequencing technology and computational methods, bioinformatics resources continue to emerge and update rapidly, including workflow for in silico ncRNA analysis, up-to-date platforms, databases, and tools dedicated to ncRNA identification and functional annotation. In this review, we aim to describe the biogenesis, biological functions, and interactions with DNA, RNA, protein, and microorganism of five major regulatory ncRNAs (miRNA, siRNA, tsRNA, circRNA, lncRNA) in plants. Then, we systematically summarize tools for analysis and prediction of plant ncRNAs, as well as databases. Furthermore, we discuss the silico analysis process of these ncRNAs and present a protocol for step-by-step computational analysis of ncRNAs. In general, this review will help researchers better understand the world of ncRNAs at multiple levels.
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Fu, Xiang-Dong. "Non-coding RNA: a new frontier in regulatory biology." National Science Review 1, no. 2 (May 14, 2014): 190–204. http://dx.doi.org/10.1093/nsr/nwu008.
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Abstract A striking finding in the past decade is the production of numerous non-coding RNAs (ncRNAs) from mammalian genomes. While it is entirely possible that many of those ncRNAs are transcription noises or by-products of RNA processing, increasing evidence suggests that a large fraction of them are functional and provide various regulatory activities in the cell. Thus, functional genomics and proteomics are incomplete without understanding functional ribonomics. As has been long suggested by the ‘RNA world’ hypothesis, many ncRNAs have the capacity to act like proteins in diverse biochemical processes. The enormous amount of information residing in the primary sequences and secondary structures of ncRNAs makes them particularly suited to function as scaffolds for molecular interactions. In addition, their functions appear to be stringently controlled by default via abundant nucleases when not engaged in specific interactions. This review focuses on the functional properties of regulatory ncRNAs in comparison with proteins and emphasizes both the opportunities and challenges in future ncRNA research.
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Abedi-Gaballu, Fereydoon, Elham Kamal Kazemi, Seyed Ahmad Salehzadeh, Behnaz Mansoori, Farhad Eslami, Ali Emami, Gholamreza Dehghan, Behzad Baradaran, Behzad Mansoori, and William C. Cho. "Metabolic Pathways in Breast Cancer Reprograming: An Insight to Non-Coding RNAs." Cells 11, no. 19 (September 23, 2022): 2973. http://dx.doi.org/10.3390/cells11192973.
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Cancer cells reprogram their metabolisms to achieve high energetic requirements and produce precursors that facilitate uncontrolled cell proliferation. Metabolic reprograming involves not only the dysregulation in glucose-metabolizing regulatory enzymes, but also the enzymes engaging in the lipid and amino acid metabolisms. Nevertheless, the underlying regulatory mechanisms of reprograming are not fully understood. Non-coding RNAs (ncRNAs) as functional RNA molecules cannot translate into proteins, but they do play a regulatory role in gene expression. Moreover, ncRNAs have been demonstrated to be implicated in the metabolic modulations in breast cancer (BC) by regulating the metabolic-related enzymes. Here, we will focus on the regulatory involvement of ncRNAs (microRNA, circular RNA and long ncRNA) in BC metabolism, including glucose, lipid and glutamine metabolism. Investigation of this aspect may not only alter the approaches of BC diagnosis and prognosis, but may also open a new avenue in using ncRNA-based therapeutics for BC treatment by targeting different metabolic pathways.
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Koscianska, Edyta, Emilia Kozlowska, and Agnieszka Fiszer. "Regulatory Potential of Competing Endogenous RNAs in Myotonic Dystrophies." International Journal of Molecular Sciences 22, no. 11 (June 4, 2021): 6089. http://dx.doi.org/10.3390/ijms22116089.
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Non-coding RNAs (ncRNAs) have been reported to be implicated in cell fate determination and various human diseases. All ncRNA molecules are emerging as key regulators of diverse cellular processes; however, little is known about the regulatory interaction among these various classes of RNAs. It has been proposed that the large-scale regulatory network across the whole transcriptome is mediated by competing endogenous RNA (ceRNA) activity attributed to both protein-coding and ncRNAs. ceRNAs are considered to be natural sponges of miRNAs that can influence the expression and availability of multiple miRNAs and, consequently, the global mRNA and protein levels. In this review, we summarize the current understanding of the role of ncRNAs in two neuromuscular diseases, myotonic dystrophy type 1 and 2 (DM1 and DM2), and the involvement of expanded CUG and CCUG repeat-containing transcripts in miRNA-mediated RNA crosstalk. More specifically, we discuss the possibility that long repeat tracts present in mutant transcripts can be potent miRNA sponges and may affect ceRNA crosstalk in these diseases. Moreover, we highlight practical information related to innovative disease modelling and studying RNA regulatory networks in cells. Extending knowledge of gene regulation by ncRNAs, and of complex regulatory ceRNA networks in DM1 and DM2, will help to address many questions pertinent to pathogenesis and treatment of these disorders; it may also help to better understand general rules of gene expression and to discover new rules of gene control.
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Balarezo-Cisneros, Laura Natalia, Steven Parker, Marcin G. Fraczek, Soukaina Timouma, Ping Wang, Raymond T. O’Keefe, Catherine B. Millar, and Daniela Delneri. "Functional and transcriptional profiling of non-coding RNAs in yeast reveal context-dependent phenotypes and in trans effects on the protein regulatory network." PLOS Genetics 17, no. 1 (January 25, 2021): e1008761. http://dx.doi.org/10.1371/journal.pgen.1008761.
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Non-coding RNAs (ncRNAs), including the more recently identified Stable Unannotated Transcripts (SUTs) and Cryptic Unstable Transcripts (CUTs), are increasingly being shown to play pivotal roles in the transcriptional and post-transcriptional regulation of genes in eukaryotes. Here, we carried out a large-scale screening of ncRNAs in Saccharomyces cerevisiae, and provide evidence for SUT and CUT function. Phenotypic data on 372 ncRNA deletion strains in 23 different growth conditions were collected, identifying ncRNAs responsible for significant cellular fitness changes. Transcriptome profiles were assembled for 18 haploid ncRNA deletion mutants and 2 essential ncRNA heterozygous deletants. Guided by the resulting RNA-seq data we analysed the genome-wide dysregulation of protein coding genes and non-coding transcripts. Novel functional ncRNAs, SUT125, SUT126, SUT035 and SUT532 that act in trans by modulating transcription factors were identified. Furthermore, we described the impact of SUTs and CUTs in modulating coding gene expression in response to different environmental conditions, regulating important biological process such as respiration (SUT125, SUT126, SUT035, SUT432), steroid biosynthesis (CUT494, SUT053, SUT468) or rRNA processing (SUT075 and snR30). Overall, these data capture and integrate the regulatory and phenotypic network of ncRNAs and protein-coding genes, providing genome-wide evidence of the impact of ncRNAs on cellular homeostasis.
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Fort, Rafael Sebastián, Santiago Chavez, Juan M. Trinidad Barnech, Carolina Oliveira-Rizzo, Pablo Smircich, José Roberto Sotelo-Silveira, and María Ana Duhagon. "Current Status of Regulatory Non-Coding RNAs Research in the Tritryp." Non-Coding RNA 8, no. 4 (July 18, 2022): 54. http://dx.doi.org/10.3390/ncrna8040054.
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Trypanosomatids are protozoan parasites that cause devastating vector-borne human diseases. Gene expression regulation of these organisms depends on post-transcriptional control in responding to diverse environments while going through multiple developmental stages of their complex life cycles. In this scenario, non-coding RNAs (ncRNAs) are excellent candidates for a very efficient, quick, and economic strategy to regulate gene expression. The advent of high throughput RNA sequencing technologies show the presence and deregulation of small RNA fragments derived from canonical ncRNAs. This review seeks to depict the ncRNA landscape in trypanosomatids, focusing on the small RNA fragments derived from functional RNA molecules observed in RNA sequencing studies. Small RNA fragments derived from canonical ncRNAs (tsRNAs, snsRNAs, sdRNAs, and sdrRNAs) were identified in trypanosomatids. Some of these RNAs display changes in their levels associated with different environments and developmental stages, demanding further studies to determine their functional characterization and potential roles. Nevertheless, a comprehensive and detailed ncRNA annotation for most trypanosomatid genomes is still needed, allowing better and more extensive comparative and functional studies.
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Li, Chunhua, Xiaorong Yu, Jianping Lu, Liyu Zheng, Dahua Xu, Zelong Xu, Liqiang Wang, et al. "Contributions of Gene Modules Regulated by Essential Noncoding RNA in Colon Adenocarcinoma Progression." BioMed Research International 2020 (March 24, 2020): 1–12. http://dx.doi.org/10.1155/2020/8595473.
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Noncoding RNAs (ncRNAs), especially microRNA (miRNA) and long noncoding RNA (lncRNA), have an impact on a variety of important biological processes during colon adenocarcinoma (COAD) progression. This includes chromatin organization, transcriptional and posttranscriptional regulation, and cell-cell signaling. The aim of this study is to identify the ncRNA-regulated modules that accompany the progression of COAD and to analyze their mechanisms, in order to screen the potential prognostic biomarkers for COAD. An integrative molecular analysis was carried out to identify the crosstalks of gene modules between different COAD stages, as well as the essential ncRNAs in the posttranscriptional regulation of these modules. 31 ncRNA regulatory modules were found to be significantly associated with overall survival in COAD patients. 17 out of the 31 modules (in which ncRNAs played essential roles) had improved the predictive ability for COAD patient survival compared to only the mRNAs of those modules, which were enriched in the core cancer hallmark pathways with closer interactions. These suggest that the ncRNAs’ regulatory modules not only exhibit close relation to COAD progression but also reflect the dynamic significant crosstalk of genes in the modules to the different malignant extent of COAD.
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Pandey, Amitkumar, Saiprasad Ajgaonkar, Nikita Jadhav, Praful Saha, Pranay Gurav, Sangita Panda, Dilip Mehta, and Sujit Nair. "Current Insights into miRNA and lncRNA Dysregulation in Diabetes: Signal Transduction, Clinical Trials and Biomarker Discovery." Pharmaceuticals 15, no. 10 (October 14, 2022): 1269. http://dx.doi.org/10.3390/ph15101269.
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Diabetes is one of the most frequently occurring metabolic disorders, affecting almost one tenth of the global population. Despite advances in antihyperglycemic therapeutics, the management of diabetes is limited due to its complexity and associated comorbidities, including diabetic neuropathy, diabetic nephropathy and diabetic retinopathy. Noncoding RNAs (ncRNAs), including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), are involved in the regulation of gene expression as well as various disease pathways in humans. Several ncRNAs are dysregulated in diabetes and are responsible for modulating the expression of various genes that contribute to the ‘symptom complex’ in diabetes. We review various miRNAs and lncRNAs implicated in diabetes and delineate ncRNA biological networks as well as key ncRNA targets in diabetes. Further, we discuss the spatial regulation of ncRNAs and their role(s) as prognostic markers in diabetes. We also shed light on the molecular mechanisms of signal transduction with diabetes-associated ncRNAs and ncRNA-mediated epigenetic events. Lastly, we summarize clinical trials on diabetes-associated ncRNAs and discuss the functional relevance of the dysregulated ncRNA interactome in diabetes. This knowledge will facilitate the identification of putative biomarkers for the therapeutic management of diabetes and its comorbidities. Taken together, the elucidation of the architecture of signature ncRNA regulatory networks in diabetes may enable the identification of novel biomarkers in the discovery pipeline for diabetes, which may lead to better management of this metabolic disorder.
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Gámez-Valero, Ana, Anna Guisado-Corcoll, Marina Herrero-Lorenzo, Maria Solaguren-Beascoa, and Eulàlia Martí. "Non-Coding RNAs as Sensors of Oxidative Stress in Neurodegenerative Diseases." Antioxidants 9, no. 11 (November 8, 2020): 1095. http://dx.doi.org/10.3390/antiox9111095.
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Oxidative stress (OS) results from an imbalance between the production of reactive oxygen species and the cellular antioxidant capacity. OS plays a central role in neurodegenerative diseases, where the progressive accumulation of reactive oxygen species induces mitochondrial dysfunction, protein aggregation and inflammation. Regulatory non-protein-coding RNAs (ncRNAs) are essential transcriptional and post-transcriptional gene expression controllers, showing a highly regulated expression in space (cell types), time (developmental and ageing processes) and response to specific stimuli. These dynamic changes shape signaling pathways that are critical for the developmental processes of the nervous system and brain cell homeostasis. Diverse classes of ncRNAs have been involved in the cell response to OS and have been targeted in therapeutic designs. The perturbed expression of ncRNAs has been shown in human neurodegenerative diseases, with these changes contributing to pathogenic mechanisms, including OS and associated toxicity. In the present review, we summarize existing literature linking OS, neurodegeneration and ncRNA function. We provide evidences for the central role of OS in age-related neurodegenerative conditions, recapitulating the main types of regulatory ncRNAs with roles in the normal function of the nervous system and summarizing up-to-date information on ncRNA deregulation with a direct impact on OS associated with major neurodegenerative conditions.
Dissertations / Theses on the topic "Regulatory ncRNAs"
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Okaro, Udoka. "A Small RNA and DNA Binding Protein Contribute to Biofilm Development in Bartonella henselae." Scholar Commons, 2019. https://scholarcommons.usf.edu/etd/7878.
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A biofilm, which is associated with 80% of chronic infections in humans, is formed when bacteria aggregate, attach to a substrate and secrete a matrix protecting the bacteria from host cell defenses and antibiotics. Bartonella henselae (B. henselae) is the causative agent of cat scratch disease, persistent bacteremia, and one of the most frequently reported causes of blood-culture negative endocarditis (BCNE) in patients. The ability of B. henselae to adhere to the heart valve, form a biofilm and vegetation to cause endocarditis increases the morbidity and mortality rate in infected patients. The presence of a trimeric autotransporter adhesin (TAA) called Bartonella adhesin A (BadA) has been linked to biofilm formation in B. henselae. BadA is a protein of 3036 amino acids and a member of the TAAs found in Bartonella and other Gram-negative bacteria. The function of BadA has been studied in vitro and is critical for agglutination, host cell adhesion and activation of a pro-angiogenic host response. However, very little is known about badA gene regulation or the molecular basis of biofilm formation. This work aims to determine whether BadA is necessary for the establishment of biofilms and how the bacteria regulate badA expression. Using genetic mutations, real-time cell adhesion assay, RT-qPCR, and microscopy, it was shown that BadA is required for biofilm formation. Using an in-frame complete deletion strain of badA, a reduced ability to form a biofilm was observed which was restored in the deletion strain complemented with a partial badA. Analysis of the B. henselae transcriptome shows nine highly transcribed, homologous RNAs, termed Bartonella regulatory transcript (Brt1-9). The Brts are short-sized (<200 >nucleotides), highly expressed, and located in an intergenic region indicative of small RNAs (sRNA). The Brts are predicted to form a stable stem and loop structure with a potential terminator/riboswitch region on the 3′ end. Located ~20 nucleotides downstream of each Brt is a poorly transcribed helix-turn-helix DNA binding protein gene termed transcriptional regulatory protein (trps 1-9). High brt transcription stops just before the start of the trp implicating the 3’ loop of the Brt as a terminating loop. Replacement of the trp with a gfp reporter gene shows that in the absence of the 3′ end of Brt1, gfp is transcribed. Also consistent with our findings, an increase in both the transcription of trp1 and badA and the formation of a biofilm in mutants of the brt1 gene was observed. Furthermore, to determine the role of the Trp in regulating badA, an electrophoretic mobility shift assay was carried out. The data confirms that Trp1 binds the promoter region of badA gene to regulate gene expression. In summary, the brt1/trp1 regulon affects badA transcription and biofilm formation in B. henselae. Understanding the mechanism and condition(s) by which the brt/trp regulatory system regulates badA is a plausible approach to the development of treatments that target the formation of biofilm-related diseases and persistent bacteremia in humans.
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Gripenland, Jonas. "Regulatory roles of two small RNAs in the human pathogen Listeria monocytogenes and the evaluation of an alternative infection model." Doctoral thesis, Umeå universitet, Institutionen för molekylärbiologi (Medicinska fakulteten), 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-55432.
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Listeriosis is a potentially lethal disease caused by the Gram-positive facultative intracellular pathogen Listeria monocytogenes (L.m.). L.m. is found ubiquitously in the environment and infects humans via ingestion of contaminated food. Contaminated products are usually derived from ruminants and involve dairy products and different kinds of processed meat. Listeriosis is a potential lifethreatening disease with a total mortality rate of 20-30 %. The development of listeriosis may lead to meningitis and septicemia or other invasive diseases. Pregnant women are of increased risk of developing listeriosis and a materno-fetal infection commonly lead to spontaneous abortion or still-birth. Regulation of gene expression, and specifically virulence gene expression, is essential for pathogenic bacteria to be equipped for handling counteractions from the host as well as thriving in the often hostile environment. In pathogenic Listeria, virulence gene expression is under the control of the global virulence gene regulator PrfA. The expression of prfA is highly regulated at the transcriptional, post-transcriptional and post- translational level. We have identified a novel type of post-transcriptional regulation of prfA-mRNA by a trans-acting riboswitch element (SreA). By binding to the leader region of prfA-mRNA, SreA negatively regulates the expression of prfA. To our knowledge, this is the first description of a cis-acting riboswitch capable of functioning as a small RNA in trans, regulating targets on distant sites. To date, there have been around 100 sRNAs identified in Listeria monocytogenes, but experimental data is still limited. We have characterized a blood induced sRNA, Rli38, which is important for full virulence during oral infection of mice. Our data suggest that Rli38 regulates the expression of at least two proteins; OppD (Oligopeptide transport protein) and IsdG (heme degrading monooxygenase). Both of these proteins have been implicated in the infectious cycle of L.m. We speculate that the virulence phenotype of an ∆rli38 mutant is possibly mediated through the effect of these proteins. L.m. is a complex pathogen, able to infect and replicate in a variety of organs and cause several distinctive forms of disease. These qualities of L.m. generate difficulties in simulating human listeriosis in animal models, as entailed by the multitude of models used in the field. In this work, we have evaluated the use of an alternative animal model in studying listeriosis. Our results describe the differentiated virulence potential of wildtype bacteria and a ∆prfA mutant strain in the chicken embryo by live/death screening and organ colonization. Large differences in mean time to death were found between wild-type and the ∆prfA strain and ∆prfA cells displayed a considerable defect in colonization of the embryonal liver. The results presented in this thesis show that the chicken embryo infection model is a valuable and convenient tool in studying end-outcome and organ colonization of Listeria monocytogenes. Taken together, this thesis describes the characterization of two previously unknown sRNAs in the human pathogen Listeria monocytogenes and the use of an alternative infection model for simulating listeriosis.
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Sousa, Neto Cecilio Martins de. "Estabilizador de sistema de pot?ncia para m?quinas s?ncronas de polos salientes utilizando a transformada Wavelet." Universidade Federal do Rio Grande do Norte, 2013. http://repositorio.ufrn.br:8080/jspui/handle/123456789/15474.
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Previous issue date: 2013-07-05Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico
The power system stabilizers are used to suppress low-frequency electromechanical oscillations and improve the synchronous generator stability limits. This master thesis proposes a wavelet-based power system stabilizer, composed of a new methodology for extraction and compensation of electromechanical oscillations in electrical power systems based on the scaling coefficient energy of the maximal overlap discrete wavelet transform in order to reduce the effects of delay and attenuation of conventional power system stabilizers. Moreover, the wavelet coefficient energy is used for electric oscillation detection and triggering the power system stabilizer only in fault situations. The performance of the proposed power system stabilizer was assessed with experimental results and comparison with the conventional power system stabilizer. Furthermore, the effects of the mother wavelet were also evaluated in this work
Os estabilizadores de sistemas de pot?ncia s?o empregados para suprimir oscila??es eletromec?nicas, de baixa frequ?ncia, e estender os limites de estabilidade de geradores s?ncronos. Prop?e-se nesta disserta??o de mestrado um estabilizador de sistema de pot?ncia baseado nas wavelets, composta por uma novametodologia para extra??o e compensa??o de oscila??es eletromec?nicas em sistemas el?tricos de pot?ncia baseada nas energias dos coeficientes de aproxima??o da transformada wavelet discreta redundante, com o objetivo de reduzir os efeitos de atraso e atenua??es dos estabilizadores de sistemas de pot?ncia convencionais. Por outro lado, as energias dos coeficientes wavelet s?o utilizadas para detec??o das oscila??es el?tricas e habilita??o do estabilizador de sistema de pot?ncia proposto apenas nas situa??es de falta. A efic?cia do desempenho do estabilizador de sistema de pot?ncia proposto foi comprovada por meio de resultados experimentais, cujo desempenho foi comparado com o desempenho do estabilizador de sistema de pot?ncia convencional. Al?m disso, os efeitos das wavelets m?es tamb?m foram avaliados
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Qu, Zhipeng. "Comprehensive identification and annotation of non-protein-coding transcriptomes from vertebrates indicates most ncRNAs are regulatory." Thesis, 2013. http://hdl.handle.net/2440/81965.
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Non-coding RNAs (ncRNAs), in particular long ncRNAs, represent a significant proportion of the vertebrate transcriptome and probably regulate many biological processes. Initially, I developed a robust pipeline for the genome wide identification and annotation of ncRNAs and used publically available bovine ESTs (Expressed Sequence Tags) from many developmental stages and tissues as input. The pipeline yielded 23,060 annotated bovine ncRNAs, the majority of which (57%) were intergenic, and were only moderately correlated with protein coding genes. I then used this pipeline to annotate ncRNAs from human, mouse and zebrafish ESTs. Comparative analysis confirmed some previously described findings about intergenic ncRNAs, such as a positionally biased distribution with respect to regulatory or development related protein-coding genes, and weak but clear sequence conservation across species. Furthermore, comparative analysis of developmental and regulatory genes proximate to long intergenic ncRNAs indicated that the relationship of these genes to neighbor long ncRNAs was not conserved, providing evidence for the rapid evolution of species-specific gene associated long ncRNA. In addition, I built protein-coding and nonprotein-coding gene co-expression networks based on available human transcriptome data. More than 30,000 human protein-coding and non-coding transcripts were annotated into tissue-specific co-expression sub-networks, indicating the possible regulatory connections between ncRNAs and protein-coding genes. In conclusion, I have reconstructed and annotated over 130,000 long ncRNAs, most of which are unannotated, in human, mouse and zebrafish. Together with the annotated bovine ncRNAs, we provide a significantly expanded number of candidates for functional testing by the research community.Thesis (Ph.D.) -- University of Adelaide, School of Molecular and Biomedical Science, 2013
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Wiegand, Sandra. "RNA-Seq and proteomics based analysis of regulatory RNA features and gene expression in Bacillus licheniformis." Doctoral thesis, 2013. http://hdl.handle.net/11858/00-1735-0000-0022-5E88-E.
Full textBook chapters on the topic "Regulatory ncRNAs"
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Swati, D. "Riboswitches: Regulatory ncRNAs in Archaea." In Biocommunication of Archaea, 277–303. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-65536-9_17.
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Skreka, Konstantinia, Michael Karbiener, Marek Zywicki, Alexander Hüttenhofer, Marcel Scheideler, and Mathieu Rederstorff. "Expression Profiling of ncRNAs Employing RNP Libraries and Custom LNA/DNA Microarray Analysis." In Regulatory RNAs, 229–51. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-662-45801-3_9.
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Safran, Marilyn, Naomi Rosen, Michal Twik, Ruth BarShir, Tsippi Iny Stein, Dvir Dahary, Simon Fishilevich, and Doron Lancet. "The GeneCards Suite." In Practical Guide to Life Science Databases, 27–56. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-16-5812-9_2.
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AbstractThe GeneCards® database of human genes was launched in 1997 and has expanded since then to encompass gene-centric, disease-centric, and pathway-centric entities and relationships within the GeneCards Suite, effectively navigating the universe of human biological data—genes, proteins, cells, regulatory elements, biological pathways, and diseases—and the connections among them. The knowledgebase amalgamates information from >150 selected sources related to genes, proteins, ncRNAs, regulatory elements, chemical compounds, drugs, splice variants, SNPs, signaling molecules, differentiation protocols, biological pathways, stem cells, genetic tests, clinical trials, diseases, publications, and more and empowers the suite’s Next Generation Sequencing (NGS), gene set, shared descriptors, and batch query analysis tools.
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Bocci, Federico, Mohit Kumar Jolly, Herbert Levine, and José Nelson Onuchic. "Quantitative Characteristic of ncRNA Regulation in Gene Regulatory Networks." In Computational Biology of Non-Coding RNA, 341–66. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-8982-9_14.
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G. Fagan, Steven, and Shona Pfeiffer. "Emerging Roles of Non-Coding RNA in Neuronal Function and Dysfunction." In Recent Advances in Neurochemistry [Working Title]. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.101327.
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Advancements in RNA sequencing technologies in recent years have contributed greatly to our understanding of the transcriptome and the now widely recognized multifaceted functions of RNA. The discovery and functional analysis of an increasing number of novel small non-coding RNAs (ncRNAs) has highlighted their importance as critical regulators of gene expression and brain function. In particular, two diverse classes of ncRNAs, microRNAs (miRNAs) and tRNA-derived small RNAs (tsRNAs), are especially abundant in the nervous system and play roles in regulation of gene expression and protein translation, cellular stress responses and complex underlying pathophysiology of neurological diseases. This chapter will discuss the most recent findings highlighting the dysregulation, functions and regulatory roles of ncRNAs in the pathophysiological mechanisms of neurological disorders and their relevance as novel biomarkers of injury and therapeutic agents.
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Al-Dahmoshi, Hussein, Noor Al-Khafaji, Moaed E. Al-Gazally, Maha F. Smaism, Zena Abdul Ameer Mahdi, and Suhad Y. Abed. "Interactions of lncRNAs and miRNAs in Digestive System Tumors." In Recent Advances in Noncoding RNAs [Working Title]. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.107374.
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Noncoding RNA (ncRNA) includes short (miRNA) and long (lncRNA) that have important regulatory role in different biological processes. One of the important issue in which ncRNA involved is tumor induction and suppression. miRNA and lncRNA were vital players in many tumors including digestive system tumors. This study includes studying the role of 140 hsa-miR including miR-1 to miR-140 and their sponger lncRNA in esophageal and stomach cancers by 249 studies. The review revealed that each miR may play as oncogene only or tumor suppressor via upregulation and downregulation regulatory proteins in cell cycles and activation of physiological cascades. Some of miR have dual role in same type of tumor as oncogene and suppressive miR. Same thing is for lncRNA tacting as oncogenic via sponging some of miR when overexpressed to upregulate oncogenic protein or acting as suppression lncRNA when overexpressed to downregulate some oncogenic proteins activated by miR. The current review concludes the vital role of ncRNA (both miRNA and lncRNA) in some digestive system tumors as oncogene-promoting cancer viability, invasiveness, proliferation, and metastasis or as tumor suppressor inhibiting tumorigenicity or inducing apoptosis.
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Kumar, Pranjal, and Nikita Bhandari. "lncRNAs: Role in Regulation of Gene Expression." In Gene Expression. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.104900.
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The long non-coding RNAs (lncRNAs) are a subclass of ncRNA which is more than 200 nucleotides long and processed similar to mRNA by RNA polymerase II with very few differences between them. In the last two decades, it has become a hot topic of research as it has been found differentially expressed in disease versus normal conditions including cancers. They regulate many biological functions including regulation of gene expression and epigenetic control. lncRNAs can control gene expression at the transcriptional level, and post-transcriptional level. Also, they can play a structural role to function as scaffolds for protein complexes. They interact with DNA, RNA, and proteins. They have been shown to possess competitive binding sites for miRNAs, which makes them a master regulator of gene expression by masking miRNAs and altering many biological functions. They are found to be associated with many cellular functions including cell proliferation, migration, and invasion. The lncRNAs can be utilized as biomarkers and can be targeted for personalized therapy.