Relevant bibliographies by topics / RNAi pathway

Academic literature on the topic 'RNAi pathway'

Author: Grafiati
Published: 4 June 2021
Last updated: 3 February 2022

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Journal articles on the topic "RNAi pathway"

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Dzianott, Aleksandra, Joanna Sztuba-Solińska, and Jozef J. Bujarski. "Mutations in the Antiviral RNAi Defense Pathway Modify Brome mosaic virus RNA Recombinant Profiles." Molecular Plant-Microbe Interactions® 25, no. 1 (January 2012): 97–106. http://dx.doi.org/10.1094/mpmi-05-11-0137.

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RNA interference (RNAi) mechanism targets viral RNA for degradation. To test whether RNAi gene products contributed to viral RNA recombination, a series of Arabidopsis thaliana RNAi-defective mutants were infected with Brome mosaic virus (BMV) RNAs that have been engineered to support crossovers within the RNA3 segment. Single-cross RNA3-RNA1, RNA3-RNA2, and RNA3-RNA3 recombinants accumulated in both the wild-type (wt) and all knock-out lines at comparable frequencies. However, a reduced accumulation of novel 3′ mosaic RNA3 recombinants was observed in ago1, dcl2, dcl4, and rdr6 lines but not in wt Col-0 or the dcl3 line. A BMV replicase mutant accumulated a low level of RNA3-RNA1 single-cross recombinants in Col-0 plants while, in a dcl2 dcl4 double mutant, the formation of both RNA3-RNA1 and mosaic recombinants was at a low level. A control infection in the cpr5-2 mutant, a more susceptible BMV Arabidopsis host, generated similar-to-Col-0 profiles of both single-cross and mosaic recombinants, indicating that recombinant profiles were, to some extent, independent of a viral replication rate. Also, the relative growth experiments revealed similar selection pressure for recombinants among the host lines. Thus, the altered recombinant RNA profiles have originated at the level of recombinant formation rather than because of altered selection. In conclusion, the viral replicase and the host RNAi gene products contribute in distinct ways to BMV RNA recombination. Our studies reveal that the antiviral RNAi mechanisms are utilized by plant RNA viruses to increase their variability, reminiscent of phenomena previously demonstrated in fungi.
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Yang, Li, Yuan Tian, Yuan-Yuan Peng, Jinzhi Niu, and Jin-Jun Wang. "Expression Dynamics of Core RNAi Machinery Genes in Pea Aphids Upon Exposure to Artificially Synthesized dsRNA and miRNAs." Insects 11, no. 2 (January 21, 2020): 70. http://dx.doi.org/10.3390/insects11020070.

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The pea aphid is an important pest of vegetables and causes serious losses worldwide. RNA interference (RNAi) is an effective pest control tool, and three sub-pathways have been described: The miRNA pathway, siRNA pathway, and piRNA pathway. A large number of genes in miRNA pathway and piRNA pathway are found to be expanded. To study the roles of these genes, the expression of 25 core RNAi genes was screened in spatiotemporal samples, artificially synthesized dsRNA and miRNA treated samples. The 25 genes were all expressed during different development stages and in different tissues. In dsRNA-treated samples and miRNA-treated samples, the expressions of genes in these three pathways were induced, especially the expanded genes. This suggests a complex network of RNAi core genes in the three sub-pathways. Treatment of miRNA seems to induce gene expression in a dosage-dependent manner. These results increase our knowledge of the siRNA pathway and related factors from RNAi pathway in aphids and promote the use of RNAi for the control of aphid pests.
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Soleimani, Saeed, Zahra Valizadeh Arshad, Sharif Moradi, Ali Ahmadi, Seyed Javad Davarpanah, and Sadegh Azimzadeh Jamalkandi. "Small regulatory noncoding RNAs in Drosophila melanogaster: biogenesis and biological functions." Briefings in Functional Genomics 19, no. 4 (March 27, 2020): 309–23. http://dx.doi.org/10.1093/bfgp/elaa005.

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Abstract RNA interference (RNAi) is an important phenomenon that has diverse genetic regulatory functions at the pre- and posttranscriptional levels. The major trigger for the RNAi pathway is double-stranded RNA (dsRNA). dsRNA is processed to generate various types of major small noncoding RNAs (ncRNAs) that include microRNAs (miRNAs), small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs) in Drosophila melanogaster (D. melanogaster). Functionally, these small ncRNAs play critical roles in virtually all biological systems and developmental pathways. Identification and processing of dsRNAs and activation of RNAi machinery are the three major academic interests that surround RNAi research. Mechanistically, some of the important biological functions of RNAi are achieved through: (i) supporting genomic stability via degradation of foreign viral genomes; (ii) suppressing the movement of transposable elements and, most importantly, (iii) post-transcriptional regulation of gene expression by miRNAs that contribute to regulation of epigenetic modifications such as heterochromatin formation and genome imprinting. Here, we review various routes of small ncRNA biogenesis, as well as different RNAi-mediated pathways in D. melanogaster with a particular focus on signaling pathways. In addition, a critical discussion of the most relevant and latest findings that concern the significant contribution of small ncRNAs to the regulation of D. melanogaster physiology and pathophysiology is presented.
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Lew, A. E., L. A. Jackson, and M. I. Bellgard. "Comparative genomic analysis of non-coding sequences and the application of RNA interference tools for bovine functional genomics." Australian Journal of Experimental Agriculture 45, no. 8 (2005): 995. http://dx.doi.org/10.1071/ea05057.

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Non-coding (nc) RNAs are important regulators of developmental genes, and essential for the modification of cellular DNA and chromatin through a process known as RNA interference (RNAi). The mediators of RNAi can be in the form of short double stranded (ds) RNAs, micro (mi) RNAs or small interfering (si) RNAs. miRNAs are involved in a translation repression pathway that inhibits protein translation in mRNA targets. Comparative genomic screens have revealed conserved regulatory non-coding sequences, which assist to predict the function of endogenous miRNAs. Only a few comparative studies include bovine genomic sequence, and RNAi has yet to be applied in bovine genome functional screens. siRNAs target homologous mRNAs for degradation, and thereby, silence specific genes. The use of synthetic siRNAs facilitates the elucidation of gene pathways by specific gene knockdown. A survey of the literature identifies a small number of reports using RNAi to examine immune pathways in bovine cell lines; however, they do not target genes involved in specific production traits. Applications of RNAi to elucidate bovine immune pathways for relevant bacterial and parasite diseases are yet to be reported. The inhibition of viral replication using RNAi has been demonstrated with bovine RNA viruses such as pestivirus and foot and mouth disease virus signifying the potential of RNAi as an antiviral therapeutic. RNAi approaches combined with genome data for protozoan parasites, insects and nematodes, will expedite the identification of novel targets for the treatment and prevention of economically important parasitic infections. This review will examine the approaches used in mammalian RNAi research, the current status of its applications to livestock systems and will discuss potential applications in beef cattle programs.
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Zhuang, Jimmy J., and Craig P. Hunter. "The Influence of Competition Among C. elegans Small RNA Pathways on Development." Genes 3, no. 4 (October 19, 2012): 671–85. http://dx.doi.org/10.3390/genes3040671.

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Small RNAs play a variety of regulatory roles, including highly conserved developmental functions. Caenorhabditis elegans not only possesses most known small RNA pathways, it is also an easy system to study their roles and interactions during development. It has been proposed that in C. elegans, some small RNA pathways compete for access to common limiting resources. The strongest evidence supporting this model is that disrupting the production or stability of endogenous short interfering RNAs (endo-siRNAs) enhances sensitivity to experimentally induced exogenous RNA interference (exo-RNAi). Here, we examine the relationship between the endo-siRNA and microRNA (miRNA) pathways, and find that, consistent with competition among these endogenous small RNA pathways, endo-siRNA pathway mutants may enhance miRNA efficacy. Furthermore, we show that exo-RNAi may also compete with both endo-siRNAs and miRNAs. Our data thus provide support that all known Dicer-dependent small RNA pathways may compete for limiting common resources. Finally, we observed that both endo-siRNA mutants and animals experiencing exo-RNAi have increased expression of miRNA-regulated stage-specific developmental genes. These observations suggest that perturbing the small RNA flux and/or the induction of exo-RNAi, even in wild-type animals, may impact development via effects on the endo-RNAi and microRNA pathways.
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Szachnowski, Ugo, Sara Andus, Dominika Foretek, Antonin Morillon, and Maxime Wery. "Endogenous RNAi pathway evolutionarily shapes the destiny of the antisense lncRNAs transcriptome." Life Science Alliance 2, no. 5 (August 28, 2019): e201900407. http://dx.doi.org/10.26508/lsa.201900407.

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Antisense long noncoding (aslnc)RNAs are extensively degraded by the nuclear exosome and the cytoplasmic exoribonuclease Xrn1 in the budding yeast Saccharomyces cerevisiae, lacking RNAi. Whether the ribonuclease III Dicer affects aslncRNAs in close RNAi-capable relatives remains unknown. Using genome-wide RNA profiling, here we show that aslncRNAs are primarily targeted by the exosome and Xrn1 in the RNAi-capable budding yeast Naumovozyma castellii, Dicer only affecting Xrn1-sensitive aslncRNAs levels in Xrn1-deficient cells. The dcr1 and xrn1 mutants display synergic growth defects, indicating that Dicer becomes critical in the absence of Xrn1. Small RNA sequencing showed that Dicer processes aslncRNAs into small RNAs, with a preference for Xrn1-sensitive aslncRNAs. Consistently, Dicer localizes into the cytoplasm. Finally, we observed an expansion of the exosome-sensitive antisense transcriptome in N. castellii compared with S. cerevisiae, suggesting that the presence of cytoplasmic RNAi has reinforced the nuclear RNA surveillance machinery to temper aslncRNAs expression. Our data provide fundamental insights into aslncRNAs metabolism and open perspectives into the possible evolutionary contribution of RNAi in shaping the aslncRNAs transcriptome.
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Mondal, Mosharrof, Judith K. Brown, and Alex Flynt. "Exploiting somatic piRNAs in Bemisia tabaci enables novel gene silencing through RNA feeding." Life Science Alliance 3, no. 10 (August 6, 2020): e202000731. http://dx.doi.org/10.26508/lsa.202000731.

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RNAi promises to reshape pest control by being nontoxic, biodegradable, and species specific. However, due to the plastic nature of RNAi, there is a significant variability in responses. In this study, we investigate small RNA pathways and processing of ingested RNAi trigger molecules in a hemipteran plant pest, the whitefly Bemisia tabaci. Unlike Drosophila, where the paradigm for insect RNAi technology was established, whitefly has abundant somatic piwi-associated RNAs (piRNAs). Long regarded as germline restricted, piRNAs are common in the soma of many invertebrates. We sought to exploit this for a novel gene silencing approach. The main principle of piRNA biogenesis is the recruitment of target RNA fragments into the pathway. As such, we designed synthetic RNAs to possess complementarity to the loci we annotated. Following feeding of these exogenous piRNA triggers knockdown as effective as conventional siRNA-only approaches was observed. These results demonstrate a new approach for RNAi technology that could be applicable to dsRNA-recalcitrant pest species and could be fundamental to realizing insecticidal RNAi against pests.
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Cánovas-Márquez, José Tomás, Sebastian Falk, Francisco E. Nicolás, Subramanian Padmanabhan, Rubén Zapata-Pérez, Álvaro Sánchez-Ferrer, Eusebio Navarro, and Victoriano Garre. "A ribonuclease III involved in virulence of Mucorales fungi has evolved to cut exclusively single-stranded RNA." Nucleic Acids Research 49, no. 9 (April 20, 2021): 5294–307. http://dx.doi.org/10.1093/nar/gkab238.

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Abstract Members of the ribonuclease III (RNase III) family regulate gene expression by processing double-stranded RNA (dsRNA). This family includes eukaryotic Dicer and Drosha enzymes that generate small dsRNAs in the RNA interference (RNAi) pathway. The fungus Mucor lusitanicus, which causes the deadly infection mucormycosis, has a complex RNAi system encompassing a non-canonical RNAi pathway (NCRIP) that regulates virulence by degrading specific mRNAs. In this pathway, Dicer function is replaced by R3B2, an atypical class I RNase III, and small single-stranded RNAs (ssRNAs) are produced instead of small dsRNA as Dicer-dependent RNAi pathways. Here, we show that R3B2 forms a homodimer that binds to ssRNA and dsRNA molecules, but exclusively cuts ssRNA, in contrast to all known RNase III. The dsRNA cleavage inability stems from its unusual RNase III domain (RIIID) because its replacement by a canonical RIIID allows dsRNA processing. A crystal structure of R3B2 RIIID resembles canonical RIIIDs, despite the low sequence conservation. However, the groove that accommodates dsRNA in canonical RNases III is narrower in the R3B2 homodimer, suggesting that this feature could be responsible for the cleavage specificity for ssRNA. Conservation of this activity in R3B2 proteins from other mucormycosis-causing Mucorales fungi indicates an early evolutionary acquisition.
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Holding, Cathy. "RNAi dissects signal pathway." Genome Biology 5 (2004): spotlight—20040624–01. http://dx.doi.org/10.1186/gb-spotlight-20040624-01.

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Lucentini, Jack. "Second RNAi pathway emerges." Genome Biology 5 (2004): spotlight—20040517–01. http://dx.doi.org/10.1186/gb-spotlight-20040817-01.

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Dissertations / Theses on the topic "RNAi pathway"

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Yu, Yi-Hsin Biotechnology &amp Biomolecular Sciences Faculty of Science UNSW. "Role of the RNAi pathway in influenza a virus infected mammalian cells." Publisher:University of New South Wales. Biotechnology & Biomolecular Sciences, 2008. http://handle.unsw.edu.au/1959.4/41545.

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The interferon (lFN) signalling and RNA interference (RNAi) pathways are the major antiviral pathways in animals and plants, respectively. Although the mechanism of RNAi remains to be completely characterised, the genes that encode the proteins involved in this process have been identified in the plant, fungi and animal kingdoms (Fagard et al., 2000, Grishok et aI., 2000, Hall et al., 2003, Kanellopoulou et al., 2005, Kolb et al., 2005); with comparative analyses indicating that RNAi is an evolutionarily conserved mechanism. Several studies have identified RNAi suppressors encoded by animal viruses, suggesting an antiviral role for the RNAi pathway in animals as well as plants (Andersson et al., 2005, Bennasser et al., 2006, Garcia et al., 2006, Li et al., 2004, Lichner et al., 2003, Lingel et al., 2005, Lu & Cullen, 2004, Wang et al., 2006). However, most of these studies were performed in non-mammalian systems and as yet, there is no direct evidence indicating that the RNAi pathway plays a significant antiviral role during the infection of mammalian cells. Interestingly, several viruses have now been shown to express their own microRNA (miRNA) in infected cells (Grey et al., 2005, Pfeffer et al., 2005, Pfeffer et al., 2004, Samols et al., 2005, Sullivan et al., 2005). Further, in the case of hepatitis C virus (HCV), there is evidence that the virus usurps the host cell miRNAs to enhance viral replication (Jopling et al., 2005). The principal aim of this project was to investigate the role of RNAi in mammalian cells during viral infection, particularly infection with the influenza A virus. This thesis is divided into six major chapters followed by a brief general discussion. Chapter 1 contains a general introduction to the RNAi pathway. It describes the history of the discovery of RNAi and summarizes the known and proposed antiviral roles of the RNAi pathway in plants and mammalian cells. Chapter 2 describes the general materials and methods used for this project. There are four main result chapters, each dealing with a specific experimental system. Each chapter is divided into a brief introduction, specific materials and methods used, followed by presentation of the experimental results and a brief discussion. Chapter 3 describes the development of an in vitro Dicer activity assay to study the effect of viral proteins on the activity of the mammalian Dicer protein. It was demonstrated that crude cell lysates derived from influenza A virus infected cells impaired the activity of Dicer and this observation was not due to degradation of the Dicer protein by virally-induced proteases. Chapter 4 describes the use of a GFP reporter assay for screening potential RNAi suppressors. This assay is suitable for studying viral proteins in isolation. The effect of the influenza NS1 protein on the RNAi pathway in HEK293 cells was investigated and it was shown that NS1 could exert modest, but nevertheless significant, suppression of the RNAi pathway. Northern studies, performed to examine the processing of shRNA in the presence of NS1, demonstrated that NSI suppressed the RNAi mechanism through interfering with the maturation ofshRNA into siRNA. Chapter 5 describes the effect of over-expressing components of the RNAi pathway on influenza A virus infection. In these experiments, Exportin 5, which encodes a protein involved in the transport of pre-miRNA/shRNA into the cytoplasm, was over-expressed during influenza A virus infection. Reduced viral infection was observed in cells over-expressing Exportin 5, suggesting that this treatment protects cells from virus infection. Chapter 6 describes the expressed small RNA profile during influenza A virus infection in MDCK cells. Novel canine miRNA homologues were identified through cloning and sequencing. No definitive evidence for virally-derived siRNA/miRNA was found but a general reduction of endogenous miRNA expression was detected.
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Aitken, Amelia. "Blocking the RNA Interference Pathway Improves Oncolytic Virus Therapy." Thesis, Université d'Ottawa / University of Ottawa, 2017. http://hdl.handle.net/10393/36821.

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Oncolytic viruses are novel candidates for cancer therapy and their efficacy relies on their capacity to overcome the host’s anti-viral barriers. In mammalian cells, the anti-viral response involves a protein-signaling cascade known as the interferon pathway, which alerts the immune system and limits the propagation of infection. Given that most cancer cells have defects in this pathway, they are susceptible to viral infection and responsive to oncolytic virotherapy. For reasons that remain unknown, many cancers are still refractory to oncolytic viruses, which suggests the existence of additional antiviral mechanisms. In this study, we investigate the potential involvement of an alternative antiviral pathway in cancer cells. Given that insects and plants rely on the RNA silencing pathway for their anti-viral protection, we investigated the presence of a similar mechanism in cancer cells. We found viral genome-derived small RNAs in various cancer cell lines upon infection, which is indicative of an RNA-mediated antiviral response. Also, various viruses encode suppressors of the RNA interference pathway. To determine if an oncolytic virus could benefit from such a factor, we engineered an oncolytic virus variant to encode the Nodamura virus B2 protein, a known inhibitor of RNA silencing-mediated immune responses. Using this virus, we observed enhanced cytotoxicity in 33 out of the 38 human cancer cell lines tested. Furthermore, our results show inhibition of viral genome cleavage and altered microRNA processing by our B2-expressing oncolytic virus. Taken together, our data suggests the blockade of RNA silencing antiviral pathways and/or antiviral microRNA processing improves the efficacy of our B2-encoding virus in a cell-line specific manner. Overall, our results establish the improved potential of our novel virus therapy and demonstrate for the first time the involvement of RNA pathways in the antiviral defense of cancer cells.
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Alagia, Adele. "Modulation of the RNAi pathway by chemically modified siRNA molecules." Doctoral thesis, Universitat de Barcelona, 2015. http://hdl.handle.net/10803/379307.

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To direct post-transcriptionally gene silencing, RNAi machinery exploits the formation of base pairs between the loaded guide strand and the complementary mRNA. The Ago2 protein is the “slicer” effector of the RISC and drives the endonucleolytic cleavage only when the siRNA guide strand is full paired with its RNA counterpart. Ago2 is able to incorporate a duplex siRNA molecule, unwinds the double helix and holds one strand while discarding the other. Ago2 bearing only the guide strand is defined “active” and can guide multiple cleavage reactions against the complementary mRNAs. Structural insights into Ago2 assembly process have speculated that early interactions between the siRNA and the Ago2 relies on specific recognition by the PAZ domain. Thus, proper PAZ domain recognition contributes to the specific and productive incorporation of siRNAs into the Ago2. Interactions between PAZ domain and siRNA molecule are essentially asymmetric. The guide strand with its 2-nt 3’overhang is involved in the majority of the contacts between the PAZ pocket and the siRNA, whereas the passenger strand interacts only with its 5’ end residue. In principle, overhang modifications (i.e. 2’-deoxy units) were just introduced to protect the RNA duplex integrity. Only after the understanding of the Ago2 architecture, overhang modifications were also harnessed to improve the siRNA potency and specificity. The comprehension of the PAZ lodging/dislodging motion during the formation of binary (Ago2 + guide) and ternary complex (Ago2 + guide + mRNA) pointed out the importance of adequate affinity between the guide overhang and the PAZ cleft during the Ago2 multi-turnover cleavage process. Affinity analysis on PAZ/siRNA overhang complex has proved the influence of the overhang presence for efficient binding. SiRNA duplexes with shorter overhang (1-nt) or blunt end have respectively highlighted 85-fold and >5000-fold reduced affinity. Hence, taking advantage of more efficient interactions between the PAZ pocket and the strand bearing the unpaired di-nucleotides structure, structural asymmetric siRNA molecules bearing only the antisense overhang were successful employed to bias the RISC strand selection. Moreover, competition between siRNAs, resulting in preferential incorporation of one siRNA type into the RISC machinery, is influenced by the distinct loading kinetics of siRNA molecules. Thus, the knockdown ability of siRNA mixtures is often compromised due to competition between siRNAs. It also has been reported that the simultaneous transfection of two or more siRNAs causes reduced silencing activity of one siRNA species whereas the potency of the other siRNAs were not affected. Even if siRNA competition effects are essentially produced by the interactions with the Ago2 protein, up to now, no available data about a specific Ago2 domain involvement into the siRNA competition have been described. We have been hypothesized that the PAZ domain, playing an important role in the first steps of the strand loading could be specifically involved in the siRNA competition. Given this background we are questioning how the di-nucleotide unpaired structure can influence the siRNA silencing efficiency and specificity. To explore the structural hallmarks critical for the PAZ pocket interaction, we modified the siRNA overhangs with several modifications. In detail, 2 units of β-L-nucleosides (mirror image L-Thymidine), 2’-deoxyribitol, GNA (glycerol nucleic acids)-Thymine and acyclic L-threoninol were introduced at overhang level and the silencing potency (IC50) was measured. Such modifications may provide fundamental clues on structural prerequisite needed for the PAZ recognition and strand loading into the Ago2.
Para dirigir el silenciamiento génico post-transcripcional, la maquinaria de RNAi explota la formación de pares de bases entre la hebra guía cargado y el ARNm complementario. La proteína Ago2 (Argonauta 2) es la "máquina de cortar" del complejo RISC y dirige la rotura endonucleolítica sólo cuando la hebra guía del siRNA está completamente apareada con su homóloga de ARN. Ago2 es capaz de incorporar una molécula de dúplex de siRNA, desenrolla la doble hélice y mantiene una hebra mientras se descarta la otra cadena. Ago2 cargada con la hebra guía se define "activa" y puede guiar múltiples reacciones de escisión contra los ARNm complementarios. El análisis estructural del proceso de ensamblaje de Ago2 ha llevado a la conclusión de que las primeras interacciones entre el siRNA y la proteina Ago2 se basa en el reconocimiento específico por el dominio PAZ. Por lo tanto, el correcto reconocimiento de dominio PAZ contribuye a la incorporación específica y productiva de los siRNAs en el Ago2. La hebra guía con su extremo 3' protuberante que tiene 2-nt está implicada en la mayoría de los contactos entre la cavidad presente en el dominio PAZ. En principio, las modificaciones en los extremos protuberantes se introdujeron para proteger la integridad del dúplex de ARN. Sólo después de la comprensión de la arquitectura de Ago2, se pensó en la utilización de las modificaciones en los extremos protuberantes para mejorar la potencia y especificidad de los siRNAs. Para explorar las características estructurales críticas para la interacción entre la cavidad PAZ, modificamos los extremos protuberantes de los siRNA con varias modificaciones. Específicamente, 2 unidades de un beta-L-nucleósido como la L-timidina (imagen especular de la timidina), de 2'-desoxiribitol, de GNA (glycerol nucleic acids)- timina y del derivado acíclico L-treoninol se introdujeron a los extremos protuberantes y se midió la potencia de silenciamiento (IC50). Tales modificaciones pueden proporcionar pistas fundamentales sobre el requisito estructural necesario para el reconocimiento y carga de la cadena del dominio PAZ de Ago2.
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Nord, Dianna M. "Knockdown of the Yes-associated Protein 1 pathway provides a basis for targeted therapy to treat infantile hemangioma." Thesis, Georgia Institute of Technology, 2015. http://hdl.handle.net/1853/53736.

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Hemangioma is a type of tumor commonly found in infants that is characterized by heavy vascularization and a disfiguring appearance. Hemangioma, though benign, can sometimes proliferate and be threatening to infants. Current treatments for infantile hemangioma include surgical removal as well as the use of topical and oral medication. However, current therapies are often ineffective at treating lesions and are commonly accompanied by dangerous side effects, creating the need for a new, safer treatment. This study targets the Yes-Associated Protein-1 (YAP-1), which has been described as an oncogene, by use of an interfering RNA technique in attempts to mediate tumor growth and progression. Western blotting of treatment and control BEND3 murine cells reveals that YAP-1 is knocked-down in treatment groups which have been infected with shYAP-1 siRNA genes. By successfully knocking down the YAP-1 protein, the potential for developing a novel targeted therapy for infantile hemangioma has been established.
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Roy, Matthew Stephen. "Development and application of a high-throughput RNAi screen to reveal novel components of the DNA sensing pathway." Thesis, Harvard University, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=3567049.

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The mammalian immune system has evolved a complex and diverse set of mechanisms to detect and respond to pathogens by recognizing conserved molecular structures and inducing protective immune responses. While many of these mechanisms are capable of sensing diverse molecular structures, a large fraction of pathogen sensors recognize nucleic acids. Pathogen-derived nucleic acids trigger nucleic acid sensors that typically induce anti-viral or anti-microbial immunity, however host-derived nucleic acids may also activate these sensors and lead to increased risk of inflammatory or autoimmune disease. Animal models and humans lacking key DNA nucleases, such as Trex1/Dnase3, accumulate intracellular DNA and develop progressive autoimmunity marked by increased Type-I Interferon (IFN) expression and inflammatory signatures.

Double-stranded DNA (dsDNA) is a potent inducer of the Type-I IFN response. Many of the sensors and signaling components that drive the IFN signature following simulation with transfected dsDNA (also called 'Interferon Stimulatory DNA' or 'ISD') remain unknown. We set out to identify novel components of the ISD pathway by developing a large-scale loss-of-function genetic perturbation screen of 1003 candidate genes. We interrogated multiple human and murine primary and immortalized cells, tested several Type-I IFN reporters, and considered multiple loss-of-function strategies before proceeding with an RNAi screen whereby mouse embryonic fibroblasts were stimulated with ISD and Type-IFN pathway activation was assessed by measuring Cxcl10 protein by ELISA.

Candidate genes for testing in the RNAi screen were curated from quantitative proteomic screens, IFN-beta and ISD stimulated mRNA expression profiles, and a selection of domain-based proteins including helicases, cytoplasmically located DNA-binding proteins and a set of potential negative regulators including phosphatases, deubiquitinases and known signaling proteins.

We identified a number of novel ISD pathway components including Abcf1, Ptpn1 and Hells. We validated hits through siRNA-resistant cDNA rescue, chemical inhibition or targeted knockout. Additionally, we evaluated protein-protein interactions of our strongest validated hits to develop a network model of the ISD pathway. In addition to the identification of novel ISD pathway components, our enriched screening data set may provide a useful resource of candidate genes involved in the response to cytosolic DNA.

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Kingham, Guy L. "Screening for inhibitors of and novel proteins within the homologous recombination DNA repair pathway." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:e2988d0b-c6d4-42a8-aef9-f320a13d6391.

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The homologous recombination (HR) pathway of DNA repair is essential for the faithful repair of double-stranded DNA breaks (DSBs) in all organisms and as such helps maintain genomic stability. Furthermore, HR is instrumental in the cellular response to exogenous DNA damaging agents such as those used in the clinic for chemo- and radiotherapy. HR in humans is a complex, incompletely understood process involving numerous stages and diverse biochemical activities. Advancing our knowledge of the HR pathway in humans aids the understanding of how chemo- and radiotherapies act and may be used to develop novel therapeutic strategies. Recent studies have identified inhibition of HR as one of the mechanisms via which a number of recently developed chemotherapeutics have their effect. Accordingly, the clinical potential of HR inhibitors is under investigation. My work has centred around the identification of both novel HR proteins and novel, small molecule HR inhibitors. To further these aims, I have successfully employed high-throughput RNAi and small molecule screening strategies. RNAi screens are commonly used to identify genes involved in a given cellular process via genetic loss of function, whilst small molecule, cell based screens are a powerful tool in the drug discovery process.
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Laxman, Navya. "miRNA and Asymmetric siRNA : Small RNAs with Large Effects on Bone Metabolism." Doctoral thesis, Uppsala universitet, Endokrinologi och mineralmetabolism, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-264451.

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RNA interference (RNAi) is a post-transcriptional gene silencing process elicited by double-stranded RNA, such as micro-RNA (miRNA) and small interfering RNA (siRNA). They are 18-25 nucleotide long, small non-coding RNAs acting as critical regulators in eukaryotic genome expression. They play an important role in regulating a wide range of biological processes such as cell cycle control, differentiation, aging and apoptosis. However, their role in supporting skeletal development and bone homeostasis is still poorly understood. Osteoporotic fractures constitute a tremendous and growing problem in our ageing populations, with an annual incidence of approximately 60000 osteoporotic fractures in Sweden. Osteoporosis is referred as the “Silent epidemic” because bone loss is gradual and a basically symptomless development until a fracture occurs. Results presented in this thesis provide a novel insight into crucial roles of   miRNAs in regulating bone homeostasis. The initial aim for the thesis was to perform global miRNA expression profiling in human bone cells, and to correlate these levels to global mRNA levels. We identified and functionally characterized several miRNAs that were differentially expressed and acted in important bone signaling pathways such as the Wnt and BMP pathways. These miRNAs included hsa-miR-29b, hsa-miR-30c2 and hsa-miR-125b, which we found targeting genes highly relevant to bone metabolism e.g. COL1A1, SPARC, RUNX2, BGLAP and FRZB. Thereafter, the effect on the microRNAome upon external stimuli (e.g., Dexamethasone and Parathyroid hormone) was assessed by SOLiD sequencing. We observed a substantial difference in the expression of miRNAs between PTH and DEX treated cells. Understanding the changes in miRNAome in human bone cells under different conditions could provide new insight in bone remodeling, specifically differentiation and functional properties of osteoblasts. Based on these studies, we furthermore identified Dlx5 as potential common target of miR-203 and miR-320b and these miRNAs negatively regulate BMP-2-induced osteoblast differentiation. To activate the RNAi pathway, siRNA or miRNA molecules must be conveyed into the cytoplasm of target cells. Since challenges in cellular delivery of these small silencing RNA molecules so far have limited their clinical utility, we developed a new siRNA design that demonstrates a novel carrier-free cellular delivery. This development could potentially have a major impact in RNAi therapeutics. In conclusion, this thesis provides novel insight of miRNAs that play a major role in the regulation of bone remodeling and differentiation and functional properties of osteoblasts. Our findings may have diagnostic and/or therapeutic implications in disorders of bone metabolism.
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Zwirek, Monika. "Improving barley for biofuel production : investigating the role of 4CL and CCR in the lignin biosynthesis pathway." Thesis, University of Dundee, 2013. https://discovery.dundee.ac.uk/en/studentTheses/6785dbbb-f8a4-46f1-b7c4-0c3d0d4dcdd4.

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One of the challenges in the 21st Century is to overcome the recalcitrance of lignocellulose for the production of liquid biofuels. Lignin is one of the key factors in this recalcitrance. Grasses such as Miscanthus and switchgrass could become major sources of lignocellulose. Barley has potential as a genetically-tractable research model for such novel bioenergy crops and also as a bioenergy crop itself. This thesis concerns the 4CL and the CCR enzymes on the lignin pathway which were chosen as the targets to manipulate lignin in barley. They were selected because there is evidence that suppression of each of them in dicot species can lead to increased saccharification. The 4CL and CCR genes constitute multigene families where members have different expression patterns. RNAi was used to down-regulate 4CL1 and CCR1 using a constitutive promoter via Agrobacterium-mediated transformation of barley. From an extensive screen of the primary transformants for changes in protein level and lignin content, six CCR and four 4CL lines were taken forward for detailed analysis. Antibodies were also raised against barley 4CL and CCR recombinant proteins and these showed substantial reductions in the respective target protein levels in the RNAi lines. Both 4CL and CCR transgenic lines had significant reductions in lignin content, and CCR lines had changes in lignin structure due to changes in the proportions of acid soluble and acid insoluble lignin. No substantial consistent adverse effects on key agronomic traits were apparent in the 4CL and CCR transgenics. Selected 4CL and CCR transgenics had improved saccharification yield after using three different pretreatment methods, which is a desirable feature for biofuel production.
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Kaimoyo, Evans. "Study of the (+)-Pisatin Biosynthetic Pathway by RNAi and Development of a Novel Method to Elicit the Production of Plant Secondary Metabolites." Tucson, Arizona : University of Arizona, 2006. http://etd.library.arizona.edu/etd/GetFileServlet?file=file:///data1/pdf/etd/azu%5Fetd%5F1434%5F1%5Fm.pdf&type=application/pdf.

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Kaimoyo, Evans. "Study of the (+)-Pisatin Biosynthetic Pathway by RNAi and Development of a Novel Method to Elicit the Production of Plant Secondary Metabolites." Diss., The University of Arizona, 2005. http://hdl.handle.net/10150/193608.

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(+)-Pisatin, ([+]-[6aR,11aR]-6a-hydroxy-3-methoxy-8,9-methylenedioxypterocarpan) is the major phytoalexin of the garden pea (Pisum sativum L.). Despite being the first phytoalexin to be chemically characterized, its biosynthesis remains to be fully elucidated. RNA-mediated genetic interference (RNAi) was used to gain further insights into the (+)-pisatin biosynthetic pathway. The expression of three genes, isoflavone reductase (IFR) catalyzing the reduction of 7,2'-dihydroxy-4',5'-methylenedioxyisoflavone to (-)-sophorol, sophorol reductase (SOR) involved in reducing (-)-sophorol to (-)-7,2'-dihydroxy-4',5'-methylenedioxyisoflavanol and hydroxymaackiain-3-O methyltransferase (HMM) involved in methylation of (+)-6a-hydroxymaackiain to (+)-pisatin was silenced. The genes are transcriptionally co-regulated during (+)-pisatin biosynthesis, with the IFR and SOR proposed to function upstream of the HMM gene.Hairy roots expressing the HMM RNAi construct, deficient in (+)-pisatin biosynthesis were identified. However, these did not accumulate (+)-6a-hydroxymaackiain, precursor to (+)-pisatin. Instead they accumulated 2,7,4'-trihydroxyisoflavanone, daidzein, liquiritigenin and isoformononetin. The amino acid sequence of HMM is very similar to that of another methyltransferase, hydroxyisoflavanone-4'-O-methyltransferase (HI4MOT), found in most legumes. HI4?MOT catalyzes the methylation of 2,7,4'-trihydroxyisoflavanone (THI) to 2,7-dihydroxy-4'-methoxyisoflavanone, one of the earliest enzymatic steps in isoflavonoid biosynthesis. In pea, HI4OMT may be the same enzyme as "HMM" catalyzing the methylation of both THI and (+)-6a-hydroxymaackiain. Preventing the methylation of THI could divert pea intermediates to the production of daidzein and isoformononetin instead of (+)-pisatin.None of the transgenic hairy roots expressing the IFR RNAi construct were totally deficient in (+)-pisatin biosynthesis. However, all produced reduced amounts of (+)-pisatin, with one culture accumulating 7,2'-dihydroxy-4',5'-methylenedioxyisoflavone, the substrate for IFR. Hairy roots expressing the SOR RNAi construct deficient in (+)-pisatin biosynthesis were identified. These accumulated (-)-sophorol, the substrate for SOR. These data provide evidence for the involvement of these genes and the intermediates with (-)-optical activity in (+)-pisatin biosynthesis.The elicitation of the biosynthesis of secondary metabolites in plant cell and tissue cultures by electric current was explored. Electric current was demonstrated to elicit the biosynthesis of secondary metabolites in pea hairy and intact roots, seedling, root and cell suspension cultures of various plant species. Electric current has potential for use as an elicitor of secondary metabolites in basic and commercial research ventures.
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Books on the topic "RNAi pathway"

1

Muise, Brandon. Examining caspase mediated apoptotic pathways through RNAi as a means of procaspase downregulation. Sudbury, Ont: Laurentian University, 2006.

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service), ScienceDirect (Online, ed. RNA turnover in eukaryotes: Nucleases, pathways and analysis of mRNA decay. San Diego, Calif: Academic, 2008.

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Kekkonen, Viktoria. Characterization of bacterial RNA and DNA signalling pathways that induce cellular dysfunction. Sudbury, Ont: Laurentian University, 2006.

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Viral Interactions with Host RNA Decay Pathways. MDPI, 2017. http://dx.doi.org/10.3390/books978-3-03842-503-8.

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Rna Turnover In Eukaryotes Analysis Of Specialized And Quality Control Rna Decay Pathways. Academic Press, 2008.

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RNA Turnover in Eukaryotes: Analysis of Specialized and Quality Control RNA Decay Pathways. Elsevier, 2008. http://dx.doi.org/10.1016/s0076-6879(08)x0013-8.

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RNA Turnover in Eukaryotes: Nucleases, Pathways and Analysis of mRNA Decay. Elsevier, 2008. http://dx.doi.org/10.1016/s0076-6879(08)x0014-x.

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D, Smolke Christina, ed. The metabolic pathway engineering handbook: Tools and applications. Boca Raton: CRC Press/Taylor & Francis, 2009.

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Signal Transduction: Pathways, Mechanisms and Diseases. Springer, 2009.

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Gluckman, Sir Peter, Mark Hanson, Chong Yap Seng, and Anne Bardsley. Vitamin B9 (folate) in pregnancy and breastfeeding. Oxford University Press, 2015. http://dx.doi.org/10.1093/med/9780198722700.003.0012.

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Folate is a coenzyme in multiple biochemical pathways involving one-carbon metabolism, including amino acid metabolism, DNA and RNA synthesis, homocysteine metabolism, and methylation of DNA. The most overt consequence of folate deficiency is megaloblastic anaemia caused by the inhibition of DNA synthesis in red blood cell production. Folate deficiency may also influence the ability to maintain DNA methylation patterns in replicating cells, resulting in lasting phenotypic changes. Embryogenesis and fetal growth require higher levels of folate, which must be supplied maternally during pregnancy. A link between low maternal folate levels and the occurrence of neural tube defects has long been recognized. Other effects in pregnancy include increased risks of pre-eclampsia and placental vascular disorders. The general recommendation is for supplementation prior to conception and throughout pregnancy with 400 #amp;#x03BC;g of folic acid in tablet form, in addition to dietary sources, which can reduce the risk of neural tube defects.
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Book chapters on the topic "RNAi pathway"

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Boisvert, Marie-Eve L., and Martin J. Simard. "RNAi Pathway in C. elegans: The Argonautes and Collaborators." In RNA Interference, 21–36. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-75157-1_2.

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Fisher, Katherine H., Stephen Brown, and Martin P. Zeidler. "Designing RNAi Screens to Identify JAK/STAT Pathway Components." In Methods in Molecular Biology, 81–97. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-242-1_6.

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Marois, Eric, and Suzanne Eaton. "RNAi in the Hedgehog Signaling Pathway: pFRiPE, a Vector for Temporally and Spatially Controlled RNAi in Drosophila." In Methods in Molecular Biology, 115–28. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-516-9_10.

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Chen, Xiaochu, and Lan Xu. "Genome-Wide RNAi Screening to Dissect the TGF-β Signal Transduction Pathway." In Methods in Molecular Biology, 365–77. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-2966-5_24.

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Trombly, Melanie I., and Xiaozhong Wang. "A Recessive Genetic Screen for Components of the RNA Interference Pathway in Mouse Embryonic Stem Cells." In RNAi and microRNA-Mediated Gene Regulation in Stem Cells, 45–63. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-769-3_4.

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Tanaka, Yoshikazu, Noriko Nakamura, and Junichi Togami. "Altering Flower Color in Transgenic Plants by RNAi-Mediated Engineering of Flavonoid Biosynthetic Pathway." In Methods in Molecular Biology™, 245–57. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-59745-191-8_17.

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Yang, Jianguo, Jing Shi, Raghavan Venkat, and Kripa Ram. "Functional Analysis of ER Stress Pathway Genes for Apoptosis of NS/0 Cell Line Using RNAi Methods." In Cells and Culture, 447–51. Dordrecht: Springer Netherlands, 2010. http://dx.doi.org/10.1007/978-90-481-3419-9_78.

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Nejepinska, Jana, Matyas Flemr, and Petr Svoboda. "The Canonical RNA Interference Pathway in Animals." In Regulatory RNAs, 111–49. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-662-45801-3_5.

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Arpaia, Salvatore, Olivier Christiaens, Paul Henning Krogh, and Kimberly M. Parker. "Environmental safety assessment of plants expressing RNAi for pest control." In RNAi for plant improvement and protection, 117–30. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789248890.0117.

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Abstract This chapter focuses on the importance of problem formulation (PF) in the environmental risk assessment process, which involves the identification of the possible hazards associated with a stressor, i.e. transgenic RNAi expressing plants or RNAi-based pesticides. The risk hypotheses developed from the PF that can be used to hypothesize pathways to risk and support the design of experimental studies to determine environmental impacts are also discussed.
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Arpaia, Salvatore, Olivier Christiaens, Paul Henning Krogh, and Kimberly M. Parker. "Environmental safety assessment of plants expressing RNAi for pest control." In RNAi for plant improvement and protection, 117–30. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789248890.0012.

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Abstract This chapter focuses on the importance of problem formulation (PF) in the environmental risk assessment process, which involves the identification of the possible hazards associated with a stressor, i.e. transgenic RNAi expressing plants or RNAi-based pesticides. The risk hypotheses developed from the PF that can be used to hypothesize pathways to risk and support the design of experimental studies to determine environmental impacts are also discussed.
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Conference papers on the topic "RNAi pathway"

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Sánchez-Rivera, Francisco J., David M. Feldser, John Doench, Arjun Bhutkar, Corbin E. Meacham, David E. Root, Michael T. Hemann, and Tyler Jacks. "Abstract 2957: Uncovering tumor-specific components of the p53 pathway using mouse models and RNAi." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-2957.

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Papageorgiou, Angela, and Joseph Avruch. "Abstract 292: Identification of new components of the mTOR signaling pathway in pancreatic cancer cells by a genome-wide RNAi screen." In Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/1538-7445.am10-292.

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Jeon, Jun W., Anthony D. Saleh, Shaleeka Cornelius, Sophie Carlson, Scott Martin, Pinar Ormanoglu, Hui Cheng, et al. "Abstract 605: Linkage of NF-κB pathway and mitosis-related molecules using integrated RNAi screening and transcriptomic analysis of head and neck squamous cell carcinoma." In Proceedings: AACR Annual Meeting 2020; April 27-28, 2020 and June 22-24, 2020; Philadelphia, PA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1538-7445.am2020-605.

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Fox, EM, TW Miller, F. Ye, Y. Shyr, and CL Arteaga. "Abstract S3-8: RNAi Screening Identifies the Insulin/Insulin-Like Growth Factor-I Receptor Pathway as a Mechanism of Escape from Hormone Dependence in Estrogen Receptor-Positive Breast Cancer." In Abstracts: Thirty-Third Annual CTRC‐AACR San Antonio Breast Cancer Symposium‐‐ Dec 8‐12, 2010; San Antonio, TX. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/0008-5472.sabcs10-s3-8.

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Ayaz, E. Serdar, and Tolga Can. "Constructing signaling pathways from RNAI data using genetic algorithms." In 2011 6th International Symposium on Health Informatics and Bioinformatics (HIBIT). IEEE, 2011. http://dx.doi.org/10.1109/hibit.2011.6450816.

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Li, Huarong. "Systemic RNAi in western corn rootworm does not involve transitive pathways." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.112159.

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Tanikawa, Chizu, Koji Ueda, Yusuke Nakamura, and Koichi Matsuda. "Abstract 2051: Regulation of RNA processing by PADI4 pathway." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-2051.

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Li, Yuan, and Shaojie Zhang. "Predicting folding pathways between RNA conformational structures guided by RNA stacks." In the 2nd ACM Conference. New York, New York, USA: ACM Press, 2011. http://dx.doi.org/10.1145/2147805.2147832.

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Guo, Sujuan, Kevin Pridham, and Zhi Sheng. "Abstract A04: LINC00467 regulates the autophagy signaling pathway STK11/AMPK." In Abstracts: AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines; December 4-7, 2015; Boston, MA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.nonrna15-a04.

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El-fadl, Rihab, Nasser Rizk, Amena Fadel, and Abdelrahman El Gamal. "The Profile of Hepatic Gene Expression of Glucose Metabolism in Mice on High Fat Diet." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2020. http://dx.doi.org/10.29117/quarfe.2020.0213.

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Obesity is a growing problem worldwide, and recent data indicated that 20% of the populations would be obese. Obesity arises as a multifactorial disease caused by inherited traits that interact with lifestyle factors such as diet and physical activity. The liver plays an essential role in the gluco-regulation via regulating glucose, lipid and protein metabolism. The process of glucose metabolism is controlled by a range of molecular mechanisms and genes which affect the metabolism of the liver during intake of high fat diet (HFD). The objective of this research is to investigate the profile of hepatic gene expression of glucose metabolism in mice on HFD treated with leptin (5 mg/kg BW Ip injection). Ten wild type CD1 mice fed on HFD is used for this study, where groups are control (vehicle - leptin) and test group (vehicle + leptin). Body weight (BW) was measured, and blood chemistry, insulin and leptin were measured at the end of the experiments. Total RNA was isolated from the liver tissue, and RTPCR profiler array technology was used to evaluate the mRNA expression of 84 essential genes of hepatic glucose metabolism. The data of the BW and blood chemistry are not significantly different between the two groups. Leptin treatment enhanced the metabolic pathways and the candidate genes of the different metabolic pathway; glycogen metabolism such as Gys1, Gys2 and Pygm, pentose phosphate shunt such as Rpia and suppressed the glycolysis such as Aldob, and TCA cycle such as Mdh1b. In conclusion, this study has shown that leptin could affect the profile of the hepatic mouse genes of glucose metabolism in the early stages of HFD to induce obesity
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Reports on the topic "RNAi pathway"

1

Guney, Isil. Dissecting Androgen-Dependent and Independent Signaling Pathways Using RNA Interference-Based Functional Genomics in Human Cells. Fort Belvoir, VA: Defense Technical Information Center, June 2008. http://dx.doi.org/10.21236/ada495676.

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Guney, Isil. Dissecting Androgen-Dependent and Independent Signaling Pathways Using RNA Interference-Based Functional Genomics in Human Cells. Fort Belvoir, VA: Defense Technical Information Center, June 2009. http://dx.doi.org/10.21236/ada505263.

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