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https://www.readbyqxmd.com/read/28209198/distribution-and-fate-of-hiv-1-unintegrated-dna-species-a-comprehensive-update
#1
REVIEW
Faysal Bin Hamid, Jinsun Kim, Cha-Gyun Shin
Reverse transcription of viral RNA and the subsequent integration of reverse transcripts are the classical early events of the HIV-1 life-cycle. Simultaneously, abundant unintegrated DNAs (uDNAs), are formed in cells ubiquitously. The uDNAs either undergo recombination or degradation or persist inactively for long periods in the nucleus as future resources. Among them, 2-LTR circles are considered a dead-end for viral spread. Their contribution to the HIV-1 infection is still poorly understood. Nevertheless, the preintegration transcription of the aberrant DNAs and the consequent alterations of cellular factors have already been reported...
February 16, 2017: AIDS Research and Therapy
https://www.readbyqxmd.com/read/28182717/error-baseline-rates-of-five-sample-preparation-methods-used-to-characterize-rna-virus-populations
#2
Jeffrey R Kugelman, Michael R Wiley, Elyse R Nagle, Daniel Reyes, Brad P Pfeffer, Jens H Kuhn, Mariano Sanchez-Lockhart, Gustavo F Palacios
Individual RNA viruses typically occur as populations of genomes that differ slightly from each other due to mutations introduced by the error-prone viral polymerase. Understanding the variability of RNA virus genome populations is critical for understanding virus evolution because individual mutant genomes may gain evolutionary selective advantages and give rise to dominant subpopulations, possibly even leading to the emergence of viruses resistant to medical countermeasures. Reverse transcription of virus genome populations followed by next-generation sequencing is the only available method to characterize variation for RNA viruses...
2017: PloS One
https://www.readbyqxmd.com/read/28142124/quantitative-real-time-monitoring-of-rca-amplification-of-cancer-biomarkers-mediated-by-a-flexible-ion-sensitive-platform
#3
Bruno Veigas, Joana Pinto, Raquel Vinhas, Tomás Calmeiro, Rodrigo Martins, Elvira Fortunato, Pedro Viana Baptista
Ion sensitive field-effect transistors (ISFET) are the basis of radical new sensing approaches. Reliable molecular characterization of specific detection of DNA and/or RNA is vital for disease diagnostics and to follow up alterations in gene expression profiles. Devices and strategies for biomolecular recognition and detection should be developed into reliable and inexpensive platforms. Here, we describe the development of a flexible thin-film sensor for label free gene expression analysis. A charge modulated ISFET based sensor was integrated with real-time DNA/RNA isothermal nucleic acid amplification: Loop-mediated isothermal amplification (LAMP) and Rolling Circle Amplification (RCA) techniques for c-MYC and BCR-ABL1 genes, allowing for the real-time quantification of template...
January 24, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28127202/tracing-overlapping-biological-signals-in-mid-infrared-using-colonic-tissues-as-a-model-system
#4
Ranjit Kumar Sahu, Ahmad Salman, Shaul Mordechai
AIM: To understand the interference of carbohydrates absorbance in nucleic acids signals during diagnosis of malignancy using Fourier transform infrared (FTIR) spectroscopy. METHODS: We used formalin fixed paraffin embedded colonic tissues to obtain infrared (IR) spectra in the mid IR region using a bruker II IR microscope with a facility for varying the measurement area by varying the aperture available. Following this procedure we could measure different regions of the crypt circles containing different biochemicals...
January 14, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28119336/large-scale-analysis-of-branchpoint-usage-across-species-and-cell-lines
#5
Allison J Taggart, Chien-Ling Lin, Barsha Shrestha, Claire Heintzelman, Seongwon Kim, William G Fairbrother
The coding sequence of each human pre-mRNA is interrupted, on average, by eleven introns that must be spliced out for proper gene expression. Each intron contains three obligate signals: a 5' splice site, a branch site and a 3' splice site. Splice site usage has been mapped exhaustively across different species, cell types and cellular states. In contrast, only a small fraction of branch sites have been identified even once. The few reported annotations of branch site are imprecise as reverse transcriptase skips several nucleotides while traversing a 2-5 linkage...
January 24, 2017: Genome Research
https://www.readbyqxmd.com/read/28117799/visualization-of-protein-protein-interaction-in-nuclear-and-cytoplasmic-fractions-by-co-immunoprecipitation-and-in-situ-proximity-ligation-assay
#6
Xinzhou Zhu, Andrea Zelmer, Sven Wellmann
Protein-protein interactions are involved in thousands of cellular processes and occur in distinct spatial context. Traditionally, co-immunoprecipitation is a popular technique to detect protein-protein interactions. Subsequent Western blot analysis is the most common method to visualize co-immunoprecipitated proteins. Recently, the proximity ligation assay has become a powerful tool to visualize protein-protein interactions in situ and provides the possibility to quantify protein-protein interactions by this method...
January 16, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28086788/comprehensive-circrna-expression-profile-and-selection-of-key-circrnas-during-priming-phase-of-rat-liver-regeneration
#7
Lifei Li, Jianlin Guo, Yanhui Chen, Cuifang Chang, Cunshuan Xu
BACKGROUND: Rat liver regeneration (LR) proceeds along a process of highly organized and ordered tissue growth in response to the loss or injury of liver tissue, during which many physiological processes may play important roles. The molecular mechanism of hepatocyte proliferation, energy metabolism and substance metabolism during rat LR had been elucidated. Further, the correlation of circular RNA (circRNA) abundance with proliferation has recently been clarified. However, the regulatory capacity of circRNA in rat LR remains a fascinating topic...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28027000/viroid-quasispecies-revealed-by-deep-sequencing
#8
Joseph R J Brass, Robert A Owens, Jaroslav Matoušek, Gerhard Steger
Viroids are non-coding single-stranded circular RNA molecules that replicate autonomously in infected host plants causing mild to lethal symptoms. Their genomes contain about 250-400 nucleotides, depending on viroid species. Members of the family Pospiviroidae, like the Potato spindle tuber viroid (PSTVd), replicate via an asymmetric rolling-circle mechanism using the host DNA-dependent RNA-Polymerase II in the nucleus, while members of Avsunviroidae are replicated in a symmetric rolling-circle mechanism probably by the nuclear-encoded polymerase in chloroplasts...
December 27, 2016: RNA Biology
https://www.readbyqxmd.com/read/27974620/will-the-circle-be-unbroken-specific-mutations-in-the-yeast-sm-protein-ring-expose-a-requirement-for-assembly-factor-brr1-a-homolog-of-gemin2
#9
Beate Schwer, Allen J Roth, Stewart Shuman
A seven-subunit Sm protein ring assembles around specific U-rich RNA segments of the U1, U2, U4, and U5 snRNPs that direct pre-mRNA splicing. Using human snRNP crystal structures to guide mutagenesis in Saccharomyces cerevisiae, we gained new insights to structure-function relationships of the SmD1 and SmD2 subunits. Of sixteen conserved amino acids comprising their RNA-binding sites or inter-subunit interfaces, only Arg88 in SmD1 and Arg97 in SmD2 were essential for growth. Tests for genetic interactions with non-Sm splicing factors identified benign mutations of SmD1 (N37A, R88K, R93A) and SmD2 (R49A, N66A, R97K, D99A) that were synthetically lethal with null alleles of U2 snRNP subunits Lea1 and/or Msl1...
December 14, 2016: RNA
https://www.readbyqxmd.com/read/27915180/self-primed-isothermal-amplification-for-genomic-dna-detection-of-human-papillomavirus
#10
Wei Lu, Qingpan Yuan, Zhiliu Yang, Bo Yao
Rolling circle amplification (RCA) is an isothermal amplification technique with high efficiency and perfect accuracy for nucleic acids detection. However, RCA technique suffers the limitation to detect short DNA or RNA molecules. For long nucleic acid molecules, enzymatic restriction as well as heat denaturation process is usually required, which makes the amplification not effective and strictly isothermal. In this article, a simple and efficient one-pot self-primed isothermal amplification (SIA) was developed for detection of genomic DNA directly based on the combination of nicking endonuclease assisted strand displacement amplification (SDA) and exponential RCA...
April 15, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27910923/protein-expression-from-unintegrated-hiv-1-dna-introduces-bias-in-primary-in-vitro-post-integration-latency-models
#11
Pawel Bonczkowski, Marie-Angélique De Scheerder, Eva Malatinkova, Alexandra Borch, Zora Melkova, Renate Koenig, Ward De Spiegelaere, Linos Vandekerckhove
To understand the persistence of latently HIV-1 infected cells in virally suppressed infected patients, a number of in vitro models of HIV latency have been developed. In an attempt to mimic the in vivo situation as closely as possible, several models use primary cells and replication-competent viruses in combination with antiretroviral compounds to prevent ongoing replication. Latency is subsequently measured by HIV RNA and/or protein production after cellular activation. To discriminate between pre- and post-integration latency, integrase inhibitors are routinely used, preventing novel integrations upon cellular activation...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27899638/structure-and-folding-of-the-tetrahymena-telomerase-rna-pseudoknot
#12
Darian D Cash, Juli Feigon
Telomerase maintains telomere length at the ends of linear chromosomes using an integral telomerase RNA (TER) and telomerase reverse transcriptase (TERT). An essential part of TER is the template/pseudoknot domain (t/PK) which includes the template, for adding telomeric repeats, template boundary element (TBE), and pseudoknot, enclosed in a circle by stem 1. The Tetrahymena telomerase holoenzyme catalytic core (p65-TER-TERT) was recently modeled in our 9 Å resolution cryo-electron microscopy map by fitting protein and TER domains, including a solution NMR structure of the Tetrahymena pseudoknot...
January 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27883258/bivalent-display-of-dicysteine-on-peptide-nucleic-acids-for-homogenous-dna-rna-detection-through-in-situ-fluorescence-labelling
#13
Ge-Min Fang, Oliver Seitz
Fluorogenic probes that signal the presence of specific DNA or RNA sequences are key enabling tools for molecular disease diagnosis and imaging studies. Usually, at least one fluorophore is attached through covalent bonding to an oligonucleotide probe. However, the additional conjugation step increases costs. Here we introduce a method that avoids the requirement for the preparation of fluorescence-labelled oligonucleotides and provides the opportunity to alter the fluorogenic reporter dye without resynthesis...
January 17, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27822856/in-situ-single-molecule-rna-genotyping-using-padlock-probes-and-rolling-circle-amplification
#14
Tomasz Krzywkowski, Thomas Hauling, Mats Nilsson
Present-day techniques allow for massively parallel and high-throughput characterization of the somatic mutation status of samples. Most of these assays rely on whole specimen extracts, where heterogeneous spatial context of the specimen is lost. This chapter describes an up-to-date protocol for multiplexed, in situ genotyping of RNA in preserved tissue and cell lines, using padlock probes and rolling circle amplification. The presented approach allows for automated quantification of mRNA expression and mutation status, in single cells or in designated specimen areas...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27809244/accumulation-of-stable-full-length-circular-group-i-intron-rnas-during-heat-shock
#15
Kasper L Andersen, Bertrand Beckert, Benoit Masquida, Steinar D Johansen, Henrik Nielsen
Group I introns in nuclear ribosomal RNA of eukaryotic microorganisms are processed by splicing or circularization. The latter results in formation of full-length circular introns without ligation of the exons and has been proposed to be active in intron mobility. We applied qRT-PCR to estimate the copy number of circular intron RNA from the myxomycete Didymium iridis. In exponentially growing amoebae, the circular introns are nuclear and found in 70 copies per cell. During heat-shock, the circular form is up-regulated to more than 500 copies per cell...
October 31, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/27797171/the-discovery-of-rolling-circle-amplification-and-rolling-circle-transcription
#16
Michael G Mohsen, Eric T Kool
Nucleic acid amplification is a hugely important technology for biology and medicine. While the polymerase chain reaction (PCR) has been highly useful and effective, its reliance on heating and cooling cycles places some constraints on its utility. For example, the heating step of PCR can destroy biological molecules under investigation and heat/cool cycles are not applicable in living systems. Thus, isothermal approaches to DNA and RNA amplification are under widespread study. Perhaps the simplest of these are the rolling circle approaches, including rolling circle amplification (RCA) and rolling circle transcription (RCT)...
November 15, 2016: Accounts of Chemical Research
https://www.readbyqxmd.com/read/27761361/paradoxical-delay-of-senescence-upon-depletion-of-brca2-in-telomerase-deficient-worms
#17
Mi-Sun Kwon, Jaewon Min, Hee-Yeon Jeon, Kwangwoo Hwang, Chuna Kim, Junho Lee, Je-Gun Joung, Woong-Yang Park, Hyunsook Lee
BRCA2 is a multifunctional tumor suppressor involved in homologous recombination (HR), mitotic checkpoint regulation, and telomere homeostasis. Absence of Brca2 in mice results in progressive shortening of telomeres and senescence, yet cells are prone to neoplastic transformation with elongated telomeres, suggesting that BRCA2 has positive and negative effects on telomere length regulation along the path to tumorigenesis. Using Caenorhabditis elegans as a model, we show here that depletion of BRC-2, an ortholog of BRCA2, paradoxically delays senescence in telomerase-deficient mutant worms...
October 2016: FEBS Open Bio
https://www.readbyqxmd.com/read/27737936/titin-forms-circles-regulation-by-heart-failure-and-the-rna-binding-protein-rbm20
#18
Nicolas Jaé, Stefanie Dimmeler
No abstract text is available yet for this article.
October 14, 2016: Circulation Research
https://www.readbyqxmd.com/read/27732664/combined-activity-of-dcl2-and-dcl3-is-crucial-in-the-defense-against-potato-spindle-tuber-viroid
#19
Konstantina Katsarou, Eleni Mavrothalassiti, Wannes Dermauw, Thomas Van Leeuwen, Kriton Kalantidis
Viroids are self replicating non-coding RNAs capable of infecting a wide range of plant hosts. They do not encode any proteins, thus the mechanism by which they escape plant defenses remains unclear. RNAi silencing is a major defense mechanism against virus infections, with the four DCL proteins being principal components of the pathway. We have used Nicotiana benthamiana as a model to study Potato spindle tuber viroid infection. This viroid is a member of the Pospiviroidae family and replicates in the nucleus via an asymmetric rolling circle mechanism...
October 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27713731/genome-based-genetic-tool-development-for-bacillus-methanolicus-theta-and-rolling-circle-replicating-plasmids-for-inducible-gene-expression-and-application-to-methanol-based-cadaverine-production
#20
Marta Irla, Tonje M B Heggeset, Ingemar Nærdal, Lidia Paul, Tone Haugen, Simone B Le, Trygve Brautaset, Volker F Wendisch
Bacillus methanolicus is a thermophilic methylotroph able to overproduce amino acids from methanol, a substrate not used for human or animal nutrition. Based on our previous RNA-seq analysis a mannitol inducible promoter and a putative mannitol activator gene mtlR were identified. The mannitol inducible promoter was applied for controlled gene expression using fluorescent reporter proteins and a flow cytometry analysis, and improved by changing the -35 promoter region and by co-expression of the mtlR regulator gene...
2016: Frontiers in Microbiology
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