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https://www.readbyqxmd.com/read/28635587/ictv-virus-taxonomy-profile-ophioviridae
#1
María Laura García, Elena Dal Bó, John V da Graça, Selma Gago-Zachert, John Hammond, Pedro Moreno, Tomohide Natsuaki, Vicente Pallás, Jose A Navarro, Carina A Reyes, Gabriel Robles Luna, Takahide Sasaya, Ioannis E Tzanetakis, Anna María Vaira, Martin Verbeek, Ictv Report Consortium
The Ophioviridae is a family of filamentous plant viruses, with single-stranded negative, and possibly ambisense, RNA genomes of 11.3-12.5 kb divided into 3-4 segments, each encapsidated separately. Virions are naked filamentous nucleocapsids, forming kinked circles of at least two different contour lengths. The sole genus, Ophiovirus, includes seven species. Four ophioviruses are soil-transmitted and their natural hosts include trees, shrubs, vegetables and bulbous or corm-forming ornamentals, both monocots and dicots...
June 21, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28622300/the-als-linked-e102q-mutation-in-sigma-receptor-1-leads-to-er-stress-mediated-defects-in-protein-homeostasis-and-dysregulation-of-rna-binding-proteins
#2
Alice Dreser, Jan Tilmann Vollrath, Antonio Sechi, Sonja Johann, Andreas Roos, Alfred Yamoah, Istvan Katona, Saeed Bohlega, Dominik Wiemuth, Yuemin Tian, Axel Schmidt, Jörg Vervoorts, Marc Dohmen, Cordian Beyer, Jasper Anink, Eleonora Aronica, Dirk Troost, Joachim Weis, Anand Goswami
Amyotrophic lateral sclerosis (ALS) is characterized by the selective degeneration of motor neurons (MNs) and their target muscles. Misfolded proteins which often form intracellular aggregates are a pathological hallmark of ALS. Disruption of the functional interplay between protein degradation (ubiquitin proteasome system and autophagy) and RNA-binding protein homeostasis has recently been suggested as an integrated model that merges several ALS-associated proteins into a common pathophysiological pathway...
June 16, 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28580104/highly-specific-imaging-of-mrna-in-single-cells-by-target-rna-initiated-rolling-circle-amplification
#3
Ruijie Deng, Kaixiang Zhang, Yupeng Sun, Xiaojun Ren, Jinghong Li
Detection of single-cell gene expression with high spatial and sequence resolution is a key challenge in single cell biology. Herein, we propose a robust method for the direct detection of mRNA, termed target RNA-initiated rolling circle amplification, which enables imaging of mRNA with single-nucleotide and near-single-molecule resolution in single cells. By utilizing a Splint R ligase capable of efficiently catalyzing the ligation of a padlock probe by the target RNA, the method can enable the efficient detection of mRNA without reverse transcription (detection efficiency over 20%)...
May 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28575409/giant-reverse-transcriptase-encoding-transposable-elements-at-telomeres
#4
Irina R Arkhipova, Irina A Yushenova, Fernando Rodriguez
Transposable elements are omnipresent in eukaryotic genomes and have a profound impact on chromosome structure, function and evolution. Their structural and functional diversity is thought to be reasonably well-understood, especially in retroelements, which transpose via an RNA intermediate copied into cDNA by the element-encoded reverse transcriptase, and are characterized by a compact structure. Here we report a novel type of expandable eukaryotic retroelements, which we call Terminons. These elements can attach to G-rich telomeric repeat overhangs at the chromosome ends, in a process apparently facilitated by complementary C-rich repeats at the 3'-end of the RNA template immediately adjacent to a hammerhead ribozyme motif...
May 30, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28525572/crosstalk-between-vertical-and-horizontal-gene-transfer-plasmid-replication-control-by-a-conjugative-relaxase
#5
Fabián Lorenzo-Díaz, Cris Fernández-López, Rudi Lurz, Alicia Bravo, Manuel Espinosa
Horizontal gene transfer is a key process in the evolution of bacteria and also represents a source of genetic variation in eukaryotes. Among elements participating in gene transfer, thousands of small (<10 kb) mobile bacterial plasmids that replicate by the rolling circle mechanism represent a driving force in the spread of antibiotic resistances. In general, these plasmids are built as genetic modules that encode a replicase, an antibiotic-resistance determinant, and a relaxase that participates in their conjugative mobilization...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28453847/human-immunodeficiency-virus-persistence-and-t-cell-activation-in-blood-rectal-and-lymph-node-tissue-in-human-immunodeficiency-virus-infected-individuals-receiving-suppressive-antiretroviral-therapy
#6
Gabriela Khoury, Rémi Fromentin, Ajantha Solomon, Wendy Hartogensis, Marisela Killian, Rebecca Hoh, Ma Somsouk, Peter W Hunt, Valerie Girling, Elizabeth Sinclair, Peter Bacchetti, Jenny L Anderson, Frederick M Hecht, Steven G Deeks, Paul U Cameron, Nicolas Chomont, Sharon R Lewin
Background.: Immune activation and inflammation remain elevated in human immunodeficiency virus (HIV)-infected individuals receiving antiretroviral therapy (ART) and may contribute to HIV persistence. Methods.: Using flow cytometry expression of CD38, HLA-DR and PD-1 were measured in blood (n = 48), lymph node (LN; n = 9), and rectal tissue (n = 17) from virally suppressed individuals. Total and integrated HIV DNA, 2-LTR circles, and cell-associated unspliced HIV RNA were quantified...
March 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28398700/differential-requirements-for-dna-repair-proteins-in-immortalized-cell-lines-using-alternative-lengthening-of-telomere-mechanisms
#7
Alaina R Martinez, Zeenia Kaul, Jeffrey D Parvin, Joanna Groden
Cancer cells require telomere maintenance to enable uncontrolled growth. Most often telomerase is activated, although a subset of human cancers are telomerase-negative and depend on recombination-based mechanisms known as ALT (Alternative Lengthening of Telomeres). ALT depends on proteins that are essential for homologous recombination, including BLM and the MRN complex, to extend telomeres. This study surveyed the requirement for requisite homologous recombination proteins, yet to be studied in human ALT cell lines, by protein depletion using RNA interference...
April 11, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28396678/identification-of-circular-rnas-in-kiwifruit-and-their-species-specific-response-to-bacterial-canker-pathogen-invasion
#8
Zupeng Wang, Yifei Liu, Dawei Li, Li Li, Qiong Zhang, Shuaibin Wang, Hongwen Huang
Research studies have recently focused on circle RNAs (circRNAs) in relation to their regulatory functions in animals. However, the systematic identification of circRNAs in plants, especially non-model plants, is limited. In addition, raw report on the prediction of the potential role of circRNAs in plant response to pathogen invasion is currently available. We conducted the systematic identification of circRNAs from four materials originating from three species belonging to genus Actinidia under different situations using ribosomal RNA (rRNA) depleted RNA-Seq data...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28388404/drosophilosophical-re-thinking-adaptive-immunity-in-the-fly
#9
Cara West, Neal Silverman
For decades, flies have been a model for innate immunity. In this issue of Cell, Tassetto et al. describe a mechanism for antiviral RNAi spreading that parallels mammalian adaptive immunity through reverse-transcribed vDNA circles and the systemic dissemination of small-RNA-containing exosomes.
April 6, 2017: Cell
https://www.readbyqxmd.com/read/28373128/rolling-circle-transcription-based-polymeric-sirna-nanoparticles-for-tumor-targeted-delivery
#10
Jae Hyeop Lee, Sook Hee Ku, Min Ju Kim, So Jin Lee, Hyun Cheol Kim, Kwangmeyung Kim, Sun Hwa Kim, Ick Chan Kwon
RNA, one of the major biological macromolecules, has been considered as an attractive building material for bottom-up fabrication of nanostructures in the past few decades due to advancements in RNA biology, RNA chemistry and RNA nanotechnology. Most recently, an isothermal enzymatic nucleic acid amplification method termed rolling circle transcription (RCT), which achieves a large-scale synthesis of RNA nanostructures, has emerged as one of fascinating techniques for RNAi-based therapies. Herein, we proposed a newly designed RCT method for synthesis of polymeric siRNA nanoflower, referred to 'RCT and annealing-generated polymeric siRNA (RAPSI)': (1) Amplification of the antisense strand of siRNA via RCT process and (2) annealing of chimeric sense strand containing 3'-terminal DNA nucleotides that provide enzyme cleavage sites...
March 31, 2017: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/28370773/a-dnazyme-feedback-amplification-strategy-for-biosensing
#11
Meng Liu, Qiang Zhang, Dingran Chang, Jimmy Gu, John D Brennan, Yingfu Li
We report a signal amplification strategy termed DNAzyme feedback amplification (DFA) that takes advantage of rolling-circle amplification (RCA) and an RNA-cleaving DNAzyme (RCD). DFA employs two specially programmed DNA complexes, one composed of a primer and a circular template containing the antisense sequence of an RCD, and the other composed of the same circular template and an RNA-containing substrate for the RCD. RCA is initiated at the first complex to produce RCD elements that go on to cleave the substrate in the second complex...
March 28, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28361879/synthesizing-topological-structures-containing-rna
#12
Di Liu, Yaming Shao, Gang Chen, Yuk-Ching Tse-Dinh, Joseph A Piccirilli, Yossi Weizmann
Though knotting and entanglement have been observed in DNA and proteins, their existence in RNA remains an enigma. Synthetic RNA topological structures are significant for understanding the physical and biological properties pertaining to RNA topology, and these properties in turn could facilitate identifying naturally occurring topologically nontrivial RNA molecules. Here we show that topological structures containing single-stranded RNA (ssRNA) free of strong base pairing interactions can be created either by configuring RNA-DNA hybrid four-way junctions or by template-directed synthesis with a single-stranded DNA (ssDNA) topological structure...
March 31, 2017: Nature Communications
https://www.readbyqxmd.com/read/28279183/circles-reshaping-the-rna-world-from-waste-to-treasure
#13
REVIEW
Jing Liu, Tian Liu, Xiaman Wang, Aili He
A new type of RNAs was identified from genes traditionally thought to express messenger or linear ncRNA (noncoding RNA) only. They were subsequently named as circRNAs (circular RNAs) due to the covalently closed structure. Accumulating studies were performed to explore the expression profile of circRNAs in different cell types and diseases, the outcomes totally changed our view of ncRNAs, which was thought to be junk by-products in the process of gene transcription, and enriched our poor understanding of its underlying functions...
March 9, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28209198/distribution-and-fate-of-hiv-1-unintegrated-dna-species-a-comprehensive-update
#14
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
#15
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
#16
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...
May 15, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28127202/tracing-overlapping-biological-signals-in-mid-infrared-using-colonic-tissues-as-a-model-system
#17
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
#18
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 11 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...
April 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
#19
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
#20
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
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