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You searched for: Subject RNA Remove constraint Subject: RNA
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1. 2-Oxopurine Riboside: A Dual Fluorescent Analog and Photosensitizer for RNA/DNA Research

Author:
Naishka E. Caldero-Rodríguez; Enrique M. Arpa; Diego J. Cárdenas; Lara Martínez-Fernández; Steffen Jockusch; Sourav Kanti Seth; Inés Corral; Carlos E. Crespo-Hernández
Source:
Journal of physical chemistry 2022 v.126 no.24 pp. 4483-4490
ISSN:
1520-5207
Subject:
DNA; RNA; absorption; aqueous solutions; fluorescence; nucleosides; photolysis; photosensitizing agents; quantum mechanics; singlet oxygen; solvents
Abstract:
... There is significant interest in developing suitable nucleoside analogs exhibiting high fluorescence and triplet yields to investigate the structure, dynamics, and binding properties of nucleic acids and promote selective photosensitized damage to DNA/RNA, respectively. In this study, steady-state, laser flash photolysis, time-resolved IR luminescence, and femtosecond broad-band transient absorpti ...
DOI:
10.1021/acs.jpcb.2c01113

2. A CRISPR-based nucleic acid detection method for severe fever with thrombocytopenia syndrome virus

Author:
Yansong Zhang; Xuanyang Bai; Jinhui Li; Jing Xie; Huan Li; Lang Yang; Peihan Li; Peng Li; Hao Dong; Qichao Chen; Xinyan Hu; Yun Wang; Tingting Jiang; Hongbin Song; Leili Jia; Lizhong Li
Source:
Virus research 2022 v.311 pp. 198691
ISSN:
0168-1702
Subject:
Huaiyangshan banyangvirus; RNA; aerosols; detection limit; equipment; fever; fluorescence; genome; immunoaffinity chromatography; mortality; research; thrombocytopenia; viruses; Asia
Abstract:
... Fever with thrombocytopenia syndrome virus (SFTS) is a tick-borne infection now known to spread among humans as an aerosol, which has resulted in several outbreaks across Asia over the past decade. As mortality is substantial, it is vital to establish a rapid, on-site nucleic acid detection method for diagnosis. Here we describe such a method for SFTSV (Dabie bandavirus) based on CRISPR-Cas13a. Sp ...
DOI:
10.1016/j.virusres.2022.198691

3. A CRISPR/dCas9-based transcription activated system developed in marine microalga Nannochloropsis oceanica

Author:
Li Wei; Zhouyi Jiang; Bingqing Liu
Source:
Aquaculture 2022 v.546 pp. 737064
ISSN:
0044-8486
Subject:
DNA; Nannochloropsis; RNA; RNA interference; aquaculture; carbon dioxide; feeds; gene overexpression; genes; methylation; methyltransferases; microalgae; photosynthesis; transactivators; transcription (genetics); transcriptional activation
Abstract:
... Nannochloropsis is one of the most important microalgae utilized as the feedstuff in aquaculture and is emerging model oleaginous microalgae. Recently, different genetic tools such as RNA interference, gene overexpression and gene editing have been developed in Nannochloropsis. However, the available genetic modification methods based on CRISPR technology are rather limited for modulating gene exp ...
DOI:
10.1016/j.aquaculture.2021.737064

4. A Comparative Analysis of Metabolic Profiles of Embryonic Skeletal Muscle from Lantang and Landrace Pigs

Author:
Shufang Cai; Tianqi Duo; Xiaoyu Wang; Xian Tong; Chenglong Luo; Yaosheng Chen; Jianhao Li; Delin Mo
Source:
Animals 2022 v.12 no.4 pp. -
ISSN:
2076-2615
Subject:
DNA; NADP-glucose-6-phosphate dehydrogenase; RNA; cell proliferation; energy; energy metabolism; enzyme activity; landraces; longissimus muscle; malate dehydrogenase; metabolites; metabolomics; muscle development; pentose phosphate cycle; pork; pork quality; pyruvate dehydrogenase (lipoamide); skeletal muscle; succinate dehydrogenase (quinone); swine; tricarboxylic acid cycle
Abstract:
... Elucidation of the complex regulation of porcine muscle development is key to increasing pork output and improving pork quality. However, the molecular mechanisms involved in early porcine embryonic muscle development in different pig breeds remain largely unknown. Here, GC–MS based metabolomics and metabolomic profiling was used to examine the longissimus lumborum (LL) of the Lantang (LT) and the ...
DOI:
10.3390/ani12040420

5. A Direct Assay for Measuring the Activity and Inhibition of Coactivator-Associated Arginine Methyltransferase 1

Author:
Yurui Zhang; Matthijs J. van Haren; Nils Marechal; Nathalie Troffer-Charlier; Vincent Cura; Jean Cavarelli; Nathaniel I. Martin
Source:
Biochemistry 2022 v.61 no.11 pp. 1055-1063
ISSN:
1520-4995
Subject:
RNA; S-adenosylmethionine; arginine; carcinogenesis; genes; histones; liquid chromatography; methylation; peptides; protein arginine methyltransferases; tandem mass spectrometry; therapeutics
Abstract:
... Coactivator-associated arginine methyltransferase 1 (CARM1) is a member of the family of protein arginine methyltransferases. CARM1 catalyzes methyl group transfer from the cofactor S-adenosyl-l-methionine (AdoMet) to both histone and nonhistone protein substrates. CARM1 is involved in a range of cellular processes, mainly involving RNA transcription and gene regulation. As the aberrant expression ...
DOI:
10.1021/acs.biochem.2c00075

6. A Novel Flavi-like Virus in Alfalfa (Medicago sativa L.) Crops along the Snake River Valley

Author:
Jennifer Dahan; Yuri I. Wolf; Gardenia E. Orellana; Erik J. Wenninger; Eugene V. Koonin; Alexander V. Karasev
Source:
Viruses 2022 v.14 no.6 pp. -
ISSN:
1999-4915
Subject:
Alfalfa mosaic virus; Alphapartitivirus; Amalgavirus; Bean leafroll virus; Deltapartitivirus; Frankliniella occidentalis; Medicago sativa; Pegivirus; RNA; RNA-directed RNA polymerase; alfalfa; cattle; forage crops; genome; host plants; phylogeny; polyproteins; river valleys; serine proteinases; virus transmission; viruses; Idaho; Snake River
Abstract:
... Alfalfa is an important perennial forage crop in Idaho supporting dairy and cattle industries that is typically grown in the same field for as many as 4 years. Alfalfa stands of different ages were subjected to screening for viruses using high-throughput sequencing and RT-PCR. The two most common viruses found were alfalfa mosaic virus and bean leafroll virus, along with Medicago sativa amalgaviru ...
DOI:
10.3390/v14061320

7. A Reduced Starch Level in Plants at Early Stages of Infection by Viruses Can Be Considered a Broad-Range Indicator of Virus Presence

Author:
Wanying Zhao; Li Wang; Meizi Liu; Dong Zhang; Ida Bagus Andika; Ying Zhu; Liying Sun
Source:
Viruses 2022 v.14 no.6 pp. -
ISSN:
1999-4915
Subject:
Cucumber mosaic virus; DNA; Geminiviridae; Nicotiana benthamiana; Potato virus Y; RNA; Tobacco mosaic virus; apples; biosynthesis; potatoes; starch; transcription (genetics); viruses
Abstract:
... The diagnosis of virus infection can facilitate the effective control of plant viral diseases. To date, serological and molecular methods for the detection of virus infection have been widely used, but these methods have disadvantages if applied for broad-range and large-scale detection. Here, we investigated the effect of infection of several different plant RNA and DNA viruses such as cucumber m ...
DOI:
10.3390/v14061176

8. A Single Amino Acid Substitution in RFC4 Leads to Endoduplication and Compromised Resistance to DNA Damage in Arabidopsis thaliana

Author:
Kan Cui; Lei Qin; Xianyu Tang; Jieying Nong; Jin Chen; Nan Wu; Xin Gong; Lixiong Yi; Chenghuizi Yang; Shitou Xia
Source:
Genes 2022 v.13 no.6 pp. -
ISSN:
2073-4425
Subject:
Arabidopsis thaliana; DNA; DNA damage; DNA repair; RNA; adenosinetriphosphatase; amino acid substitution; cell cycle; cell proliferation; dwarfing; genomics; genotoxicity; homozygosity; mutagens; mutants; phenotype; site-directed mutagenesis
Abstract:
... Replication factor C (RFC) is a heteropentameric ATPase associated with the diverse cellular activities (AAA+ATPase) protein complex, which is composed of one large subunit, known as RFC1, and four small subunits, RFC2/3/4/5. Among them, RFC1 and RFC3 were previously reported to mediate genomic stability and resistance to pathogens in Arabidopsis. Here, we generated a viable rfc4e (rfc4−1/RFC4ᴳ⁵⁴ᴱ ...
DOI:
10.3390/genes13061037

9. A Test and Refinement of Folding Free Energy Nearest Neighbor Parameters for RNA Including N6-Methyladenosine

Author:
Marta Szabat; Martina Prochota; Ryszard Kierzek; Elzbieta Kierzek; David H. Mathews
Source:
Journal of molecular biology 2022 pp. 167632
ISSN:
0022-2836
Subject:
Gibbs free energy; RNA; models; molecular biology; nucleotides; prediction
Abstract:
... RNA folding free energy change parameters are widely used to predict RNA secondary structure and to design RNA sequences. These parameters include terms for the folding free energies of helices and loops. Although the full set of parameters has only been traditionally available for the four common bases and backbone, it is well known that covalent modifications of nucleotides are widespread in nat ...
DOI:
10.1016/j.jmb.2022.167632

10. A brief review of RNA modification related database resources

Author:
Jiani Ma; Lin Zhang; Shutao Chen; Hui Liu
Source:
Methods 2022 v.203 pp. 342-353
ISSN:
1046-2023
Subject:
RNA; biosynthesis; databases; pathogenesis; ribonucleotides
Abstract:
... To date, over 150 different RNA modifications have been identified, playing crucial roles in biological processes and disease pathogenesis. Thanks to the advancement of high-throughput sequencing technologies employed for transcriptome-wide mapping, a bunch of RNA modification databases have emerged as an exciting area, which promotes further investigation of the mechanisms and functions of these ...
DOI:
10.1016/j.ymeth.2021.03.003

11. A chromosome‐anchored genome assembly for Lake Trout (Salvelinus namaycush)

Author:
Seth R. Smith; Eric Normandeau; Haig Djambazian; Pubudu M. Nawarathna; Pierre Berube; Andrew M. Muir; Jiannis Ragoussis; Chantelle M. Penney; Kim T. Scribner; Gordon Luikart; Chris C. Wilson; Louis Bernatchez
Source:
Molecular ecology resources 2022 v.22 no.2 pp. 679-694
ISSN:
1755-098X
Subject:
DNA; Esox lucius; RNA; Salvelinus namaycush; autotetraploidy; chromosome mapping; data collection; doubled haploids; ecology; females; genome assembly; genomics; liver; mitochondrial genome; models; population genetics; pseudogenes
Abstract:
... Here, we present an annotated, chromosome‐anchored, genome assembly for Lake Trout (Salvelinus namaycush) – a highly diverse salmonid species of notable conservation concern and an excellent model for research on adaptation and speciation. We leveraged Pacific Biosciences long‐read sequencing, paired‐end Illumina sequencing, proximity ligation (Hi‐C) sequencing, and a previously published linkage ...
DOI:
10.1111/1755-0998.13483

12. A comparative transcriptomic analysis of glucagon-like peptide-1 receptor- and glucose-dependent insulinotropic polypeptide receptor-expressing cells in the hypothalamus

Author:
Christopher Smith; Ryan Patterson-Cross; Orla Woodward; Jo Lewis; Davide Chiarugi; Florian Merkle; Fiona Gribble; Frank Reimann; Alice Adriaenssens
Source:
Appetite 2022 v.174 pp. 106022
ISSN:
0195-6663
Subject:
RNA; appetite; astrocytes; bioinformatics; body weight; energy balance; fluorescence; gastric inhibitory polypeptide; glucagon-like peptide 1; humans; hypothalamus; mice; neurons; oligodendroglia; pharmacology; secretin; smooth muscle; surveys; synergism; transcriptomics; weight loss
Abstract:
... The hypothalamus is a key region of the brain implicated in homeostatic regulation, and is an integral centre for the control of feeding behaviour. Glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP) are incretin hormones with potent glucoregulatory function through engagement of their respective cognate receptors, GLP-1R and GIPR. Recent evidence indicates that ...
DOI:
10.1016/j.appet.2022.106022

13. A comparison of total RNA extraction methods for RT-PCR based differential expression of genes from Trichoderma atrobrunneum

Author:
Sobia Mushtaq; Asima Tayyeb; Firdaus-e-Bareen
Source:
Journal of microbiological methods 2022 pp. 106535
ISSN:
0167-7012
Subject:
RNA; Trichoderma; agar gel electrophoresis; biofertilizers; biological control; bioremediation; cetyltrimethylammonium bromide; enzymes; gene expression regulation; polyvinylpyrrolidone; qualitative analysis; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; sodium dodecyl sulfate; spectroscopy; ubiquitin
Abstract:
... The genus Trichoderma is ubiquitous in various niches and is currently used for biocontrol, biofertilizer, enzyme production and bioremediation. However, molecular mechanisms underlying its diverse biological functions are yet not fully elucidated. Extraction of high-quality RNA for downstream applications such as quantitative polymerase chain reaction is a prerequisite. The current study aims to ...
DOI:
10.1016/j.mimet.2022.106535

14. A fungal microRNA‐like RNA subverts host immunity and facilitates pathogen infection by silencing two host receptor‐like kinase genes

Author:
Ming Xu; Guangyao Li; Yan Guo; Yuqi Gao; Lihua Zhu; Zhaoyang Liu; Runze Tian; Chen Gao; Pengliang Han; Ning Wang; Feiran Guo; Jiyuan Bao; Conghui Jia; Hao Feng; Lili Huang
Source:
The new phytologist 2022 v.233 no.6 pp. 2503-2519
ISSN:
0028-646X
Subject:
RNA; Valsa mali; apples; callose; eukaryotic cells; fungi; histology; immunity; pathogens; reactive oxygen species; virulence
Abstract:
... Small RNAs (sRNAs) play important roles in various biological processes by silencing their corresponding target genes in most eukaryotes. However, cross‐kingdom regulation mediated by fungal microRNA‐like RNAs (milRNAs) in plant–pathogen interactions is still largely unknown. Using molecular, genetic, histological, and biochemical approaches, we found that the apple tree Valsa canker pathogen Vals ...
DOI:
10.1111/nph.17945

15. A lateral flow dipstick combined with reverse transcription recombinase polymerase amplification for rapid and visual detection of the BVDV and BPIV3

Author:
Sen Yang; Qian-Ying Wang; Bin Tan; Peng-Fei Shi; Lian-Jiang Qiao; Zhi-Jie Li; Ke-Xin Liu; Zhi-Gang Cao; Shu-Qin Zhang; Fei-Yan Sun
Source:
Journal of virological methods 2022 v.299 pp. 114343
ISSN:
0166-0934
Subject:
Bovine alphaherpesvirus 1; Bovine respirovirus 3; Bovine viral diarrhea virus 1; Classical swine fever virus; RNA; ambient temperature; bovine respiratory disease; cattle; cross reaction; diagnostic techniques; feedlots; genes; phosphoproteins; recombinase polymerase amplification; China
Abstract:
... Bovine respiratory disease complex (BRDC) is a serious disease affecting feedlot cattle in China and likely other places worldwide. Bovine viral diarrhea virus (BVDV) and bovine parainfluenza virus type 3 (BPIV3) are principally responsible for causing BRDC, and are a major strain to the industrial economy. Eradication of these viruses/disease requires swift viral identification and treatment. Hen ...
DOI:
10.1016/j.jviromet.2021.114343

16. A multi-omics study to boost continuous bolaform sophorolipid production

Author:
Sven Dierickx; Karolien Maes; Sophie L.K.W. Roelants; Beata Pomian; Lieven Van Meulebroek; Sofie L. De Maeseneire; Lynn Vanhaecke; Wim K. Soetaert
Source:
New biotechnology 2022 v.66 pp. 107-115
ISSN:
1871-6784
Subject:
RNA; Starmerella bombicola; biodegradability; biomarkers; biomass; bioreactors; biosurfactants; decline; genome; genomics; metabolites; metabolomics; microfiltration; multiomics; petroleum; phosphates; sophorolipids; yeasts
Abstract:
... Biodegradable and biobased surface active agents are renewable and environmentally friendly alternatives to petroleum derived or oleochemical surfactants. However, they are accompanied by relatively high production costs. In this study, the aim was to reduce the production costs for an innovative type of microbial biosurfactant: bolaform sophorolipids, produced by the yeast Starmerella bombicola Δ ...
DOI:
10.1016/j.nbt.2021.11.002

17. A nanovaccine for enhancing cellular immunity via cytosolic co-delivery of antigen and polyIC RNA

Author:
Carcia S. Carson; Kyle W. Becker; Kyle M. Garland; Hayden M. Pagendarm; Payton T. Stone; Karan Arora; Lihong Wang-Bishop; Jessalyn J. Baljon; Lorena D. Cruz; Sebastian Joyce; John T. Wilson
Source:
Journal of controlled release 2022 v.345 pp. 354-370
ISSN:
0168-3659
Subject:
RNA; adjuvants; antigens; cancer vaccines; cell-mediated immunity; composite polymers; cytokines; cytosol; disulfides; lymph; mice; models; neoplasms; pharmacokinetics
Abstract:
... Traditional approaches to cancer vaccines elicit weak CD8⁺ T cell responses and have largely failed to meet clinical expectations. This is in part due to inefficient antigen cross-presentation, inappropriate selection of adjuvant and its formulation, poor vaccine pharmacokinetics, and/or suboptimal coordination of antigen and adjuvant delivery. Here, we describe a nanoparticle vaccine platform for ...
DOI:
10.1016/j.jconrel.2022.03.020

18. A nationwide indicator to smooth and normalize heterogeneous SARS-CoV-2 RNA data in wastewater

Author:
Nicolas Cluzel; Marie Courbariaux; Siyun Wang; Laurent Moulin; Sébastien Wurtzer; Isabelle Bertrand; Karine Laurent; Patrick Monfort; Christophe Gantzer; Soizick Le Guyader; Mickaël Boni; Jean-Marie Mouchel; Vincent Maréchal; Grégory Nuel; Yvon Maday; Obépine consortium
Source:
Environment international 2022 v.158 pp. 106998
ISSN:
0160-4120
Subject:
RNA; Severe acute respiratory syndrome coronavirus 2; algorithms; automatic detection; complement; genome; humans; viral load; viruses; wastewater; wastewater treatment; France
Abstract:
... Since many infected people experience no or few symptoms, the SARS-CoV-2 epidemic is frequently monitored through massive virus testing of the population, an approach that may be biased and may be difficult to sustain in low-income countries. Since SARS-CoV-2 RNA can be detected in stool samples, quantifying SARS-CoV-2 genome by RT-qPCR in wastewater treatment plants (WWTPs) has been carried out a ...
DOI:
10.1016/j.envint.2021.106998

19. A nonsequencing approach for the rapid detection of rna editing

Author:
Ruchika; Tshukahara Toshifumi; Biyani Manish
Source:
Journal of visualized experiments 2022 no.182 pp. e63591
ISSN:
1940-087X
Subject:
DNA fragmentation; RNA; cost effectiveness; gel electrophoresis; gels; molecular biology; polyacrylamide; rapid methods; single-stranded DNA
Abstract:
... RNA editing is a process that leads to posttranscriptional sequence alterations in RNAs. Detection and quantification of RNA editing rely mainly on Sanger sequencing and RNA sequencing techniques. However, these methods can be costly and time-consuming. In this protocol, a portable microtemperature gradient gel electrophoresis (µTGGE) system is used as a nonsequencing approach for the rapid detect ...
DOI:
10.3791/63591

20. A novel technology for the one-step detection of prune dwarf virus: Colorimetric reverse transcription loop-mediated isothermal amplification assay

Author:
Ali Çelik
Source:
Crop protection 2022 v.155 pp. 105910
ISSN:
0261-2194
Subject:
Apple mosaic virus; Prune dwarf virus; Prunus avium; Prunus necrotic ringspot virus; RNA; coat proteins; color; colorimetry; detection limit; genome; genomics; monitoring; plant protection; reverse transcription loop-mediated isothermal amplification; technology
Abstract:
... A one-step colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to target the coat protein region of genomic RNA of prune dwarf virus (PDV). WarmStart 2X Master Mix from NEB (New England Biolabs) was used for naked eye observation of positive LAMP reactions, where the changing in color from pink to yellowish indicates a positive result. The detect ...
DOI:
10.1016/j.cropro.2022.105910