18,850 results match your criteria extracts rna


Informosomes Travel in Time: An Early mRNA Concept in the Current mRNP Landscape.

Authors:
Pavel Ivanov

Biochemistry (Mosc) 2021 Sep;86(9):1044-1052

Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA 02115, USA.

Messenger RNA is complexed with proteins throughout its life cycle. The first mRNA-containing particles of non-ribosomal nature, named informosomes, were discovered in cytoplasmic extracts of fish embryos by the laboratory of Alexander Spirin, and later described in live cells. Over time, various other nuclear and cytoplasmic mRNA-containing ribonucleoproteins (mRNPs) have been found and characterized. Read More

View Article and Full-Text PDF
September 2021

In vitro effects of bufotenine against RNA and DNA viruses.

Braz J Microbiol 2021 Sep 25. Epub 2021 Sep 25.

Instituto Pasteur, Av. Paulista, São Paulo, 393, Brazil.

Bufotenine, an alkaloid that can be found in plant extracts and skin secretions of amphibians, is reported to have potential antiviral activity. The present study evaluated the antiviral activity of bufotenine against different genetic lineages of rabies virus (RABV, a single-stranded, negative-sense RNA virus), canine coronavirus (CCoV, a positive-sense RNA virus) and two double-stranded DNA viruses (two strains of herpes simplex virus type 1/HSV-1 [KOS and the acyclovir-resistant HSV-1 strain 29R] and canine adenovirus 2, CAV-2). The maximal non-toxic bufotenine concentrations in Vero and BHK-21 cells were determined by MTT assays. Read More

View Article and Full-Text PDF
September 2021

ncDLRES: a novel method for non-coding RNAs family prediction based on dynamic LSTM and ResNet.

BMC Bioinformatics 2021 Sep 20;22(1):447. Epub 2021 Sep 20.

College of Computer Science and Technology, Jilin University, Changchun, China.

Background: Studies have proven that the same family of non-coding RNAs (ncRNAs) have similar functions, so predicting the ncRNAs family is helpful to the research of ncRNAs functions. The existing calculation methods mainly fall into two categories: the first type is to predict ncRNAs family by learning the features of sequence or secondary structure, and the other type is to predict ncRNAs family by the alignment among homologs sequences. In the first type, some methods predict ncRNAs family by learning predicted secondary structure features. Read More

View Article and Full-Text PDF
September 2021

DNAzyme based three-way junction assay for antibody-free detection of locus-specific N-methyladenosine modifications.

Biosens Bioelectron 2021 Sep 11;194:113625. Epub 2021 Sep 11.

Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, PR China. Electronic address:

N-methyladenosine (m6A) is the most abundant post-transcriptional modification in RNA and has important implications in physiological processes and tumor development. However, sensitive and specific quantification of locus-specific m6A modification levels remains a challenging task. In the present work, a novel m6A-sensitive DNAzyme was utilized to directly detect m6A by coupling with a three-way junction-mediated isothermal exponential CRISPR amplification reaction for the first time. Read More

View Article and Full-Text PDF
September 2021

Fluorophore-PNA-Quencher/Quencher-DNA probe for miRNA detection.

Bioorg Med Chem Lett 2021 Sep 14;51:128359. Epub 2021 Sep 14.

Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan. Electronic address:

Micro RNAs (miRNAs) are involved in a variety of biological functions and are attracting attention as diagnostic and prognostic markers for various diseases. Highly sensitive RNA detection methods are required to determine miRNA expression levels and intracellular localization. In this study, we designed new double-stranded peptide nucleic acid (PNA)/DNA probes consisting of a fluorophore-PNA-quencher (fPq) and a quencher-DNA (qD) for miR-221 detection. Read More

View Article and Full-Text PDF
September 2021

Ethyl Acetate Fraction of (L.) Medic Flowers Exerts Inhibitory Effects Against Oxidative Stress in HO-Induced HepG2 Cells and D-Galactose-Induced Aging Mice.

J Med Food 2021 Sep;24(9):997-1009

College of Food Science and Biology, Hebei University of Science and Technology, Shijiazhuang, China.

Oxidative stress has been demonstrated to be associated with numerous aging-related diseases. Ethyl acetate fraction of (L.) Medic (EA) had been reported to possess strong radical-scavenging activity due to its rich content of flavonoids. Read More

View Article and Full-Text PDF
September 2021

Detection of tRNA-specific adenosine deaminase activity and wobble inosine modification in human cell lysates.

Methods Enzymol 2021 24;658:311-334. Epub 2021 Jul 24.

Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, United States. Electronic address:

The wobble inosine modification plays a central role in translation by enabling a single tRNA to decode multiple synonymous codons. In eukaryotes, the formation of wobble inosine is catalyzed by a heterodimeric adenosine deaminase complex comprised of the ADAT2 and ADAT3 subunits. Notably, pathogenic variants in the ADAT3 subunit have been identified as the cause of autosomal recessive intellectual disability in the human population by impacting wobble inosine levels. Read More

View Article and Full-Text PDF
September 2021

Photoinduced atom transfer radical polymerization combined with click chemistry for highly sensitive detection of tobacco mosaic virus RNA.

Talanta 2021 Dec 13;235:122803. Epub 2021 Aug 13.

Pharmacy College, Henan University of Chinese Medicine, Zhengzhou, 450046, PR China. Electronic address:

An electrochemical biosensor for highly sensitive detection of tobacco mosaic virus (TMV) RNA (tRNA) based on click chemistry and photoinduced atom transfer radical polymerization (photoATRP) is developed for the first time. Herein, tRNA is recognized and captured by hairpin DNA immobilized on the gold electrode surface by Au-S self-assembly. Propyl 2-bromoisobutyrate (PBIB), a photoATRP initiator containing an alkyne group, is conjugated to the azide group of hairpin DNA via a Cu(I)-catalyzed azidoalkyl cyclization reaction (CuAAC). Read More

View Article and Full-Text PDF
December 2021

DNA functionalized double quantum dots-based fluorescence biosensor for one-step simultaneous detection of multiple microRNAs.

Talanta 2021 Dec 30;235:122763. Epub 2021 Jul 30.

School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China. Electronic address:

The disease diagnosis by detecting single microRNAs (miRNAs) can produce high false positive rate. Herein, a novel fluorescence biosensor method for one-step simultaneous detection of multiple miRNAs was proposed by using single-stranded DNA (ssDNA) functionalized double quantum dots (QDs) and black hole quencher (BHQ)-decorated magnetic nanobeads (MNs). MNs were linked with two black hole quenchers (BHQ1 and BHQ3) via a complementary DNA (cDNA). Read More

View Article and Full-Text PDF
December 2021

Identification of SARS-CoV-2 inhibitors from extracts of Thunb.

Saudi J Biol Sci 2021 Sep 6. Epub 2021 Sep 6.

Department of Botany and Microbiology, College of Science, King Saud University, Riyadh-11451, Saudi Arabia.

Thunb., a perennial herb belonging to the Saururaceae family is a well-known ingredient of Traditional Chinese medicine (TCM) with several therapeutic properties. During the severe acute respiratory syndrome (SARS) outbreak in China, it was one of the approved ingredients in SARS preventative formulations and therefore, the plant may contain novel bioactive chemicals that can be used to suppress the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a virus for which there are currently no effective drugs available. Read More

View Article and Full-Text PDF
September 2021

The temperature-regulated DEAD-box RNA helicase CrhR interactome: Autoregulation and photosynthesis-related transcripts.

J Exp Bot 2021 Sep 9. Epub 2021 Sep 9.

Faculty of Biology, University of Freiburg, Schänzlestr., Freiburg, Germany.

RNA helicases play crucial functions in RNA biology. In plants, RNA helicases are encoded by large gene families, performing roles in abiotic stress responses, development, the post-transcriptional regulation of gene expression as well as house-keeping functions. Several of these RNA helicases are targeted to the organelles, mitochondria and chloroplasts. Read More

View Article and Full-Text PDF
September 2021

DeepLncLoc: a deep learning framework for long non-coding RNA subcellular localization prediction based on subsequence embedding.

Brief Bioinform 2021 Sep 9. Epub 2021 Sep 9.

Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan, 410083, China.

Long non-coding RNAs (lncRNAs) are a class of RNA molecules with more than 200 nucleotides. A growing amount of evidence reveals that subcellular localization of lncRNAs can provide valuable insights into their biological functions. Existing computational methods for predicting lncRNA subcellular localization use k-mer features to encode lncRNA sequences. Read More

View Article and Full-Text PDF
September 2021

Decentralizing Cell-Free RNA Sensing With the Use of Low-Cost Cell Extracts.

Front Bioeng Biotechnol 2021 23;9:727584. Epub 2021 Aug 23.

ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile.

Cell-free gene expression systems have emerged as a promising platform for field-deployed biosensing and diagnostics. When combined with programmable toehold switch-based RNA sensors, these systems can be used to detect arbitrary RNAs and freeze-dried for room temperature transport to the point-of-need. These sensors, however, have been mainly implemented using reconstituted PURE cell-free protein expression systems that are difficult to source in the Global South due to their high commercial cost and cold-chain shipping requirements. Read More

View Article and Full-Text PDF

Application of the amplification-free SERS-based CRISPR/Cas12a platform in the identification of SARS-CoV-2 from clinical samples.

J Nanobiotechnology 2021 Sep 8;19(1):273. Epub 2021 Sep 8.

Department of Bioengineering, Guangdong Province Engineering Research Center of Antibody Drug and Immunoassay, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People's Republic of China.

The control of contagious or refractory diseases requires early, rapid diagnostic assays that are simple, fast, and easy-to-use. Here, easy-to-implement CRISPR/Cas12a-based diagnostic platform through Raman transducer generated by Raman enhancement effect, term as SERS-CRISPR (S-CRISPR), are described. The S-CRISPR uses high-activity noble metallic nanoscopic materials to increase the sensitivity in the detection of nucleic acids, without amplification. Read More

View Article and Full-Text PDF
September 2021

Two ISREs cooperatively regulate ISG expression in West Nile virus infected IFNAR MEFs.

J Virol 2021 Sep 8:JVI0104021. Epub 2021 Sep 8.

Georgia State University, Atlanta, GA 30033.

We previously identified a subset of interferon stimulated genes (ISGs) upregulated by West Nile virus (WNV) infection in wildtype mouse embryo fibroblasts (MEFs) after viral proteins had inhibited type 1 interferon (IFN)-mediated JAK-STAT signaling and also in WNV-infected RIG-I, MDA5, STAT1, STAT2, IFNAR, IRF3, IRF7, and IRF3/7 MEFs. In this study, ISG upregulation by WNV infection in IFNAR MEFs was confirmed by RNA-seq. ISG upregulation by WNV infection was inhibited in RIG-I/MDA5 MEFs. Read More

View Article and Full-Text PDF
September 2021

Detection of microorganisms with antibacterial activities from different industrial wastes and GC-MS analysis of crude microbial extract.

Braz J Biol 2021 6;83:e245585. Epub 2021 Sep 6.

The University of Haripur, Department of Biology, Khyber Pakhtunkhwa, Pakistan.

Many soil microorganisms' i.e., bacteria and fungi produce secondary metabolites called antibiotics. Read More

View Article and Full-Text PDF
September 2021

Baicalin attenuates angiotensin II-induced blood pressure elevation and modulates MLCK/p-MLC signaling pathway.

Biomed Pharmacother 2021 Sep 4;143:112124. Epub 2021 Sep 4.

Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, China; Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, China; Chen Keji Academic Thought Inheritance Studio, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, China. Electronic address:

Scutellaria baicalensis Georgi is an extensively used medicinal herb for the treatment of hypertension in traditional Chinese medicine. Baicalin, is an important flavonoid in Scutellaria baicalensis Georgi extracts, which exhibits therapeutic effects on anti-hypertension, but its underlying mechanisms remain to be further explored. Therefore, we investigated the effects and molecular mechanisms of Baicalin on anti-hypertension. Read More

View Article and Full-Text PDF
September 2021

DNA-Based Smart Reagent for Detecting Alzheimer's Associated MicroRNAs.

ACS Sens 2021 Sep 7;6(9):3176-3181. Epub 2021 Sep 7.

The RNA Institute, University of Albany, State University of New York, Albany, New York 12222, United States.

Alzheimer's disease (AD) is the most common neurodegenerative disorder, with significant research efforts devoted to identifying new biomarkers for clinical diagnosis and treatment. MicroRNAs have emerged as likely disease regulators and biomarkers for AD, now implicated as having roles in several biological processes related to progression of the disease. In this work, we use the assay (croNA ctivated onditional ooping of ngineered witches) for single-step detection of AD-related microRNAs. Read More

View Article and Full-Text PDF
September 2021

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework.

F1000Res 2021 11;10:103. Epub 2021 Feb 11.

University of Minnesota, Twin Cities, MN, 55455, USA.

The Earth Microbiome Project (EMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the 'microbiome') and microbial diversity patterns across the habitats of our planet. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on the environment and human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data analysis have helped researchers to gain an in-depth knowledge about the taxonomic and genetic composition of microbial communities. Read More

View Article and Full-Text PDF
September 2021

Virucidal and antiviral activities of pomegranate (Punica granatum) extract against the mosquito-borne Mayaro virus.

Parasit Vectors 2021 Sep 3;14(1):443. Epub 2021 Sep 3.

Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.

Background: The arthropod-borne Mayaro virus (MAYV) causes "Mayaro fever," a disease of medical significance, primarily affecting individuals in permanent contact with forested areas in tropical South America. Recently, MAYV has attracted attention due to its likely urbanization. There are currently no licensed drugs against most mosquito-transmitted viruses. Read More

View Article and Full-Text PDF
September 2021

Which East Asian herbal medicines can decrease viral infections?

Phytochem Rev 2021 Aug 27:1-19. Epub 2021 Aug 27.

Faculty of Pharmacy, Nagasaki International University, 2825-7, Sasebo, Nagasaki 859-3298 Japan.

Whilst Western research for the COVID-19 crisis focuses on vaccination, in East Asia traditional herbal prescriptions are studied for SARS-CoV2 therapy. In Japan, Maoto (Ephedrae herba 4 g, Armeniacae semen 4 g, Cinnamomi cortex 3 g, and Glycyrrhizae radix 2 g, JPXVII) is used based on clinical evidence for its effect on early phase influenza (also caused by RNA viruses) comparable to that of oseltamivir. The Health Ministry of Thailand has approved (Jap. Read More

View Article and Full-Text PDF

Efficient and Rapid Analysis of Polysomes and Ribosomal Subunits in Cells and Tissues Using Ribo Mega-SEC.

Bio Protoc 2021 Aug 5;11(15):e4106. Epub 2021 Aug 5.

Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom.

Polysome profile analysis is a popular method for separating polysomes and ribosomal subunits and is typically achieved using a sucrose density gradient (SDG). This has remained the gold standard method since ribosomes were first discovered; however, this method is time-consuming and requires multiple steps from making the gradient and long ultracentrifugation to collecting and analyzing the fractions. Each of these steps in the SDG workflow can introduce potential technical variation that affects the reproducibility of gradient profiles between samples. Read More

View Article and Full-Text PDF

Silver Nanoparticles Derived by   Reveal Anticancer and Apoptosis-Inducing Effects.

Int J Mol Sci 2021 Aug 11;22(16). Epub 2021 Aug 11.

Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy.

The fight against cancer is one of the main challenges for medical research. Recently, nanotechnology has made significant progress, providing possibilities for developing innovative nanomaterials to overcome the common limitations of current therapies. In this context, silver nanoparticles (AgNPs) represent a promising nano-tool able to offer interesting applications for cancer research. Read More

View Article and Full-Text PDF

Anti-Fibrotic and Anti-Angiogenic Activities of Leaf Extracts in Thioacetamide-Induced Experimental Liver Cirrhosis.

Molecules 2021 Aug 10;26(16). Epub 2021 Aug 10.

Department of Animal Science, Faculty of Agriculture, University of Peradeniya, Peradeniya 20400, Sri Lanka.

Chronic liver inflammation has become a major global health concern. In the absence of clinical surrogate markers to diagnose inflammatory liver disease, the intervention with effective drugs in modern medicine tends to be late. In Sri Lanka, traditional medical practitioners prescribe herbal preparations from for the prevention and treatment of liver disorders. Read More

View Article and Full-Text PDF

Severe Acute Respiratory Syndrome Coronavirus-2 Inactivation Activity of the Polyphenol-Rich Tea Leaf Extract with Concentrated Theaflavins and Other Virucidal Catechins.

Molecules 2021 Aug 8;26(16). Epub 2021 Aug 8.

Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada, Obihiro 080-8555, Japan.

Since severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is producing a large number of infections and deaths globally, the development of supportive and auxiliary treatments is attracting increasing attention. Here, we evaluated SARS-CoV-2-inactivation activity of the polyphenol-rich tea leaf extract TY-1 containing concentrated theaflavins and other virucidal catechins. The TY-1 was mixed with SARS-CoV-2 solution, and its virucidal activity was evaluated. Read More

View Article and Full-Text PDF

Phenolics-Rich Extracts of Dietary Plants as Regulators of Fructose Uptake in Caco-2 Cells via GLUT5 Involvement.

Molecules 2021 Aug 5;26(16). Epub 2021 Aug 5.

Faculty of Biotechnology and Food Sciences, Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Stefanowskiego 2/22, 90-537 Łódź, Poland.

The latest data link the chronic consumption of large amounts of fructose present in food with the generation of hypertension and disturbances in carbohydrate and lipid metabolism, which promote the development of obesity, non-alcoholic fatty liver disease, insulin resistance, and type 2 diabetes. This effect is possible after fructose is absorbed by the small intestine cells and, to a lesser extent, by hepatocytes. Fructose transport is dependent on proteins from the family of glucose transporters (GLUTs), among which GLUT5 selectively absorbs fructose from the intestine. Read More

View Article and Full-Text PDF

bCNN-Methylpred: Feature-Based Prediction of RNA Sequence Modification Using Branch Convolutional Neural Network.

Genes (Basel) 2021 Jul 28;12(8). Epub 2021 Jul 28.

Core Research Institute of Intelligent Robots, Jeonbuk National University, Jeonju 54896, Korea.

RNA modification is vital to various cellular and biological processes. Among the existing RNA modifications, N-methyladenosine (m6A) is considered the most important modification owing to its involvement in many biological processes. The prediction of m6A sites is crucial because it can provide a better understanding of their functional mechanisms. Read More

View Article and Full-Text PDF

First report of Grapevine enamovirus 1 in Vitis vinifera cultivar 'Meunier' in France.

Plant Dis 2021 Aug 22. Epub 2021 Aug 22.

Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000 Colmar, France, Colmar, France;

Grapevine enamovirus 1 (GEV-1) is a member of the genus Enamovirus in the family Solemoviridae. GEV-1 was first described in 2017 in a few grapevine cultivars in Brazil (Silva et al. 2017) and subsequently in China (Ren et al. Read More

View Article and Full-Text PDF

A simple and fast spectroscopy-based technique for Covid-19 diagnosis.

Sci Rep 2021 08 18;11(1):16740. Epub 2021 Aug 18.

Anoual Laboratory, Boulevard d'Alexandrie, 20360, Casablanca, Morocco.

The coronavirus pandemic, which appeared in Wuhan, China, in December 2019, rapidly spread all over the world in only a few weeks. Faster testing techniques requiring less resources are key in managing the pandemic, either to enable larger scale testing or even just provide developing countries with limited resources, particularly in Africa, means to perform tests to manage the crisis. Here, we report an unprecedented, rapid, reagent-free and easy-to-use screening spectroscopic method for the detection of SARS-CoV-2 on RNA extracts. Read More

View Article and Full-Text PDF

Cooperative recruitment of RDR6 by SGS3 and SDE5 during small interfering RNA amplification in .

Proc Natl Acad Sci U S A 2021 Aug;118(34)

Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan.

Small interfering RNAs (siRNAs) are often amplified from transcripts cleaved by RNA-induced silencing complexes (RISCs) containing a small RNA (sRNA) and an Argonaute protein. Amplified siRNAs, termed secondary siRNAs, are important for reinforcement of target repression. In plants, target cleavage by RISCs containing 22-nucleotide (nt) sRNA and Argonaute 1 (AGO1) triggers siRNA amplification. Read More

View Article and Full-Text PDF