keyword
https://read.qxmd.com/read/38469716/the-role-of-the-5-sensing-function-of-ribonuclease-e-in-cyanobacteria
#21
JOURNAL ARTICLE
Ute A Hoffmann, Elisabeth Lichtenberg, Said N Rogh, Raphael Bilger, Viktoria Reimann, Florian Heyl, Rolf Backofen, Claudia Steglich, Wolfgang R Hess, Annegret Wilde
RNA degradation is critical for synchronising gene expression with changing conditions in prokaryotic and eukaryotic organisms. In bacteria, the preference of the central ribonucleases RNase E, RNase J and RNase Y for 5'-monophosphorylated RNAs is considered important for RNA degradation. For RNase E, the underlying mechanism is termed 5' sensing, contrasting to the alternative 'direct entry' mode, which is independent of monophosphorylated 5' ends. Cyanobacteria, such as Synechocystis sp. PCC 6803 ( Synechocystis ), encode RNase E and RNase J homologues...
January 2024: RNA Biology
https://read.qxmd.com/read/38467975/endosomal-toll-like-receptors-as-therapeutic-targets-for-autoimmune-diseases
#22
JOURNAL ARTICLE
Kensuke Miyake, Takuma Shibata, Ryutaro Fukui, Yusuke Murakami, Ryota Sato, Ryosuke Hiranuma
Nucleic acid (NA)-sensing Toll-like receptors (TLRs) reside in the endosomal compartment of innate immune cells, such as macrophages and dendritic cells. NAs transported to the endosomal compartment are degraded by DNases and RNases. Degradation products, including single-stranded DNA, oligoRNA, and nucleosides, are recognized by TLR7, TLR8, and TLR9 to drive the defense responses against pathogens. NA degradation influences endosomal TLR responses by generating and degrading TLR ligands. TLR ligand accumulation because of impaired NA degradation causes constitutive TLR activation, leading to autoinflammatory and autoimmune diseases...
2024: Advances in Experimental Medicine and Biology
https://read.qxmd.com/read/38453747/a-rapid-inexpensive-and-effective-method-for-the-efficient-isolation-of-genomic-dna-from-gram-negative-bacteria
#23
JOURNAL ARTICLE
Lihini Ranesha Weerakkody, Chamindri Witharana
Currently, there are several protocols to extract bacterial DNA based on different principles. However, the quantity and the quality of the DNA obtained by each method are highly variable and microorganism dependent. In most of these classical crude methods, highly toxic and hazardous organic solvents such as phenol and chloroform are used for deproteinization, whereas in certain protocols, expensive enzymes including RNases and Proteinases are used. This study was designed to introduce a simple, rapid, inexpensive and effective genomic DNA isolation procedure for Gram-negative bacteria, without the usage of toxic chemicals and costly enzymes...
March 7, 2024: Molecular Genetics and Genomics: MGG
https://read.qxmd.com/read/38453211/the-protein-only-rnase-ps-endonucleases-that-cleave-pre-trna-biological-relevance-molecular-architectures-substrate-recognition-and-specificity-and-protein-interactomes
#24
JOURNAL ARTICLE
Catherine A Wilhelm, Kipchumba Kaitany, Abigail Kelly, Matthew Yacoub, Markos Koutmos
Protein-only RNase P (PRORP) is an essential enzyme responsible for the 5' maturation of precursor tRNAs (pre-tRNAs). PRORPs are classified into three categories with unique molecular architectures, although all three classes of PRORPs share a mechanism and have similar active sites. Single subunit PRORPs, like those found in plants, have multiple isoforms with different localizations, substrate specificities, and temperature sensitivities. Most recently, Arabidopsis thaliana PRORP2 was shown to interact with TRM1A and B, highlighting a new potential role between these enzymes...
2024: Wiley Interdisciplinary Reviews. RNA
https://read.qxmd.com/read/38452582/emerging-role-of-tumor-suppressing-micrornas-as-therapeutics-in-managing-non-small-cell-lung-cancer
#25
REVIEW
Shubham Singh, Sangeeta Saxena, Himani Sharma, Keshav Raj Paudel, Amlan Chakraborty, Ronan MacLoughlin, Brian G Oliver, Gaurav Gupta, Poonam Negi, Sachin Kumar Singh, Kamal Dua
Lung cancer (LC) is the second leading cause of death across the globe after breast cancer. There are two types of LC viz. small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). NSCLC accounts for approximately 85% of all LC cases. NSCLC affects smokers and people who do not smoke and mainly arises in bronchi and peripheral lungs tissue. LC is often characterized by the alterations of key genes such as EGFR, Wnt/β-catenin signaling, ALK, MET, K-Ras and p53 and downstream signaling pathways associated with tumor growth, differentiation, and survival...
February 23, 2024: Pathology, Research and Practice
https://read.qxmd.com/read/38452081/prophage-proteins-alter-long-noncoding-rna-and-dna-of-developing-sperm-to-induce-a-paternal-effect-lethality
#26
JOURNAL ARTICLE
Rupinder Kaur, Angelina McGarry, J Dylan Shropshire, Brittany A Leigh, Seth R Bordenstein
The extent to which prophage proteins interact with eukaryotic macromolecules is largely unknown. In this work, we show that cytoplasmic incompatibility factor A (CifA) and B (CifB) proteins, encoded by prophage WO of the endosymbiont Wolbachia, alter long noncoding RNA (lncRNA) and DNA during Drosophila sperm development to establish a paternal-effect embryonic lethality known as cytoplasmic incompatibility (CI). CifA is a ribonuclease (RNase) that depletes a spermatocyte lncRNA important for the histone-to-protamine transition of spermiogenesis...
March 8, 2024: Science
https://read.qxmd.com/read/38447345/rna-quality-score-evaluation-a-preliminary-study-of-rna-integrity-number-rin-and-rna-integrity-and-quality-number-rna-iq
#27
JOURNAL ARTICLE
Suyu Li, Jing Liu, Mengyao Zhao, Yonglin Su, Bin Cong, Zheng Wang
In the past several years, with the in-depth development of RNA-related research, exploring the application of transcriptome and corresponding RNA biomarkers has become one of the research hotspots in the field of forensic science. High-quality RNA is essential for successful downstream workflows, especially in the steps of screening biomarkers by microarray or RNA sequencing (RNA-seq). Thus, accurately evaluating the quality of RNA samples is a critical step in obtaining meaningful expression data. The RNA integrity number (RIN) generated from the Agilent Bioanalyzer system has been widely used for RNA quality control in the past two decades...
March 2, 2024: Forensic Science International
https://read.qxmd.com/read/38443797/integrated-metabolome-and-transcriptome-analyses-reveal-the-molecular-mechanism-underlying-dynamic-metabolic-processes-during-taproot-development-of-panax-notoginseng
#28
JOURNAL ARTICLE
Xuejiao Li, Yan Zhao, Shuilian He, Jing Meng, Yingchun Lu, Huineng Shi, Chunlan Liu, Bing Hao, Qingyan Tang, Shuangyan Zhang, Guanghui Zhang, Yu Luo, Shengchao Yang, Jianli Yang, Wei Fan
BACKGROUND: Panax notoginseng (Burk) F. H. Chen is one of the most famous Chinese traditional medicinal plants. The taproot is the main organ producing triterpenoid saponins, and its development is directly linked to the quality and yield of the harvested P. notoginseng. However, the mechanisms underlying the dynamic metabolic changes occurring during taproot development of P. notoginseng are unknown. RESULTS: We carried out metabolomic and transcriptomic analyses to investigate metabolites and gene expression during the development of P...
March 5, 2024: BMC Plant Biology
https://read.qxmd.com/read/38443657/crosstalk-between-vault-rnas-and-innate-immunity
#29
REVIEW
Rodolfo Gamaliel Avila-Bonilla, Juan Pablo Martínez-Montero
PURPOSE: Vault (vt) RNAs are noncoding (nc) RNAs transcribed by RNA polymerase III (RNA Pol III) with 5'-triphosphate (5'-PPP) termini that play significant roles and are recognized by innate immune sensors, including retinoic acid-inducible protein 1 (RIG-I). In addition, vtRNAs adopt secondary structures that can be targets of interferon-inducible protein kinase R (PKR) and the oligoadenylate synthetase (OAS)/RNase L system, both of which are important for activating antiviral defenses...
March 5, 2024: Molecular Biology Reports
https://read.qxmd.com/read/38441909/covalent-organic-frameworks-as-nano-reservoir-for-room-temperature-rna-storage
#30
JOURNAL ARTICLE
Satyapriya Nath, Kiran Devi Tulsiyan, Binayak Mohapatra, Adithyan Puthukkudi, Pankaj V Alone, Himansu S Biswal, Bishnu P Biswal
The emerging role of Ribonucleic acids (RNAs) as therapeutics is alluring. However, RNAs are extremely labile under ambient conditions and typically need to be stored in cryogenic conditions (-20 ᵒC to -80 ᵒC). Hence, storage, stabilization, and transportation of RNA under ambient conditions have been an arduous task and remain an unsolved problem. In this work, a guanidinium-based ionic covalent organic framework (COF), TTGCl with nanotubular morphology, was synthesized and used as nano-reservoirs for room-temperature storage of RNA...
March 5, 2024: Chemistry: a European Journal
https://read.qxmd.com/read/38441369/deformable-smart-dna-nanomachine-for-synergistic-intracellular-cancer-related-mirnas-imaging-and-chemo-gene-therapy-of-drug-resistant-tumors
#31
JOURNAL ARTICLE
Chen Dong, Yeran Wang, Zhilong Chen, Chenlong Yan, Jingjing Zhang, Chunyuan Song, Lianhui Wang
Diagnosis and treatment of tumor especially drug-resistant tumor remains a huge challenge, which requires intelligent nanomedicines with low toxic side effects and high efficacy. Herein, deformable smart DNA nanomachines are developed for synergistic intracellular cancer-related miRNAs imaging and chemo-gene therapy of drug-resistant tumors. The tetrahedral DNA framework (MA-TDNA) with fluorescence quenched component and five antennas is self-assembled first, and then DOX molecules are loaded on the MA-TDNAs followed by linking MUC1-aptamer and Mcl-1 siRNA to the antennas of MA-TDNA, so that the apt-MA-TDNA@DOX-siRNA (DNA nanomachines) is constructed...
March 5, 2024: Small
https://read.qxmd.com/read/38439836/the-effects-of-transcription-factor-7-like-2-rs7903146-and-paired-box-4-rs2233580-variants-associated-with-type-2-diabetes-on-the-therapeutic-efficacy-of-hypoglycemic-agents
#32
JOURNAL ARTICLE
Nipaporn Teerawattanapong, Lanraphat Srisawat, Tassanee Narkdontri, Pa-Thai Yenchitsomanus, Watip Tangjittipokin, Nattachet Plengvidhya
AIM: This study aims to investigate the effects of the TCF7L2 rs7903146 and PAX4 rs2233580 (R192H) variants associated with T2D on the therapeutic efficacies of various HAs in patients with T2D after follow-up for 3 years. METHODS: A total of 526 patients who were followed up at the Diabetic Clinic of Siriraj Hospital during 2016-2019 were enrolled. The variants TCF7L2 rs7903146 and PAX4 rs2233580 (R192H) were genotyped using the RNase H2 enzyme-based amplification (rhAmp) technique and the associations between genotypes and glycemic control after treatments with different combinations HA were evaluated using Generalized Estimating Equations (GEE) analysis...
March 15, 2024: Heliyon
https://read.qxmd.com/read/38432358/an-optimised-protocol-for-the-expression-and-purification-of-adenovirus-core-protein-vii
#33
JOURNAL ARTICLE
Ajani Athukorala, Karla J Helbig, Brian P McSharry, Jade K Forwood, Subir Sarker
Adenovirus protein VII (pVII) is a highly basic core protein, bearing resemblance to mammalian histones. Despite its diverse functions, a comprehensive understanding of its structural intricacies and the mechanisms underlying its functions remain elusive, primarily due to the complexity of producing a good amount of soluble pVII. This study aimed to optimise the expression and purification of recombinant pVII from four different adenoviruses with a simple vector construct. This study successfully determined the optimal conditions for efficiently purifying pVII across four adenovirus species, revealing the differential preference for bacterial expression systems...
March 1, 2024: Journal of Virological Methods
https://read.qxmd.com/read/38432074/a-novel-ultrasensitive-rnase-h-assay-based-on-phosphorothioated-terminal-hairpin-formation-and-self-priming-extension-reaction
#34
JOURNAL ARTICLE
Junhyeok Yoon, Jinhwan Lee, Jaemin Kim, Sang Mo Lee, Soohyun Kim, Hyun Gyu Park
We herein present a novel ultrasensitive RNase H assay based on phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP) reaction. The detection probe employed as a key component in this technique serves as a substrate for RNase H and triggers the PS-THSP reaction upon the RNase H-mediated degradation of the probe. As a consequence, a large number of long concatemeric amplification products could be produced and used to identify the RNase H activity through the fluorescence signals produced by the nucleic acid-specific fluorescent dye, SYTO 9...
February 29, 2024: Biosensors & Bioelectronics
https://read.qxmd.com/read/38431617/rtf2-controls-replication-repriming-and-ribonucleotide-excision-at-the-replisome
#35
JOURNAL ARTICLE
Brooke A Conti, Penelope D Ruiz, Cayla Broton, Nicolas J Blobel, Molly C Kottemann, Sunandini Sridhar, Francis P Lach, Tom F Wiley, Nanda K Sasi, Thomas Carroll, Agata Smogorzewska
DNA replication through a challenging genomic landscape is coordinated by the replisome, which must adjust to local conditions to provide appropriate replication speed and respond to lesions that hinder its progression. We have previously shown that proteasome shuttle proteins, DNA Damage Inducible 1 and 2 (DDI1/2), regulate Replication Termination Factor 2 (RTF2) levels at stalled replisomes, allowing fork stabilization and restart. Here, we show that during unperturbed replication, RTF2 regulates replisome localization of RNase H2, a heterotrimeric enzyme that removes RNA from RNA-DNA heteroduplexes...
March 2, 2024: Nature Communications
https://read.qxmd.com/read/38426261/ribonuclease-a-polymer-conjugates-via-in-situ-growth-for-cancer-treatment
#36
JOURNAL ARTICLE
Lin Jiang, Xiao Liang, Jiaxin Jia, Haobo Han, Jun Tang, Quanshun Li
Efficient delivery of therapeutic proteins is a critical aspect for protein-based cancer treatment. Herein, an in situ growth approach was employed to prepare ribonuclease A (RNase A)-polymer conjugates by incorporating a cationic polymer, poly( N , N '-dimethylamino-2-ethyl methacrylate) (P(DMAEMA)), and a hydrophobic polymer, poly( N -isopropylacrylamide) (P(NIPAM)), through atom transfer radical polymerization (ATRP). The synthesized RNase A-polymer conjugates (namely R-P(D- b -N)) could preserve the integrity of RNase A and exhibit a unique combination of cationic and hydrophobic properties, leading to enhanced intracellular delivery efficiency...
March 1, 2024: Journal of Materials Chemistry. B, Materials for Biology and Medicine
https://read.qxmd.com/read/38425334/a-methodological-primer-of-extracellular-vesicles-isolation-and-characterization-via-different-techniques
#37
JOURNAL ARTICLE
Farhang Aliakbari, Noah B Stocek, Maxximuss Cole-André, Janice Gomes, Giovanni Fanchini, Stephen H Pasternak, Gunna Christiansen, Dina Morshedi, Kathryn Volkening, Michael J Strong
We present four different protocols of varying complexity for the isolation of cell culture-derived extracellular vesicles (EVs)/exosome-enriched fractions with the objective of providing researchers with easily conducted methods that can be adapted for many different uses in various laboratory settings and locations. These protocols are primarily based on polymer precipitation, filtration and/or ultracentrifugation, as well as size-exclusion chromatography (SEC) and include: (i) polyethylene glycol and sodium chloride supplementation of the conditioned medium followed by low-speed centrifugation; (ii) ultracentrifugation of conditioned medium; (iii) filtration of conditioned media through a 100-kDa exclusion filter; and (iv) isolation using a standard commercial kit...
2024: Biology Methods and Protocols
https://read.qxmd.com/read/38423012/oligoadenylate-synthetase-1-displays-dual-antiviral-mechanisms-in-driving-translational-shutdown-and-protecting-interferon-production
#38
JOURNAL ARTICLE
Munesh K Harioudh, Joseph Perez, Zhenlu Chong, Sharmila Nair, Lomon So, Kevin D McCormick, Arundhati Ghosh, Lulu Shao, Rashmi Srivastava, Frank Soveg, Thomas S Ebert, Maninjay K Atianand, Veit Hornung, Ram Savan, Michael S Diamond, Saumendra N Sarkar
In response to viral infection, how cells balance translational shutdown to limit viral replication and the induction of antiviral components like interferons (IFNs) is not well understood. Moreover, how distinct isoforms of IFN-induced oligoadenylate synthetase 1 (OAS1) contribute to this antiviral response also requires further elucidation. Here, we show that human, but not mouse, OAS1 inhibits SARS-CoV-2 replication through its canonical enzyme activity via RNase L. In contrast, both mouse and human OAS1 protect against West Nile virus infection by a mechanism distinct from canonical RNase L activation...
February 23, 2024: Immunity
https://read.qxmd.com/read/38416645/the-apparent-loss-of-prc2-chromatin-occupancy-as-an-artifact-of-rna-depletion
#39
JOURNAL ARTICLE
Evan Healy, Qi Zhang, Emma H Gail, Samuel C Agius, Guizhi Sun, Michael Bullen, Varun Pandey, Partha Pratim Das, Jose M Polo, Chen Davidovich
RNA has been implicated in the recruitment of chromatin modifiers, and previous studies have provided evidence in favor and against this idea. RNase treatment of chromatin is commonly used to study RNA-mediated regulation of chromatin modifiers, but the limitations of this approach remain unclear. RNase A treatment during chromatin immunoprecipitation (ChIP) reduces chromatin occupancy of the H3K27me3 methyltransferase Polycomb repressive complex 2 (PRC2). This led to suggestions of an "RNA bridge" between PRC2 and chromatin...
February 27, 2024: Cell Reports
https://read.qxmd.com/read/38416641/apparent-rna-bridging-between-prc2-and-chromatin-is-an-artifact-of-non-specific-chromatin-precipitation-upon-rna-degradation
#40
JOURNAL ARTICLE
Alexander Hall Hickman, Richard G Jenner
Polycomb repressive complex 2 (PRC2) modifies chromatin to maintain repression of genes specific for other cell lineages. In vitro, RNA inhibits PRC2 activity, but the effect of RNA on PRC2 in cells is less clear, with studies concluding that RNA either antagonizes or promotes PRC2 chromatin association. The addition of RNase A to chromatin immunoprecipitation reactions has been reported to reduce detection of PRC2 target sites, suggesting the existence of RNA bridges connecting PRC2 to chromatin. Here, we show that the apparent loss of PRC2 chromatin association after RNase A treatment is due to non-specific chromatin precipitation...
February 27, 2024: Cell Reports
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