keyword
https://read.qxmd.com/read/38535801/hortensins-type-1-ribosome-inactivating-proteins-from-seeds-of-red-mountain-spinach-isolation-characterization-and-their-effect-on-glioblastoma-cells
#1
JOURNAL ARTICLE
Sara Ragucci, Veronica Russo, Angela Clemente, Maria Giuseppina Campanile, Maria Antonietta Oliva, Nicola Landi, Paolo Vincenzo Pedone, Antonietta Arcella, Antimo Di Maro
Ribosome inactivating proteins (RIPs) are specific N-β-glycosylases that are well-characterized in plants. Their enzymatic action is to damage ribosomes, thereby blocking protein translation. Recently, several research groups have been working on the screening for these toxins in edible plants to facilitate the use of RIPs as biotechnological tools and biopesticides and to overcome public prejudice. Here, four novel monomeric (type 1) RIPs have been isolated from the seeds of Atriplex hortensis L. var...
March 4, 2024: Toxins
https://read.qxmd.com/read/38523232/detection-of-the-phosphorothioate-oligonucleotide-fomivirsen-using-a-ligase-detection-reaction-with-polymerase-chain-reaction
#2
JOURNAL ARTICLE
Naoki Harikai, Haruka Kakuda, Takumi Uchiyama, Tsubaki Yamamoto, Kazumasa Zaima, Kazufusa Shinomiya
This study aimed to develop a simple and sensitive detection method for fomivirsen, a 21-nucleotide phosphorothioate oligonucleotide used as a nucleic acid medicine, using a ligase detection reaction. A ligation probe was designed to hybridize with fomivirsen and polymerase chain reaction (PCR) primers, with a deoxyuridine part between the primer binding sites. The probe was ligated to a circular product by Taq DNA ligase, and the resulting product was converted to a linear form through the removal of the uracil base using uracil DNA glycosylase...
March 25, 2024: Analytical Sciences: the International Journal of the Japan Society for Analytical Chemistry
https://read.qxmd.com/read/38522610/dissecting-gene-expression-networks-in-the-developing-hippocampus-through-the-lens-of-neil3-depletion
#3
JOURNAL ARTICLE
Anna M Bugaj, Nicolas Kunath, Vidar Langseth Saasen, Marion S Fernandez-Berrocal, Ana Vankova, Pål Sætrom, Magnar Bjørås, Jing Ye
Gene regulation in the hippocampus is fundamental for its development, synaptic plasticity, memory formation, and adaptability. Comparisons of gene expression among different developmental stages, distinct cell types, and specific experimental conditions have identified differentially expressed genes contributing to the organization and functionality of hippocampal circuits. The NEIL3 DNA glycosylase, one of the DNA repair enzymes, plays an important role in hippocampal maturation and neuron functionality by shaping transcription...
March 22, 2024: Progress in Neurobiology
https://read.qxmd.com/read/38509454/an-rrm-domain-protein-soe-suppresses-transgene-silencing-in-rice
#4
JOURNAL ARTICLE
Rui Zhao, Wen-Ai Wu, Yi-Hua Huang, Xin-Kai Li, Jia-Qi Han, Wu Jiao, Yin-Na Su, He Zhao, Yang Zhou, Wu-Qiang Cao, Xun Zhang, Wei Wei, Wan-Ke Zhang, Qing-Xin Song, Xin-Jian He, Biao Ma, Shou-Yi Chen, Jian-Jun Tao, Cui-Cui Yin, Jin-Song Zhang
Gene expression is regulated at multiple levels, including RNA processing and DNA methylation/demethylation. How these regulations are controlled remains unclear. Here, through analysis of a suppressor for the OsEIN2 over-expressor, we identified an RNA recognition motif protein SUPPRESSOR OF EIN2 (SOE). SOE is localized in nuclear speckles and interacts with several components of the spliceosome. We find SOE associates with hundreds of targets and directly binds to a DNA glycosylase gene DNG701 pre-mRNA for efficient splicing and stabilization, allowing for subsequent DNG701-mediated DNA demethylation of the transgene promoter for proper gene expression...
March 20, 2024: New Phytologist
https://read.qxmd.com/read/38504497/gene-doping-control-analysis-of-human-erythropoietin-transgene-in-equine-plasma-by-pcr-liquid-chromatography-high-resolution-tandem-mass-spectrometry
#5
JOURNAL ARTICLE
Bruce Pui-Nam Yuen, Kin-Sing Wong, Yat-Ming So, Wai Him Kwok, Hiu Wing Cheung, Terence See Ming Wan, Emmie Ngai-Man Ho, Wing-Tak Wong
Gene doping involves the misuse of genetic materials to alter an athlete's performance, which is banned at all times in both human and equine sports. Quantitative polymerase chain reaction (qPCR) assays have been used to control the misuse of transgenes in equine sports. Our laboratory recently developed and implemented duplex as well as multiplex qPCR assays for transgenes detection. To further advance gene doping control, we have developed for the first time a sensitive and definitive PCR-liquid chromatography high-resolution tandem mass spectrometry (PCR-LC-HRMS/MS) method for transgene detection with an estimated limit of detection of below 100 copies/mL for the human erythropoietin (hEPO) transgene in equine plasma...
March 19, 2024: Analytical Chemistry
https://read.qxmd.com/read/38471078/fshing-for-dna-damage-key-features-of-muty-detection-of-8-oxoguanine-adenine-mismatches
#6
JOURNAL ARTICLE
Chandrima Majumdar, Merve Demir, Steven R Merrill, Mohammad Hashemian, Sheila S David
ConspectusBase excision repair (BER) enzymes are genomic superheroes that stealthily and accurately identify and remove chemically modified DNA bases. DNA base modifications erode the informational content of DNA and underlie many disease phenotypes, most conspicuously, cancer. The "OG" of oxidative base damage, 8-oxo-7,8-dihydroguanine (OG), is particularly insidious due to its miscoding ability that leads to the formation of rare, pro-mutagenic OG:A mismatches. Thwarting mutagenesis relies on the capture of OG:A mismatches prior to DNA replication and removal of the mis-inserted adenine by MutY glycosylases to initiate BER...
March 12, 2024: Accounts of Chemical Research
https://read.qxmd.com/read/38467300/hogg1-a-novel-mediator-in-nitrosamine-induced-esophageal-tumorigenesis
#7
JOURNAL ARTICLE
De-Rong Tang, Cheng-Lin Li, Zhi-Yun Xu, Zhen-Zhong Zhang, Qian-Wei Wang, Jian-Qiang Zhao
BACKGROUND: The effect of human 8-Oxoguanine DNA Glycosylase (hOGG1) on exogenous chemicals in esophageal squamous cell carcinoma (ESCC) remain unclear. The study plans to determine hOGG1 expression levels in ESCC and possible interactions with known environmental risk factors in ESCC. MATERIAL AND METHODS: We analyzed levels of exposure to urinary nitrosamines in volunteers from high and low prevalence areas by GC-MS. And we performed the interaction between hOGG1 gene and nitrosamine disinfection by-products by analyzing hOGG1 gene expression in esophageal tissues...
March 9, 2024: Food and Chemical Toxicology
https://read.qxmd.com/read/38462345/construction-of-single-molecule-counting-based-biosensors-for-dna-modifying-enzymes-a-review
#8
REVIEW
Qian Zhang, Juan Hu, Dong-Ling Li, Jian-Ge Qiu, Bing-Hua Jiang, Chun-Yang Zhang
DNA-modifying enzymes act as critical regulators in a wide range of genetic functions (e.g., DNA damage & repair, DNA replication), and their aberrant expression may interfere with regular genetic functions and induce various malignant diseases including cancers. DNA-modifying enzymes have emerged as the potential biomarkers in early diagnosis of diseases and new therapeutic targets in genomic research. Consequently, the development of highly specific and sensitive biosensors for the detection of DNA-modifying enzymes is of great importance for basic biomedical research, disease diagnosis, and drug discovery...
April 15, 2024: Analytica Chimica Acta
https://read.qxmd.com/read/38451471/three-state-diffusion-model-of-dna-glycosylase-translocation-along-stretched-dna-as-revealed-by-free-energy-landscapes-at-the-all-atom-level
#9
JOURNAL ARTICLE
Hyeonjun Kim, Youngshang Pak
DNA glycosylases play key roles in the maintenance of genomic integrity. These enzymes effectively find rare damaged sites in DNA and participate in subsequent base excision repair. Single-molecule and ensemble experiments have revealed key aspects of this damage-site searching mechanism and the involvement of facilitated diffusion. In this study, we describe free energy landscapes of enzyme translocation along nonspecific DNA obtained using a fully atomistic molecular dynamics (MD) simulation of a well-known DNA glycosylase, human 8-oxoguanine DNA glycosylase 1 (hOGG1)...
March 7, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38435525/cellular-repair-of-synthetic-analogs-of-oxidative-dna-damage-reveals-a-key-structure-activity-relationship-of-the-cancer-associated-mutyh-dna-repair-glycosylase
#10
JOURNAL ARTICLE
Savannah G Conlon, Cindy Khuu, Carlos H Trasviña-Arenas, Tian Xia, Michelle L Hamm, Alan G Raetz, Sheila S David
The base excision repair glycosylase MUTYH prevents mutations associated with the oxidatively damaged base, 8-oxo-7,8-dihydroguanine (OG), by removing undamaged misincorporated adenines from OG:A mispairs. Defects in OG:A repair in individuals with inherited MUTYH variants are correlated with the colorectal cancer predisposition syndrome known as MUTYH -associated polyposis (MAP). Herein, we reveal key structural features of OG required for efficient repair by human MUTYH using structure-activity relationships (SAR)...
February 28, 2024: ACS Central Science
https://read.qxmd.com/read/38432775/hydrogen-inhalation-in-vivo-rat-genotoxicity-tests
#11
JOURNAL ARTICLE
Cordélia Salomez-Ihl, Stéphane Tanguy, Jean-Pierre Alcaraz, Chloé Davin, Victor Pascal-Moussellard, Mariem Jabeur, Pierrick Bedouch, Ludovic Le Hegarat, Valérie Fessard, Anne-Louise Blier, Sylvie Huet, Philippe Cinquin, François Boucher
Preclinical and clinical studies have shown that molecular hydrogen (H2 ) has anti-oxidant, anti-inflammatory, and anti-apoptotic properties. Safety data are available in the literature and acute toxicity has been tested in isolated cells and laboratory animals. We have evaluates the genotoxicity of H2 in vivo in rats after 72 h exposure, following the International Council for Harmonization guidelines ICH S2 (R1). The study was conducted on three groups of male Wistar rats: a negative control group, a positive control group receiving methyl methanesulfonate, and a H2 -treated group receiving a 3...
2024: Mutation Research. Genetic Toxicology and Environmental Mutagenesis
https://read.qxmd.com/read/38420825/genotoxicity-assessment-of-quinoin-a-ribosome-inactivating-protein-from-quinoa-seeds-in-the-teleost-danio-rerio
#12
JOURNAL ARTICLE
Filomena Mottola, Sara Ragucci, Maria Carannante, Nicola Landi, Rosaria Scudiero, Antimo Di Maro, Lucia Rocco
BACKGROUND: Ribosome inactivating proteins (RIPs) are N-glycosylases found in various plants that are able to specifically and irreversibly inhibit protein translation, thereby leading to cell death. Their cytotoxic properties have attracted attention in the medical field in the context of developing new anticancer therapies. Quinoin is a novel toxic enzyme obtained from quinoa seeds and classified as a type 1 RIP ( Chenopodium quinoa Willd.). Recently, quinoin was found to be cytotoxic to normal fibroblasts and keratinocytes in vitro , as well as to several tumor cell lines...
February 4, 2024: Frontiers in Bioscience (Landmark Edition)
https://read.qxmd.com/read/38405940/potent-pollen-gene-regulation-by-dna-glycosylases-in-maize
#13
Yibing Zeng, Julian Somers, Harrison S Bell, R Kelly Dawe, John E Fowler, Brad Nelms, Jonathan I Gent
Although DNA methylation primarily represses transposable elements (TEs) in plants, it also represses select endosperm and pollen genes. These genes, or their cis-regulatory elements, are methylated in plant body tissues but are demethylated by DNA glycosylases (DNGs) in endosperm and pollen, enabling their transcription. Activity of either one of two DNGs, MDR1 or DNG102, is essential for pollen viability in maize. Using single-pollen mRNA sequencing on pollen segregating mutations in both genes, we identified 58 candidate DNG target genes, whose expression is strongly decreased in double mutant pollen (124-fold decrease on average)...
February 15, 2024: bioRxiv
https://read.qxmd.com/read/38397143/cognitive-function-is-associated-with-the-genetically-determined-efficiency-of-dna-repair-mechanisms
#14
JOURNAL ARTICLE
Nicolas Cherbuin, Hardip Patel, Erin I Walsh, Ananthan Ambikairajah, Richard Burns, Anne Brüstle, Lene Juel Rasmussen
Several modifiable risk factors for neurodegeneration and dementia have been identified, although individuals vary in their vulnerability despite a similar risk of exposure. This difference in vulnerability could be explained at least in part by the variability in DNA repair mechanisms' efficiency between individuals. Therefore, the aim of this study was to test associations between documented, prevalent genetic variation (single nucleotide polymorphism, SNP) in DNA repair genes, cognitive function, and brain structure...
January 24, 2024: Genes
https://read.qxmd.com/read/38396961/analysis-of-the-model-of-atherosclerosis-formation-in-pig-hearts-as-a-result-of-impaired-activity-of-dna-repair-enzymes
#15
JOURNAL ARTICLE
Robert Paslawski, Paweł Kowalczyk, Urszula Paslawska, Jerzy Wiśniewski, Piotr Dzięgiel, Adrian Janiszewski, Liliana Kiczak, Maciej Zacharski, Barbara Gawdzik, Karol Kramkowski, Andrzej Szuba
Excessive consumption of food rich in saturated fatty acids and carbohydrates can lead to metabolic disturbances and cardiovascular disease. Hyperlipidemia is a significant risk factor for acute cardiac events due to its association with oxidative stress. This leads to arterial wall remodeling, including an increase in the thickness of the intima media complex (IMT), and endothelial dysfunction leading to plaque formation. The decreased nitric oxide synthesis and accumulation of lipids in the wall result in a reduction in the vasodilating potential of the vessel...
February 14, 2024: International Journal of Molecular Sciences
https://read.qxmd.com/read/38391916/a-knockout-of-poly-adp-ribose-polymerase-1-in-a-human-cell-line-an-influence-on-base-excision-repair-reactions-in-cellular-extracts
#16
JOURNAL ARTICLE
Svetlana N Khodyreva, Ekaterina S Ilina, Nadezhda S Dyrkheeva, Alina S Kochetkova, Alexandra A Yamskikh, Ekaterina A Maltseva, Anastasia A Malakhova, Sergey P Medvedev, Suren M Zakian, Olga I Lavrik
Base excision repair (BER) is the predominant pathway for the removal of most forms of hydrolytic, oxidative, and alkylative DNA lesions. The precise functioning of BER is achieved via the regulation of each step by regulatory/accessory proteins, with the most important of them being poly(ADP-ribose) polymerase 1 (PARP1). PARP1's regulatory functions extend to many cellular processes including the regulation of mRNA stability and decay. PARP1 can therefore affect BER both at the level of BER proteins and at the level of their mRNAs...
February 6, 2024: Cells
https://read.qxmd.com/read/38384388/human-nthl1-expression-and-subcellular-distribution-determines-cisplatin-sensitivity-in-human-lung-epithelial-and-non-small-cell-lung-cancer-cells
#17
JOURNAL ARTICLE
Anirban Kar, Natalya P Degtyareva, Paul W Doetsch
Base excision repair is critical for maintaining genomic stability and for preventing malignant transformation. NTHL1 is a bifunctional DNA glycosylase/AP lyase that initiates repair of oxidatively damaged pyrimidines. Our recent work established that transient over-expression of NTHL1 leads to acquisition of several hallmarks of cancer in non-tumorigenic immortalized cells likely through interaction with nucleotide excision repair protein XPG. Here, we investigate how NTHL1 expression levels impact cellular sensitivity to cisplatin in non-tumorigenic immortalized cells and five non-small cell lung carcinomas cell lines...
March 2024: NAR cancer
https://read.qxmd.com/read/38381482/epistasis-between-mutator-alleles-contributes-to-germline-mutation-spectrum-variability-in-laboratory-mice
#18
JOURNAL ARTICLE
Thomas A Sasani, Aaron R Quinlan, Kelley Harris
Maintaining germline genome integrity is essential and enormously complex. Although many proteins are involved in DNA replication, proofreading, and repair, mutator alleles have largely eluded detection in mammals. DNA replication and repair proteins often recognize sequence motifs or excise lesions at specific nucleotides. Thus, we might expect that the spectrum of de novo mutations - the frequencies of C>T, A>G, etc. - will differ between genomes that harbor either a mutator or wild-type allele. Previously, we used quantitative trait locus mapping to discover candidate mutator alleles in the DNA repair gene Mutyh that increased the C>A germline mutation rate in a family of inbred mice known as the BXDs (Sasani et al...
February 21, 2024: ELife
https://read.qxmd.com/read/38377993/protein-language-models-assisted-optimization-of-a-uracil-n-glycosylase-variant-enables-programmable-t-to-g-and-t-to-c-base-editing
#19
JOURNAL ARTICLE
Yan He, Xibin Zhou, Chong Chang, Ge Chen, Weikuan Liu, Geng Li, Xiaoqi Fan, Mingsun Sun, Chensi Miao, Qianyue Huang, Yunqing Ma, Fajie Yuan, Xing Chang
Current base editors (BEs) use DNA deaminases, including cytidine deaminase in cytidine BE (CBE) or adenine deaminase in adenine BE (ABE), to facilitate transition nucleotide substitutions. Combining CBE or ABE with glycosylase enzymes can induce limited transversion mutations. Nonetheless, a critical demand remains for BEs capable of generating alternative mutation types, such as T>G corrections. In this study, we leveraged pre-trained protein language models to optimize a uracil-N-glycosylase (UNG) variant with altered specificity for thymines (eTDG)...
February 9, 2024: Molecular Cell
https://read.qxmd.com/read/38375718/tet-enzymes-and-5hmc-epigenetic-mark-new-key-players-in-carcinogenesis-and-progression-in-gynecological-cancers
#20
JOURNAL ARTICLE
A E Zacapala-Gómez, M A Mendoza-Catalán, V Antonio-Véjar, H Jiménez-Wences, J Ortíz-Ortíz, P A Ávila-López, C J Baños-Hernández, E G Salmerón-Bárcenas
DNA methylation is an epigenetic mechanism involving the transfer of a methyl group onto the C5 position of the cytosine to form 5-methylcytosine (5mC). In general, DNA methylation in cancer is associated with the repression of the expression of tumor suppressor genes (TSG) and the demethylation with the overexpression of oncogenes. DNA methylation was considered a stable modification for a long time, but in 2009, it was reported that DNA methylation is a dynamic modification. The Ten-Eleven-Translocations (TET) enzymes include TET1, TET2, and TET3 and participate in DNA demethylation through the oxidation of 5mC to 5-hydroxymethylcytosine (5hmC)...
February 2024: European Review for Medical and Pharmacological Sciences
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