Nucleosides, Nucleotides & Nucleic Acids最新文献_第5页

Evaluation and normalization of a set of reliable reference genes for quantitative sgk-1 gene expression analysis in Caenorhabditis elegans-focused cancer research. 在以 elegans 为重点的癌症研究中，对一组用于 sgk-1 基因表达定量分析的可靠参考基因进行评估和归一化。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2025-01-01 Epub Date: 2024-02-15 DOI: 10.1080/15257770.2024.2317413

Özgür Ülkü Özdemir, Kübra Yurt, Ayşe Nur Pektaş, Şeyda Berk

{"title":"Evaluation and normalization of a set of reliable reference genes for quantitative sgk-1 gene expression analysis in Caenorhabditis elegans-focused cancer research.","authors":"Özgür Ülkü Özdemir, Kübra Yurt, Ayşe Nur Pektaş, Şeyda Berk","doi":"10.1080/15257770.2024.2317413","DOIUrl":"10.1080/15257770.2024.2317413","url":null,"abstract":"Multiple signaling pathways have been discovered to play a role in aging and longevity, including the insulin/IGF-1 signaling system, AMPK pathway, TOR signaling, JNK pathway, and germline signaling. Mammalian serum and glucocorticoid-inducible kinase 1 (sgk-1), which has been associated with various disorders including hypertension, obesity, and tumor growth, limits survival in C. elegans by reducing DAF-16/FoxO activity while suppressing FoxO3 activity in human cell culture. C. elegans provides significant protection for a number of genes associated with human cancer. The best known of these are the lin-35/pRb (mammalian ortholog pRb) and CEP-1 (mammalian ortholog p53) genes. Therefore, in this study, we aimed to investigate the expression analyzes of sgk-1, which is overexpressed in many types of mammalian cancer, in mutant lin-35 and to demonstrate the validation of reference genes in wild-type N2 and mutant lin-35 for C. elegans-focused cancer research. To develop functional genomic studies in C. elegans, we evaluated the expression stability of five candidate reference genes (act-1, ama-1, cdc-42, pmp-3, iscu-1) by quantitative real-time PCR using five algorithms (geNorm, NormFinder, Delta Ct method, BestKeeper, RefFinder) in N2 and lin-35 worms. According to our findings, act-1 and cdc-42 were effective in accurately normalizing the levels of gene expression in N2 and lin-35. act-1 and cdc-42 also displayed the most consistent expression patterns, therefore they were utilized to standardize expression level of sgk-1. Furthermore, our results clearly showed that sgk-1 was upregulated in lin-35 worms compared to N2 worms. Our results highlight the importance of definitive validation using mostly expressed reference genes.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"91-110"},"PeriodicalIF":1.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139741536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Downregulation of MGLL and microRNAs (miR-302b-5p, miR-190a-3p, miR-450a-2-3p) in non-small cell lung cancer: potential roles in pathogenesis. 非小细胞肺癌中MGLL和microrna （miR-302b-5p, miR-190a-3p, miR-450a-2-3p）的下调：在发病机制中的潜在作用

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2024-12-14 DOI: 10.1080/15257770.2024.2439904

Cilem Ozdemır, Ozgur Ilhan Celık, Arife Zeybek, Tugba Suzek, Younes Aftabı, Sevim Karakas Celık, Tuba Edgunlu

{"title":"Downregulation of MGLL and microRNAs (miR-302b-5p, miR-190a-3p, miR-450a-2-3p) in non-small cell lung cancer: potential roles in pathogenesis.","authors":"Cilem Ozdemır, Ozgur Ilhan Celık, Arife Zeybek, Tugba Suzek, Younes Aftabı, Sevim Karakas Celık, Tuba Edgunlu","doi":"10.1080/15257770.2024.2439904","DOIUrl":"https://doi.org/10.1080/15257770.2024.2439904","url":null,"abstract":"Genes involved in lipid metabolism have been considered potential therapeutic targets in lung cancer because lipid metabolism is severely disrupted in this cancer. Monoglyceride lipase (MGLL) is a lipolytic enzyme that converts monoacylglycerides to fatty acids and glycerol. MicroRNAs (miRNA), one of the most important epigenetic regulators of gene expression, are also considered potential biomarkers in diagnosing, treating, and prognosis lung cancer. This study aimed to investigate the potential effects of MGLL and related miRNAs (miR-302b-5p, miR-190a-3p, miR-450a-2-3p) in the pathogenesis of non-small cell lung cancer (NSCLC) by examining their expression levels and regulatory mechanisms. We analysed the expression levels of MGLL and miRNAs in 30 NSCLC and 20 non-cancerous tissues by qPCR. We performed in silico analyses to determine the biological functions of MGLL and miRNAs in NSCLC. A protein-protein interaction (PPI) network was constructed for MGLL, and gene ontology (GO) analysis, and the interacting genes were analysed using the TCGAnalyzer tool. Our study showed that the expression levels of MGLL, miR-302b-5p, miR-190a-3p and miR-450a-2-3p were significantly decreased in NSCLC tissues (p < 0.05). Also, according to TCGAnalyzer, MSRB3, HTR4, and FCER1G genes were downregulated genes for NSCLC. We showed that miR-302b-5p, miR-190a-3p, and miR-450a-2-3p significantly regulate the TGF-β signalling pathway. In conclusion, this study provides evidence for the potential role of MGLL and microRNAs (miR-302b-5p, miR-190a-3p, miR-450a-2-3p) in NSCLC. In subsequent studies, it was determined that MSRB3, FCER1G and LTB4R2 genes, especially the HTR4 gene, could be potential target genes for lung cancer.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-17"},"PeriodicalIF":1.1,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142824458","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Convenient syntheses of isotopically labeled pyrimidine 2'-deoxynucleosides and their 5-hydroxy oxidation products. 方便合成同位素标记嘧啶2′-脱氧核苷及其5-羟基氧化产物。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2024-12-09 DOI: 10.1080/15257770.2024.2437038

Yixuan Gao, Eric T Kool

引用次数: 0

System biology analysis of miRNA-gene interaction network reveals novel drug targets in breast cancer. mirna -基因相互作用网络的系统生物学分析揭示了乳腺癌的新药物靶点。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2024-12-04 DOI: 10.1080/15257770.2024.2436421

Jing Huang, Yichun Gao, Jipan Liu, Zhiyuan Yang, Xiaoli Zhang

{"title":"System biology analysis of miRNA-gene interaction network reveals novel drug targets in breast cancer.","authors":"Jing Huang, Yichun Gao, Jipan Liu, Zhiyuan Yang, Xiaoli Zhang","doi":"10.1080/15257770.2024.2436421","DOIUrl":"https://doi.org/10.1080/15257770.2024.2436421","url":null,"abstract":"Breast cancer is a heterogeneous disease that is ranked as one of the most common cancers worldwide. Currently, although there are existing molecules such as progesterone receptor and estrogen receptor for breast cancer treatment, discovering more effective drug targets is still in urgent need. In this study, we have obtained six sequencing datasets of breast cancer from GEO database and identified a set of differentially expressed molecules, including 67 miRNAs and 133 genes. Function enrichment analysis by miRPathDB database indicated that targets of 11 miRNAs could be enriched in breast cancer pathway with a p-value ≤ .05. A special miRNA-gene interaction network was constructed for analysis of the progression of breast cancer. We then ranked the importance of each molecule (i.e. miRNA and gene) by their node centrality indexes in the network and selected the top 10% of molecules. The statistical analysis of these molecules showed three miRNAs (hsa-miR-1275, hsa-miR-2392, hsa-miR-3141) have significant effects on the prognosis and survival of patients. By searching for potential drugs in Drugbank database, we have identified four candidates (phenethyl isothiocyanate, amuvatinib, theophylline, trifluridine) for targeting these genes. In conclusion, we believe that these drugs and their analogs could be used in the targeted therapy of breast cancer in the future.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-16"},"PeriodicalIF":1.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142780707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The association of piR-651 and piR-823 on metastatic and invasive characteristics of triple negative breast cancer cells. piR-651和piR-823与三阴性乳腺癌细胞转移和侵袭特性的关系

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2024-12-04 DOI: 10.1080/15257770.2024.2437037

Çağrı Öner, Faruk Köser, Ertuğrul Çolak

{"title":"The association of piR-651 and piR-823 on metastatic and invasive characteristics of triple negative breast cancer cells.","authors":"Çağrı Öner, Faruk Köser, Ertuğrul Çolak","doi":"10.1080/15257770.2024.2437037","DOIUrl":"https://doi.org/10.1080/15257770.2024.2437037","url":null,"abstract":"PIWI-Interacting RNAs are small non-coding RNAs derived from single-stranded RNAs which plays a crucial role in epigenetic regulation through transposon silencing and mRNA degradation via deamination. This study aimed to inhibit piR-651 and piR-823 in MDA-MB-231 triple-negative breast cancer cells and to explore their potential effects on healthy HUVEC cells. Non-target, anti-piR-651, and anti-piR-823 sequences were transfected in bothHUVEC and MDA-MB-231 cells using Lipofectamine. Proliferation and motility were assessed at 24, 48, and 72 h post-transfection in both cell lines. Based on the motility findings, MDA-MB-231 cells were underwent an invasion assay using crystal violet staining. The expressions of Ki-67, HIF-1α, MMP-2, and MMP-9 genes were measured at 48 h, when both cell lines exhibited the most significant effects of inhibition. The optimal time for proliferation of anti-piR-651 and anti-piR-823 transfected MDA-MB-231 cells was determined to be at 48 h, as indicated by decreased motility and invasion assay results (p < 0.001). NeverthelessHowever, there was no significant difference in the motility and proliferation of HUVECss transfected with anti-piR-651 and anti-piR-823 compared to the control group (p > 0.05). Asides from MMP-2 in anti-piR-823 transfected HUVECs and HIF-1α in anti-piR-823 transfected MDA-MB-231 cells, gene expressions of Ki-67, HIF-1α, MMP-2, and MMP-9 were reduced in both cell lines (p < 0.001). Inhibition of piR-651 and piR-823 decreased the survival and metastasis of cancer cells, without causing vital structural changes in healthy cells. Future research in cancer gene therapy or genetic modification may benefit from investigating piR-651 and piR-823 as possible inhibitors of breast cancer invasion and metastasis.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-17"},"PeriodicalIF":1.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142780719","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Revolutionizing DNA: advanced modification techniques for next-gen nanotechnology. 革新 DNA：新一代纳米技术的先进修饰技术。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2024-11-26 DOI: 10.1080/15257770.2024.2432992

Pratikeswar Panda, Rajaram Mohapatra

{"title":"Revolutionizing DNA: advanced modification techniques for next-gen nanotechnology.","authors":"Pratikeswar Panda, Rajaram Mohapatra","doi":"10.1080/15257770.2024.2432992","DOIUrl":"https://doi.org/10.1080/15257770.2024.2432992","url":null,"abstract":"The comprehensive advancement in DNA modification and coupling is driving DNA nanotechnology to new heights, paving the way for groundbreaking innovations in healthcare, materials science, and beyond. The ability to engineer DNA with tailored properties and functionalities underscores its immense potential in creating novel materials and devices. Utilizing a spectrum of techniques-such as amino handles, thiol groups, alkynes, azides, Diels-Alder reactions, hydrazides, and aminooxy functions-enables diverse coupling strategies, including Palladium-Catalyzed Couplings, to construct intricate DNA nanostructures. Further coupling modifications encompass hydrophobic alterations, redox-active moieties, chemical crosslinking agents, and Biotinylation. These modifications significantly broaden DNA's functional repertoire, offering precise control over interactions, structures, and features. By leveraging these advanced techniques, alongside next-generation sequencing (NGS)-based DNA modifications, researchers can design and implement DNA nanostructures with specific capabilities and applications, showcasing DNA's versatility as a programmable biomaterial. Through meticulous design and strategic implementation, DNA nanotechnology achieves unprecedented levels of precision and functionality, ushering in a new era of technological advancements and applications. These advanced DNA modification techniques hold great potential for transformative applications in nanotechnology, paving the way for innovations in drug delivery, diagnostics, and bioengineering.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-32"},"PeriodicalIF":1.1,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142716383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Clinical relevance and function of HMGB1 gene polymorphism and expression in colorectal cancer. 结直肠癌中 HMGB1 基因多态性和表达的临床相关性及功能。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2024-11-26 DOI: 10.1080/15257770.2024.2432991

Fang Wang, Zhijun Huang, Jianping Li, Xueren Gao

{"title":"Clinical relevance and function of HMGB1 gene polymorphism and expression in colorectal cancer.","authors":"Fang Wang, Zhijun Huang, Jianping Li, Xueren Gao","doi":"10.1080/15257770.2024.2432991","DOIUrl":"https://doi.org/10.1080/15257770.2024.2432991","url":null,"abstract":"High HMGB1 levels contribute to the development and metastasis of tumors such as colorectal cancer (CRC). The current investigation sought to evaluate the association of a functional InDel polymorphism (rs34000982) on the HMGB1 gene with CRC susceptibility and tumor stage and the clinical relevance of HMGB1 gene expression. A total of 600 CRC patients and 600 healthy control individuals were genotyped by a polymerase chain reaction-polyacrylamide gel electrophoresis assay. The findings demonstrated that the rs34000982 Ins allele or Ins/Ins genotype was associated not only with reduced susceptibility to CRC, especially stage III-IV CRC (Ins vs. Del: OR = 0.65, 95%CI = 0.51-0.82, p < 0.001; Ins/Ins vs. Del/Del: OR = 0.29, 95%CI = 0.14- 0.60, p < 0.001), but also with tumor stage. CRC patients carrying the Ins allele or Ins/Ins genotype had a significantly lower risk of stage III-IV tumors (Ins vs. Del: OR = 0.69, 95%CI = 0.53- 0.91; Ins/Ins vs. Del/Del: OR = 0.41, 95%CI = 0.18-0.94). Functional research revealed that the rs34000982 Ins allele enabled hsa-miR-944 to interact with the 3' untranslated region of HMGB1. In addition, HMGB1 gene expression levels were associated not only with multiple immune cell infiltration, but also with multiple anti-CRC drug sensitivities. The current findings suggest that the HMGB1 rs34000982 polymorphism may serve as a marker of CRC susceptibility and progression in the Chinese population, and HMGB1 levels may serve as an anti-CRC drug sensitivity marker.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-11"},"PeriodicalIF":1.1,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142716310","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomic determinants in pathogenicity of SARS-CoV-2 versa common cold coronaviruses. SARS-CoV-2 与普通感冒冠状病毒致病性的基因组决定因素。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2024-11-21 DOI: 10.1080/15257770.2024.2430397

Zahra Arab-Bafrani, Majid Nikoubin-Boroujeni, Saeedeh Ebrahimi, Ali Teimoori, Elham Heidari, Elham Mousavi

{"title":"Genomic determinants in pathogenicity of SARS-CoV-2 versa common cold coronaviruses.","authors":"Zahra Arab-Bafrani, Majid Nikoubin-Boroujeni, Saeedeh Ebrahimi, Ali Teimoori, Elham Heidari, Elham Mousavi","doi":"10.1080/15257770.2024.2430397","DOIUrl":"https://doi.org/10.1080/15257770.2024.2430397","url":null,"abstract":"Determination of the different short oligonucleotide features in the full genome of fatal and mild coronavirus strains can show the researchers how these viruses evolved and became virulent strains. To this aim, at first, in the full genome of all coronavirus strains included in this study, the observed and expected frequency of dinucleotide to hexanucleotide was obtained using Markov method. Then odds ratio (observed/expected abundances) of short oligonucleotide was computed and considered as the raw data (features). Finally, ten distinct weighting algorithms approaches (Information Gain, Information Gain Ratio, Rule, Deviation, Chi Squared, Gini Index, Uncertainty, Relief, Support Vector Machine (SVM), and PCA) was employed on the features to identify oligonucleotide distribution differences across the full genome of SARS-related viruses compared to common cold coronaviruses. Totally among 5440 features (16 dinucleotides, 64 trinucleotides, 256 tetra nucleotides, 1024 penta-nucleotides, and 4096 Hexa-nucleotides), CC, CCA, CCAC, ACCAC, and CACCAC motifs were selected by 80 -90% of all weighting algorithms models to distinguish virulent strains from mild coronaviruses. These remarkable oligonucleotides might point toward the existence of some particular RNA elements that might be involved in viral virulence and thus can be targeted for viral treatment in the future.","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-13"},"PeriodicalIF":1.1,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142687620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Neurotransmitters and neural hormone-based probes for quadruplex DNA sequences associated with neurodegenerative diseases. 基于神经递质和神经激素的探针，用于检测与神经退行性疾病相关的四重 DNA 序列。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2024-11-19 DOI: 10.1080/15257770.2024.2431145

Callie Rohrer, Alexis Palumbo, Marissa Paul, Erin Reese, Swarna Basu

引用次数: 0

Design and synthesis of fluorescence-labeled nucleotide with a cleavable aryl-triazene linker for DNA sequencing by synthesis. 设计并合成带有可裂解芳基三氮烯连接体的荧光标记核苷酸，用于 DNA 测序合成。

IF 1.1 4区生物学

Nucleosides, Nucleotides & Nucleic Acids Pub Date : 2024-11-18 DOI: 10.1080/15257770.2024.2429696

Bo-Wei Tang, Ping-Yang Wang, Yu-Mei Shen

引用次数: 0