EFFECT OF FLANKING SEQUENCES ON THE ACCURACY OF THE RECOGNITION OF TRANSCRIPTION FACTOR BINDING SITES by T. M. Khlebodarova, D. Yu. Oshchepkov, V. G. Levitsky, O. A. Podkolodnaya, E. V. Ignatieva, E. A. Ananko, I. L. Stepanenko, N. A. Kolchanov

“…For 20 % of TFs, binding site sequences selected in vitro had a broader range of permissible significant nucleotides not found in natural sites. The optimum lengths of DNA sequences including natural binding sites, at which they are recognized most accurately, were estimated by the weight matrix method. …”
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Effect of different drying methods on the taste and volatile compounds, sensory characteristics of Takifugu obscurus by Youyou Li, Shui Jiang, Yiwen Zhu, Wenzheng Shi, Yin Zhang, Yuan Liu

“…Different drying methods had significant influence on the color, rehydration, 5'-nucleotides, free amino acids and volatile components (P < 0.05). …”
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Long Noncoding RNA LOC100129940-N Is Upregulated in Papillary Thyroid Cancer and Promotes the Invasion and Progression by Manting Choy, Yan Guo, Hai Li, Guohong Wei, Runyi Ye, Weiwei Liang, Haipeng Xiao, Yanbing Li, Hongyu Guan

“…Long noncoding RNAs (lncRNAs), a class of noncoding RNAs (ncRNAs) longer than 200 nucleotides, are aberrantly expressed in malignant diseases, including PTC. …”
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Influence of allelic polymorphism in the 3’ untranslated region of the <i>StTCP23</i> gene on the tolerance of potato cultivars to the potato spindle tuber viroid by N. V. Mironenko, A. V. Kochetov, O. S. Afanasenko

“…Cultivars with the A allele (‘Gala’, ‘Colomba’, ‘Favorit’, and ‘Fioletovy’) identical to the reference genome or a high dose of the C allele with a deletion of four nucleotides (cv. ‘Impala’) were characterized by high susceptibility already at the primary (firstyear) infection with the PSTVd. …”
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Multi-locus CRISPRi targeting with a single truncated guide RNA by Molly M. Moore, Siddarth Wekhande, Robbyn Issner, Alejandro Collins, Anna J. Cruz, Yanjing V. Liu, Nauman Javed, Salvador Casaní-Galdón, Jason D. Buenrostro, Charles B. Epstein, Eugenio Mattei, John G. Doench, Bradley E. Bernstein, Noam Shoresh, Fadi J. Najm

“…We screen over 13,000 possible CTCF binding sites with 24 guides at 10 nucleotides in spacer length. These truncated guides direct CRISPRi-mediated deposition of repressive H3K9me3 marks and disrupt transcription factor binding at most sequence match target sites. …”
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Metabolite Profiling of Sorghum Seeds of Different Colors from Different Sweet Sorghum Cultivars Using a Widely Targeted Metabolomics Approach by Yaxing Zhou, Zhenguo Wang, Yan Li, Zhigang Li, Hui Liu, Wei Zhou

“…We identified 651 metabolites that were divided into 24 categories, including fatty acids, glycerolipids, flavonoids, benzoic acid derivatives, anthocyanins, and nucleotides and its derivatives. Among them, 217 metabolites were selected as significantly differential metabolites which could be related to the seed color by clustering analysis, principal component analysis (PCA), and orthogonal signal correction and partial least squares-discriminant analysis (OPLS-DA). …”
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Genomic, Evolutionary, and Pathogenic Characterization of a New <i>Polerovirus</i> in Traditional Chinese Medicine <i>Viola philippica</i> by Yuanling Chen, Gaoxiang Chen, Jiaping Yu, Yali Zhou, Shifang Fei, Haorong Chen, Jianxiang Wu, Shuai Fu

“…VPPV possesses a linear, positive-sense, single-stranded RNA genome consisting of 5535 nucleotides (nt) and encodes seven highly overlapping open reading frames (ORFs). …”
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Analysis of MicroRNA -155-5p Expression in Patients with Primary Myelofibrosis. by Sarah I. Khaleel, Jaffar N. AlAlsaidissa

“…MicroRNAs (miRNAs) are short, non-protein-coding RNA molecules, typically 18–24 nucleotides in length. Dysregulation of miRNAs may contribute to the disease phenotype. …”
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Discrimination of superficial lymph nodes using ultrasonography and tissue metabolomics coupled with machine learning by Lu Li, Xinyue Wang, Hongyan Deng, Wenjuan Lu, Yasu Zhou, Xinhua Ye, Yong Li, Jie Wang

“…Specifically, the lymphoma group exhibited higher levels of nucleotides (inosine monophosphate and adenosine diphosphate) as well as glutamic acid, and the metastasis group was characterized by higher levels of carbohydrates, acylcarnitines, glycerophospholipids, and uric acid. …”
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Correlation between dominant bacterial community and non-volatile organic compounds during the fermentation of shrimp sauces by Ruichang Gao, Huijie Liu, Ying Li, Hongying Liu, Yue Zhou, Li Yuan

“…The results showed that the AAN, TVB-N, organic acid, 5'-nucleotide and FAA content were in range of 0.93–1.42 g/100mL, 49.91–236.27 mg/100mL, 6.65–20.68 mg/mL, 3.51–6.56 mg/mL and 81.27–102.90 mg/mL. …”
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Complexed Crystal Structure of Saccharomyces cerevisiae Dihydroorotase with Inhibitor 5-Fluoroorotate Reveals a New Binding Mode by Hong-Hsiang Guan, Yen-Hua Huang, En-Shyh Lin, Chun-Jung Chen, Cheng-Yang Huang

“…DHOase catalyzes the reversible cyclization of N-carbamoyl aspartate (CA-asp) to dihydroorotate (DHO) in the third step of the pathway for the biosynthesis of pyrimidine nucleotides and is an attractive target for potential anticancer and antimalarial chemotherapy. …”
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The SpxA1-TenA toxin-antitoxin system regulates epigenetic variations of Streptococcus pneumoniae by targeting protein synthesis. by Shaomeng Wang, Xiu-Yuan Li, Mengran Zhu, Haiteng Deng, Juanjuan Wang, Jing-Ren Zhang

“…Because spontaneous variations frequently occur during bacterial growth in the number of the AT di-nucleotides in the promoter region of the spxA1-tenA operon, this locus acts as a programmed genetic switch that generates pneumococcal subpopulations with epigenetic and phenotypic diversity.…”
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Transmission of potato spindle tuber viroid between <i>Phytophthora infestans</i> and host plants by O. S. Afanasenko, A. V. Khiutti, N. V. Mironenko, N. M. Lashina

“…Potato spindle tuber viroid (PSTVd) is a naked, circular, single-stranded RNA (356–363 nucleotides in length) which lacks any protein-coding sequences. …”
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MicroRNA and Putative Target Discoveries in Chrysanthemum Polyploidy Breeding by Fengjiao Zhang, Jingya Zhao, Sujuan Xu, Weimin Fang, Fadi Chen, Nianjun Teng

“…MicroRNAs (miRNAs), around 22 nucleotides (nt) in length, are a class of endogenous and noncoding RNA molecule that play an essential role in plant development, either by suppressing the transcription of target genes at a transcriptional level or inhibiting translation at a posttranscriptional level. …”
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SequenceCraft: machine learning-based resource for exploratory analysis of RNA-cleaving deoxyribozymes by M. Eremeyeva, Y. Din, N. Shirokii, N. Serov

“…This became possible with the development of a unique curated database of > 350 RNA-cleaving catalytic cores, property-based sequence representations allowing to work with both conventional and chemically modified nucleotides, and optimized kobs predicting algorithm achieving Q2 > 0.9 on experimental data published to date. …”
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Energy status regulated umami compound metabolism in harvested shiitake mushrooms (Lentinus edodes) with spores triggered to release by Rongrong Xia, Xuemei Zhao, Guang Xin, Libin Sun, Heran Xu, Zhenshan Hou, Yunting Li, Yafei Wang

“…Meanwhile, the activities of phosphohexose isomerase, succinate dehydrogenase, glucose-6-phosphate dehydrogenase and cytochrome c oxidase and the contents of umami nucleotides and amino acids were maintained at higher levels in mushrooms with spore release. …”
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Effects of Reheating Methods on the Quality of Prepared Pork Rib Soup with Carrot and Corn by LU Jiaxin, REN Weizhao, REN Jingnan, DONG Huilong, FAN Gang, WEI Jianying, WANG Zhuo, HUANG Shengwei, WU Qufang, ZHANG Benpeng, QIU Xiaoxiao

“…The steam reheated soup exhibited a good combination of umami amino acids and nucleotides, presenting the strongest umami taste with an equivalent umami concentration (EUC) of 178.4 g/100 g, followed by those reheated by microwave, open flame, and water bath (EUC of 109.9, 100.2, and 56.5 g/100 g, respectively). …”
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Polymorphism of <i>Sdr</i> genes regulating seed dormancy in <i>Triticum persicum</i> Vav. and <i>Triticum aethiopicum</i> Jakubz. by M. S. Bazhenov, E. D. Guseva, V. S. Rubets

“…Previously unknown polymorphisms were found in the promoter of the Sdr-B1 gene in the studied accessions. A deletion of 16 nucleotides was detected in the 3’-terminal region of the TraesCS2B02G215200 gene, located on the complementary DNA chain close to the 3’-end of the Sdr-B1 gene. …”
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Synthesis and Antiviral Evaluation of 5-(4-Aryl-1,3-butadiyn-1-yl)-uridines and Their Phosphoramidate Pronucleotides by Evan Saillard, Otmane Bourzikat, Koffi Assa, Vincent Roy, Luigi A. Agrofoglio

“…Nucleoside analogs, which mimic natural nucleotides, have shown promise in targeting RNA-dependent RNA polymerases (RdRps). …”
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Exploring serum miR-33b as a novel diagnostic marker for hypercholesterolemia and obesity: insights from a pilot case-control study by Yaser Masoumi-Ardakani, Mostafa Eghbalian, Hossein Fallah, Alireza Jafari, Beydolah Shahouzehi

“…MicroRNAs (miRNAs) are small, conserved, non-coding RNA sequences consisting of approximately 22 nucleotides, playing crucial roles in biological and pathological functions. …”
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