Analysis of Gene Expression in an Inbred Line of Soft-Shell Clams (Mya arenaria) Displaying Growth Heterosis: Regulation of Structural Genes and the NOD2 Pathway by John J. Wilson, Janelle Grendler, Azaline Dunlap-Smith, Brian F. Beal, Shallee T. Page

“…Also differentially expressed was the nucleotide-binding oligomerization domain 2 (NOD2) receptor pathway that contributes to determination of growth, immunity, apoptosis, and proliferation. …”
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SRC enhanced cisplatin resistance in bladder cancer by reprogramming glycolysis and pentose phosphate pathway by Yuwen Gong, Dongyang Gao, Yibo Shi, Guangrui Fan, Xiaoquan Yu, Enguang Yang, Hui Cheng, Junqiang Tian, Hui Ding, Shanhui Liu, Shengjun Fu, Yan Tao, Yuan Shui, Liang Cheng, Lanlan Li, Zhiping Wang

“…SRC activates hexokinase2 which up-regulates glycolysis and especially the pentose phosphate pathway that leading to increased nucleotide synthesis and NADPH production which can neutralize reactive oxygen species (ROS) induced by cisplatin, thereby protecting bladder cancer cells from cisplatin-induced DNA damage. …”
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Characterization of a Small Supernumerary Marker Chromosome Derived from Xq28 and 14q11.2 Detected Prenatally by Akihiro Hasegawa, Osamu Samura, Taisuke Sato, Tomona Matsuoka, Yuki Ito, Kazuhiro Kajiwara, Hiroaki Aoki, Yuka Inage, Masahisa Kobayashi, Aikou Okamoto

“…Additionally, the single nucleotide polymorphism array analysis revealed copy number gains at Xq28 and 14q11.2. …”
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The complete mitochondrial genome and phylogenetic implications of Paradoxopsyllus custodis and Stenischia montanis yunlongensis by Bin Chen, Mingna Duan, Shuang Liu, Yafang Liu, Shaobo Tang, Dandan Jiang, Wei Gu, Quanfu Zhang, Xing Yang

“…The lengths of these genomes were 15,375 bp and 15,651 bp respectively, encompassing a total of 37 genes. Notably, all nucleotide combinations displayed a marked AT preference, with ATN as start codon for all 13 protein-coding genes in both species. …”
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NLRP3 Deficiency Attenuates Renal Fibrosis and Ameliorates Mitochondrial Dysfunction in a Mouse Unilateral Ureteral Obstruction Model of Chronic Kidney Disease by Honglei Guo, Xiao Bi, Ping Zhou, Shijian Zhu, Wei Ding

“…Background and Aims. The nucleotide-binding domain and leucine-rich repeat containing PYD-3 (NLRP3) inflammasome has been implicated in the pathogenesis of chronic kidney disease (CKD); however, its exact role in glomerular injury and tubulointerstitial fibrosis is still undefined. …”
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Genome Sequencing Reveals the Adaptation of Chickens to High Altitudes in Different Regions by Yizhou Hu, Xing Li, Qixin Guo, Lan Huang, Hao Bai, Guobin Chang

“…In total, 21,672,487 high-quality single-nucleotide polymorphisms were selected and used for subsequent analyses. …”
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The association of codon 392 polymorphism in ESR2 gene with breast cancer in Iran by Sakineh Abbasi, Samira Kalbasi

“…In codon 392 of exon 7, showed a silent SNP (silent single nucleotide polymorphism). The frequency of allele G in codon 392 (CTC ? …”
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Evidence for Directed Evolution of Larger Size Motif in Arabidopsis thaliana Genome by Rajesh Mehrotra, Amit Yadav, Purva Bhalothia, Ratna Karan, Sandhya Mehrotra

“…As we increased the spacer length, one nucleotide at a time, the probability of its occurrence in genome decreased. …”
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Regulation of stress granule maturation and dynamics by poly(ADP-ribose) interaction with PARP13 by Shang-Jung Cheng, Temitope Gafaar, Jijin R. A. Kuttiyatveetil, Aleksandr Sverzhinsky, Carla Chen, Minghui Xu, Allison Lilley, John M. Pascal, Anthony K. L. Leung

“…This fragmented stress granule phenotype is also apparent in PARP13 variants with cancer-associated single-nucleotide polymorphisms (SNPs) that disrupt PAR binding. …”
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A mechanism-informed deep neural network enables prioritization of regulators that drive cell state transitions by Xi Xi, Jiaqi Li, Jinmeng Jia, Qiuchen Meng, Chen Li, Xiaowo Wang, Lei Wei, Xuegong Zhang

“…Some regulators reveal potential new therapeutic targets, drug repurposing possibilities, and putative causal single nucleotide polymorphisms. This method to analyze single-cell multi-omics data demonstrates how the interpretable design of neural networks can better decode biological systems.…”
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Role of Inflammasomes in Neuroimmune and Neurodegenerative Diseases: A Systematic Review by Yue Lang, Fengna Chu, Donghui Shen, Weiguanliu Zhang, Chao Zheng, Jie Zhu, Li Cui

“…Several components of inflammasomes, such as nucleotide-binding oligomerization domain- (NOD-) like receptor, absent in melanoma 2- (AIM2-) like receptors (ALRs), apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC), and caspase-1, as well as the upstream factors and downstream effectors, are associated with the initiation and development of MS and its animal model, experimental autoimmune encephalomyelitis. …”
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Crown Gall Induced by a Natural Isolate of <i>Brucella</i> (<i>Ochrobactrum</i>) <i>pseudogrignonense</i> Containing a Tumor-Inducing Plasmid by Marjolein J. G. Hooykaas, Paul J. J. Hooykaas

“…Whole-genome sequencing revealed that this bacterium contained three large DNA circles with rRNA and tRNA genes, representing one chromosome and two chromids, respectively, and two megaplasmids, including a Ti plasmid. Average nucleotide identity (ANIb, ANIm) and genome-to-genome distance (GGDC) values above the thresholds of 96% and 70%, respectively, showed that NBC51/LBA8980 belonged to the species <i>Brucella</i> (<i>Ochrobactrum) pseudogrignonense.…”
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Enrichment of rare alleles within epigenetic chromatin marks in the first intron by Shin-Sang Jo, Sun Shim Choi

“…We estimated the proportions of rare single nucleotide polymorphisms with a minor allele frequency < 0.01 located in several histone marks in the first introns of various genes, and compared them with those in other introns and those in 2-kb upstream regions. …”
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DNA Damage Induced by Alkylating Agents and Repair Pathways by Natsuko Kondo, Akihisa Takahashi, Koji Ono, Takeo Ohnishi

“…N-methylations are removed by base excision repair, AlkB homologues, or nucleotide excision repair (NER). O6-methylguanine (MeG), which can eventually become cytotoxic and mutagenic, is repaired by O6-methylguanine-DNA methyltransferase, and O6MeG:T mispairs are recognized by the mismatch repair system (MMR). …”
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The Relationship between Cadherin Polymorphisms and the Risk of Delayed Encephalopathy after Acute Carbon Monoxide Poisoning in the Chinese Han Population by Xuejiao Liu, Jiao Zeng, Xiaoli Zhang, Jiapeng Gu, Fan Zhang, Yongkai Han, Ping Zhang, Wenqiang Li, Renjun Gu

“…The purpose of this study was to analyze the relationship between cadherin gene single-nucleotide polymorphisms (SNPs) and the risk of delayed encephalopathy after acute carbon monoxide poisoning (DEACMP). …”
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Shared mechanisms of enhanced plasmid maintenance and antibiotic tolerance mediated by the VapBC toxin:antitoxin system by Sarah Hollingshead, Gareth McVicker, Maria R. Nielsen, YuGeng Zhang, Giulia Pilla, Rebekah A. Jones, Jonathan C. Thomas, Sarah E. H. Johansen, Rachel M. Exley, Ditlev E. Brodersen, Christoph M. Tang

“…We found that the plasmid in CS14 is stabilized by a single nucleotide polymorphism (SNP) in its vapBC TA system. …”
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Association of TNF-α gene promoter polymorphism with primary open-angle glaucoma by A.V. Shevchenko, V.F. Prokof’ev, V.I. Konenkov, A.V. Eremina, A.N. Trunov, V.V. Chernykh

“…We failed to identify any single nucleotide polymorphism or complexes negatively associated with POAG.…”
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Genomic insights into genetic diversity and seed coat color change in common bean composite populations by Eva Plestenjak, Eva Plestenjak, Mohamed Neji, Lovro Sinkovič, Vladimir Meglič, Barbara Pipan

“…More than 8.6 million high-confidence single nucleotide polymorphisms (SNPs) were identified. Genetic diversity metrics such as nucleotide diversity (π), observed heterozygosity (Ho), expected heterozygosity (He) and allelic richness (Ar) were calculated. …”
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Investigating mobile element variations by statistical genetics by Shohei Kojima

“…The use of MEVs in eQTL analysis and GWAS has a minimal impact on the discovery of genome loci associated with gene expression and disease; most disease-associated haplotypes can be identified by single nucleotide variations (SNVs). On the other hand, it helps make hypotheses about causal variants or effector variants. …”
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MsDpo4—a DinB Homolog from Mycobacterium smegmatis—Is an Error-Prone DNA Polymerase That Can Promote G:T and T:G Mismatches by Amit Sharma, Deepak T. Nair

“…We show that a representative homolog from Mycobacterium smegmatis (MsDpo4) can carry out template-dependent nucleotide incorporation and therefore is a DNA polymerase. …”
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