Chromosome 1 Sequence Analysis of C57BL/6J-Chr1KM Mouse Strain by Fuyi Xu, Tianzhu Chao, Yiyin Zhang, Shixian Hu, Yuxun Zhou, Hongyan Xu, Junhua Xiao, Kai Li

“…With 36.6× average coverage of the entire genome, 0.48 million single nucleotide polymorphisms (SNPs) and 96,679 indels were detected on Chr 1 through comparison with reference strain C57BL/6J. …”
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The transcriptional regulation effects of histidine, isoleucine and glutamate on free exopolysaccharide biosynthesis of Streptococcus thermophilus 937 by Yunchao Wa, Yunchao Wa, Xia Zhao, Xia Zhao, Chenchen Zhang, Chenchen Zhang, Hengxian Qu, Hengxian Qu, Dawei Chen, Dawei Chen, Xia Chen, Xia Chen, Yujun Huang, Yujun Huang, Ruixia Gu, Ruixia Gu

“…Our previous studies showed f-EPS production from S. thermophilus 937 was increased 2-fold in the presence of 15 mM of glutamate, isoleucine, and histidine in the chemically defined medium.MethodsIn this study, we used transcriptomics and qPCR to further explore the specific mechanism of the enhanced effect of 3 amino acids on the f-EPS biosynthesis of S. thermophilus 937.ResultsThe mRNA-seq analysis and targeted pathway analysis indicated that genes associated with histidine/valine/leucine/ isoleucine/phenylalanine/tyrosine/tryptophan synthesis, galactose metabolism, purine metabolism and quorum sensing in S. thermophilus 937 were significantly upregulated under increasing concentrations of histidine, isoleucine and glutamate in chemically defined medium (CDM). qPCR results showed that the significant upregulation of galactose metabolism- and nucleotide sugar synthesis-related genes was attributed to the increase in glutamate concentration, and glutamate could induce the expression of galR. …”
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Updates on hosts and distribution of pepper yellow leaf curl Indonesia virus and squash leaf curl China virus in Central Java Province, Indonesia by Adyatma Irawan Santosa, Adenisa Hanifah Irbati, Geby Nandita Cahyaning Pratiwi, Antama Surwadinata, Putri Laeshita, Krisnanda Surya Dharma, Reko Saputra Jaya, Annisa Lisa Andriyani, Chilya Qurrota A'yun, Chusnu Naura Syifa Fatika

“…PepYLCIV OR924279 and OR924280 formed a subgroup with LC542629 from Bali in the phylogenetic tree constructed using MEGA11, and shared 95.8 – 96.7% identities at nucleotide (nt) and 98.4 – 99.5% at amino acid (aa) levels according to Sequence Demarcation Tool v1.2 software. …”
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Association between IFN-γ +874A/T and IFN-γR1 (-611A/G, +189T/G, and +95C/T) Gene Polymorphisms and Chronic Periodontitis in a Sample of Iranian Population by Zahra Heidari, Hamidreza Mahmoudzadeh-Sagheb, Mohammad Hashemi, Somayeh Ansarimoghaddam, Bita Moudi, Nadia Sheibak

“…Materials and Methods. 310 individuals were enrolled in the study including 210 CP patients and 100 healthy controls. Single nucleotide polymorphisms at IFN-γ (+874A/T) and IFN-γR1 (-611A/G, +189T/G, and +95C/T) were analyzed by ARMS-PCR and PCR-RFLP methods. …”
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Population features of prevalence and clinical-diagnostic role of NOD2 gene polymorphisms associated with Crohn’s disease by D. A. Kuznetsova, M. V. Merzlyakov, G. V. Vavin, A. S. Razumov, V. L. Emanue

“…According to literature data analysis it is possible to conclude that there are clear populationrelated features of the prevalence, clinical and diagnostic role of NOD2 genetic polymorphism associated to Crohn's disease that requires development of the international data bank of all genetic nucleotide polymorphisms associated to various stages of CD pathogenesis in different countries and populations. …”
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Causality between insulin use and malignant tumors of the digestive system: a two-sample mendelian randomized study by DengZhuo Chen, YongLi Ma, JingHui Li, Liang Wen, GuoSheng Zhang, ChengZhi Huang, XueQing Yao

“…Methods We selected single nucleotide polymorphisms (SNPs) strongly associated with insulin use as instrumental variables and used aggregated statistics on digestive system neoplasms as the outcome event. …”
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Molecular identification of Newcastle disease virus isolated on the poultry farm of the Moscow Oblast in summer of 2022 by А. А. Treshchalina, А. А. Rtishchev, Е. Yu. Shustova, А. V. Belyakova, A. S. Gambaryan, Е. Yu. Boravleva

“…The Newcastle disease virus, which is a representative of the Paramyxoviruses family, was isolated from the dead poultry. We determined the nucleotide sequences of fragments in F gene (encodes the fusion surface protein) and in NP gene (encodes the nucleocapsid protein). …”
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In the coevolution of cotton and pathogenic fungi, resistant cotton varieties lead to an escalation in the virulence of Verticillium dahliae by Yalin Zhang, Lifang Cui, Ruibing Liu, Zili Feng, Hongjie Feng, Jinglong Zhou, Lihong Zhao, Feng Wei, Heqin Zhu

“…Moreover, whole genome resequencing revealed that the Ka/Ks ratio of single nucleotide polymorphism (SNPs) in the majority of the offspring strains was about 0.6, indicating an adverse selection impact in the offspring strains. …”
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Bacteriophage LDT325 enhances Pseudomonas syringae tolerance by improving antioxidant defense in tea plant [Camellia sinensis (L.) O. Kuntze] by Li Liu, Anqi Huang, Hua Zhang, Yubao Li, Lei Wang, Lei Wang

“…Using NCBI BLASTn to compare the entire genome with other nucleotide sequences, we found that the phage LDT325 exhibited cross-species characteristics that had not been previously reported. …”
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Targeting the CLK2/SRSF9 splicing axis in prostate cancer leads to decreased ARV7 expression by Jasper Van Goubergen, Miroslav Peřina, Florian Handle, Elisa Morales, Anika Kremer, Oliver Schmidt, Glen Kristiansen, Marcus V. Cronauer, Frédéric R. Santer

“…Here, we set out to evaluate the applicability of the ARV7 3′UTR as a therapy target. A common single nucleotide polymorphism, rs5918762, was found to affect the splicing rate and thus the expression of ARV7 in cellular models and patient specimens. …”
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Glucocorticoid receptor (NR3C1) genetic polymorphisms and the outcomes of sudden sensorineural hearing loss by Chen-Yu Chien, Shu-Yu Tai, Kuan-Hui Li, Hua-Ling Yang, Ling-Feng Wang, Kuen-Yao Ho, Ning-Chia Chang

“…Materials and methods We conducted a comparison study of 93 cases with a poor outcome (control) and 100 cases with a good outcome (case) in SSNHL patients. Six single nucleotide polymorphisms (SNPs) were selected. The genotypes were determined using TaqMan technology. …”
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The <i>MCPH7</i> Gene Product STIL Is Essential for Dendritic Spine Formation by Tohru Matsuki, Hidenori Tabata, Masashi Ueda, Hideaki Ito, Koh-ichi Nagata, Yumi Tsuneura, Shima Eda, Kenji Kasai, Atsuo Nakayama

“…ARHGEF7, also known as ß-PIX, is a guanine nucleotide exchange factor for Rac1 and Cdc42, thereby activating Rac1/Cdc42 and the downstream pathway, leading to the upregulation of spine formation/maintenance. …”
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Genome‐wide association study of tuberculosis in the western Chinese Han and Tibetan population by Hao Bai, Mengyuan Song, Shikun Lei, Lin Jiao, Xuejiao Hu, Tao Wu, Jiajia Song, Tangyuheng Liu, Wu Peng, Zhenzhen Zhao, Zirui Meng, Binwu Ying

“…And different susceptibility single nucleotide polymorphisms (SNP) have been reported in different studies. …”
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Hepatitis C Virus Clearance after Discontinuation of Pegylated Interferon Alpha-2a Monotherapy in a Child by Takeshi Endo, Koichi Ito, Tokio Sugiura, Kenji Goto

“…The pretreatment liver biopsy revealed no fibrosis or malignancy and mild chronic hepatitis; his Knodell's histological activity (HAI) score was 4. Single nucleotide polymorphism of IL28B (rs8099917) was major type. …”
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Genetic Markers Associated to Dyslipidemia in HIV-Infected Individuals on HAART by Rosmeri K. Lazzaretti, Aline S. Gasparotto, Marina G. de M. Sassi, Carísi A. Polanczyk, Regina Kuhmmer, Jussara M. Silveira, Rossana P. Basso, Cezar A. T. Pinheiro, Mariângela F. Silveira, Eduardo Sprinz, Vanessa S. Mattevi

“…This study evaluated the impact of 9 single nucleotide polymorphisms (SNPs) in 6 candidate genes (APOB, APOA5, APOE, APOC3, SCAP, and LDLR) over dyslipidemia in HIV-infected patients on stable antiretroviral therapy (ART) with undetectable viral loads. …”
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Genetic Variation for Wild Populations of the Rare and Endangered Plant <i>Glyptostrobus pensilis</i> Based on Double-Digest Restriction Site-Associated DNA Sequencing by Yongrong Huang, Yu Li, Xiaojie Hong, Suzhen Luo, Dedan Cai, Xiangxi Xiao, Yunpeng Huang, Yushan Zheng

“…A total of 3,687,189 single-nucleotide polymorphisms (SNPs) were identified, and 15,158 high-quality SNPs were obtained after filtering. …”
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Association of Polymorphisms in Toll-Like Receptors 4 and 9 with Autoimmune Thyroid Disease in Korean Pediatric Patients by Won Kyoung Cho, Jung-Pil Jang, Eun-Jeong Choi, Moonbae Ahn, Shin Hee Kim, Kyoung Soon Cho, So Hyun Park, In Cheol Baek, Min Ho Jung, Tai-Gyu Kim, Byung-Kyu Suh

“…Methods. Fifteen single-nucleotide polymorphisms in 7 TLR genes were analyzed in 104 Korean children (girls = 86, boys = 18) with AITD (Hashimoto disease (HD) = 44, Graves’ disease (GD) = 60, thyroid-associated ophthalmopathy (TAO) = 29, and non-TAO = 31) with 183 controls. …”
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Production of recombinant norovirus VP1 protein and its antigenic and immunogenic properties by Vladislav A. Lapin, Dmitry V. Novikov, Ekaterina V. Mokhonova, Dmitry A. Melentyev, Maria I. Tsyganova, Dmitry E. Zaitsev, Viktor V. Novikov

“…Computer analysis of nucleotide and amino acid sequences, molecular cloning, polymerase chain reaction, electrophoresis of nucleic acids in agarose gel and proteins in polacrylamide gel, affinity chromatography, enzyme immunoassay. …”
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Comparative analysis of allele frequencies for DNA polymorphisms associated with disease and economically important traits in the genomes of Russian and foreign cattle breeds by A. V. Igoshin, G. A. Romashov, E. N. Chernyaeva, N. P. Elatkin, N. S. Yudin, D. M. Larkin

“…The aim of this study was a comparative analysis of frequencies for known causative nucleotide substitutions, insertions and deletions associated with disease and economically important traits in Russian and foreign cattle breeds. …”
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Associations of miR-499 and miR-34b/c Polymorphisms with Susceptibility to Hepatocellular Carcinoma: An Evidence-Based Evaluation by Zhongxia Wang, Junhua Wu, Guang Zhang, Yin Cao, Chunping Jiang, Yitao Ding

“…Hepatocellular carcinoma (HCC) represents the sixth common cancer in the world. Single nucleotide polymorphisms (SNPs) in microRNA genes may be associated with susceptibility to HCC. …”
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