Phage resistance formation and fitness costs of hypervirulent Klebsiella pneumoniae mediated by K2 capsule-specific phage and the corresponding mechanisms by Miran Tang, Zeyu Huang, Xiaodong Zhang, Jingchun Kong, Beibei Zhou, Yijia Han, Yi Zhang, Lijiang Chen, Tieli Zhou

“…WGS revealed single nucleotide polymorphism (SNP) in genes encoding RfaH, galU, sugar glycosyltransferase, and polysaccharide deacetylase family protein in the mutants. …”
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Key <i>FAD2</i>, <i>FAD3</i>, and <i>SAD</i> Genes Involved in the Fatty Acid Synthesis in Flax Identified Based on Genomic and Transcriptomic Data by Ekaterina M. Dvorianinova, Olga L. Zinovieva, Elena N. Pushkova, Daiana A. Zhernova, Tatiana A. Rozhmina, Liubov V. Povkhova, Roman O. Novakovskiy, Elizaveta A. Sigova, Anastasia A. Turba, Elena V. Borkhert, George S. Krasnov, Chengjiang Ruan, Alexey A. Dmitriev, Nataliya V. Melnikova

“…In most cases, two genes from a pair differed by a significant number of gene-specific SNPs (single nucleotide polymorphisms) or even InDels (insertions/deletions), except for <i>FAD2a-1</i> and <i>FAD2a-2</i>, where only seven SNPs distinguished these genes. …”
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Genetically Predicted Body Mass Index and Breast Cancer Risk: Mendelian Randomization Analyses of Data from 145,000 Women of European Descent. by Yan Guo, Shaneda Warren Andersen, Xiao-Ou Shu, Kyriaki Michailidou, Manjeet K Bolla, Qin Wang, Montserrat Garcia-Closas, Roger L Milne, Marjanka K Schmidt, Jenny Chang-Claude, Allison Dunning, Stig E Bojesen, Habibul Ahsan, Kristiina Aittomäki, Irene L Andrulis, Hoda Anton-Culver, Volker Arndt, Matthias W Beckmann, Alicia Beeghly-Fadiel, Javier Benitez, Natalia V Bogdanova, Bernardo Bonanni, Anne-Lise Børresen-Dale, Judith Brand, Hiltrud Brauch, Hermann Brenner, Thomas Brüning, Barbara Burwinkel, Graham Casey, Georgia Chenevix-Trench, Fergus J Couch, Angela Cox, Simon S Cross, Kamila Czene, Peter Devilee, Thilo Dörk, Martine Dumont, Peter A Fasching, Jonine Figueroa, Dieter Flesch-Janys, Olivia Fletcher, Henrik Flyger, Florentia Fostira, Marilie Gammon, Graham G Giles, Pascal Guénel, Christopher A Haiman, Ute Hamann, Maartje J Hooning, John L Hopper, Anna Jakubowska, Farzana Jasmine, Mark Jenkins, Esther M John, Nichola Johnson, Michael E Jones, Maria Kabisch, Muhammad Kibriya, Julia A Knight, Linetta B Koppert, Veli-Matti Kosma, Vessela Kristensen, Loic Le Marchand, Eunjung Lee, Jingmei Li, Annika Lindblom, Robert Luben, Jan Lubinski, Kathi E Malone, Arto Mannermaa, Sara Margolin, Frederik Marme, Catriona McLean, Hanne Meijers-Heijboer, Alfons Meindl, Susan L Neuhausen, Heli Nevanlinna, Patrick Neven, Janet E Olson, Jose I A Perez, Barbara Perkins, Paolo Peterlongo, Kelly-Anne Phillips, Katri Pylkäs, Anja Rudolph, Regina Santella, Elinor J Sawyer, Rita K Schmutzler, Caroline Seynaeve, Mitul Shah, Martha J Shrubsole, Melissa C Southey, Anthony J Swerdlow, Amanda E Toland, Ian Tomlinson, Diana Torres, Thérèse Truong, Giske Ursin, Rob B Van Der Luijt, Senno Verhoef, Alice S Whittemore, Robert Winqvist, Hui Zhao, Shilin Zhao, Per Hall, Jacques Simard, Peter Kraft, Paul Pharoah, David Hunter, Douglas F Easton, Wei Zheng

“…Single marker analyses identified 17 of the 84 BMI-associated single nucleotide polymorphisms (SNPs) in association with breast cancer risk at p < 0.05; for 16 of them, the allele associated with elevated BMI was associated with reduced breast cancer risk.…”
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Identification of New Copy Number Variation and the Evaluation of a CNV Detection Tool for NGS Panel Data in Polish Familial Hypercholesterolemia Patients by Lena Rutkowska, Iwona Pinkier, Kinga Sałacińska, Łukasz Kępczyński, Dominik Salachna, Joanna Lewek, Maciej Banach, Paweł Matusik, Ewa Starostecka, Andrzej Lewiński, Rafał Płoski, Piotr Stawiński, Agnieszka Gach

“…The first-line strategy is to identify possible pathogenic SNVs (single nucleotide variants) using multiple PCR, Sanger sequencing, or with more comprehensive approaches, such as NGS (next-generation sequencing), WES (whole-exome sequencing) or WGS (whole-genome sequencing). …”
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First Report of <i>Bartonella</i> spp. in Marsupials from Brazil, with a Description of <i>Bartonella harrusi</i> sp. nov. and a New Proposal for the Taxonomic Reclassification of... by Renan Bressianini do Amaral, Marita Vedovelli Cardozo, Alessandro de Mello Varani, Maria Eduarda Chiaradia Furquim, Clara Morato Dias, William Oliveira de Assis, Alanderson Rodrigues da Silva, Heitor Miraglia Herrera, Rosangela Zacarias Machado, Marcos Rogério André

“…In addition, this strain exhibited an average nucleotide identity (ANI) of 85% with <i>Bartonella</i> species belonging to the <i>B. vinsonii</i> group and 91% with <i>B. machadoae</i>. …”
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8q Gain Has No Additional Predictive Value in SF3B1MUT Uveal Melanoma but Is Predictive for a Worse Prognosis in Patients with BAP1MUT Uveal Melanoma by Josephine Q.N. Nguyen, MD, Wojtek Drabarek, MD, PhD, Jolanda Vaarwater, BS, Serdar Yavuzyigitoglu, MD, PhD, Robert M. Verdijk, MD, PhD, Dion Paridaens, MD, PhD, Nicole C. Naus, MD, PhD, Annelies de Klein, PhD, Erwin Brosens, PhD, Emine Kiliç, MD, PhD, Emine Kilic, Annelies de Klein, Erwin Brosens, Nicole C. Naus, Dion Paridaens, Serdar Yavuzyigitoglu, Wojtek Drabarek, Josephine Q.N. Nguyen, Jolanda Vaarwater, Robert M. Verdijk

“…Copy number status and gene expression were assessed using either a single nucleotide polymorphism array, fluorescence in situ hybridization, and karyotyping, or a combination of these techniques. …”
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An exploration of the correlations between seven psychiatric disorders and the risks of breast cancer, breast benign tumors and breast inflammatory diseases: Mendelian randomizatio... by Fei Ren, Qingyao Shang, Shuangtao Zhao, Chenxuan Yang, Kexin Feng, Jiaxiang Liu, Xiyu Kang, Ruixuan Zhang, Xiang Wang, Xin Wang

“…This study aims to investigate if mental disorders influence the risks of overall breast cancer, the two subtypes of breast cancer (ER+ and ER-), breast benign tumors and breast inflammatory diseases.MethodsDuring our research, genome-wide association study (GWAS) data for seven psychiatric disorders (schizophrenia, major depressive disorder, bipolar disorder, post-traumatic stress disorder, panic disorder, obsessive-compulsive disorder and anorexia nervosa) from the Psychiatric Genomics Consortium (PGC) and the UK Biobank were selected, and single-nucleotide polymorphisms (SNPs) significantly linked to these mental disorders were identified as instrumental variables. …”
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SLC44A2 Frequency, a New TaqMan Real-Time Polymerase Chain Reaction Method for HNA-3A/3B Genotyping, and a New Application of Droplet Digital PCR by Yufeng Wang, Yufeng Wang, Yufeng Wang, Xihui Chen, Xihui Chen, Qi Chen, Qi Chen, Tangdong Chen, Tangdong Chen, Kun Chen, Yuanming Wu, Yuanming Wu, Li Wang, Li Wang, Li Wang

“…Background: Human neutrophil antigen-3A (HNA-3A) and human neutrophil antigen-3B (HNA-3B) are generated by a single-nucleotide polymorphism (rs2288904, c.461G &gt; A) in exon 7 of the choline transporter-like protein-2 gene (CTL2, also known as SLC44A2). …”
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XBP1-mediated activation of the STING signalling pathway in macrophages contributes to liver fibrosis progression by Qi Wang, Qingfa Bu, Mu Liu, Rui Zhang, Jian Gu, Lei Li, Jinren Zhou, Yuan Liang, Wantong Su, Zheng Liu, Mingming Wang, Zhexiong Lian, Ling Lu, Haoming Zhou

“…X-box binding protein 1 (XBP1) has been shown to promote macrophage nucleotide-binding oligomerization domain, leucine-rich repeat and pyrin domain-containing 3 (NLRP3) activation in steatohepatitis. …”
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Screening of Indica-Japonica Specific Molecular Markers and Establishment of Discrimination System by Jingfang DONG, Xuezhong LI, Shaohong ZHANG, Bin LIU, Junliang ZHAO, Tifeng YANG

“…Molecular markers designed based on nucleotide sequence differences between indica rice and japonica rice have been widely used to discriminate indica-japonica in rice. …”
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Interleukin Variants Are Associated with the Development and Progression of IgA Nephropathy: A Candidate-Gene Association Study and Meta-Analysis by Ioanna Chronopoulou, Maria Tziastoudi, Georgios Pissas, Efthimios Dardiotis, Maria Dardioti, Spyridon Golfinopoulos, Georgios Filippidis, Peter R. Mertens, Evangelia E. Tsironi, Vassilios Liakopoulos, Theodoros Eleftheriadis, Ioannis Stefanidis

“…Genotypes were assessed for two promoter-region single-nucleotide polymorphisms, C-899T (rs1800587) in <i>IL1A</i> and C-511T (rs16944) in <i>IL1B</i>, and for one penta-allelic variable-length tandem repeat polymorphism (VNTR 86 bp intron 2) in <i>IL1RN</i>. …”
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Outbreak of Klebsiella pneumoniae ST11 Resistant To Ceftazidime-Avibactam Producing KPC-31 and the Novel Variant KPC-115 during COVID-19 Pandemic in Argentina by Federico Nicola, Daniela Cejas, Francisco González-Espinosa, Silvia Relloso, Fabián Herrera, Pablo Bonvehí, Jorgelina Smayevsky, Roque Figueroa-Espinosa, Gabriel Gutkind, Marcela Radice

“…Based on whole-genome sequencing results of selected isolates, less than 7 single-nucleotide polymorphisms were identified among them, which was indicative of the presence of a unique clone. …”
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Molecular epidemiology and genomic dynamics of Pseudomonas aeruginosa isolates causing relapse infections by Cong Shen, Jinxiang Zeng, Dexiang Zheng, Yinglun Xiao, Jieying Pu, Li Luo, Hongyun Zhou, Yimei Cai, Liling Zhang, Meina Wu, Xuan Zhang, Guangyuan Deng, Song Li, Qiwei Li, Jianming Zeng, Zhaohui Sun, Bin Huang, Cha Chen

“…Fast adaptation and evolution of P. aeruginosa isolates were reflected by dynamic changes of antimicrobial resistance, gene loss and acquisition, and single-nucleotide polymorphisms during relapse episodes. Remarkably, a convergent non-synonymous mutation that occurs in a pyochelin-associated virulence gene fptA (T1056C, M252T) could be a considerable target for the diagnosis and treatment of relapse P. aeruginosa infection. …”
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3p Arm Loss and Survival in Head and Neck Cancer: An Analysis of TCGA Dataset by Hugh Andrew Jinwook Kim, Mushfiq Hassan Shaikh, Mark Lee, Peter Y. F. Zeng, Alana Sorgini, Temitope Akintola, Xiaoxiao Deng, Laura Jarycki, Halema Khan, Danielle MacNeil, Mohammed Imran Khan, Adrian Mendez, John Yoo, Kevin Fung, Pencilla Lang, David A. Palma, Krupal Patel, Joe S. Mymryk, John W. Barrett, Paul C. Boutros, Luc G. T. Morris, Anthony C. Nichols

“…We downloaded the clinical, single nucleotide variation (SNV), copy number aberration (CNA), RNA sequencing, and reverse phase protein assay (RPPA) data from The Cancer Genome Atlas (TCGA) and The Cancer Proteome Atlas HNSCC cohorts. …”
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Brevundimonas brasiliensis sp. nov.: a New Multidrug-Resistant Species Isolated from a Patient in Brazil by Gabriela Guerrera Soares, Emeline Boni Campanini, Roumayne Lopes Ferreira, Marcelo Silva Folhas Damas, Saulo Henrique Rodrigues, Leslie Camelo Campos, Jucimária Dantas Galvão, Andrea Soares da Costa Fuentes, Caio César de Melo Freire, Iran Malavazi, André Pitondo-Silva, Anderson Ferreira da Cunha, Maria-Cristina da Silva Pranchevicius

“…Multilocus sequence analysis, Type (Strain) Genome Server, digital DNA-DNA hybridization, and average nucleotide identity confirmed that the Brevundimonas sp. studied represents a distinct species, for which we propose the name Brevundimonas brasiliensis sp. nov. …”
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Whole-genome informed circulating tumor DNA analysis by multiplex digital PCR for disease monitoring in B-cell lymphomas: a proof-of-concept study by Zahra Haider, Tove Wästerlid, Tove Wästerlid, Linn Deleskog Spångberg, Leily Rabbani, Cecilia Jylhä, Cecilia Jylhä, Birna Thorvaldsdottir, Aron Skaftason, Hero Nikdin Awier, Aleksandra Krstic, Aleksandra Krstic, Anna Gellerbring, Anna Lyander, Moa Hägglund, Ashwini Jeggari, Georgios Rassidakis, Georgios Rassidakis, Kristina Sonnevi, Kristina Sonnevi, Birgitta Sander, Richard Rosenquist, Richard Rosenquist, Richard Rosenquist, Emma Tham, Emma Tham, Karin E. Smedby, Karin E. Smedby

“…In this study, we assessed the clinical potential of using whole-genome sequencing (WGS) of lymphomas at diagnosis to identify patient-specific structural (SVs) and single nucleotide variants (SNVs) to enable longitudinal, multi-targeted droplet digital PCR analysis (ddPCR) of cell-free DNA (cfDNA).MethodsIn 9 patients with B-cell lymphoma (diffuse large B-cell lymphoma and follicular lymphoma), comprehensive genomic profiling at diagnosis was performed by 30X WGS of paired tumor and normal specimens. …”
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The protective effects of Levilactobacillus brevis FZU0713 on lipid metabolism and intestinal microbiota in hyperlipidemic rats by Xiaoyun Fan, Qing Zhang, Weiling Guo, Qi Wu, Jinpeng Hu, Wenjian Cheng, Xucong Lü, Pingfan Rao, Li Ni, Youting Chen, Lijiao Chen

“…Furthermore, liver metabolomics analysis demonstrated that L. brevis FZU0713 had a significant regulatory effect on the composition of liver metabolites in hyperlipidemic rats, especially the levels of some important biomarkers involved in the metabolic pathways of arachidonic acid metabolism, primary bile acid biosynthesis, amino sugar and nucleotide sugar metabolism, taurine and hypotaurine metabolism, biosynthesis of unsaturated fatty acid, fructose and mannose metabolism, tyrosine metabolism, etc. …”
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Arachidonic acid activates NLRP3 inflammasome in MDSCs via FATP2 to promote post-transplant tumour recurrence in steatotic liver grafts by Hui Liu, Wai Ho Oscar Yeung, Li Pang, Jiang Liu, Xiao Bing Liu, Kevin Tak Pan Ng, Qingmei Zhang, Wen Qi Qiu, Yueqin Zhu, Tao Ding, Zhe Wang, Ji Ye Zhu, Chung Mau Lo, Kwan Man

“…Methods: MDSC populations and nucleotide-binding oligomerisation domain-like receptor family pyrin domain containing 3 (NLRP3) inflammasome levels were investigated in a clinical cohort and a rat liver transplantation model. …”
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RNA-Seq Transcriptome Analysis and Evolution of <i>OsEBS</i>, a Gene Involved in Enhanced Spikelet Number per Panicle in Rice by Fuan Niu, Mingyu Liu, Shiqing Dong, Xianxin Dong, Ying Wang, Can Cheng, Huangwei Chu, Zejun Hu, Fuying Ma, Peiwen Yan, Dengyong Lan, Jianming Zhang, Jihua Zhou, Bin Sun, Anpeng Zhang, Jian Hu, Xinwei Zhang, Shicong He, Jinhao Cui, Xinyu Yuan, Jinshui Yang, Liming Cao, Xiaojin Luo

“…<i>Indica</i> (<i>XI</i>) subspecies harbored higher nucleotide diversity than <i>japonica</i> (<i>GJ</i>) subspecies in the <i>OsEBS</i> region, and <i>XI</i> experienced strong balancing selection during evolution, while selection in <i>GJ</i> was neutral. …”
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Steady Decline of HBV DNA Load under NAs in Lymphoma Patients and a Higher Level of qAnti-HBc Predict HBV Reactivation by Yiqi Liu, Reyizha Nuersulitan, Chi Zhang, Na Huo, Jun Li, Yuqin Song, Jun Zhu, Weiping Liu, Hong Zhao

“…<b>Background:</b> Patients with lymphoma and chronic hepatitis B virus infection need to be treated with both chemotherapy and nucleotide analogue (NA) therapy. However, dynamic changes in HBV DNA loads with increasing chemotherapy cycles are lacking. …”
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