Identified VCAM1 as prognostic gene in gastric cancer by co-expression network analysis by Wenjuan Li, Hong Gao, Jianjun Liu

“…This study aims to identify genetic variances and potential diagnostic and therapeutic approaches for diverse types of gastric cancer utilizing an extensive dataset. Data from RNA sequencing and clinical pathological details were acquired from The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) dataset. …”
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Distribution of the arctic variant of the CPT1A gene in indigenous populations of Siberia by B. A. Malyarchuk, M. V. Derenko, G. A. Denisova, A. N. Litvinov

“…Five polymorphic loci relevant to the haplotypic structure of CPT1A gene (rs2278908, rs2278907, rs2924699, rs7112615 and rs2229738) were revealed by high-throughput DNA sequencing in addition to locus rs80356779 studied here. …”
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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

“…In this study, <i>V. philippica</i> plants exhibiting symptoms such as leaf yellowing, mottled leaves, and vein chlorosis were collected and subjected to RNA sequencing to identify potential viral pathogens. A novel polerovirus, named Viola Philippica Polerovirus (VPPV), was identified in <i>V. philippica</i>. …”
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TB drug susceptibility testing in high fluoroquinolone resistance settings by F. Saluzzo, F. Masood, V. Batignani, F. Di Marco, U. Majeed, A. Ghazal, D.M. Cirillo, S. Tahseen

“…Xpert® MTB/RIF Ultra, MTB/XDR, Genotype® MTBDRplus, Genotype® MTBDRsl, culture, and phenotypic drug susceptibility testing (pDST) for relevant drugs (including bedaquiline and levofloxacin) were performed. Next-generation sequencing (NGS) resolved discordances between MTB/XDR and pDST results. …”
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Navigating uncertainty in environmental DNA detection of a nuisance marine macroalga. by Patrick K Nichols, Kaʻuaʻoa M S Fraiola, Alison R Sherwood, Brian B Hauk, Keolohilani H Lopes, Colt A Davis, James T Fumo, Chelsie W W Counsell, Taylor M Williams, Heather L Spalding, Peter B Marko

“…Results were subsequently validated with high-throughput sequencing of amplified eDNA and negative control samples. …”
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Dynamic changes in physicochemical property, biogenic amines content and microbial diversity during the fermentation of Sanchuan ham by Zhongai Chen, Hong Chen, Huan Du, Cong Chen, Kaixiang Lu, Qiaoli Xue, Yongjin Hu

“…In this study, we explored the physicochemical property, biogenic amines concentration and microbial diversity of external and internal Sanchuan ham by high-throughput sequencing during the processing of Sanchuan ham. Results showed that the nitrite remained at a stable level of 0.15 mg/kg which was significantly lower than the national health standard safety level of 20 mg/kg. …”
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Bioprospecting Saccharomyces cerevisiae in fruits from Amazonian region for beer brewing by Luan Reis Honorato da Silva, Flávia da Silva Fernandes, Jocélia Pinheiro Santos, Érica Simplício de Souza, Lívia Melo Carneiro, João Paulo Alves Silva, Jacqueline da Silva Batista, João Vicente Braga de Souza

“…Identification of the isolated strains was achieved through biochemical assays and ITS rDNA (Internal Transcribed Spacer ribosomal DNA), sequencing, with emphasis on determining their affiliation to S. cerevisiae and assessing phylogenetic ties. …”
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Differentiation of <i>Escherichia coli</i> and <i>Shigella flexneri</i> by Metabolite Profiles Obtained Using Gold Nanoparticles-Based Surface-Assisted Laser Desorption/Ionization... by Adrian Arendowski

“…<i>Escherichia coli</i> and <i>Shigella flexneri</i> are challenging to differentiate using methods such as phenotyping, 16S rRNA sequencing, or protein profiling through matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) due to their close relatedness. …”
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Heavy metal contamination and eutrophication effects on bacterial communities in the Han River basin by Fei Xiong, Cejia Yao, Dongdong Zhai, Hongyan Liu, Wang Dong, Yuanyuan Chen

“…This study analyzed microbial communities in sediment samples from 15 sites using 16S rDNA sequencing. Our findings revealed a significant decrease in α-diversity with increasing copper (Cu) concentration, with the downstream region (group L) exhibiting higher diversity compared to the upstream region (group U). …”
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When a sore throat turns into deadly multiple serous cavity effusions: the role of Prevotella oris in rapidly progressing infection—a case report by Fangqi Zhang, Juan-Li Wang, Jian Zhu, Shaokui Si, Hao Guo, Xiang Yue, Wei Wen

“…After multiple cultures of the patient’s sputum yielded no identifiable pathogenic bacteria, the metagenomic next-generation sequencing (mNGS) revealed Prevotella oris as the predominant pathogen present in both the patient’s peripheral blood and the pericardial drainage fluid. …”
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Pediatric kidney transplant recipients are at an increased risk for dysbiosis by Gizem Yılmaz, Seha Saygılı, Ayşe Ağbaş, Esra Karabağ Yılmaz, Ahmet Variş, Nur Canpolat

“…The gut microbiota was assessed using 16S rRNA gene sequencing, with alpha and beta diversity, as well as all statistical analyses, conducted using the Phyloseq library in the R programming language. …”
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Automation-aided construction and characterization of Bacillus subtilis PrsA strains for the secretion of amylases by Felix Hamburger, Niels Schlichting, Michael Eichenlaub, Paul Igor Costea, Christopher Sauer, Stefan Jenewein, Johannes Kabisch, Johannes Kabisch

“…Following strain selection and deletion of major extracellular proteases, several hundred individual strains were created and screened using a stepwise and modular automation approach combined with amplicon sequencing. In addition to providing the key learnings from the workflow, it was revealed that no single PrsA molecule consistently improved amylase production, but genetic constructs combining different elements showed up to a 10-fold variation in yield. …”
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Sex disparities in the association between rare earth elements exposure and genetic mutation frequencies in lung cancer patients by Mengyuan Liu, Jiali Zhang, Xiaohong Duan, Qiming Zhou, Jing Chen, Siyao Liu, Junyan Su, Li Han, Fan Yang, Niansong Qian

“…A cohort of 53 LUAD patients underwent tumor DNA sequencing (1123 cancer-related genes) and plasma REE (lanthanum (La), cerium (Ce), praseodymium (Pr), neodymium (Nd), and yttrium (Y)) quantification. …”
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Near complete genome assembly of Yadong trout (Salmo trutta) by Chen Li, Shenglei Han, Shuo Li, Kaiqiang Liu, Yuyan Liu, Hong-yan Wang, Qian Wang, Changlin Liu, Changwei Shao

“…In this study, we assembled a near-complete genome of the S. trutta, integrating PacBio HiFi, Hi-C, and ONT sequencing technologies. The genome assembly spans 2.49 Gb, with 96.87% of the sequence anchored onto 40 chromosomes. …”
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Identification of the gene coding for seed cotyledon albumin SCA in the pea (Pisum L.) genome by A. V. Mglinets, V. S. Bogdanova, O. E. Kosterin

“…Then we sequenced them in a number of pea accessions. Concordance of the earlier electrophoretic data and sequence variation indicated the sequence Psat0s797g0160 of the reference pea genome to be the SCA gene. …”
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Host 3' flap endonuclease Mus81 plays a critical role in trimming the terminal redundancy of hepatitis B virus relaxed circular DNA during covalently closed circular DNA formation. by Hu Zhang, Quanxin Long, Yuanjie Liu, Alexander L Marchetti, Cheng-Der Liu, Ning Sun, Haitao Guo

“…To address these questions, a mutant HBV cell line HepDES-C1822G was established with a C1822G mutation in the pgRNA coding sequence, altering the sequence of 3' TR of (-) strand DNA while the 5' TR remained wild type (wt). …”
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Microbial Community, Fatty Acid Composition, and Health Potential of Horse Oil Fermented with Barley Nuruk by Jeong-Ha Lee, Sung-Eun Bae, Ho-Min Kang, Yu-Jin Ha, Chang-Gu Hyun

“…Molecular docking demonstrated that the amide structures play a key role in α-glucosidase inhibition through essential hydrogen bonding interactions. Next-generation sequencing (NGS) analysis showed a notable reduction in pathogenic bacteria, such as <i>Salmonella enterica</i>, and a dominance of <i>Lactobacillus acidophilus</i> (95.2%) by day 10. …”
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A Genomic‐Based Workflow for eDNA Assay Development for a Critically Endangered Turtle, Myuchelys georgesi by Holly V. Nelson, Arthur Georges, Katherine A. Farquharson, Elspeth A. McLennan, Jane L. DeGabriel, Katherine Belov, Carolyn J. Hogg

“…Consequently, the development of eDNA assays has relied on mitochondrial reference sequences available in online databases, or in cases where such data are unavailable, de novo DNA extraction and sequencing of mtDNA. …”
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Asymptomatic lung abscess of aspergillus in a female without previous lung diseases or immunocompromise: a case report by Hanxue Xiang, Ling Zhang, Liu Yang, Miaotian Cai, Yingmin Ma, Yulin Zhang

“…Then Aspergillus terreus was detected by both fluid culture and metagenomics next-generation sequencing. Interestingly, this patient had no history of tuberculosis or chronic pulmonary diseases. …”
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Molecular Detection and Phylogenetic Analysis of the alkB Gene in Klebsiella oxytoca Strains Isolated from the Gut of Tenebrio molitor by Tsitsi Lynn Mupamhadzi, Oleen Machona, Farisai Chidzwondo, Rumbidzai Mangoyi

“…The amplified alkB gene was then sequenced using the Sanger sequencing technique, blasted on NCBI to look for similar sequences, and a phylogenetic tree was constructed. …”
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