NAPTUNE: nucleic acids and protein biomarkers testing via ultra-sensitive nucleases escalation by Tao Hu, Xinxin Ke, Yingying Yu, Hongmei Feng, Senfeng Zhang, Yinuo Cui, Boyang Zhang, Min He, Yinbing Tang, Lei Liu, Yu Lin, Quanquan Ji, Chuanxia Chen, Chunlong Xu, Chunyi Hu

“…Using a tandem cascade of endonucleases, NAPTUNE employs apurinic/apyrimidinic endonuclease 1 (APE1) to generate DNA guides, enabling the detection of target nucleic acids at femtomolar levels. …”
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A sensitivity analysis of methodological variables associated with microbiome measurements by Samuel P. Forry, Stephanie L. Servetas, Jennifer N. Dootz, Monique E. Hunter, Jason G. Kralj, James J. Filliben, Scott A. Jackson

“…This report details a full factorial exploration of 48 experimental protocols by systematically varying microbiome sample, iterations of material production, laboratory personnel, DNA extraction kit, marker gene selection, and reference databases. …”
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Global proteomics and affinity mass spectrometry analysis of human Schwann cells indicates that variation in and loss of neurofibromin (NF1) alters protein expression and cellular... by Christian X Fay, Elizabeth R.M. Zunica, Elias Awad, William Bradley, Cameron Church, Jian Liu, Hui Liu, David K. Crossman, James A. Mobley, John P. Kirwan, Christopher L. Axelrod, Erik Westin, Robert A. Kesterson, Deeann Wallis

“…When we evaluated the proteome of NF1 null cells stably transfected with tagged mNf1 cDNAs we again identified an overall trend of metabolic differences pertaining to “oxidative phosphorylation”, “mitochondria dysfunction”, and “glycolysis” in the variant cDNA expressing cells. We then validated differential expression of the following proteins: LAMC1, CYB5R3, and SOD2 that are observed in the altered pathways. …”
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The Combinational Effect of Enhanced Infection Control Measures and Targeted Clinical Metagenomics Surveillance on the Burden of Endemic Carbapenem and Other β-Lactam Resistance Am... by Athina Giampani, Maria Simitsopoulou, Maria Sdougka, Christos Paschaloudis, Emmanuel Roilides, Elias Iosifidis

“…The presence of four carbapenemase genes, <i>bla</i>_KPC, <i>bla</i>_OXA-48-like, <i>bla</i>_VIM, and <i>bla</i>_NDM, as well as the β-lactamase genes <i>bla</i>_TEM and <i>bla</i>_SHV, was evaluated by PCR after DNA isolation directly from stool samples. The results were compared to culture-based phenotypic analysis. …”
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Association of ATM Gene Polymorphism with PTC Metastasis in Female Patients by Yulu Gu, Xiaoli Liu, Yaqin Yu, Jieping Shi, Lizhe Ai, Hui Sun, Joseph Sam Kanu, Chong Wang, Yawen Liu

“…Ataxia telangiectasia mutated (ATM) gene is critical in the process of recognizing and repairing DNA lesions and is related to invasion and metastasis of malignancy. …”
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Dysbiosis of the human skin mycobiome in patients receiving systemic IL-23 inhibitors by Yuta Koike, Sayaka Kuwatsuka, Daisuke Motooka, Hiroyuki Murota

“…Swab samples were collected from the psoriasis-free skin of antecubital fossa, post-auricular, and the tongue surface before and after 16 weeks of treatment with anti-IL-23 antibodies. Fungal DNA was sequenced by ITS1 metagenomic analysis, and taxonomic classification was performed. …”
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Development of a colloidal gold immunochromatographic assay utilizing dual-antibody sandwich method for detecting Orientia tsutsugamushi by Qingyu Lu, Shiyin Yu, Sibo Wang, Min Cao, Liuxin Li, Miao Xin, Weilong Tan, Yong Qi, Yichen Lu, Xiaohui Xiong

“…Furthermore, a detection limit of 1 × 106 copies/μL DNA of O. tsutsugamushi was determined for both PT and SJ infected cell strains by constructing a relationship between cell number and copy number of the pathogen using a quantitative PCR-based standard curve. …”
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Choosing the most suitable NGS technology to combine with a standardized viral enrichment protocol for obtaining complete avian orthoreovirus genomes from metagenomic samples by Sonsiray Álvarez-Narváez, Sonsiray Álvarez-Narváez, Telvin L. Harrell, Islam Nour, Sujit K. Mohanty, Steven J. Conrad

“…The results suggest that our ARV genome enrichment protocol caused some fragmentation of the viral cDNA that impacted the length of the long reads (but not the short reads) and, as a result, caused a failure to produce complete genomes via de novo assembly. …”
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Efficacy of Abatacept for Arthritis in Patients with an Overlap Syndrome between Rheumatoid Arthritis and Systemic Lupus Erythematosus by Kei Ikeda, Yoshie Sanayama, Sohei Makita, Junichi Hosokawa, Mieko Yamagata, Daiki Nakagomi, Katsuhiko Takabayashi, Hiroshi Nakajima

“…In addition, the levels of immunoglobulin G and anti-DNA antibody significantly decreased between baseline and 24 weeks ( and , resp.). …”
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A novel homozygous intronic variant in CDT1 that alters splicing causes Meier–Gorlin syndrome, and a review of published mutations and growth hormone treatments by Qing Li, Yichi Wu, Fucheng Meng, Zhuxi Li, Di Zhan, Xiaoping Luo

“…Pathogenic variants in 13 genes involved in DNA replication initiation have been identified in this disease, but homozygous intronic variants have never been reported. …”
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655Val and 1170Pro ERBB2 SNPs in Familial Breast Cancer Risk and BRCA1 Alterations by Stefania Tommasi, Vita Fedele, Rosanna Lacalamita, Michele Bruno, Francesco Schittulli, David Ginzinger, Gery Scott, Serenella Eppenberger-Castori, Daniele Calistri, Silvia Casadei, Ian Seymour, Salvatore Longo, Gianluigi Giannelli, Brunella Pilato, Giovanni Simone, Christopher C. Benz, Angelo Paradiso

“…A consecutive series of 628 patients with first diagnosis of breast cancer and 169 healthy people had DNA analyzed for both SNPs. Genotypic or allelic frequencies of ERBB2 SNPs in breast cancer patients were similar than in controls. …”
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Achievements and prospects of applying high-throughput sequencing techniques to potato genetics and breeding by I. V. Bykova, N. A. Shmakov, D. A. Afonnikov, A. V. Kochetov, E. K. Khlestkina

“…This information should prove useful while planning comparative assays of potato transcriptome or application of DNA-markers. Sequencing of the genome as well as transcriptomes and microRNomes of cultivated potato and its wild relatives, on one hand, is of fundamental interest, assisting in detecting features of genome evolution, ontogenetic development and mechanisms of various environmental stresses responses. …”
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In vitro study of resveratrol as an antioxidant for boar semen preservation: A systematic review by Ragil Angga Prastiya, Trilas Sardjito, Amung Logam Saputro, Sari Yanti Hayanti, Nining Haryuni, Samira Musa Sasi

“…Data extracted from these studies included parameters such as sperm motility, viability, DNA integrity, and lipid peroxidation levels. …”
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PPARγ Regulates Genes Involved in Triacylglycerol Synthesis and Secretion in Mammary Gland Epithelial Cells of Dairy Goats by Hengbo Shi, Jun Luo, Jiangjiang Zhu, Jun Li, Yuting Sun, Xianzi Lin, Liping Zhang, Dawei Yao, Huaiping Shi

“…To explore the function of PPARγ in the goat mammary gland, we cloned the whole cDNA of the PPARγ gene. Homology alignments revealed that the goat PPARγ gene is conserved among goat, bovine, mouse, and human. …”
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Antibody response to Plasmodium vivax in the context of Epstein-Barr virus (EBV) co-infection: A 14-year follow-up study in the Amazon rainforest. by Luiz F F Guimarães, Bárbara A Rodrigues, Michelle H F Dias, Matheus G Barcelos, Maria F A Nascimento, Sâmick L Moreira-Nascimento, Sofia L Afonso, Barbara G S Abreu, Jaap M Middeldorp, Francis B Ntumngia, John H Adams, Camila Fabbri, Stefanie Lopes, Cor J F Fernandes, Flora S Kano, Luzia H Carvalho

“…In parallel, the status of EBV infection was determined over time by the detection of circulating EBV DNA (EBV-DNAemia) and EBV-specific antibodies to lytic (VCAp18) or latent (EBNA1) antigens. …”
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Genetic history of the Koryaks and Evens of the Magadan region based on Y chromosome polymorphism data by B. A. Malyarchuk, M. V. Derenko

“…The genetic contribution of the European males’ Y chromosome significantly prevails over that of maternally inherited mitochondrial DNA. The study of the Y chromosome haplogroup diversity has shown that only relatively young phylogenetic branches have been preserved in the Koryak gene pool. …”
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Discovery and characterization of complete genomes of 38 head-tailed proviruses in four predominant phyla of archaea by Tianqi Xu, Yimin Ni, Hailing Li, Shuang Wu, Shuling Yan, Lanming Chen, Yongxin Yu, Yongjie Wang

“…Eleven proviruses contain genes linked to antiviral defense mechanisms, including those involved in restriction modification (RM), clustered regularly interspaced short palindromic repeat (CRISPR)-associated (CRISPR–Cas) nucleases, defense island system associated with restriction-modification (DISARM), and DNA degradation (Dnd). Moreover, auxiliary metabolic genes were identified in the proviruses of Bathyarchaeia and Halobacteriota archaea, including those involved in carbohydrate and amino acid metabolism. …”
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Detailed cytogenetic analysis of three duck species (the northern pintail, mallard, and common goldeneye) and karyotype evolution in the family Anatidae (Anseriformes, Aves) by V. R. Beklemisheva, K. V. Tishakova, S. A. Romanenko, D. A. Andreushkova, V. A. Yudkin, E. А. Interesova, F. Yang, M. A. Ferguson-Smith, A. S. Graphodatsky, A. A. Proskuryakova

“…Localization of clusters of ribosomal DNA and telomere repeats revealed that the duck karyotypes contain some microchromosomes that bear ribosomal RNA genes and/or are enriched for telomere repeats and constitutive heterochromatin. …”
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Exploring the genetic correlation and causal relationships between breast cancer and meningioma using bidirectional Mendelian randomization by Lu Ding, Bo Chen, Zhou Zhou, Zhaojun Mei, Kan Cao, Xinyu Lu, Wei Chen

“…ER-related signaling pathways and the regulation of DNA damage may play a critical role in the pathogenesis of both diseases.…”
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First Report on the Frequency and Subtype Distribution of <i>Blastocystis</i> sp. in Extensively Reared Holstein-Friesian Cattle from Terceira Island, Azores Archipelago, Portugal by Sara Gomes-Gonçalves, Alexandra Silva, Guilherme Moreira, Nausicaa Gantois, Rubén Garcia Dominguez, Eric Viscogliosi, Magali Chabé, João R. Mesquita

“…A total of 116 stool samples were thus collected from dairy cows, and <i>Blastocystis</i> sp. DNA was detected using qPCR. The results revealed a 14.7% occurrence rate (17/116), with seven STs identified including ST3, ST5, ST7, ST10, ST14, ST25, and ST42, with variable frequency. …”
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