Harmonized Datasets of microbiological parameters from a French national-scale soil monitoring survey by Aurélien Cottin, Samuel Dequiedt, Christophe Djemiel, Nicolas Chemidlin Prévost-Bouré, Julie Tripied, Mélanie Lelièvre, Lucie Terreau, Tiffanie Régnier, Battle Karimi, Claudy Jolivet, Antonio Bispo, Nicolas Saby, Pierre-Alain Maron, Lionel Ranjard, Sébastien Terrat

“…Based on the 2,240 sites of the 2000–2015 RMQS, molecular tools were applied to characterize soil microbiota. Soil DNA analysis yielded molecular microbial biomass for 2,168 sites, bacterial and fungal qPCR for 2,073 sites, and high-throughput amplicon sequencing of targeted 16S rDNA bacterial and archaeal genes for 1,842 sites. …”
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Building a reliable 16S mini-barcode library of wild bees from Occitania, south-west of France by Anaïs Marquisseau, Kamila Canale-Tabet, Emmanuelle Labarthe, Géraldine Pascal, Christophe Klopp, André Pornon, Nathalie Escaravage, Rémi Rudelle, Alain Vignal, Annie Ouin, Mélodie Ollivier, Magalie Pichon

“…The COI (Cytochrome Oxydase subunit 1) gene, the most used in barcoding/metabarcoding of arthropods, suffers from primer bias and difficulties for covering all wild bee species using the classical Folmer primers.We present here a curated database for a 250 bp mini-barcode region of the 16S rRNA gene, suitable for low-cost metabarcoding wild bees in applications, such as eDNA analysis or for sequencing ancient or degraded DNA. …”
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First assessment of biofouling assemblages in the northern Red Sea, an important region for marine non-indigenous species transfer by Juan Sempere-Valverde, Juan Sempere-Valverde, Eva Aylagas, Vitaly Syomin, Vitaly Syomin, Marcos A. L. Teixeira, Glafira D. Kolbasova, Glafira D. Kolbasova, Sofía Ruiz-Velasco, Sahar Chebaane, Arthur Anker, João Curdia, Ronald Cadiz, Dylan M. Cottrell, Andrea Desiderato, Luiz F. Andrade, Chakkiath Paul Antony, Carolina Bocanegra-Castano, Matilde Marzucchi, Angelo Poliseno, Doaa Baker, Basmah Alabdulaziz, Flor Torres, Ameer A. Eweida, Ameer A. Eweida, Susana Carvalho, Susana Carvalho

“…The eDNA analysis of seawater confirmed these spatial differences, also detecting a variation between sampling times that was not observed with the other approaches. …”
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High-coverage whole-genome sequencing of a Jakun individual from the “Orang Asli” Proto-Malay subtribe from Peninsular Malaysia by Wai-Sum Yap, Alvin Cengnata, Woei-Yuh Saw, Thuhairah Abdul Rahman, Yik-Ying Teo, Renee Lay-Hong Lim, Boon-Peng Hoh

“…The ADMIXTURE analysis further revealed potential admixture from the EA and North Borneo populations, as corroborated by the results from the F3, F4, and TreeMix analyses. Mitochondrial DNA analysis revealed that the Jakun genome carried the N21a haplogroup (estimated to have occurred ~19 kya), which is commonly found among Malays from Malaysia and Indonesia. …”
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HER2-related biomarkers predict clinical outcomes with trastuzumab deruxtecan treatment in patients with HER2-expressing metastatic colorectal cancer: biomarker analyses of DESTINY... by Salvatore Siena, Kanwal Raghav, Toshiki Masuishi, Kensei Yamaguchi, Tomohiro Nishina, Elena Elez, Javier Rodriguez, Ian Chau, Maria Di Bartolomeo, Hisato Kawakami, Fumitaka Suto, Makito Koga, Koichiro Inaki, Yusuke Kuwahara, Issey Takehara, Daniel Barrios, Kojiro Kobayashi, Axel Grothey, Takayuki Yoshino

“…Baseline circulating tumor DNA (ctDNA) analysis suggests antitumor activity of T-DXd in patients who had baseline activating RAS, PIK3CA, or HER2 mutations detected in ctDNA.…”
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MTIOT: Identifying HPV subtypes from multiple infection data by Qi Zhao, Tianjun Zhou, Lin Li, Guofan Hong, Luonan Chen

“…To address these limitations, we introduce MTIOT (Multiple subTypes In One Time), a novel detection method that utilizes machine learning with a new multichannel integration scheme to enhance HPV-DNA analysis. This approach may enable more accurate and rapid identification of multiple hrHPV types within a single sample. …”
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Protein-DNA interactions: statistical analysis of interatomic contacts in major and minor grooves by A. A. Anashkina, E. N. Kuznetsov, A. V.  Batianovskii, L. A. Uroshlev, V. G. Tumanyan, N. G. Esipova

“…It was shown that conformationally stable peptides occur sometimes in the binding regions with DNA. Analysis of the residues in a predefined conformation in 3 518 protein­DNA complexes revealed 159 amino acid residues in a predefined β­bend type I conformation, 15 residues in the conformation of β­bend type I’, and 6 residues in the conformation of β­bend type II. …”
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Evaluation of de novo donor specific antibodies after kidney transplantation in the era of donor-derived cell-free DNA by Yuan Tian, Lukas Frischknecht, Anna Mallone, Fabian Rössler, Thomas Schachtner, Jakob Nilsson

“…A strong correlation between cumulative dnDSA MFI and dd-cfDNA levels was observed, especially in patients with “true” HLA-DQ-directed dnDSA. Sequential dd-cfDNA analysis showed dynamic changes in 25% of patients, all from the “true” dnDSA group, which tended to align with shifts in cumulative MFI over time.ConclusionThese findings highlight the correlation between cumulative dnDSA MFI and dd-cfDNA levels, particularly in HLA-DQ-directed dnDSA, and suggest graft injury is dynamic in dnDSA-positive patients. …”
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Genetic structure of the population of wild-growing vines of the Utrish Nature Reserve by E. T. Ilnitskaya, M. V. Makarkina, I. V. Gorbunov, I. V. Stepanov, T. D. Kozina, E. A. Kozhevnikov, V. K. Kotlyar

“…Statistical processing of DNA analysis data made it possible to identify two genetically different populations among the wild discovered vines. …”
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Exercise-induced methylation of the Serhl2 promoter and implication for lipid metabolism in rat skeletal muscle by Mutsumi Katayama, Kazuhiro Nomura, Jonathan M. Mudry, Alexander V. Chibalin, Anna Krook, Juleen R. Zierath

“…Additional methods included promoter luciferase assays, fluorescence microscopy, and RNA/DNA analysis to investigate exercise-induced molecular changes. …”
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Complete mitochondrial genome sequence analysis revealed double matrilineal components in Indian Ghoongroo pigs by Pranab Jyoti Das, Satish Kumar, Manasee Choudhury, Seema Rani Pegu, K. Meera, Rajib Deb, Sunil Kumar, Santanu Banik, Vivek Kumar Gupta

“…This study underscores the significance of mitochondrial DNA analysis in uncovering hidden genetic diversity within seemingly uniform populations. …”
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The promising role of nanopore sequencing in cancer diagnostics and treatment by Xinming Su, Qingyuan Lin, Bin Liu, Chuntao Zhou, Liuyi Lu, Zihao Lin, Jiahua Si, Yuemin Ding, Shiwei Duan

“…In the context of DNA analysis, nanopore sequencing excels in identifying structural variations (SVs), copy number variations (CNVs), gene fusions within SVs, and mutations in specific genes, including those involving DNA modifications and DNA adducts. …”
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Statistical optimization of pectinases from thermophilic Aspergillus fumigatus BT-4 employing response surface methodology through submerged fermentation using agricultural wastes by Imran Ali, Roheena Abdullah, Sana Saqib, Kinza Nisar, Afshan Kaleem, Mehwish Iqtedar, Irfana Iqbal, Xiaoming Chen

“…Among all the isolates, strain No. 4 was identified as Aspergillus fumigatus BT-4 based on its morphology and 18 S rDNA analysis. This strain was employed to screen various fermentation media to enhance pectinase production. …”
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Genetic Predictors of Poor Prognosis in Portuguese Patients with Juvenile Idiopathic Arthritis: Data from Reuma.pt by Ana Filipa Mourão, Maria José Santos, Sílvia Mendonça, Filipa Oliveira-Ramos, Manuel Salgado, Paula Estanqueiro, José Melo-Gomes, Fernando Martins, Ana Lopes, Bruno Filipe Bettencourt, Jácome Bruges-Armas, José Costa, Carolina Furtado, Ricardo Figueira, Iva Brito, Jaime Branco, João Eurico Fonseca, Helena Canhão

“…We collected prospectively patient and disease characteristics and a blood sample for DNA analysis. Poor prognosis was defined as CHAQ/HAQ >0.75 at the last visit and/or the treatment with biological therapy. …”
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Set of 15 SNP-SNP Markers for Detection of Unbalanced Degraded DNA Mixtures and Noninvasive Prenatal Paternity Testing by Ranran Zhang, Yu Tan, Li Wang, Hui Jian, Jing Zhu, Yuanyuan Xiao, Mengyu Tan, Jiaming Xue, Fan Yang, Fan Yang, Weibo Liang

“…Unbalanced and degraded mixtures (UDM) are very common in forensic DNA analysis. For example, DNA signals from criminal suspects are masked by a large amount of DNA from victims, or cell-free fetal DNA (cffDNA) in maternal plasma is masked by a high background of maternal DNA. …”
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A low-protein soybean-free diet improves carcass traits and meat quality and modulates the colonic microbiota in Daweizi pigs by Haohua Fu, Taoming Yang, Hengjia Ni, Hengjia Ni, Jing Li, Fenfen Liu, Jingbo Liu, Yulong Yin, Yulong Yin

“…Moreover, the purine content in the meat substantially decreased with the LPNS diet. The 16S rDNA analysis revealed that the LPNS diet greatly modified the composition of the colonic microbiota community, with a decrease in the Firmicutes/Bacteroidetes ratio and an increase in the abundance of Lactobacillus spp.DiscussionThe use of functional herbs along with a low-protein diet helped to regulate fat and purine metabolism in fatty-type pigs. …”
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Multi-omics elucidates the kidney damage caused by aquatic Cu via the gut-kidney axis in ducks by Mingcai Duan, Jinyu Liu, Zhaoxia Cai, Li Chen, Yong Tian, Wenwu Xu, Tao Zeng, Tiantian Gu, Lizhi Lu

“…Results indicate that Cu exposure causes pathological damage to the kidney, with a significant increase in the levels of TNFα, IL-6, and IL-1β in both serum and renal tissue. 16S rDNA analysis revealed that the relative abundances of Candidatus_Saccharimonas and Bacteroides were significantly reduced in the Cu-induced group. …”
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Evaluation of circulating tumor DNA as a prognostic and predictive biomarker in BRAF V600E mutated colorectal cancer—results from the FIRE‐4.5 study by Susanne Klein‐Scory, Alexander Baraniskin, Wolff Schmiegel, Thomas Mika, Roland Schroers, Swantje Held, Kathrin Heinrich, David Tougeron, Dominik P. Modest, Ingo Schwaner, Jan Eucker, Rudolf Pihusch, Martina Stauch, Florian Kaiser, Christoph Kahl, Meinolf Karthaus, Christian Müller, Christof Burkart, Sebastian Stintzing, Volker Heinemann

“…This study was accompanied by a prospective translational project analyzing cell‐free circulating tumor DNA (ctDNA) in plasma to test whether ctDNA analysis may help to guide clinical treatment decision making. …”
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Clinical Significance of Perioperative Minimal Residual Disease Detected by Circulating Tumor DNA in Patients With Lung Cancer With a Long Follow-up Data: An Exploratory Study by Shuta Ohara, MD, PhD, Kenichi Suda, MD, PhD, Sumedha Sudhaman, PhD, Akira Hamada, MD, PhD, Masato Chiba, MD, PhD, Masaki Shimoji, MD, PhD, Toshiki Takemoto, MD, PhD, Ekaterina Kalashnikova, PhD, Samantha K. Cheung, PhD, Michael Krainock, MD, PhD, Jordan Feeney, BS, Himanshu Sethi, MPH, Minetta C. Liu, MD, Junichi Soh, MD, PhD, Yasuhiro Tsutani, MD, PhD, Tetsuya Mitsudomi, MD, PhD

“…Here, we report on a cohort of patients with NSCLC who underwent definitive surgery and ctDNA analysis in the pre-operative, adjuvant, and surveillance settings. …”
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De Novo or inherited: gonosomal mosaicism in hereditary angioedema due to C1 inhibitor deficiency by Laura Batlle-Masó, Laura Batlle-Masó, Laura Batlle-Masó, Janire Perurena-Prieto, Janire Perurena-Prieto, Janire Perurena-Prieto, Laura Viñas-Giménez, Laura Viñas-Giménez, Laura Viñas-Giménez, Aina Aguiló-Cucurull, Aina Aguiló-Cucurull, Paula Fernández-Álvarez, Johana Gil-Serrano, Johana Gil-Serrano, Johana Gil-Serrano, Mar Guilarte, Mar Guilarte, Mar Guilarte, Roger Colobran, Roger Colobran, Roger Colobran, Roger Colobran

“…In the patient, we identified a novel splice site mutation in SERPING1 (c.890-1G>C) and, by cDNA analysis, we confirmed its pathogenicity. Despite normal C1-INH function in the parents, we found that the mother was, unexpectedly, a mutation carrier. …”
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