Formamide denaturation of double-stranded DNA for fluorescence in situ hybridization (FISH) distorts nanoscale chromatin structure. by Anne R Shim, Jane Frederick, Emily M Pujadas, Tiffany Kuo, I Chae Ye, Joshua A Pritchard, Cody L Dunton, Paola Carrillo Gonzalez, Nicolas Acosta, Surbhi Jain, Nicholas M Anthony, Luay M Almassalha, Igal Szleifer, Vadim Backman

“…As imaging techniques rapidly evolve to probe nanoscale genome organization at higher resolution, it is critical to consider how the reagents and procedures involved in sample preparation affect chromatin at the relevant length scales. …”
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Multi-purpose utility of circulating plasma DNA testing in patients with advanced cancers. by Geraldine Perkins, Timothy A Yap, Lorna Pope, Amy M Cassidy, Juliet P Dukes, Ruth Riisnaes, Christophe Massard, Philippe A Cassier, Susana Miranda, Jeremy Clark, Katie A Denholm, Khin Thway, David Gonzalez De Castro, Gerhardt Attard, L Rhoda Molife, Stan B Kaye, Udai Banerji, Johann S de Bono

“…We also observed high detection concordance for critical 'hot-spot' mutations (KRAS, BRAF, PIK3CA) in matched cpDNA and archival tumor tissue, and important differences between archival tumor and cpDNA. This multiplex sequencing assay can be utilized to detect somatic mutations from plasma in advanced cancer patients, when safe repeat tumor biopsy is not feasible and genomic analysis of archival tumor is deemed insufficient. …”
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Analysis of genetic diversity of Zymoseptoria tritici populations in central and south-eastern Ethiopia by Ayantu Tucho, Ayantu Tucho, Tilahun Mekonnen, Farideh Ghadamgahi, Samrat Ghosh, Diriba Muleta, Kassahun Tesfaye, Kassahun Tesfaye, Eu Shang Wang, Tesfaye Alemu, Ramesh Raju Vetukuri

“…The pathogen’s genetic structure was further examined using 12 simple sequence repeat (SSR) markers. The microsatellite markers were highly polymorphic and informative, with mean number of alleles (Na), effective alleles (Ne), Nei’s gene diversity of 6.23, 2.90, and 0.59, respectively. …”
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Uncovering <i>Fusarium</i> Species Associated with Fusarium Wilt in Chickpeas (<i>Cicer arietinum</i> L.) and the Identification of Significant Marker–Trait Associations for Resist... by Sojida M. Murodova, Tohir A. Bozorov, Ilkham S. Aytenov, Bekhruz O. Ochilov, Dilafruz E. Qulmamatova, Ilkhom B. Salakhutdinov, Marufbek Z. Isokulov, Gavkhar O. Khalillaeva, Laylo A. Azimova, Sodir K. Meliev

“…An analysis of the genetic diversity of chickpeas, using 69 polymorphic simple sequence repeat (SSR) markers, revealed a total of 191 alleles across all markers, with, on average, each SSR marker detecting approximately 2.8 alleles. …”
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Gemcitabine resistance by CITED4 upregulation via the regulation of BIRC2 expression in pancreatic cancer by Eun-Jeong Jeong, Yuna Roh, Eunsun Jung, Jin-Seong Hwang, Taesang Son, Hyun Seung Ban, Tae-Su Han, Young-Kug Choo, Jang-Seong Kim

“…Results From the RNA sequencing data of isolated GEM-resistant PC cells and The Cancer Genome Atlas dataset, 15 GEM resistance-related genes were found to be upregulated, including CITED4, the gene encoding a type of CBP/p300-interacting transactivator implicated in several cancers. …”
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Parkinson’s families project: a UK-wide study of early onset and familial Parkinson’s disease by Clodagh Towns, Zih-Hua Fang, Manuela M. X. Tan, Simona Jasaityte, Theresa M. Schmaderer, Eleanor J. Stafford, Miriam Pollard, Russel Tilney, Megan Hodgson, Lesley Wu, Robyn Labrum, Jason Hehir, James Polke, Lara M. Lange, Anthony H. V. Schapira, Kailash P. Bhatia, Parkinson’s Families Project (PFP) Study Group, Global Parkinson’s Genetics Program (GP2), Andrew B. Singleton, Cornelis Blauwendraat, Christine Klein, Henry Houlden, Nicholas W. Wood, Paul R. Jarman, Huw R. Morris, Raquel Real

“…Where possible, we also recruited affected and unaffected relatives. We analysed DNA samples with a combination of single nucleotide polymorphism (SNP) array genotyping, multiplex ligation-dependent probe amplification (MLPA), and whole-genome sequencing (WGS). …”
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Amplification of select autonomous HERV loci and surrounding host gene transcription in monocytes from patients with post-acute sequelae of COVID-19 by Hyunmin Koo, Casey D. Morrow

“…These autonomous HERV proviral genomes include long terminal repeats (LTRs) capable of promoting RNA transcription. …”
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Paternal identification of mango controlled-pollination seedling progenies based on fluorescent SSR markers by YAN Jinyuan, ZHENG Bin, WANG Songbiao, MA Xiaowei, XU Wentian, XIE Kunliang, WU Hongxia

“…The genomic DNA of the samples was extracted using an improved CTAB method. …”
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Molecular investigation of coronaviruses in Hungarian bats by Dr Henrik Károlyi, Dr Gábor Kemenesi, Dr Enikő Fehér, Ágnes Nagy, Ágota Ábrahám, Dr Zsófia Lanszki, Csaba I Pereszlényi, Dr Tamás Görföl

“…Positive samples were Sanger sequenced and certain viruses were subjected to Illumina sequencing and de novo genome assembly. …”
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Genetic Polymorphisms and Forensic Parameters of Thirteen X-Chromosome Markers in the Iraqi Kurdish Population by Ara K. Mohammad, Bahez Ismael, Khanzad Ahmed Ali, Balnd M. Albarzinji

“…The system was optimized and tested for species specificity, sensitivity, stability, and DNA mixture using 9947A female and 9948 male control genomic DNA. The amplified products of nine loci were sequenced to determine the correct amplicon length. …”
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An appropriate DNA input for bisulfite conversion reveals LINE-1 and Alu hypermethylation in tissues and circulating cell-free DNA from cancers. by Trang Thi Quynh Tran, Tung The Pham, Than Thi Nguyen, Trang Hien Do, Phuong Thi Thu Luu, Uyen Quynh Nguyen, Linh Dieu Vuong, Quang Ngoc Nguyen, Son Van Ho, Hang Viet Dao, Tong Van Hoang, Lan Thi Thuong Vo

“…The autonomous and active Long-Interspersed Element-1 (LINE-1, L1) and the non-autonomous Alu retrotransposon elements, contributing to 30% of the human genome, are the most abundant repeated sequences. …”
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Novel protocol for mapping virus integration sites in genes involved in therapy resistance by Michele Massimino, Zhangzan Huang, Jean Helmijr, Camilla Muritti, Anna Uijtdewillegen, Paolo Vigneri, John W. M. Martens, Maurice P. H. M. Jansen

“…This study defines a sequencing-based protocol to rapidly characterize genomic loci near VIS. …”
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SYBR GreenⅠReal-Time Fluorescence Quantitative PCR for Parasitic Boveria labialis Identification from the Sea Cucumber Apostichopus japonicus by Wenyue HAO, Jinjin WANG, Jianlong GE, Bin LI, Yingeng WANG, Meijie LIAO, Xiaojun RONG, Hongjing ZHAO, Minqi JIANG, Wenguang ZHAO, Licheng NIU, Jiao PAN

“…Based on the partial mitochondrial genome sequence of B. labialis obtained using sequencing, primers were designed to amplify nad10 and a SYBR GreenⅠreal-time fluorescent quantitative PCR detection method was established. …”
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Predictive symptoms for COVID-19 in the community: REACT-1 study of over 1 million people. by Joshua Elliott, Matthew Whitaker, Barbara Bodinier, Oliver Eales, Steven Riley, Helen Ward, Graham Cooke, Ara Darzi, Marc Chadeau-Hyam, Paul Elliott

“…Participants were asked about symptoms occurring in the week prior to testing. Viral genome sequencing was carried out for PCR-positive samples with N-gene cycle threshold value < 34 (N = 1,079) in round 8 (January 2021). …”
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Innovative exploration of Hep-2 cell culture in the isolation and culture of Mycoplasma pneumoniae by Weiwei Wu, Wenwen Zhu, Jing Tong, Qiang Zhou, Yanping Xu, Xiuxiu Zhou, Yu Du, Jun Bi, Liguo Zhu

“…The isolated strains were identified by nucleic acid and whole-genome sequencing. Results: Among the 20 throat swab samples collected from individuals with influenza-like illness, 10 MP-positive samples were detected by qPCR. …”
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Assessment of Microsatellite Genetic Diversity of Cultured Eriocheir sinensis Populations from Jiangsu and Anhui by Yuting HU, Jun LING, He JIANG, Huan WANG, Tingshuang PAN, Guoqing DUAN, Huaxing ZHOU, Min YANG, Tong LI

“…The leg muscle of the sampled crabs was extracted, and genomic DNA was extracted according to the instructions of the genome extraction kit (TianGen DP304). …”
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Characterizing spatial epidemiology in a heterogeneous transmission landscape using the spatial transmission count statistic by Leke Lyu, Gabriella Veytsel, Guppy Stott, Spencer Fox, Cody Dailey, Lambodhar Damodaran, Kayo Fujimoto, Pamela Brown, Roger Sealy, Armand Brown, Magdy Alabady, Justin Bahl

“…Intensive and widespread efforts to collect and sequence SARS-CoV-2 viral samples have enabled the development of comparative genomic approaches to reconstruct spatial transmission history and understand viral transmission across different scales. …”
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Composition and Functional Capacity of Gut Microbes are Associated with Arterial Stiffness: A Prospective Study by Jing Li, Yixuan Zhong, Jingjing Bai, Shuohua Chen, Jun Cai, Shouling Wu, Weili Zhang

“…“Shotgun” metagenomics sequencing were undertaken in 96 individuals from a hypertension-associated gut-microbiota study in the Kailuan cohort, who measured brachial-ankle pulse wave velocity (baPWV) and provided fecal samples between September 2014 and February 2015 at Kailuan General Hospital and 11 affiliated hospitals. …”
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Using de novo assembly to identify structural variation of eight complex immune system gene regions. by Jia-Yuan Zhang, Hannah Roberts, David S C Flores, Antony J Cutler, Andrew C Brown, Justin P Whalley, Olga Mielczarek, David Buck, Helen Lockstone, Barbara Xella, Karen Oliver, Craig Corton, Emma Betteridge, Rachael Bashford-Rogers, Julian C Knight, John A Todd, Gavin Band

“…Characterizing this variation is challenging due to the complexity of these loci, which contain extensive regions of paralogy, segmental duplication and high copy-number repeats, but recent progress in long-read sequencing and optical mapping techniques suggests this problem may now be tractable. …”
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Establishment of a TaqMan qPCR method with MGB probe for the specific detection of BVDV field strains circulating in China by Lele An, Lele An, Xiaoting Ren, Yetao Zhang, Shubin Zhang, Yongqing Zhao, Yongqing Zhao

“…Intra- and inter-assay coefficients of variation were below 1.5%, indicating excellent repeatability and reproducibility. When applied to field serum samples collected from free-range cattle in various regions of China, the assay achieved a 100% concordance rate with a commercial reference kit (IDEXX RealPCR™ BVDV RNA Test). …”
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