A Novel p.G141R Mutation in ILDR1 Leads to Recessive Nonsyndromic Deafness DFNB42 in Two Chinese Han Families by Xueling Wang, Longhao Wang, Hu Peng, Tao Yang, Hao Wu

“…In this study, targeted next-generation sequencing (NGS) in two Chinese Han families identified a novel p.G141R homozygous mutation in ILDR1 as the genetic cause of the deafness. …”
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Devilish Details in Apes and Atoms

“…Nature leads with a preview of an upcoming workshop on sequencing the ape genome. Science leads off this week with a story about a new measurement that comes tantalizingly close to overturning the longstanding Standard Model of particle physics.…”
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Unveiling early-life microbial colonization profile through characterizing low-biomass maternal-infant microbiomes by 2bRAD-M by Shuwen Hou, Yuesong Jiang, Feng Zhang, Tianfan Cheng, Dan Zhao, Jilong Yao, Ping Wen, Ping Wen, Lijian Jin, Shi Huang

“…We collected breast milk samples, maternal feces, and infant meconium, comparing the results from 2bRAD-M with those from both commonly used 16S rRNA amplicon sequencing and the gold-standard whole metagenomics sequencing (WMS).ResultsThe accuracy and robustness of 2bRAD-M were demonstrated through its consistently high correlation of microbial individual abundance and low whole-community-level distance with the paired WMS samples. …”
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Detection of I491F and V170F rpoB mutations associated with misdiagnosis of rifampicin resistance among patients with drug-susceptible tuberculosis treatment failure, Myanmar, 2022 by Phyu Win Ei, Mi Mi Htwe, Myat Htut Nyunt, Aye Su Mon, Zaw Myint, Wint Wint Nyunt, Su Mon Win, Sandar Aung, Wai Myat Thwe, Wah Wah Aung

“…Whole genome or Deeplex-targeted next-generation sequencing was performed using Illumina Miseq. Mutation analysis was done by PhyResSE and SAM-TB online platforms. …”
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Molecular genetic detection and differentiation of <i>Xanthomonas oryzae</i> pv. <i>oryzicola</i>, bacterial leaf streak agents of rice by M. L. Koroleva, S. A. Blinova, A. A. Shvartsev, V. E. Kurochkin, Ya. I. Alekseev

“…The SeqX.o.all sequencing primers were selected for the hrp gene cluster sequence, namely for the nucleotide sequence encoding the Hpa1 protein, the sequencing of which allows for eff icient differentiation of X. oryzae species. …”
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Assessing the impact of sewage and wastewater on antimicrobial resistance in nearshore Antarctic biofilms and sediments by Melody S Clark, Benjamin H Gregson, Carla Greco, Harisree Paramel Nair, Marlon Clark, Claire Evans, Kevin A. Hughes, Kudzai Hwengwere, Marcus Leung, Lloyd S Peck, Caray A. Walker, William Chow

“…Analysis of AMR genes generated from long-reads Nanopore MinION sequencing showed similar site variability in both drug class and resistance mechanism. …”
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Impact of Improved Sanitation Standard Operating Procedures on Microbial Populations at Three Tree Fruit Packing Facilities by M. Laura Rolon, Marysabel Mendez Acevedo, Priscilla Sinclair, Dumitru Macarisin, Luke F. LaBorde, Jasna Kovac

“…Total aerobic bacteria were quantified using a standard plate count method, and Listeria spp. and L. monocytogenes concentration was quantified using a Most Probable Number method. Amplicon sequencing was used to determine bacterial and fungal microbiota composition, and Nanopore sequencing was used to detect functional elements in the microbiota that could promote the survival and persistence of L. monocytogenes in the studied environments. …”
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Transcriptome Analysis of Effect of Cordyceps militaris Aqueous Extract in Human Gastric Cancer Cell BGC-823 on Different RCD Pathways by Mingqi CUI, Kaiwen YU, Yang SONG, Fangxu XU, Shenghou WANG, Ze WANG

“…A total of 5885 differentially expressed genes were identified through transcriptome sequencing analysis, with significant enrichment in the apoptosis (P=0.001) and autophagy (P=0.008) signaling pathways. …”
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Multimodal cell-free DNA whole-genome TAPS is sensitive and reveals specific cancer signals by Dimitrios V. Vavoulis, Anthony Cutts, Nishita Thota, Jordan Brown, Robert Sugar, Antonio Rueda, Arman Ardalan, Kieran Howard, Flavia Matos Santo, Thippesh Sannasiddappa, Bronwen Miller, Stephen Ash, Yibin Liu, Chun-Xiao Song, Brian D. Nicholson, Helene Dreau, Carolyn Tregidgo, Anna Schuh

“…Most existing methods focus on targeted deep sequencing, but few integrate multiple data modalities. …”
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First VIM-producing representative of Pseudomonas putida group from the largest Bulgarian hospital by Atanaska Petrova, Ivan N. Ivanov, Liubomir Paunov, Angel Uchikov, Ivan Stoikov, Todor Kantardjiev, Marianna Murdjeva

“…The species group P. putida was confirmed with MALDI-TOF system and whole genome sequencing defined it as P. kurunegalensis. Antibiotic susceptibility testing revealed susceptibility only to tobramycin and colistin. …”
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Progression from Sustained BK Viruria to Sustained BK Viremia with Immunosuppression Reduction Is Not Associated with Changes in the Noncoding Control Region of the BK Virus Genome by Imran A. Memon, Bijal A. Parikh, Monique Gaudreault-Keener, Rebecca Skelton, Gregory A. Storch, Daniel C. Brennan

“…We performed PCR amplification and sequencing of (1) stored urine and (2) plasma samples from the time of peak viremia from 11 patients with sustained viremia who participated in a 200-patient clinical trial. …”
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Mutations in Mycobacterium tuberculosis Isolates with Discordant Results for Drug-Susceptibility Testing in Peru by L. Solari, D. Santos-Lazaro, Z. M. Puyen

“…Discordance was confirmed by repeating both tests, and WGS was performed, using the Next Generation Sequencing methodology. Obtained sequences were aligned “through reference” (genomic mapping) using the program BWA with the algorithm “mem”, using as a reference the genome of the M. tuberculosis H37Rv strain. …”
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Copper Tolerance of <i>Trichoderma koningii</i> Tk10 by Kehe Fu, Lili Fan, Jiaming Ji, Xiayu Qiu

“…Whole-genome sequencing revealed six genes associated with copper tolerance, including one superoxide dismutase gene, one peroxidase gene, and three catalase genes linked to copper stress. …”
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Identification and Characterization of Arcanobacterium canis from Companion Animals in Germany and The United Kingdom by Siti Gusti Ningrum, Antonia Kreitlow, Christoph Lämmler, Ellen Prenger-Berninghoff, Christa Ewers, Geoffrey Foster, Madeleine Plötz, Amir Abdulmawjood

“…Both isolates were analyzed using culture methods, biochemical analysis, MALDI-TOF MS, real-time PCR amplification and sequencing of the 16S rRNA gene, and rpoB, gap, and tuf genes. …”
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Miniature-inverted-repeat transposable elements contribute to phenotypic variation regulation of rice induced by space environment by Lishan Chen, Qing Yang, Yan Zhang, Yeqing Sun

“…Rice leaves samples at the heading stage from three space-mutagenic lines were subjected to high coverage whole-genome bisulfite sequencing and whole-genome sequencing. These analyses were conducted to investigate the effects of MITEs related epigenetic and genetic variations on space-mutagenic phenotypes.Results and discussionStudies have indicated that MITEs within gene regulatory regions might contribute to the formation and differentiation of space-mutagenic phenotypes. …”
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Novel frameshift variant of WNT10A in a Japanese patient with hypodontia by Michiyo Ando, Yoshihiko Aoki, Yasuto Sano, Junya Adachi, Masatoshi Sana, Satoru Miyabe, Satoshi Watanabe, Shogo Hasegawa, Hitoshi Miyachi, Junichiro Machida, Mitsuo Goto, Yoshihito Tokita

“…Here, we investigated the genetic causes of sporadic congenital tooth agenesis. Exome sequencing, followed by Sanger sequencing, identified a novel single-nucleotide deletion in WNT10A (NC_000002.12(NM_025216.3):c.802del), which was not found in the healthy parents of the patient. …”
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Targeted Next-Generation Resequencing of Gene Identifies Novel Multiple Variants Pattern in Severe Hereditary Factor V Deficiency by Piotr K. Janicki, Sonia Vaida, Hamid A. B. AL-Mondhiry

“…The present study investigated the genetic defects underlying severe Factor V deficiency in a 26-year-old Columbian (South America) female and her immediate family (both parents and newborn child) by next generation sequencing (NGS) of the entire gene locus. Five mutations in the coding sequence of , including three missense single-nucleotide variants (R2102H, R513K, D107H) and two synonymous variants (A135A , S184S), were identified and confirmed by the Sanger sequencing in the investigated proband (homozygote for all detected mutations), her parents, and her newborn child (all heterozygotic carriers for identified mutations). …”
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Advances in multi-omics integrated analysis methods based on the gut microbiome and their applications by Dongdong Duan, Mingyu Wang, Jinyi Han, Mengyu Li, Zhenyu Wang, Shenping Zhou, Wenshui Xin, Xinjian Li, Xinjian Li

“…With the emergence of new technologies including next-generation sequencing (NGS) and advanced techniques such as microbial community sequencing, people have begun to explore the interaction mechanisms between microorganisms and hosts at various omics levels such as genomics, transcriptomics, metabolomics, and proteomics. …”
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Genome-Wide Approach Identifies Natural Large-Fragment Deletion in ASFV Strains Circulating in Italy During 2023 by Claudia Torresi, Roberta Biccheri, Cesare Cammà, Carmina Gallardo, Maurilia Marcacci, Simona Zoppi, Barbara Secondini, Caterina Riverso, Alejandro Soler, Cristina Casciari, Michela Pela, Elisabetta Rossi, Claudia Pellegrini, Carmen Iscaro, Francesco Feliziani, Monica Giammarioli

“…Complete genomic sequencing of 30 strains revealed large-fragment deletions and translocations. …”
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Detection of gene mutation in a case of Nagashima-type palmoplantar keratoderma by CAO Yuanyuan, YUAN Zhaojun, JIN Chuanyang, WANG Tianzi, LIAO Xiaojie, LIU Hong

“…Whole exome high-throughput sequencing was used to identify the pathogenic mutation, and Sanger sequencing was applied to verify the mutation site. …”
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