Editorial Material
Multidisciplinary Sciences
Heidi Ledford
Summary: The article tells the story of a human genome scientist who sequenced the genes of the ocean, set up a health-screening company after checking his own genes, and explains why he has no plans to stop.
Article
Multidisciplinary Sciences
Yukiko Matsuda, Arikuni Uchimura, Yasunari Satoh, Naohiro Kato, Masaaki Toshishige, Junko Kajimura, Kanya Hamasaki, Kengo Yoshida, Tomonori Hayashi, Asao Noda, Osamu Tanabe
Summary: The spectra and frequencies of somatic mutations in mouse long-term hematopoietic stem cells (LT-HSCs) were studied using whole-genome sequencing. Spontaneous and X-ray-induced mutations were identified, with SNVs and small indels being the most common types of mutations. The role of reactive oxygen species in radiation mutagenesis and the presence of microhomology sequences in DNA repair mechanisms were also analyzed. The study also revealed the radiation-specificity of different mutation types, as well as the clonality and dynamics of LT-HSCs after irradiation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biology
Chu Cheng, Pengfeng Xiao
Summary: Next-generation sequencing holds great potential for precision medicine, but current technologies have limitations in accuracy. To overcome this, a correctable decoding sequencing strategy with conservative error rates is proposed. This strategy shows promise in sequence decoding, error correction, and sequencing accuracy, and can be used as an alternative to existing NGS platforms.
LIFE SCIENCE ALLIANCE
(2022)
Article
Plant Sciences
Zeyu Zhang, Huihui Wang, Yongsheng Wang, Feihu Xi, Huiyuan Wang, Markus Kohnen, Pengfei Gao, Wentao Wei, Kai Chen, Xuqing Liu, Yubang Gao, Ximei Han, Kaiqiang Hu, Hangxiao Zhang, Qiang Zhu, Yushan Zheng, Bo Liu, Ayaz Ahmad, Yau-Heiu Hsu, Steven E. Jacobsen, Lianfeng Gu
Summary: The study found that CHH methylation gradually accumulates during the transition from vegetative to reproductive growth in moso bamboo, with differentially methylated regions mainly occurring at transcription start and termination sites. Genes with CG methylation changes are enriched in 'vegetative to reproductive phase transition of meristem' GO categories, while circRNA flanking introns are hypermethylated and enriched in LTR retrotransposons.
Article
Medicine, Research & Experimental
Wen-Xuan Zhou, Shu Wang, Ting-Chao Wu, Ling-Chao Cheng, Yao Du, Wei Wu, Chen Lin, Xin-Ying Li, Zhong-Liang Hu
Summary: In this study, the transcriptome and DNA methylation profiles of parathyroid adenoma were analyzed, and several candidate genes that may be involved in the pathogenesis of PHPT were identified. Among them, hypermethylation of the POMC promoter may contribute to its low expression, which may be involved in the development of PHPT.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Article
Environmental Sciences
Miodrag Stojkovic, Francisco Manuel Ortuno Guzman, Dongjun Han, Petra Stojkovic, Joaquin Dopazo, Konstantina M. Stankovic
Summary: Plastic pollution is rapidly increasing, but its impact on human health is poorly understood. This study demonstrates the use of human cellular models to identify molecular biomarkers of environmental pollution and potentially decipher the origins of environmental diseases.
ENVIRONMENTAL POLLUTION
(2023)
Article
Plant Sciences
Alessia Russo, Baptiste Mayjonade, Daniel Frei, Giacomo Potente, Roman T. Kellenberger, Lea Frachon, Dario Copetti, Bruno Studer, Juerg E. Frey, Ueli Grossniklaus, Philipp M. Schluter
Summary: This article describes a method for extracting high molecular weight (HMW) DNA from low input plant material, which is easy to follow and quick. It successfully enables HMW DNA extraction from different plant species and is suitable for long-read sequencing on the Oxford Nanopore Technologies PromethION(R) platform.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Yiqin Wang, Xiaoxian Guo, Kaixiong Ye, Michael Orth, Zhenglong Gu
Summary: Mitochondrial dysfunction is accelerated in patients with Huntington's disease due to the presence of pathogenic mtDNA heteroplasmies, particularly in lymphoblasts. The expansion of these heteroplasmies is correlated with disease progression and severity, as well as decline in functional capacity. Additionally, elongated CAG repeats in the HTT gene contribute to the age-dependent expansion of pathogenic mtDNA heteroplasmies in HD patients.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Microbiology
Melanie A. Mallory, Weston C. Hymas, Keith E. Simmon, Michael T. Pyne, Jeffery B. Stevenson, Adam P. Barker, David R. Hillyard, Kimberly E. Hanson
Summary: This study developed and validated an amplicon-based Ion Torrent NGS method for simultaneous analysis of CMV resistance mutations in multiple genes. Compared to standard Sanger sequencing, the NGS assay had a low error rate and high accuracy, and generated high-quality sequence from low viral load specimens. The assay showed excellent agreement with Sanger and detected resistance mutations missed by Sanger in low-frequency variants.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Jinyue Zhang, Yu Wang, Yuqin Wang, Panke Zhang, Hong-Yuan Chen, Shuo Huang
Summary: DNA lesions induced by alkylating agents can be directly distinguished by observing the enzymatic stalling kinetics, which is not interfered with by the sequence context.
Article
Food Science & Technology
Meng-Yue Zhou, Ran -Ran Xing, Ke-Han Liu, Yi-Qiang Ge, Ying Chen
Summary: This study aimed to develop a DNA barcoding method for the species identification of culinary spices. Five barcodes were evaluated to detect 19 culinary spices, but they could not definitively identify all the species. The combination of ITS2 and psbA-trnH barcodes improved the identification ability, successfully identifying all tested spices except for Cambodian cardamom. The method can be used to standardize labels on commercial culinary spices.
Review
Medicine, Research & Experimental
Fang Liu, Yunfei Wang, Hongcang Gu, Xiaoxue Wang
Summary: DNA methylation is a stable epigenetic modification occurring at CpG dinucleotides, playing essential roles in both physiological and pathological processes. In human diseases, especially cancer, aberrant DNA methylation has been observed. However, conventional methods for DNA methylation profiling require a large amount of DNA from heterogeneous cell populations, making it impractical for rare or circulating tumor cells. Therefore, the development of sequencing technologies that can accurately profile DNA methylation using small numbers of cells, or even single cells, is crucial. Excitingly, various single-cell DNA methylation sequencing and omics sequencing technologies have been developed, greatly advancing our understanding of the molecular mechanisms of DNA methylation. In this review, we summarize these methods, their applications in biomedical sciences, discuss technical challenges, and provide prospects for future research directions.
Article
Biophysics
Qiuxiang He, Longhua Tang
Summary: This article reviews the fabrication methods and applications of nanogap electrodes in the field of biological/chemical sensing. It outlines the challenges of nanogap electrodes in single molecule sensing/sequencing and suggests future directions for sensing perspectives.
BIOSENSORS & BIOELECTRONICS
(2022)
Article
Chemistry, Multidisciplinary
Zheng Yuan, Dapeng Zhang, Fangzhi Yu, Yangde Ma, Yan Liu, Xiangjun Li, Hailin Wang
Summary: This study demonstrates a new supernuclease's capability for highly efficient cutting of DNA segments, leading to the development of a method that allows precise sequencing of single protected-DNA fragment molecules, and the direct measurement of RecA filament length. This innovative assay shows promise as an analytical tool for studying various protein-DNA interactions involved in DNA replication, transcription, recombination, repair, and gene editing.
Article
Computer Science, Information Systems
Wenjie Hu, Yuxin Zhang, Hongrui Zhang, Weigang Chen
Summary: This paper proposes a hardware accelerator for accelerating the recognition of DNA sequencing barcodes using a barcode identification scheme combining cyclic shifting with dynamic programming. The experimental results demonstrate that the accelerator can achieve a speedup of two orders of magnitude for longer barcodes.
Article
Multidisciplinary Sciences
Linda Ye, Mingu Kang, Junwei Liu, Felix von Cube, Christina R. Wicker, Takehito Suzuki, Chris Jozwiak, Aaron Bostwick, Eli Rotenberg, David C. Bell, Liang Fu, Riccardo Comin, Joseph G. Checkelsky
Article
Chemistry, Multidisciplinary
Richard Li, Erica F. Antunes, Estelle Kalfon-Cohen, Akira Kudo, Luiz Acauan, Wei-Chang D. Yang, Canhui Wang, Kehang Cui, Andrew H. Liotta, Ananth Govind Rajan, Jules Gardener, David C. Bell, Michael S. Strano, J. Alexander Liddle, Renu Sharma, Brian L. Wardle
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2019)
Article
Chemistry, Physical
Cedric Barroo, Austin J. Akey, David C. Bell
APPLIED SURFACE SCIENCE
(2019)
Article
Biology
Tobias W. Giessen, Benjamin J. Orlando, Andrew A. Verdegaal, Melissa G. Chambers, Jules Gardener, David C. Bell, Gabriel Birrane, Maofu Liao, Pamela A. Silver
Review
Chemistry, Multidisciplinary
Cedric Barroo, Austin J. Akey, David C. Bell
APPLIED SCIENCES-BASEL
(2019)
Article
Chemistry, Physical
Mingu Kang, Linda Ye, Shiang Fang, Jhih-Shih You, Abe Levitan, Minyong Han, Jorge I. Facio, Chris Jozwiak, Aaron Bostwick, Eli Rotenberg, Mun K. Chan, Ross D. McDonald, David Graf, Konstantine Kaznatcheev, Elio Vescovo, David C. Bell, Efthimios Kaxiras, Jeroen Van den Brink, Manuel Richter, Madhav Prasad Ghimire, Joseph G. Checkelsky, Riccardo Comin
Article
Chemistry, Inorganic & Nuclear
Geronimo Perez, Maria Paulina Romero, Elisa Baggio Saitovitch, Fred Jochen Litterst, Jefferson F. D. F. Araujo, David C. Bell, Guillermo Solorzano
SOLID STATE SCIENCES
(2020)
Article
Multidisciplinary Sciences
A. Devarakonda, H. Inoue, S. Fang, C. Ozsoy-Keskinbora, T. Suzuki, M. Kriener, L. Fu, E. Kaxiras, D. C. Bell, J. G. Checkelsky
Article
Materials Science, Multidisciplinary
M. E. Mendoza, A. P. Campos, Yutao Xing, David C. Bell, I. G. Solorzano
DIAMOND AND RELATED MATERIALS
(2020)
Article
Chemistry, Multidisciplinary
Jessi E. S. van der Hoeven, Stephan Kramer, Simone Dussi, Tanya Shirman, Kyoo-Chul K. Park, Chris H. Rycroft, David C. Bell, Cynthia M. Friend, Joanna Aizenberg
Summary: RCT catalysts have a unique structure where all nanoparticles reside on the pore wall, with over 50% of their surface embedded in the matrix, increasing thermal and mechanical stability. Epitaxial growth of silver on the supported nanoparticles reveals that both the nanoparticle surface exposed to the pore and the embedded interface remained chemically accessible. This understanding offers valuable guidance for designing stable catalytic materials.
ADVANCED FUNCTIONAL MATERIALS
(2021)
Article
Multidisciplinary Sciences
Anyuan Gao, Yu-Fei Liu, Chaowei Hu, Jian-Xiang Qiu, Christian Tzschaschel, Barun Ghosh, Sheng-Chin Ho, Damien Berube, Rui Chen, Haipeng Sun, Zhaowei Zhang, Xin-Yue Zhang, Yu-Xuan Wang, Naizhou Wang, Zumeng Huang, Claudia Felser, Amit Agarwal, Thomas Ding, Hung-Ju Tien, Austin Akey, Jules Gardener, Bahadur Singh, Kenji Watanabe, Takashi Taniguchi, Kenneth S. Burch, David C. Bell, Brian B. Zhou, Weibo Gao, Hai-Zhou Lu, Arun Bansil, Hsin Lin, Tay-Rong Chang, Liang Fu, Qiong Ma, Ni Ni, Su-Yang Xu
Summary: This study explores the internal structure of topological antiferromagnets, revealing the layer Hall effect and the layer-locked Berry curvature characteristics. The research presents new pathways for detecting and manipulating the internal spatial structure of fully compensated topological antiferromagnets.
Article
Chemistry, Multidisciplinary
Lila Bazina, Dimitrios Bitounis, Xiaoqiong Cao, Glen M. DeLoid, Dorsa Parviz, Michael S. Strano, Hao-Yu Greg Lin, David C. Bell, Brian D. Thrall, Philip Demokritou
Summary: The study evaluated the biotransformations and cytotoxicity of 11 2-dimensional nanomaterials in the gastrointestinal tract, revealing significant agglomeration during digestion and dissolution of MoS2. Despite a slight increase in cytotoxicity with inorganic materials and graphene dispersed in PF108, no adverse effects were observed in the exposed cell model. Further research is needed to clarify the inflammatory or genotoxic potential of these nanomaterials after short- or long-term ingestion.
ENVIRONMENTAL SCIENCE-NANO
(2021)
Article
Microscopy
Cedric Barroo, Austin J. Akey, David C. Bell
Article
Nanoscience & Nanotechnology
Adriana Mendoza-Garcia, Caitlin M. Masterson, Arjun Prakash, Melissa L. Nakamoto, Daniel Garcia-Rojas, Cigdem Ozsoy-Keskinbora, David C. Bell, Vicki L. Colvin
ACS APPLIED NANO MATERIALS
(2019)
Article
Chemistry, Physical
Kun Jiang, Robert B. Sandberg, Austin J. Akey, Xinyan Liu, David C. Bell, Jens K. Norskov, Karen Chan, Haotian Wang