Article
Multidisciplinary Sciences
Shuhei Yasumoto, Toshiya Muranaka
Summary: Genome editing is a powerful breeding technique that introduces mutations into specific gene sequences in genomes. However, there is still no widely authorized method for detecting foreign genes in genome-edited crops.
SCIENTIFIC REPORTS
(2023)
Article
Plant Sciences
Jiyeong Choi, Anya Clara Osatuke, Griffin Erich, Kristian Stevens, Min Sook Hwang, Maher Al Rwahnih, Marc Fuchs
Summary: Pawpaw trees in New York were found to be infected with tobacco ringspot virus (TRSV) and tomato ringspot virus (ToRSV) based on high-throughput sequencing and testing. The study also revealed high similarity between different isolates of these viruses in pawpaw trees.
Article
Virology
Solomon Maina, Linda Zheng, Brendan C. Rodoni
Summary: The study developed a targeted genome sequencing (TG-Seq) approach that can detect multiple plant viruses simultaneously with high sensitivity and potential. It successfully detected all expected viral amplicons in mPCR reactions, providing more accurate and detailed virus detection.
Article
Genetics & Heredity
Dave J. Baker, Alp Aydin, Thanh Le-Viet, Gemma L. Kay, Steven Rudder, Leonardo de Oliveira Martins, Ana P. Tedim, Anastasia Kolyva, Maria Diaz, Nabil-Fareed Alikhan, Lizzie Meadows, Andrew Bell, Ana Victoria Gutierrez, Alexander J. Trotter, Nicholas M. Thomson, Rachel Gilroy, Luke Griffith, Evelien M. Adriaenssens, Rachael Stanley, Ian G. Charles, Ngozi Elumogo, John Wain, Reenesh Prakash, Emma Meader, Alison E. Mather, Mark A. Webber, Samir Dervisevic, Andrew J. Page, Justin O'Grady
Summary: CoronaHiT is a flexible sequencing method for SARS-CoV-2 genomes, suitable for rapid expansion of global sequencing efforts. In experiments, CoronaHiT demonstrated good performance on both nanopore and Illumina platforms.
Article
Biotechnology & Applied Microbiology
Jie Gao, Xin Hu, Chunyan Gao, Guang Chen, Hui Feng, Zhen Jia, Peimin Zhao, Haiyang Yu, Huaiwen Li, Zedong Geng, Jingbo Fu, Jun Zhang, Yikeng Cheng, Bo Yang, Zhanghan Pang, Daoquan Xiang, Jizeng Jia, Handong Su, Hailiang Mao, Caixia Lan, Wei Chen, Wenhao Yan, Lifeng Gao, Wanneng Yang, Qiang Li
Summary: This study used a non-invasive and high-throughput phenotyping platform to monitor a diverse wheat panel and investigate the genetic controls of growth and yield-related traits. By conducting whole genome re-sequencing and a genome-wide association analysis, the study identified numerous marker-trait associations and quantitative trait loci (QTLs) that contribute to wheat growth and yield production. The temporal dynamics of these QTLs were also revealed. This research provides insights into optimizing wheat growth and yield, and offers the potential for high-throughput early selection to accelerate breeding.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Virology
Izabela Fabianska, Stefan Borutzki, Benjamin Richter, Hon Q. Tran, Andreas Neubert, Dietmar Mayer
Summary: High-throughput sequencing (HTS) is effective in detecting both known and unknown viruses in samples, providing support for determining the safety of biological products such as vaccines. Due to the complexity of bioinformatics, standardized and reliable methods are necessary for managing HTS data. The LABRADOR analysis pipeline demonstrates reliable detection of viruses in mixtures of model viruses, vaccines, and clinical samples.
Article
Biotechnology & Applied Microbiology
Michael Alonge, Ludivine Lebeigle, Melanie Kirsche, Katie Jenike, Shujun Ou, Sergey Aganezov, Xingang Wang, Zachary B. Lippman, Michael C. Schatz, Sebastian Soyk
Summary: This study introduces RagTag, a toolset for automating assembly scaffolding and patching, and establishes chromosome-scale reference genomes for tomato genotypes M82 and Sweet-100. This provides convenience for functional genomics and genome editing in tomato.
Review
Microbiology
Mark Paul Selda Rivarez, Ana Vucurovic, Natasa Mehle, Maja Ravnikar, Denis Kutnjak
Summary: The pace of tomato virus discovery has increased in the past decade due to the use of high-throughput sequencing (HTS), but further characterization lags behind, especially for economically devastating viruses. There are at least 312 virus, satellite virus, or viroid species associated with tomato, the highest number recorded for any plant, according to databases and literature review.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Immunology
Cristina Galli, Erika Ebranati, Laura Pellegrinelli, Martina Airoldi, Carla Veo, Carla Della Ventura, Arlinda Seiti, Sandro Binda, Massimo Galli, Gianguglielmo Zehender, Elena Pariani
Summary: The study successfully validated a rapid and reliable high-throughput sequencing protocol for obtaining the complete genome sequence of A(H3N2) influenza viruses directly from clinical specimens, providing important reference for influenza surveillance and outbreak investigation.
Article
Immunology
Lauren M. Walker, Andrea R. Shiakolas, Rohit Venkat, Zhaojing Ariel Liu, Steven Wall, Nagarajan Raju, Kelsey A. Pilewski, Ian Setliff, Amyn A. Murji, Rebecca Gillespie, Nigel A. Makoah, Masaru Kanekiyo, Mark Connors, Lynn Morris, Ivelin S. Georgiev
Summary: The development of novel technologies for discovering human monoclonal antibodies has been extremely valuable in combating infectious diseases. LIBRA-seq with epitope mapping is a next-generation sequencing technology that can determine residue-level epitopes for thousands of single B cells simultaneously, making it an efficient tool for high-throughput identification of antibodies against specific antigen epitopes.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemical Research Methods
Hannah K. Wayment-Steele, Wipapat Kladwang, Alexandra I. Strom, Jeehyung Lee, Adrien Treuille, Alex Becka, Rhiju Das
Summary: This study evaluates the accuracy of commonly used RNA structure modeling packages in ensemble-oriented prediction tasks and finds that packages with parameters derived through statistical learning achieve higher accuracy than those derived from thermodynamic experiments. Training a multitask model can improve performance in ensemble-based prediction tasks.
Article
Virology
Tomoyuki Nabeshima, Junya Abe
Summary: Vitis coignetiae samples from northern Japan were found to be infected with multiple RNA viruses, with three newly identified virus species assigned to different genera based on sequence identity and phylogenetic analysis.
Article
Horticulture
Yue Wang, Sheng Zhao, Peng Chen, Yongkang Liu, Zhigang Ma, Waqar Afzal Malik, Zhenghang Zhu, Zhenyu Peng, Haorong Lu, Yanli Chen, Yuxiao Chang
Summary: By studying 162 hollyhock accessions from China, extensive variation and strong correlations among quantitative traits were found. Whole-genome re-sequencing of 32 accessions identified 10,468,760 core single-nucleotide polymorphisms and calculated the average nucleotide diversity to be 0.00397. The results provide valuable information for hollyhock breeding.
Article
Plant Sciences
Leonardo Velasco, Carlos V. Padilla
Summary: Biological indexing is the primary method for certifying propagative grapevines, with HTS proposed as an alternative. Research findings indicate that HTS is more effective than biological indexing in terms of identifying viruses, saving time, and reducing costs.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Plant Sciences
Cheng Song, Yan Wang, Muhammad Aamir Manzoor, Di Mao, Peipei Wei, Yunpeng Cao, Fucheng Zhu
Summary: High-throughput sequencing technology and gene editing technologies are of great significance in orchid genomics research, helping to identify trait-related genes, improve genetic transformation, and investigate gene function.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Nanoscience & Nanotechnology
Yuying Lu, Qianlin Li, Huahao Fan, Conghui Liao, Jingsong Zhang, Huan Hu, Huaimin Yi, Yuanli Peng, Jiahai Lu, Zeliang Chen
Summary: Nanobodies screened from high-throughput libraries have shown potential as candidates for developing preventive and therapeutic antibodies. In particular, the multivalent nanobody LS-B-B2 demonstrated superior neutralizing activity against the Omicron (B.1.1.529) variant.
INTERNATIONAL JOURNAL OF NANOMEDICINE
(2023)
Article
Virology
Shi-ting He, Hongbo Qin, Lin Guan, Ke Liu, Bixia Hong, Xiaoxu Zhang, Fuxing Lou, Maochen Li, Wei Lin, Yangzhen Chen, Chengzhi He, Feitong Liu, Shanshan Lu, Shengdong Luo, Shaozhou Zhu, Xiaoping An, Lihua Song, Huahao Fan, Yigang Tong
Summary: Lactoferrin and milk fat globule membrane are key components in breast milk that inhibit coronavirus infection, but the exact mechanism is still unknown.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Immunology
Shanshan Lu, Shengdong Luo, Chang Liu, Muli Li, Xiaoping An, Mengzhe Li, Jun Hou, Huahao Fan, Panyong Mao, Yigang Tong, Lihua Song
Summary: This study reports the rapid adaptation of the GX_P2V variant, isolated from Guangxi pangolins, to Vero cells through two genomic mutations. The variant shows high attenuation in vitro and in vivo infection models. These findings contribute to our understanding of pangolin coronavirus pathogenesis and provide insights for the design of live attenuated vaccines against SARS-CoV-2.
EMERGING MICROBES & INFECTIONS
(2023)
Article
Microbiology
Yahao Li, Mingfang Pu, Pengjun Han, Mengzhe Li, Xiaoping An, Lihua Song, Huahao Fan, Zeliang Chen, Yigang Tong
Summary: In recent years, Stenotrophomonas maltophilia has become an important and highly pathogenic pathogen in clinically acquired infections. Additionally, multidrug-resistant S. maltophilia infections have become a serious challenge. Bacteriophages, with their unique antibacterial mechanism and superior bactericidal ability, offer a promising alternative for the treatment of these infections.
MICROBIOLOGY SPECTRUM
(2023)
Review
Biochemistry & Molecular Biology
Shan Xu, Duanyang Wang, Wenqi Zhao, Qinglin Wei, Yigang Tong
Summary: The influenza virus has been spreading globally for over 100 years since the first epidemic in 1918. Its unpredictable gene variation poses a potential threat of another pandemic in the future. Therefore, it is urgent to find effective broad-spectrum antiviral treatments. Trace elements, such as selenium and zinc, show potential in modulating host immune responses and directly targeting viral proteins to inhibit influenza virus replication.
Review
Virology
Qihang Tu, Mingfang Pu, Yahao Li, Yuer Wang, Maochen Li, Lihua Song, Mengzhe Li, Xiaoping An, Huahao Fan, Yigang Tong
Summary: This paper describes the different drug resistances and basic properties of Acinetobacter baumannii (A. baumannii), and analyzes the interaction between phages and their hosts. It also focuses on A. baumannii phage therapies, discussing the chance and challenge of phage therapy. The aim of this paper is to provide a more comprehensive understanding of A. baumannii phages and theoretical support for their clinical application.
Article
Chemistry, Multidisciplinary
Hao Tang, Hongbo Qin, Shiting He, Qizhen Li, Huan Xu, Mengsi Sun, Jiaan Li, Shanshan Lu, Shengdong Luo, Panyong Mao, Pengjun Han, Lihua Song, Yigang Tong, Huahao Fan, Xingyu Jiang
Summary: Antivirals capable of fighting against coronaviruses, including SARS-CoV-2 and its variants, are urgently needed but lacking. By simultaneously targeting the physical structure and replication cycle of the virus, antivirals can exhibit sustainable and broad-spectrum efficacy against coronaviruses, a feat that is difficult to achieve with single small-molecule antivirals. In this study, a library of nanomaterials on a SARS-CoV-2-like coronavirus of pangolin origin was screened, and a surface-functionalized gold nanocluster (TMA-GNC) was identified as the most effective candidate.
Review
Immunology
Lin Jiang, Ao Tang, Lihua Song, Yigang Tong, Huahao Fan
Summary: Rotavirus causes 200,000 deaths per year and poses a significant burden to public health and livestock farming worldwide. Currently, rehydration remains the main strategy for treatment and no specific drugs are available. This review discusses the viral replication cycle and possible therapeutic approaches, highlighting the potential use of Chinese medicine and natural compounds. It provides an important reference for rotavirus prevention and treatment.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Microbiology
Xiaoxuan Zhang, Yanze Mi, Shan Xu, Lihua Song, Huahao Fan, Mengzhe Li, Yigang Tong
Summary: We report the complete genome sequence of the phage BUCT-3589, which infects multidrug-resistant Klebsiella pneumoniae 3589. It belongs to the genus Przondovirus in the Autographiviridae family and has a 40,757 bp double-stranded DNA genome with a GC content of 53.13%. The genome sequence will support its use as a therapeutic agent.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Review
Biochemistry & Molecular Biology
Ke Liu, Bixia Hong, Shuqi Wang, Fuxing Lou, Yecheng You, Ruolan Hu, Amna Shafqat, Huahao Fan, Yigang Tong
Summary: Cepharanthine, a natural bisbenzylisoquinoline alkaloid, is the only approved drug of its kind for human use. It has been used in the clinic for over 70 years and has various medicinal properties, including anti-tumor, anti-inflammatory, anti-pathogen activities, among others. Recently, it has been found to greatly inhibit SARS-CoV-2 infection. This article provides a comprehensive description of the pharmacological properties, mechanisms, safety, and potential clinical applications of cepharanthine, highlighting its potential as a drug for the treatment of different diseases.
Letter
Biotechnology & Applied Microbiology
Evelien M. M. Adriaenssens, Simon Roux, J. Rodney Brister, Ilene Karsch-Mizrachi, Jens H. H. Kuhn, Arvind Varsani, Tong Yigang, Alejandro Reyes, Cedric Lood, Elliot J. J. Lefkowitz, Matthew B. B. Sullivan, Robert A. A. Edwards, Peter Simmonds, Luisa Rubino, Sead Sabanadzovic, Mart Krupovic, Bas E. E. Dutilh
NATURE BIOTECHNOLOGY
(2023)
Correction
Biotechnology & Applied Microbiology
Evelien M. M. Adriaenssens, Simon Roux, J. Rodney Brister, Ilene Karsch-Mizrachi, Jens H. Kuhn, Arvind Varsani, Tong Yigang, Alejandro Reyes, Cedric Lood, Elliot J. Lefkowitz, Matthew B. B. Sullivan, Robert A. A. Edwards, Peter Simmonds, Luisa Rubino, Sead Sabanadzovic, Mart Krupovic, Bas E. E. Dutilh
NATURE BIOTECHNOLOGY
(2023)
Article
Microbiology
Jialiang Xu, Jia Li, Yi Yan, Pengjun Han, Yigang Tong, Xu Li
Summary: A lytic phage SW16-7 was isolated from medical sewage, showing high infectivity against Salmonella enterica serovar Weltevreden and other strains. In vitro inhibition assays demonstrated its effective antibacterial effect for up to 12 h. The phage's genome lacks virulence factors and antibiotic resistance genes, suggesting its potential as a biocontrol agent against S. Weltevreden.
Article
Virology
Pengjun Han, Mingfang Pu, Yahao Li, Huahao Fan, Yigang Tong
Summary: This study reports a novel bacteriophage, BUCT631, that can specifically lyse capsule-type K1 Klebsiella pneumoniae with good thermal and pH stability. The phage has distinct characteristics in terms of infection multiplicity and burst size. Genomic analysis revealed that it belongs to a new species in the subfamily Slopekvirinae. Furthermore, this phage efficiently inhibits the growth of K. pneumoniae in vitro and improves the survival rate in infected larvae.