Review
Biology
Heena Satam, Kandarp Joshi, Upasana Mangrolia, Sanober Waghoo, Gulnaz Zaidi, Shravani Rawool, Ritesh P. Thakare, Shahid Banday, Alok K. Mishra, Gautam Das, Sunil K. Malonia
Summary: Next-generation sequencing (NGS) is a powerful tool that can sequence millions of DNA fragments simultaneously, providing detailed information about genomes, genetic variations, gene activity, and changes in gene behavior. Recent advancements have focused on improving sequencing speed and accuracy, reducing costs, and enhancing data analysis. These advancements have great potential for advancing genomics research and improving our understanding of diseases and personalized healthcare.
Review
Plant Sciences
Longlong Gao, Wenjie Xu, Tianyi Xin, Jingyuan Song
Summary: Traditional medicine has a long history of use, but little genetic information is known about the plants used, limiting their potential exploitation. Third-generation sequencing techniques, specifically PacBio SMRT and Oxford Nanopore, offer valuable insights into the genetic makeup of medicinal plants. This review compares these techniques with Illumina, the current dominant next-generation sequencing method, and summarizes the assembly of nuclear and organelle genomes of commonly used medicinal plants. Furthermore, it discusses the advantages and disadvantages of using these third-generation sequencing techniques in genomics, transcriptomics, molecular identification, and epigenomics research concerning medicinal organisms.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Pei-Ling Yu, James C. Fulton, Owen H. Hudson, Jose C. Huguet-Tapia, Jeremy T. Brawner
Summary: This study developed a broad-spectrum fungal identification tool using high-throughput Nanopore sequencing and enrichment probes. It provides a fast and accurate method for fungal identification, and also offers a platform for identifying other plant pathogens.
Article
Fisheries
Zhengyuan Liang, Bingbing Feng, Linghong Miao, Wenbin Zhu, Yan Lin, Mingkun Luo, Siyu Yang, Lanmei Wang, Jianjun Fu, Huangen Chen, Zaijie Dong
Summary: This study used Illumina and PacBio sequencing technologies to analyze the transcriptome of American shad at different developmental stages, revealing significant differences in gene expression profiles. The molecular developmental profile showed distinct differences between larva, embryo, and fingerling, with variations related to organ formation, visual system development, digestion, and stress response.
AQUACULTURE REPORTS
(2022)
Article
Food Science & Technology
Maria del Socorro Toxqui Rodriguez, Joran Vanhollebeke, Sofie Derycke
Summary: Seafood is a highly traded food commodity, but its supply and labeling accuracy are often uncertain. This study evaluated the feasibility of using the MinION sequencer and DNA barcoding to authenticate seafood products. The results showed that MinION sequencing could accurately identify some species, but its ability to detect mixed samples still needs improvement.
Article
Immunology
Jing Zhang, Lin Gao, Chi Zhu, Jiajia Jin, Chao Song, Hang Dong, Zhenzhong Li, Zheng Wang, Yubao Chen, Zhenhua Yang, Yan Tan, Li Wang
Summary: This study evaluated the clinical value of mNGS by Illumina and Nanopore in pathogen detection in suspected CAP patients, showing that Nanopore detected a wider range of species, especially in viruses, fungi, and mycobacteria, with a shorter TAT. However, it had similar diagnostic performance and treatment guidance compared to Illumina.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Domenico Tierno, Gabriele Grassi, Serena Scomersi, Marina Bortul, Daniele Generali, Fabrizio Zanconati, Bruna Scaggiante
Summary: The poor survival of triple-negative breast cancer (TNBC) is attributed to its aggressive behavior, large heterogeneity, and high risk of recurrence. Next-generation sequencing (NGS) has been used to investigate the molecular characteristics of TNBC, revealing recurrent pathogenic alterations in TP53, immunocheckpoint response genes, and PIK3CA and DNA repair pathways. NGS has also identified potential personalized treatments and novel biomarkers such as AURKA, MYC, and JARID2 mutations. Additionally, NGS studies have identified ethnicity-specific alterations in African and African American TNBC, including EZH2 overexpression, BRCA1 alterations, and a BRCA2-delaAAGA mutation. The development of long-read sequencing methods and their combination with optimized short-read techniques hold promise for improving the efficiency of NGS approaches in future clinical use.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Ryan R. R. Wick, Louise M. M. Judd, Kathryn E. E. Holt
Summary: A perfect bacterial genome assembly requires improved long-read sequencing, assemblers, and polishers. By combining Oxford Nanopore Technologies long reads and Illumina short reads, we suggest using Trycycler long-read assembly, Medaka long-read polishing, Polypolish short-read polishing, and additional short-read polishing tools and manual curation. We also discuss potential challenges and provide an online tutorial for reference.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Yafei Wang, Jinai Yao, Xinyao Xia, Zhiqiang Li, Shaoqun Zhou, Wende Liu, Hanxiang Wu
Summary: This study provided an annotated draft of the assembled genome of the K. zeae field strain KZ1 through PacBio and Illumina sequencing, revealing its high completeness and GC content. It is the first report of the K. zeae genome, contributing to further research on its genetic variation and pathogenic mechanism.
MOLECULAR PLANT-MICROBE INTERACTIONS
(2021)
Article
Food Science & Technology
Lijin Duan, Shasha Zhang, Yingxia Yang, Qian Wang, Qingkuo Lan, Yong Wang, Wentao Xu, Wujun Jin, Liang Li, Rui Chen
Summary: This study introduces a novel GMO testing method, "SSH-seq", based on suppressive subtractive hybridization and next-generation sequencing, which can be used to detect unknown GMOs and has shown promising results in experiments. Although the method may be influenced by multiple factors, further optimizations could make SSH-seq a powerful tool in the field of GMO testing.
Article
Genetics & Heredity
Shougang Wang, Xiaoyan Su, Han Cui, Meng Wang, Xiaoli Hu, Wei Ding, Weipeng Zhang
Summary: This study compared the ability of full-length 16S rRNA gene sequencing technique on the PacBio platform and partial 16S rRNA gene sequencing on the traditional Illumina platform to identify microbes in marine biofilms. The results showed that marine biofilms had higher microbial species richness compared to seawater communities, and PacBio sequencing detected more specific species unique to biofilms. The enrichment of specific species in biofilms, such as Vibrio, Arcobacter, Photobacterium, Pseudoalteromonas, and Thalassomonas, confirms previous understanding of species adapted to a surface-associated lifestyle.
Article
Chemistry, Multidisciplinary
Vasilka Chopkova, Mariana Petkova, Stefan Shilev
Summary: This study investigated the bacterial diversity of mesophilic and thermophilic phases of composting in two different sites using Illumina HiSeq sequencing and phylogenetic analysis. The results showed that the mesophilic phase had a higher number of bacterial species compared to the thermophilic phase, and there were differences in bacterial diversity between the two composting sites.
APPLIED SCIENCES-BASEL
(2023)
Article
Virology
Kathy K. Li, Betty Lau, Nicolas M. Suarez, Salvatore Camiolo, Rory Gunson, Andrew J. Davison, Richard J. Orton
Summary: Nanopore sequencing is increasingly used in clinical settings due to its portability, cost-effectiveness, and real-time operation. Despite initial challenges, improvements in sequencing hardware and software have mitigated high sequencing error rates. In this study, we evaluated the feasibility of using nanopore sequencing to determine the complete genomes of human cytomegalovirus (HCMV) directly from high-viral-load clinical samples without viral DNA enrichment, PCR amplification, or prior sequence knowledge. Our hybrid bioinformatic approach achieved highly accurate HCMV genomes from urine and lung samples, demonstrating the capability of nanopore sequencing for clinical diagnostics.
Article
Microbiology
Michael T. Pyne, Keith E. Simmon, Melanie A. Mallory, Weston C. Hymas, Jeffery Stevenson, Adam P. Barker, David R. Hillyard
Summary: HIV-1 antiretroviral therapy management requires sequencing of different portions of the HIV-1 pol gene. Traditional Sanger sequencing has limited ability to detect minor variants. Next generation sequencing enables detection of variants at frequencies as low as 1%, allowing for earlier detection of resistance. However, implementation of NGS in the clinical laboratory is hindered by complicated design and analysis.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Editorial Material
Chemistry, Multidisciplinary
Judith Nicholson
Summary: This study demonstrates a significant step in adapting nanopore technology for directly sequencing proteins.
Article
Integrative & Complementary Medicine
Yat-Tung Lo, Ming Li, Pang-Chui Shaw
Article
Chemistry, Analytical
Li-Li Jiang, Yat-Tung Lo, Wei-Ting Chen, Pang-Chui Shaw
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2016)
Article
Chemistry, Analytical
Yat-Tung Lo, Pang-Chui Shaw
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2017)
Review
Chemistry, Applied
Yat-Tung Lo, Pang-Chui Shaw
Article
Chemistry, Analytical
Yat-Tung Lo, Pang-Chui Shaw
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2018)
Article
Integrative & Complementary Medicine
Yat-Tung Lo, Mavis Hong-Yu Yik, Pang-Chui Shaw
Meeting Abstract
Biotechnology & Applied Microbiology
Pang-Chui Shaw, Ka-Lok Wong, Yat-Tung Lo
Review
Biotechnology & Applied Microbiology
Zhi-Min Zhao, Zhi-Hua Liu, Tongtong Zhang, Rongqian Meng, Zhiqun Gong, Yibing Li, Jing Hu, Arthur J. Ragauskas, Bing-Zhi Li, Ying-Jin Yuan
Summary: Bioconversion of bioresources/wastes using Rhodococcus is a promising approach for producing lipid-derived bioproducts. However, bioconversion involves living cells and is a complex system that requires further understanding. This review highlights the potential of Rhodococcus for producing lipids from various wastes and presents genetic modifications using emerging tools for promoting bioconversion. Additionally, strategies for enhancing the bioaccessibility of lignin and its derived aromatics and synthesizing biodiesel and aviation fuels from lignin and lipids are discussed. The synergistic modification of microbial strains, substrates, and fermentation processes is proposed for sustainable biological lignin valorization.
BIOTECHNOLOGY ADVANCES
(2024)
Review
Biotechnology & Applied Microbiology
Maddy L. Newby, Joel D. Allen, Max Crispin
Summary: A key aspect of successful viral vaccine design is the elicitation of neutralizing antibodies targeting viral attachment and fusion glycoproteins. Glycosylation can influence the antigenicity and immunogenicity of vaccines, with native-like glycosylation potentially enhancing immunogenicity. Understanding viral glycosylation can guide the development of future vaccines in various enveloped viruses.
BIOTECHNOLOGY ADVANCES
(2024)
Review
Biotechnology & Applied Microbiology
Uganeeswary Suparmaniam, Man Kee Lam, Jun Wei Lim, Inn Shi Tan, Bridgid Lai Fui Chin, Siew Hoong Shuit, Steven Lim, Yean Ling Pang, Peck Loo Kiew
Summary: Microalgae have the ability to synthesize high-value phytochemicals, and subjecting them to abiotic stress can enhance the accumulation of valuable metabolites within their cells. This study explores the effects of manipulating abiotic stress on microalgae yields and discusses approaches to increase HVPCs production using abiotic stress.
BIOTECHNOLOGY ADVANCES
(2024)
Review
Biotechnology & Applied Microbiology
Pei Zhou, Cong Gao, Wei Song, Wanqing Wei, Jing Wu, Liming Liu, Xiulai Chen
Summary: The engineering status of protein is crucial for the efficient bioproduction in microbial cell factories. Strategies such as protein engineering, protein modification, and protein assembly can effectively modify the protein status and enhance production efficiency.
BIOTECHNOLOGY ADVANCES
(2024)