Article
Plant Sciences
Jin Guan, Shuxia Yin, Yuesen Yue, Lingyun Liu, Yidi Guo, Hui Zhang, Xifeng Fan, Ke Teng
Summary: This study presents a full-length reference transcriptome of Zoysia japonica using PacBio single-molecule long-read sequencing for the first time. The results identified numerous novel transcripts and transcription factors, and revealed alternative splicing events and alternative polyadenylation sites in Z. japonica. In addition, the underlying transcriptional mechanism of senescence was explored through bioinformatics analysis.
Article
Plant Sciences
Tun Xu, Xiaofei Yang, Yanyan Jia, Zihang Li, Guangbo Tang, Xiujuan Li, Bo Wang, Tingjie Wang, Jiadong Lin, Li Guo, Kai Ye
Summary: By applying IsoSeq on opium poppy, we enhanced gene annotation and identified tissue and development-specific alternative splicing modes using a custom-made correction tool. Through the newly discovered transcribed loci, we uncovered distinct characteristics of splicing sites between young and old genes.
Review
Cell Biology
Fatu Badiane Markey, Vijay Parashar, Mona Batish
Summary: RNA serves as a messenger of genetic information and a regulatory molecule, playing a crucial role in gene expression. Imaging RNA in fixed and live cells is essential for understanding the regulatory steps in RNA's journey. Single-cell and single-molecule imaging techniques provide a deep insight into cellular biology and help predict the functions of RNA species.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2021)
Article
Genetics & Heredity
Fiza Liaquat, Muhammad Farooq Hussain Munis, Samiah Arif, Urooj Haroon, Jianxin Shi, Saddam Saqib, Wajid Zaman, Shengquan Che, Qunlu Liu
Summary: Schima superba is a subtropical evergreen tree that tolerates salt and accumulates elevated amounts of manganese. The PacBio sequencing technology was used to generate the transcriptome of S. Superba, providing a significant number of full-length transcripts for advanced genetic analyses. The study also identified a large number of non-coding RNAs and revealed gene expression patterns under manganese treatment.
FRONTIERS IN GENETICS
(2021)
Review
Chemistry, Analytical
Elba Mauriz, Laura M. Lechuga
Summary: This review summarizes the latest advances in plasmonic technologies for monitoring clinically relevant biomarkers at the single-molecule level, discussing design and functional applications targeting individual molecules, and a wide variety of analytes involved in new analytical developments. It also provides an overview of the utility of plasmonic-based single-molecule analysis for personalized medicine.
Review
Chemistry, Multidisciplinary
Yanfang Wu, J. Justin Gooding
Summary: This review provides an overview of the concepts, fabrication, and applications of nanopore sensors, with a focus on their potential and recent developments in quantitative analysis.
CHEMICAL SOCIETY REVIEWS
(2022)
Article
Chemistry, Analytical
Hong Sun, Chuan Yao, Kaibo You, Can Chen, Shuoshuo Liu, Zhihong Xu
Summary: In this study, a dynamic monitoring approach based on nanopore single-molecule biosensor was developed to detect the folding and unfolding transitions of proteins. By gradually increasing the concentration of denaturant guanidine hydrochloride (GdmCl), sensitive responses were observed with lysozyme unfolding. The existence of a stable intermediate was experimentally confirmed, providing insights into the conformation of the intermediate and the manner of denaturant towards lysozyme.
ANALYTICA CHIMICA ACTA
(2023)
Article
Biotechnology & Applied Microbiology
Runxuan Zhang, Richard Kuo, Max Coulter, Cristiane P. G. Calixto, Juan Carlos Entizne, Wenbin Guo, Yamile Marquez, Linda Milne, Stefan Riegler, Akihiro Matsui, Maho Tanaka, Sarah Harvey, Yubang Gao, Theresa Wiessner-Kroh, Alejandro Paniagua, Martin Crespi, Katherine Denby, Asa Ben Hur, Enamul Huq, Michael Jantsch, Artur Jarmolowski, Tino Koester, Sascha Laubinger, Qingshun Quinn Li, Lianfeng Gu, Motoaki Seki, Dorothee Staiger, Ramanjulu Sunkar, Zofia Szweykowska-Kulinska, Shih-Long Tu, Andreas Wachter, Robbie Waugh, Liming Xiong, Xiao-Ning Zhang, Ana Conesa, Anireddy S. N. Reddy, Andrea Barta, Maria Kalyna, John W. S. Brown
Summary: This study introduces a new comprehensive Arabidopsis transcriptome dataset, AtRTD3, which contains over 169,000 transcripts and provides accurate splice junctions and transcription start/end sites. Additionally, novel methods for identifying accurate splice junctions and transcription start/end sites have been developed, and the effectiveness of AtRTD3 has been validated through analysis of a cold response RNA-seq time-series.
Article
Biochemistry & Molecular Biology
Shuang-Yan Zheng, Lu-Xia Pan, Fu-Ping Cheng, Meng-Jie Jin, Zi-Long Wang
Summary: In this study, the full-length transcriptome of A. mellifera was sequenced using PacBio technology. A total of 116,535 transcripts and 30,045 genes were identified. Compared to the reference genome, 18,915 gene loci and 96,176 transcripts were newly identified. Additionally, alternative splicing events, alternative polyadenylation sites and long non-coding RNAs were detected. These findings expand our understanding of the complexity and diversity of the honey bee transcriptome.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Haihan He, Chuhong Wu, Muhammad Saqib, Rui Hao
Summary: Proteins are crucial building blocks of life, and their detection and sequencing are important for understanding diseases and biological processes. Single-molecule protein detection/sequencing tools can greatly advance clinical research and enable the early diagnosis of diseases. Fluorescence-based methods have emerged as powerful tools for single protein detection/sequencing, providing higher sensitivity and accuracy.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Plant Sciences
Estefania Mancini, Antoni Garcia-Molina
Summary: This study investigated the effect of alternative splicing (AS) on the transcriptome of rosette leaves under single and simultaneous copper (Cu) and iron (Fe) deficiency. It was found that differentially spliced genes (DSGs) and differentially expressed genes (DEGs) showed minimal overlap in number, indicating distinct responses to the double deficiency. Furthermore, it was observed that AS might act as a regulatory mechanism to modify the stability and/or functionality of enzymes involved in amino acid production during the combinatorial response to simultaneous Cu and Fe deficiency.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biology
Nadia M. Huisjes, Thomas M. Retzer, Matthias J. Scherr, Rohit Agarwal, Lional Rajappa, Barbara Safaric, Anita Minnen, Karl E. Duderstadt
Summary: The rapid development of new imaging approaches has led to the generation of larger and more complex datasets, allowing us to uncover the time evolution of individual cells and biomolecules. However, there are currently few standards for processing these information-rich datasets, which poses challenges for wider dissemination. In this study, we introduce Mars, an open-source platform that stores and processes image-derived properties of biomolecules. Mars provides a flexible solution for reproducible analysis of image-derived properties and facilitates the discovery and quantitative classification of new biological phenomena.
Article
Biochemistry & Molecular Biology
Lingyun Liu, Ke Teng, Xifeng Fan, Chao Han, Hui Zhang, Juying Wu, Zhihui Chang
Summary: This study successfully obtained the full-length transcriptome information of Pennisetum setaceum cv. 'Rubrum' using a combination of single-molecule long-read and Illumina sequencing, and revealed the molecular mechanism of anthocyanin accumulation. The results provide important baseline information for gene function studies and breeding projects.
PLANT MOLECULAR BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Johnson Chung, Bruce L. Goode, Jeff Gelles
Summary: This study used single-molecule fluorescence imaging to observe the debranching process of actin networks by GMF and cofilin. The study found that cofilin, like GMF, is an authentic debrancher independent of its filament-severing activity and that the debranching activities of the two proteins are additive. Cofilin selectively accumulates on branch-junction daughter filaments, while GMF directly binds to the Arp2/3 complex. These observations suggest that GMF and cofilin promote debranching by distinct yet complementary mechanisms.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Nanoscience & Nanotechnology
Abhinav Banerjee, Micky Anand, Simanta Kalita, Mahipal Ganji
Summary: DNA-PAINT super-resolution imaging is used to measure the free energy of dinucleotide base stacking at the single-molecule level. Results show that addition of a single dinucleotide base stacking can greatly stabilize the DNA duplex nanostructure. These findings are important for designing functional DNA nanostructures and predicting the local DNA structure.
NATURE NANOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Spyros Darmanis, Rachel Yuan Nong, Maria Hammond, Jijuan Gu, Anders Alderborn, Johan Vanelid, Agneta Siegbahn, Sigrun Gustafsdottir, Olle Ericsson, Ulf Landegren, Masood Kamali-Moghaddam
MOLECULAR & CELLULAR PROTEOMICS
(2010)
Article
Biochemical Research Methods
Mingyue He, Oda Stoevesandt, Elizabeth A. Palmer, Farid Khan, Olle Ericsson, Michael J. Taussig
Article
Biochemistry & Molecular Biology
Olle Ericsson, Jonas Jarvius, Edith Schallmeiner, Mathias Howell, Rachel Yuan Nong, Hendrik Reuter, Meinhard Hahn, Johan Stenberg, Mats Nilsson, Ulf Landegren
NUCLEIC ACIDS RESEARCH
(2008)
Article
Biochemistry & Molecular Biology
H. Johansson, M. Isaksson, E. Falk Sorqvist, F. Roos, J. Stenberg, T. Sjoblom, J. Botling, P. Micke, K. Edlund, S. Fredriksson, H. Goransson Kultima, Olle Ericsson, Mats Nilsson
NUCLEIC ACIDS RESEARCH
(2011)
Article
Multidisciplinary Sciences
Spyros Darmanis, Rachel Yuan Nong, Johan Vanelid, Agneta Siegbahn, Olle Ericsson, Simon Fredriksson, Christofer Backlin, Marta Gut, Simon Heath, Ivo Glynne Gut, Lars Wallentin, Mats G. Gustafsson, Masood Kamali-Moghaddam, Ulf Landegren
Article
Multidisciplinary Sciences
Maria Hammond, Rachel Yuan Nong, Olle Ericsson, Katerina Pardali, Ulf Landegren
Article
Biochemical Research Methods
Johan Baner, Peter Gyarmati, Alia Yacoub, Mikhayil Hakhverdyan, Johan Stenberg, Olle Ericsson, Mats Nilsson, Ulf Landegren, Sandor Belak
JOURNAL OF VIROLOGICAL METHODS
(2007)
Article
Biochemical Research Methods
Edith Schallmeiner, Elli Oksanen, Olle Ericsson, Lena Spangberg, Susann Eriksson, Ulf-Hakan Stenman, Kim Pettersson, Ulf Landegren
Article
Biochemistry & Molecular Biology
U Landegren, E Schallmeiner, M Nilsson, S Fredriksson, J Banér, M Gullberg, J Jarvius, S Gustafsdottir, F Dahl, O Söderberg, O Ericsson, J Stenberg
JOURNAL OF MOLECULAR RECOGNITION
(2004)
Article
Biochemistry & Molecular Biology
U Landegren, F Dahl, M Nilsson, S Fredriksson, J Banér, M Gullberg, J Jarvius, S Gustafsdottir, O Söderberg, O Ericsson, J Stenberg, E Schallmeiner
COMPARATIVE AND FUNCTIONAL GENOMICS
(2003)
Article
Biochemical Research Methods
O Ericsson, Å Sivertsson, J Lundeberg, A Ahmadian