Article
Chemistry, Analytical
Yan Peng, Linjuan Shu, Xiongfei Deng, Xin Huang, Xianming Mo, Feng Du, Zhuo Tang
Summary: We developed a genetically encoded sensor for sensitive imaging and tracking of endogenous RNA in living cells. This sensor can specifically recognize target RNAs and induce structural changes to enable fluorescence imaging. We successfully demonstrated its application in monitoring mRNA expression and confirming RNA distribution in cancer cells and zebrafish embryos, respectively. This study provides an effective molecular tool for RNA imaging and has potential applications in disease diagnosis and treatment evaluation.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Xiaowen Cao, Feng Chen, Jing Xue, Yue Zhao, Min Bai, Yongxi Zhao
Summary: Here, we present a hierarchical DNA branch assembly-encoded fluorescent nanoladders for denoised and highly multiplexed signal amplification of single-cell transcripts. Our method achieves independent RNA-primed rolling circle amplification without nonspecific amplification and allows for programmable DNA branch assembly to encode virtual signals for visualizing numbers of targets. We demonstrate accurate RNA profiling in different cancer cells and reveal diverse localization patterns for spatial regulation of transcripts.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Analytical
Asuka Tada, Nanami Takeuchi, Kan Shoji, Ryuji Kawano
Summary: This paper presents a method using nanopore technology for real-time counting and extraction of DNA molecules at the single-molecule level. The method eliminates the need for labeling or partitioning sample solutions and utilizes an alpha-hemolysin (αHL) nanopore to develop a DNA filtering system. The translocation of DNA through nanopores is observed by measuring the channel current, and the number of translocated molecules can be verified by quantitative polymerase chain reaction (qPCR). However, the issue of contamination proves to be a challenging problem in single-molecule counting, for which the authors propose optimizations and techniques to reduce contamination and improve accuracy.
ANALYTICAL CHEMISTRY
(2023)
Article
Microbiology
Joyce Odeke Akello, Erika Bujaki, Alexander G. Shaw, Adnan Khurshid, Yasir Arshad, Catherine Troman, Manasi Majumdar, Aine O'Toole, Andrew Rambaut, Muhammad Masroor Alam, Javier Martin, Nicholas C. Grassly
Summary: This article examines the effects of 11 nucleic acid extraction methods on the detection of poliovirus. The study found that the choice of RNA extraction method is an important factor in nucleic acid amplification-based diagnostics.
MICROBIOLOGY SPECTRUM
(2023)
Article
Chemistry, Analytical
Xing Xu, Mingxia Zhang, Xuebing Zhang, Yilong Liu, Linfeng Cai, Qianqian Zhang, Qin Chen, Li Lin, Shichao Lin, Yanling Song, Zhi Zhu, Chaoyong Yang
Summary: The study introduces the multi-Paired-seq technology, which allows efficient and accurate measurement of mRNA and proteins at the single-cell level, enabling multimodal measurements and the study of correlations and dynamics of gene and protein expressions at the cellular level.
ANALYTICAL CHEMISTRY
(2022)
Review
Chemistry, Analytical
Yulin Ren, Lei Cao, Minli You, Jingcheng Ji, Yan Gong, Hui Ren, Feng Xu, Hui Guo, Jie Hu, Zedong Li
Summary: Liquid biopsy based on detection of circulating nucleic acid (NA) biomarkers has emerged as a promising strategy for lung cancer monitoring. Digital NA amplification technologies, such as digital polymerase chain reaction and digital isothermal amplification, show high sensitivity and specificity for early diagnosis, minimal residual disease detection, prognosis prediction, and companion diagnosis of lung cancer. This paper summarizes the evolution of digital NA amplification technologies and proposes SMART digital NA amplification technologies for wider applications in lung cancer monitoring. Moreover, it summarizes the existing NA biomarkers at different stages of lung cancer and introduces the existing digital NA amplification methods for detecting these biomarkers. Conclusions and future perspectives are also provided.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Bruna Winkert Raddatz, Edson Yu Sin Kim, Louise Matie Imamura, Gisleine Jarenko Steil, Erika Bergamo Santiago, Santiago Pedro Timm Soares, Victor Henrique Alves Ribeiro, Bernardo Montesanti Machado de Almeida, Sergio Renato Rogal Jr, Marcus Vinicius Mazega Figueredo
Summary: The coronavirus pandemic increased the demand for molecular diagnostic tests. PCR is a commonly used technique but requires trained personnel, expensive equipment, and is time-consuming. LAMP, as an alternative, is similar to PCR in sensitivity and specificity but does not require sample purification or expensive equipment. In this study, we developed an optimized colorimetric RT-LAMP Point-of-Care test to diagnose COVID-19, which showed improved sensitivity through variables testing and the incorporation of mineral oil.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Multidisciplinary
Jiri Frantisek Potuznik, Ondrej Nesuta, Anton Skriba, Barbora Volenikova, Maria-Bianca Mititelu, Flaminia Mancini, Valentina Serianni, Henri Fernandez, Kristina Spustova, Jana Trylcova, Pavel Vopalensky, Hana Cahova
Summary: The expansion of RNA chemical modifications has revealed new aspects of gene regulation. We discovered a new non-canonical RNA cap, Ap(4)A, which is abundant in human and rat cell lines. Our study showed that Ap(4)A-RNA is recognized as self by the cell and does not elicit an immune response.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Analytical
Luca Miglietta, Ke Xu, Priya Chhaya, Louis Kreitmann, Kerri Hill-Cawthorne, Frances Bolt, Alison Holmes, Pantelis Georgiou, Jesus Rodriguez-Manzano
Summary: This study proposes a novel framework to identify and filter out nonspecific and low-efficient reactions from qdPCR data using outlier detection algorithms, aiming to improve the accuracy of machine learning methods. Additionally, an adaptive mapping filter strategy is developed to adjust the percentage of outliers removed based on the number of positive counts in qdPCR.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Ning Shao, Yufu Zhou, Jun Yao, Pengchao Zhang, Yanni Song, Kai Zhang, Xin Han, Bin Wang, Xuewu Liu
Summary: Dendritic cell migration is crucial for the development of allergy treatments, vaccines, and cancer immunotherapies. This study introduces a microfluidics-based platform for high-throughput and precise single-cell migration assays, allowing for the retrieval of subpopulations with different migratory potentials. By using this platform, the researchers investigate the migration of dendritic cells in response to various chemoattractants and inhibitors, quantitatively describe their migration patterns, and analyze differential gene expression of different migratory subpopulations. This platform provides a new avenue for precise characterization of cell migration and potential discovery of therapeutic modulators.
Review
Immunology
Binyao Chen, Lei Zhu, Shizhao Yang, Wenru Su
Summary: Advances in single-cell RNA sequencing have provided detailed insights into the heterogeneity and multifunctionality of dendritic cells, as well as their reclassification and ontogeny. Researchers have discussed the challenges and future trends of scRNA-seq technologies in dendritic cell research.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Polymer Science
Jingyuan Deng, Sean Bailey, Ruiwen Ai, Anthony Delmonico, Gregory Denbeaux, Shaoyi Jiang, Christopher K. Ober
Summary: Conventional chemically amplified resists (CARs) face the trade-off between resolution, line edge roughness, and sensitivity (RLS) due to acid diffusion. This study proposes an end-cap enabled chain scissionable resist based on the self-immolative property of polyphthalaldehyde (PPA) derivatives for extreme ultraviolet (EUV) lithography, and demonstrates its feasibility through experimental validation.
Review
Immunology
Mahdi Abdoli Shadbad, Khalil Hajiasgharzadeh, Afshin Derakhshani, Nicola Silvestris, Amir Baghbanzadeh, Vito Racanelli, Behzad Baradaran
Summary: Although melanoma remains the deadliest skin cancer, immunotherapy has provided more tolerable approaches and revolutionized cancer therapy. However, the undesirable response rates of traditional approaches and the immunosuppressive tumor microenvironment have raised questions about their clinical translation. Additional research on oncogenic pathways and novel tumor antigens is essential for developing more effective dendritic cell-based vaccines.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Immunology
Ahsen Ustaoglu, Fatema Arif Daudali, Manfredi D'afflitto, Stephen Murtough, Chung Lee, Estefania Moreno, Diana C. Blaydon, David P. Kelsell, Daniel Sifrim, Philip Woodland, Madusha Peiris
Summary: This study identified increased expression of nerve growth factor (NGF) and decreased abundance of dendritic cells in the mucosa of GERD patients, which may be related to neuronal sprouting and immune responses in GERD.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Multidisciplinary Sciences
Gatikrushna Singh, Bradley Seufzer, Zhenwei Song, Dora Zucko, Xiao Heng, Kathleen Boris-Lawrie
Summary: This study reveals the relationship between incomplete processing and hypermethylation of HIV-1 transcripts, as well as the role of trimethylguanosine synthetase-1 in HIV-1 infectivity and protein synthesis. The study also uncovers the interaction between nuclear RNA helicase A and the shape of the 5' untranslated region primer binding site, and the relationship between HIV-1 virion protein synthesis and host translation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)