Article
Biochemical Research Methods
Paul H. Dannenberg, Jisoo Kang, Nicola Martino, Anokhi Kashiparekh, Sarah Forward, Jiamin Wu, Andreas C. Liapis, Jie Wang, Seok-Hyun Yun
Summary: This article demonstrates a cell barcode technology using laser particles, which can be used for cell sorting and routing through a microfluidic platform integrated with a high-speed spectrometer. By utilizing the spectral emission of laser particles, individual cells labeled with different laser colors can be distinguished and sorted.
Article
Chemistry, Analytical
Li Wu, Shihan Xu, Jingang Wang, Amy L. Paguirigan, Jerald P. Radich, Yuling Qin, Daniel T. Chiu
Summary: Researchers have developed a single cell dispenser inspired by electrohydrodynamic jet printing, which can be used for single-cell multiomics studies, achieving accurate droplet generation and single-cell dispensing through systematic parameter optimization.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Jiao Feng, Chun-Miao Xu, Hou-Fu Xia, Hai-Ming Liu, Man Tang, Yi-Shen Tian, Gang Chen, Zhi-Ling Zhang
Summary: Liquid biopsy technology involves minimally invasive sampling of body fluids to analyze tumor markers for early tumor diagnosis and efficacy evaluation. This study presents a 3D magnetic chip-based extracorporeal circulation system for in vivo detection and real-time monitoring of circulating tumor cells (CTCs). By utilizing biofunctionalized magnetic nanospheres (MNs) with CTC recognition function, this 3DMC system enables efficient real-time monitoring of CTCs with good stability and strong anti-interference. In vivo detection not only detects more CTCs compared to in vitro detection but also identifies CTCs at an early stage of tumor presence in the blood. With its flexible chip design, the system can easily integrate cancer diagnosis and treatment. The biocompatibility and stability of the 3DMC system make it a promising tool for personalized medical programs for cancer patients.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Shu-Ting Xu, Cheng Yang, Xiu-Ping Yan
Summary: The study introduces an all-in-one system for rapid single-HeLa-cell screening and in-depth profiling of cellular metabolites and drugs. Utilizing zinc oxide nanothorn-decorated filters for efficient online lysis of cell membrane, the system showed promising results for subcellular discrimination and signal response improvements. This system has the potential for high-coverage single-cell metabolome analysis in cell biology and cancer research.
ANALYTICAL CHEMISTRY
(2021)
Article
Polymer Science
Kriti Kapil, Shirley Xu, Inseon Lee, Hironobu Murata, Seok-Joon Kwon, Jonathan S. Dordick, Krzysztof Matyjaszewski
Summary: Well-defined multifunctional copolymers with rhodamine B dye were synthesized by ATRP, enabling efficient and specific bioimaging of Staphylococcus aureus. The combination of multifunctional polymeric dyes and strain-specific Ab or CBD showed enhanced fluorescence and target selectivity, making them potential biosensors for the detection of target DNA, protein, or bacteria.
Article
Chemistry, Analytical
Chengxin Wu, Xing Wei, Xue Men, Xuan Zhang, Yong-Liang Yu, Zhang-Run Xu, Ming-Li Chen, Jian-Hua Wang
Summary: CytoLM is a two-dimensional cytometry platform developed for single-particle and single-cell sampling and analysis, featuring high sensitivity and high temporal resolution. It combines VCCS-LIF and ICP-MS technologies to enable high-throughput, multi-dimensional, and multi-parameter characterization of particles and cells, showing vast potential in life science analysis.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Yiyang Li, Boqian Wang, Zara Ahmad Khan, Jie He, Edwin Cheung, Wenqiong Su, Aiting Wang, Hui Jiang, Lai Jiang, Xianting Ding
Summary: This study introduces a method of mass cytometry profiling for analyzing samples with limited or rare cell subsets using a platinum-chimeric carrier cell strategy. The results demonstrate the effectiveness of this method in preserving rare target cells and performing comprehensive single-cell subtype classification analysis.
ANALYTICAL CHEMISTRY
(2023)
Article
Immunology
Francesca Di Rosa, Andrea Cossarizza, Adrian C. Hayday
Summary: The study introduces a more sensitive and effective method for T cell cycle analysis - T-DS cells, identified by Ki-67/DNA dual staining and refined flow cytometric methods in experiments on mice and humans. This approach can reflect the dynamics of human lymphocytes in peripheral blood, while providing more than just a snapshot of static phenotypes.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Chemistry, Analytical
Chengxin Wu, Xue Men, Meijun Liu, Yujia Wei, Xing Wei, Yong-Liang Yu, Zhang-Run Xu, Ming-Li Chen, Jian-Hua Wang
Summary: A 2D flow cytometry platform called CytoLM Plus was developed for multi-parameter single-cell analysis. This platform combines fluorescence and side scattering optical detection with ICP-MS detection for a comprehensive analysis of single cells. The performance of CytoLM Plus was evaluated using fluorescent microspheres and cells, and it showed comparable results to a commercial flow cytometer.
ANALYTICAL CHEMISTRY
(2023)
Article
Urology & Nephrology
Franziska Buescheck, Christoph Fraune, Martina Kluth, Maximilian Lennartz, Ronald Simon, Claudia Hube-Magg, Christian Morlock, Silvano Barbieri, Carolin Wahl, Christian Eichelberg, Christina Moeller-Koop, Doris Hoeflmayer, Corinna Wittmer, Waldemar Wilczak, Guido Sauter, Margit Fisch, Till Eichenauer, Michael Rink
Summary: In summary, the study results identify a non-diploid DNA content as a predictor of unfavorable prognosis in clear cell and papillary carcinoma.
WORLD JOURNAL OF UROLOGY
(2021)
Article
Chemistry, Analytical
Margarita Khariton, Conor J. McClune, Kara K. Brower, Sandy Klemm, Elizabeth S. Sattely, Polly M. Fordyce, Bo Wang
Summary: Microfluidic droplet assays enable single-cell PCR and sequencing analyses at unprecedented scales. Encapsulating cells within picoliter double emulsion allows sorting droplets with commercially available FACS machines, making it possible to isolate single cells based on phenotypes of interest. However, sorting DE droplets with standard cytometers requires small droplets that can pass FACS nozzles. Therefore, this study overcame limitations by using a plate-based RT-PCR assay to ameliorate the inhibition and demonstrated one-step RT-PCR from single cells in 20 pL DE droplets with fluorescence quantifiable via FACS.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Margarita Khariton, Conor J. McClune, Kara K. Brower, Sandy Klemm, Elizabeth S. Sattely, Polly M. Fordyce, Bo Wang
Summary: Microfluidic droplet assays enable single-cell PCR and sequencing analyses at unprecedented scales. However, sorting small droplets for FACS poses challenges for molecular biology. To overcome this, we used a plate-based RT-PCR assay and showed that heat lysis can alleviate inhibition for most cell lines, allowing RT-PCR to proceed in low-picoliter volumes.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Jing Yang, Zhenqing Li, Dawei Zhang, Yoshinori Yamaguchi, Wen Xiao
Summary: A method based on a microfluidic chip with a gradual change in inner size was developed to count 2 μm fluorescent microspheres (FMs). The results showed that there was a linear relationship between the number of peaks in the electropherogram and concentration of FMs if they were running in the microchannel for more than 20 min. About 2 x 10(4) FMs can be counted within 30 min by this microfluidic chip.
ANALYTICAL METHODS
(2023)
Article
Mathematical & Computational Biology
Yi Li, Chance M. Nowak, Uyen Pham, Khai Nguyen, Leonidas Bleris
Summary: In this study, machine learning architectures were employed to classify healthy and apoptotic cells using only forward and side scatter flow cytometry information. By training the models, automated and reliable classification of healthy and apoptotic cells based on size and granularity information was achieved.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2021)
Article
Chemistry, Analytical
Diwakar M. Awate, Cicero C. Pola, Erica Shumaker, Carmen L. Gomes, Jaime J. Juarez
Summary: Despite the limitations of flow cytometers, a 3D-printed imaging platform (3DPIP) has been developed to accurately count particles and conduct fluorescence microscopy efficiently. The 3DPIP utilizes a custom particle counter code and machine vision-based algorithm to identify and count particles, showing comparable accuracy to commercial particle counters. Additionally, the platform can perform static experiments and flow-through experiments effectively, making it a promising tool for use in resource-limited clinical environments.
Review
Biochemistry & Molecular Biology
Soumya Sethi, Hiroshi Sugiyama, Masayuki Endo
Summary: DNA nanotechnology is a promising toolkit for mimicking cell-cell and cell-matrix interactions, aiding in understanding and manipulating cellular functions. Future innovations in the field can be inspired by exploring the potentials of DNA-based nanostructures and addressing current challenges.
Article
Biochemistry & Molecular Biology
Yuki Hirose, Tomo Ohno, Sefan Asamitsu, Kaori Hashiya, Toshikazu Bando, Hiroshi Sugiyama
Summary: A cyclic pyrrole-imidazole polyamide (cPIP) was synthesized to bind to the abnormal expanded CAG/CTG repeat DNA sequences, showing high binding affinity and specificity for its target DNA sequence.
Article
Biochemistry & Molecular Biology
Ryu Tashiro, Ji Hye Yum, Soyoung Park, Hiroshi Sugiyama
Summary: The study showed that the photoreactivity of U-Br changes dramatically from hydrogen abstraction to cross-linking by changing the conformation of the duplex from the B-form to the A-form. Among three A-form structures, the largest amount of cross-linked products was observed when U-Br was incorporated into the RNA strand and the pyrene was conjugated to the 5 ' end of the DNA. These results indicate that the contact manner of pyrene was different between A- and B-form duplexes.
Article
Biochemistry & Molecular Biology
Kai Yu, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo, Shigeyoshi Matsumura, Yoshiya Ikawa
Summary: Naturally occurring ribozymes with modular architecture are promising for designing and assembling three-dimensional RNA nanostructures with catalytic abilities. In this study, RNA nanostructures with polygonal-shaped ribozyme oligomers were constructed using unit RNAs from the Tetrahymena group I intron, and ribozyme trimers with a triangular shape were dimerized by introducing pillar units. The resulting double-decker nanostructures containing six ribozyme units showed higher catalytic activity than the parent ribozyme trimers.
Article
Biochemistry & Molecular Biology
Sagun Jonchhe, Shankar Pandey, Christian Beneze, Tomoko Emura, Hiroshi Sugiyama, Masayuki Endo, Hanbin Mao
Summary: Researchers found that a DNA nanobowl significantly increased the stability of a human telomeric G-quadruplex and its binding with a ligand. By minimizing the proximity effect and attributing the increased affinity to the nanoconfinement effect, they provided insights into the mechanisms of binding events in nanocavities.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Vinodh J. Sahayasheela, Zutao Yu, Yuki Hirose, Ganesh N. Pandian, Toshikazu Bando, Hiroshi Sugiyama
Summary: Research suggests that targeting Gli-mediated transcription to inhibit the proliferation of cancer stem cells may be a promising strategy.
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN
(2022)
Article
Biochemistry & Molecular Biology
Shingo Hirashima, Hiroshi Sugiyama, Soyoung Park
Summary: This study characterized 2FA-containing DNA molecules and found that they have similar structure and properties to native adenine due to their small size, but exhibit unique features due to their high electronegativity. This provides valuable information for future applications of 2FA-modified DNA.
Article
Biochemistry & Molecular Biology
Junnosuke Hatanaka, Yuki Hirose, Kaori Hashiya, Toshikazu Bando, Hiroshi Sugiyama
Summary: In this study, we synthesized linear pyrrole-imidazole polyamides (PIPs) that can selectively bind to DNA. These linear PIPs have lower molecular weights compared to commonly used hairpin PIPs. The binding affinity of the PIPs to DNA was improved by modifying the N-terminus of the linear PIPs. These findings provide insights for the design of effective linear PIPs.
Article
Materials Science, Multidisciplinary
Atsushi Nakayama, Yasuaki Kumamoto, Masafumi Minoshima, Kazuya Kikuchi, Atsushi Taguchi, Katsumasa Fujita
Summary: This study demonstrates the use of photopolymerization without photoinitiators to fabricate 3D structures using biocompatible materials. The material properties of poly(ethylene glycol) diacrylate (PEGda) and collagen are preserved, making them suitable for applications with live cells.
ADVANCED OPTICAL MATERIALS
(2022)
Article
Chemistry, Multidisciplinary
Masafumi Minoshima, Taro Umeno, Kohei Kadooka, Margaux Roux, Namiko Yamada, Kazuya Kikuchi
Summary: To understand protein function in live cells, it is important to monitor protein dynamics and sense their environment in real-time. We developed a versatile chemical protein-labeling tool that efficiently forms stable carbamoylated complexes with beta-lactamase, allowing long-term visualization of labeled proteins in live cells. The use of an alpha-fluorinated carboxylate ester-based prodrug enables cell membrane permeability and stable labeling of intracellular proteins. Combining this labeling tool with a pH-activatable fluorescent probe enables visual monitoring of lysosomal protein translocation during autophagy.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Multidisciplinary Sciences
Sefan Asamitsu, Yasushi Yabuki, Kazuya Matsuo, Moe Kawasaki, Yuki Hirose, Gengo Kashiwazaki, Anandhakumar Chandran, Toshikazu Bando, Dan Ohtan Wang, Hiroshi Sugiyama, Norifumi Shioda
Summary: In this study, DNAPTP6 was identified as an RNA binding protein that plays a critical role in coordinating the assembly of stress granules (SGs) in a rG4-dependent manner. The recruitment of mRNAs into SGs through DNAPTP6 promotes RNA self-assembly and DNAPTP6 phase separation, which is essential for neuronal function.
Article
Chemistry, Multidisciplinary
Ryu Hashimoto, Masafumi Minoshima, Souhei Sakata, Fumihito Ono, Hirokazu Ishii, Yuki Watakabe, Tomomi Nemoto, Saeko Yanaka, Koichi Kato, Kazuya Kikuchi
Summary: In this study, visible-light-sensitive protecting groups with high uncaging cross sections were developed for precise control of bioactivity. Two-photon photolysis reactions were achieved using near-infrared laser, and green-light illumination enabled optical control of biological functions.
Article
Biochemistry & Molecular Biology
Takuya Hidaka, Kaori Hashiya, Toshikazu Bando, Ganesh N. Pandian, Hiroshi Sugiyama
Summary: This study constructed a class of compounds that can selectively alkylate mutant mitochondrial DNA, with the potential to treat mitochondrial diseases. These compounds have programmability and can be used to target pathogenic mutations associated with mitochondrial diseases in future studies.
CELL CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Gengo Kashiwazaki, Ryo Watanabe, Akihiro Nishikawa, Koyori Kawamura, Takashi Kitayama, Takao Hibi
Summary: Researchers have designed and synthesized a novel fluorescent probe for fructose detection, which shows a linear fluorescence response within the concentration range of 100-1000 μM and a low detection limit of 32 μM. This probe offers a simple and sensitive method for fructose determination.
Article
Chemistry, Multidisciplinary
Haruhiko Eki, Katsuhiko Abe, Hiroshi Sugiyama, Masayuki Endo
Summary: This study used atomic force microscopy to directly observe the formation and degradation of tensegrity triangle DNA crystals at a molecular level, visualizing the dynamic process and characterizing them with nanoscale resolution.
CHEMICAL COMMUNICATIONS
(2021)
