Article
Biotechnology & Applied Microbiology
Yu Liu, Yan-Hui Bi, Zhi-Gang Zhou
Summary: This study reported the precise karyotype of Saccharina japonica, which provides important basis for genomic physical mapping and genetic breeding of this marine alga.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2022)
Article
Microbiology
Andreia S. Azevedo, Ricardo M. Fernandes, Ana R. Faria, Oscar F. Silvestre, Jana B. Nieder, Chenguang Lou, Jesper Wengel, Carina Almeida, Nuno F. Azevedo
Summary: This study aimed to combine nucleic acid mimics (NAMs) and spectral image analysis to develop a new FISH variant, spectral imaging-NAM-FISH (SI-NAM-FISH), for multiplexed, robust, and rapid detection of clinical pathogens.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Jill Jasmine Dalimot, Ilka Mc Cormick Smith, Jasmin Gerkrath, Sylvia Hartmann, Oliver A. Cornely, Soo Chan Lee, Joseph Heitman, Volker Rickerts
Summary: This study focused on improving the accuracy of mucormycosis diagnosis from tissue samples using fluorescence in situ hybridization (FISH) targeting specific regions of fungal ribosomal RNA (rRNA) of Mucorales. While the probe combination showed success in targeting Mucorales and enhancing diagnosis, autofluorescence and variations in physiological states of fungi and antifungal therapy may impact the FISH signal obtained. Further studies are needed to determine the value of FISH in diagnosing mucormycosis from different clinical samples.
Article
Biochemical Research Methods
Jenny M. Vo-Phamhi, Kevin A. Yamauchi, Rafael Gomez-Sjoberg
Summary: This paper introduces an open-source toolkit and framework that incorporates crowdsourced and expert annotations as a source of ground truth for in situ transcriptomics image analysis. Through exploring and demonstrating the use of crowdsourced annotations for validating spot-calling algorithms and tuning parameters, it confirms that consensus crowdsourced annotations can substitute expert-generated ground truth. Advancements in in situ methods deepen our understanding of spatial organization in biological processes within tissues.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Yu-Sheng Wang, Jia Guo
Summary: The ability to quantify a large number of varied transcripts in single cells in their native spatial context is crucial for understanding health and disease, and recent advances in multiplexed FISH methods have enabled comprehensive RNA profiling in individual cells.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Genetics & Heredity
Regina L. Binz, Rupak Pathak
Summary: This study investigated the cytogenetic integrity of primary human umbilical vein endothelial cells (HUVECs) and found that approximately 50% of the cells have a deletion of the Xq terminal region. Additionally, a similar Xq deletion was identified in the daughter cell line generated by fusing HUVECs with A549 cells.
Article
Microbiology
Demosthenes P. Morales, Aaron J. Robinson, Andrew C. Pawlowski, Caitlyn Ark, Julia M. Kelliher, Pilar Junier, James H. Werner, Patrick S. G. Chain
Summary: This study evaluates the challenges in resolving bacterial-fungal interactions and proposes the use of fluorescence in situ hybridization (FISH) for microscopy imaging to obtain more conclusive evidence on the nature of specific relationships between bacteria and fungi.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Bowen Zhang, Taoran Tian, Dexuan Xiao, Shaojingya Gao, Xiaoxiao Cai, Yunfeng Lin
Summary: A DNA-enhanced HCR detection system (T-probe system) is introduced for the detection of cancer-related targets, demonstrating its versatility and efficiency by detecting miRNA-21 and nucleolin. The T-probe system shows high detection rate and rapid recognition of both membrane and intracellular cancer-related targets, and exhibits superior fluorescence for imaging tumor-related biomarkers in vitro and in vivo, indicating its great potential for clinical diagnosis and therapeutic applications.
ADVANCED FUNCTIONAL MATERIALS
(2022)
Article
Cell Biology
Lu Xiao, Joshua Labaer, Jia Guo
Summary: A high sensitivity and specificity multiplexed in situ RNA profiling approach was developed, allowing for successful analysis of multiple RNA species in various types of tissues through cycles of RNA staining, signal amplification, and probe stripping.
Article
Multidisciplinary Sciences
Gerrit G. Tamminga, Gijsbert J. Jansen, Marit Wiersma
Summary: This study evaluated a non-invasive fluorescence in situ hybridization (FISH) method for the detection of SARS-CoV-2 in saliva and found it to have high sensitivity and specificity, making it suitable for general population testing.
Article
Marine & Freshwater Biology
Zeyu Jia, Yijing Dong, Heng Xu, Fengping Wang
Summary: The study optimized the HCR-FISH protocol to address the issues of low signal intensity and false-positive signals, successfully identifying HCR initiator/amplifier pairs with high efficiency and specificity. Through the optimization of sample pretreatment methods, HCR-FISH protocol combinations, and image processing, false positive signals were reduced.
MARINE LIFE SCIENCE & TECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Irfan Akhtar, Fiona A. Stewart, Anna Haerle, Andrea Droste, Mathias Beller
Summary: The researchers optimized a FISH protocol to detect major bacteria genera in the Drosophila gut microbiome, aiming to investigate their spatial localization. This study contributes to answering questions about regionalization and establishment of the gut microbiome.
Article
Plant Sciences
Denisa Simonikova, Jana Cizkova, Veronika Zoulova, Pavla Christelova, Eva Hribova
Summary: Bananas are an important staple food crop and trade commodity in tropical and subtropical countries. The most important edible banana clones have originated from crosses between two different purebred varieties, which has led to chromosomal changes that may contribute to lower fertility in these vegetatively propagated clones. This article reviews the development of molecular cytogenetic approaches in studying the genome evolution of edible bananas, including the use of specific cytogenetic probes and comparative karyotype analysis.
Article
Chemistry, Multidisciplinary
Sylvie Egloff, Nina Melnychuk, Elisabete Cruz Da Silva, Andreas Reisch, Sophie Martin, Andrey S. Klymchenko
Summary: The study introduces a method named AmpliFISH for RNA imaging, utilizing small and ultrabright dye-loaded polymeric nanoparticles (NPs) functionalized with DNA. The optimized NPs enabled sequence-specific imaging of different mRNA targets and multiplexed detection of three mRNA targets simultaneously. AmpliFISH provided a stronger signal and shorter processing time compared to commercial locked nucleic acid (LNA)-based FISH technique.
Article
Chemistry, Physical
Min Seok Lee, Hwi Hyun, Inwon Park, Sungho Kim, Dong-Hyun Jang, Seonghye Kim, Jae-Kyeong Im, Hajin Kim, Jae Hyuk Lee, Taejoon Kwon, Joo H. Kang
Summary: This study developed a novel technology called mu FISH, which uses mu FISH probes based on 16S rRNA sequences to quantitatively identify and detect bacteria in blood samples. It is a more sensitive method compared to traditional bacterial detection methods.
Article
Oncology
Takuya Ishikawa, Hiroki Kawashima, Eizaburo Ohno, Hiroshi Matsubara, Yoji Sasaki, Koichi Achiwa, Akira Kanamori, Hajime Sumi, Takanori Hirai, Koji Nonogaki, Tomoyuki Tsuzuki, Masanori Kuroiwa, Masashi Hattori, Shinya Maruta, Takeshi Hiramatsu, Masahiko Ando, Senju Hashimoto, Yoshiki Hirooka
Article
Gastroenterology & Hepatology
Hiroki Kawashima, Senju Hashimoto, Eizaburo Ohno, Takuya Ishikawa, Tomomasa Morishima, Hiroshi Matsubara, Hiroyuki Sugimoto, Koji Nonogaki, Akira Kanamori, Kazuo Hara, Takamichi Kuwahara, Masanao Nakamura, Ryoji Miyahara, Masatoshi Ishigami, Masahiko Ando, Yoshiki Hirooka
DIGESTIVE ENDOSCOPY
(2019)
Article
Chemistry, Organic
Kotaro Yubata, Hiroshi Matsubara
TETRAHEDRON LETTERS
(2019)
Review
Chemistry, Organic
Hiroshi Matsubara
JOURNAL OF SYNTHETIC ORGANIC CHEMISTRY JAPAN
(2019)
Article
Chemistry, Organic
Takuji Kawamoto, Kyohei Oritani, Atsushi Kawabata, Tsubasa Morioka, Hiroshi Matsubara, Akio Kamimura
JOURNAL OF ORGANIC CHEMISTRY
(2020)
Article
Gastroenterology & Hepatology
Takuya Ishikawa, Hiroki Kawashima, Eizaburo Ohno, Hiroki Suhara, Daijuro Hayashi, Takeshi Hiramatsu, Hiroshi Matsubara, Takahisa Suzuki, Takamichi Kuwahara, Eri Ishikawa, Yoshie Shimoyama, Fumie Kinoshita, Yoshiki Hirooka, Mitsuhiro Fujishiro
Article
Biochemistry & Molecular Biology
Miyu Sakaguchi, Yasushi Makino, Hiroshi Matsubara
GLYCOCONJUGATE JOURNAL
(2020)
Article
Chemistry, Organic
Nene Soga, Tomo Yoshiki, Aoi Sato, Takuji Kawamoto, Ilhyong Ryu, Hiroshi Matsubara
Summary: In this study, borane was generated in situ using a PV method from NaBH4 or (Bu4NBH4)-Bu-n and reacted with alkenes to produce alcohols. The evolved borane was also used for selective reduction of carboxylic acids and successful Suzuki-Miyaura coupling. The PV system allowed easy and safe reactions with borane in common test tubes.
TETRAHEDRON LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Takuji Kawamoto, Kohki Noguchi, Ryotaro Takata, Rio Sasaki, Hiroshi Matsubara, Akio Kamimura
Summary: The redox-neutral tetrafluoroethylation of alkynes with TFESA and AIBN proceeds through the formation of vinyl tetrafluoroethanesulfonates followed by a radical tetrafluoroethylation. Both experimental and theoretical results support an intermolecular reaction mechanism.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Ayato Ikeda, Yasushi Makino, Hiroshi Matsubara
Summary: Glycogen debranching enzyme (GDE) has both 4-alpha-glucanotransferase and amylo-alpha-1,6-glucosidase activities. This study analyzed the substrate specificities of these enzymes and proposed a macroscopic debranching pathway.
GLYCOCONJUGATE JOURNAL
(2022)
Article
Chemistry, Organic
Yuji Nishidai, Toshiki Kawabata, Kotaro Yubata, Fumiya Ota, Hiroki Takamiya, Hideki Fujiwara, Hiroshi Matsubara
Summary: In this study, a new method for the preparation of hetero-halogen compounds was developed. Two novel air-stable hetero-halogen complexes were synthesized and utilized for the one-step synthesis of various hetero-halogen compounds.
Article
Chemistry, Applied
Motohiro Yasui, Naoko Tahara, Hiroshi Matsubara, Norihiko Takeda, Masafumi Ueda
Summary: This study developed a sequential gold-catalyzed reaction for synthesizing 4-aryl-3-(2H)-isoxazolones with a hydroxy group. The method allows the introduction of an aryl and hydroxy group in a single procedure, exhibiting good chemoselectivity and tolerance towards reactive functional groups.
ADVANCED SYNTHESIS & CATALYSIS
(2022)
Article
Chemistry, Organic
Toshiki Kawabata, Hiroshi Matsubara
Summary: Although diazomethane is highly explosive, the phase-vanishing method using highly fluorinated solvents was employed to safely generate it for organic synthesis. A two-chamber reactor was used to gradually evolve and consume diazomethane under PV conditions, such as the methylation of carboxylic acids. This PV system provides a facile and safe method for the generation of hazardous diazomethane.
TETRAHEDRON LETTERS
(2023)
Article
Chemistry, Physical
Kenichi Iwamoto, Genki Inoue, Hiroshi Matsubara
Summary: The C5H7+ fragment ion derived from 3-methyl1,4-pentadiene (MPD) was investigated using an ion mobility/mass spectrometer. The reduced mobilities (K0) of the C5H7+ fragment ions generated by MPD and cyclohexene correlated with effective temperature in He buffer gas, indicating that these fragments were identical cyclopentenium cations. Density functional theory calculations revealed the feasibility of the dissociation of MPD to cyclopentenium cations.
CHEMICAL PHYSICS LETTERS
(2023)
Article
Chemistry, Organic
Masahiro Ueda, Atsuki Kitano, Hiroshi Matsubara
Summary: The selective hydrogen abstraction reactions on sp(3) carbons with oxyradicals were investigated using ab initio and DFT calculations. It was found that beta-hydrogen abstraction was favorable, consistent with experimental findings. NBO analysis revealed that the transferred hydrogen atom is partially positively charged when abstracted by an oxyradical, and hydrogens bonded to the most positively charged carbon in the substrate were predominantly abstracted, providing a simple compass for predicting regioselectivity in the functionalization of C(sp(3))-H bonds with oxyradicals.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2021)