Article
Chemistry, Multidisciplinary
Tom Baladi, Jesper R. Nilsson, Audrey Gallud, Emanuele Celauro, Cecile Gasse, Fabienne Levi-Acobas, Ivo Sarac, Marcel R. Hollenstein, Anders Dahlen, Elin K. Esbjorner, L. Marcus Wilhelmsson
Summary: The study introduces a stealth labeling strategy to efficiently generate RNA transcripts and translate them into correct proteins, providing an important tool for biological research and RNA delivery studies.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Multidisciplinary Sciences
Christian H. Gabriel, Marta del Olmo, Amin Zehtabian, Marten Jaeger, Silke Reischl, Hannah van Dijk, Carolin Ulbricht, Asylkhan Rakhymzhan, Thomas Korte, Barbara Koller, Astrid Grudziecki, Bert Maier, Andreas Herrmann, Raluca Niesner, Tomasz Zemojtel, Helge Ewers, Adrian E. Granada, Hanspeter Herzel, Achim Kramer
Summary: The study introduces an efficient strategy for generating knock-in reporter cell lines using the CRISPR technology to investigate the dynamics of circadian clock proteins. The findings reveal highly rhythmic expressions of PER2 and CRY1 proteins in the nucleus of human cells, with notable differences in abundance and transcriptional rhythms between the two proteins.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Li Zhou, Qing-Liang Wang, Lin-Hong Mao, Si-Yuan Chen, Zi-Han Yang, Xue Liu, Yu-Hua Gao, Xiao-Qin Li, Zhi-Hang Zhou, Song He
Summary: NFIB plays an important role in inhibiting the urea cycle, and the knockout of NFIB gene in hepatocytes contributes to the aggravation of hepatocellular carcinoma.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Plant Sciences
Meng Li, Xufang Niu, Shuang Li, Shasha Fu, Qianfang Li, Meizhi Xu, Chunhua Wang, Shuang Wu
Summary: CRISPR/Cas9-mediated gene knockout is an important tool for studying gene function. Engineering the Cas9 system to achieve cell-type-specific knockout of functional genes is useful for understanding the specific functions of genes in different cell types.
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
Chemistry, Multidisciplinary
Michael Holtmannspoetter, Eike Wienbeuker, Timo Dellmann, Isabelle Watrinet, Ana J. Garcia-Saez, Kai Johnsson, Rainer Kurre, Jacob Piehler
Summary: Self-labeling enzymes (SLE) like the HaloTag are valuable tools in high and super-resolution fluorescence microscopy. New fluorogenic substrates for SLE allow imaging with excess dye. Two engineered variants of HaloTag7 with restored dehalogenase activity, reHaloTagS (approx. 0.006 s(-1)) and reHaloTagF (approx. 0.055 s(-1)), showed different turnover kinetics in vitro. Imaging with reHaloTag labeling demonstrated 3-5 times enhanced photostability, and single molecule imaging enabled controlled and stable labeling density over extended periods. Combination with structured illumination allowed simultaneous visualization of single molecule diffusion and organellar dynamics. These applications showcase the potential of reHaloTag labeling in advancing fluorescence microscopy techniques.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Neurosciences
Ian D. Tomlinson, Oleg Kovtun, Ruben Torres, Laurel G. Bellocchio, Travis Josephs, Sandra J. Rosenthal
Summary: The study focused on developing a novel ligand, IDT785, that effectively studied the cellular trafficking and membrane dynamics of SERT, providing valuable insights into SERT localization and function. The ligand demonstrated biological activity by inhibiting SERT-mediated reuptake of serotonin and enabling membrane labeling of SERT for further research.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2021)
Review
Plant Sciences
Noriyoshi Yagi, Akira Yoshinari, Ryu J. Iwatate, Reika Isoda, Wolf B. Frommer, Masayoshi Nakamura
Summary: Fluorescent probes are essential tools for visualizing cellular structures and molecular dynamics in living cells, with a wide variety of small-molecule dyes synthesized for labeling purposes. Self-labeling technologies allow these probes to be attached to cellular domains or specific proteins, and are now being increasingly utilized in plant research.
PLANT AND CELL PHYSIOLOGY
(2021)
Article
Cell Biology
Satoshi Uchino, Yuma Ito, Yuko Sato, Tetsuya Handa, Yasuyuki Ohkawa, Makio Tokunaga, Hiroshi Kimura
Summary: A genetically encoded modification-specific intracellular antibody probe was developed to detect RNAP2 Ser2 phosphorylation in living cells, revealing its specific role in transcription complexes and providing insights into genome and cell function.
JOURNAL OF CELL BIOLOGY
(2022)
Article
Physiology
Yubo Peng, Yusuke Tsuno, Ayako Matsui, Yuichi Hiraoka, Kohichi Tanaka, Shin-ichi Horike, Takiko Daikoku, Michihiro Mieda
Summary: The researchers successfully created Vip(tTA) knock-in mice expressing tetracycline transactivator (tTA) specifically in VIP neurons, providing a new genetic tool for studying the role of VIP neurons in the SCN neural network.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Zheng Lv, Zhongwei Man, Hongtu Cui, Zhenzhen Xu, Huanhuan Cao, Shuai Li, Qing Liao, Qihua He, Lemin Zheng, Hongbing Fu
Summary: This study presents two efficient red-emitting aggregation-induced emission (AIE) luminogens with off-on fluorescence characteristic for specific lysosomes and mitochondria targeting. The AIE luminogens show good biocompatibility, excellent photostability, and a Stokes' shift larger than 100 nm, enabling high fidelity imaging of lysosomes and mitochondria. Moreover, dynamic lysosomal fusion and mitochondrial fission are imaged with a high resolution of 65.6 nm using stimulated emission depletion (STED) imaging. Additionally, interactions between lysosomes and mitochondria during mitophagy are recorded, providing practical guidance for designing specific organelle targeting probes for live cell dynamic super-resolution imaging.
ADVANCED FUNCTIONAL MATERIALS
(2021)
Article
Multidisciplinary Sciences
Kohdai P. Nakajima, Clari Valansi, Daisuke Kurihara, Narie Sasaki, Benjamin Podbilewicz, Tetsuya Higashiyama
Summary: The interaction of adhesion molecules in gametes plays a crucial role in successful gamete fusion. By developing a live imaging-based adhesion molecule assay, researchers were able to observe and study the interaction of adhesion molecules in cultured cells. They found that IZUMO1 and JUNO from different species may have interchangeable combinations and play important roles in gamete adhesion.
SCIENTIFIC REPORTS
(2022)
Article
Nanoscience & Nanotechnology
Yi-Teng Hsiao, Chia-Ni Tsai, Ching-Ya Cheng, Chia-Lung Hsieh
Summary: Optical interference microscopy is a powerful bioimaging technique that allows for direct visualization of very small biological nanoparticles and unlabeled macro-molecules. The stable and indefinite linear scattering signal enables continuous observation of samples at high speeds, offering opportunities to investigate single-molecule biophysics with unprecedented details. Additionally, exploring complex biological samples using interference microscopy is emerging as an exciting research field.
Article
Neurosciences
Priyadharshini Prabhakar, Rainer Pielot, Peter Landgraf, Josef Wissing, Anne Bayrhammer, Marco van Ham, Eckart D. Gundelfinger, Lothar Jaensch, Daniela C. Dieterich, Anke Mueller
Summary: Astrocytes display regional heterogeneity in morphology, function, and molecular composition, and play a role in supporting and modulating neuronal function and signaling. Using mass spectrometry and gene enrichment analysis, we discovered subtle differences in astrocytic proteomes among different brain regions, with the cerebellum showing a strong association with the calcium signaling pathway or bipolar disorder. Additionally, our toolbox proved to be applicable for studying astrocytic proteome differences in vivo.
Article
Geochemistry & Geophysics
Luca Maggiolo, Diego Marcos, Gabriele Moser, Sebastiano B. Serpico, Devis Tuia
Summary: Convolutional neural networks are a strong method for semantic segmentation, but their accuracy is influenced by the quality of ground truth data. Often, ground truth data is sparsely annotated which can lead to smoothed object boundaries in CNN models. To address this issue, a semi-supervised approach is proposed to bridge the performance gap compared to densely annotated ground truth.
IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING
(2022)
Article
Anatomy & Morphology
Sook Kyung Park, Sang Jin Ko, Sang Kyoo Paik, Jong-Cheol Rah, Kea Joo Lee, Yong Chul Bae
BRAIN STRUCTURE & FUNCTION
(2018)
Article
Biochemical Research Methods
Dennis C. Wylie, Hans A. Hofmann, Boris V. Zemelman
Article
Neurosciences
Gergely Farkas Turi, Wen-Ke Li, Spyridon Chavlis, Ioanna Pandi, Justin O'Hare, James Benjamin Priestley, Andres Daniel Grosmark, Zhenrui Liao, Max Ladow, Jeff Fang Zhang, Boris Valery Zemelman, Panayiota Poirazi, Attila Losonczy
Article
Cell Biology
Preeti Mehta, Lauren Kreeger, Dennis C. Wylie, Jagruti J. Pattadkal, Tara Lusignan, Matthew J. Davis, Gergely F. Turi, Wen-Ke Li, Matthew P. Whitmire, Yuzhi Chen, Bridget L. Kajs, Eyal Seidemann, Nicholas J. Priebe, Attila Losonczy, Boris V. Zemelman
Article
Biochemistry & Molecular Biology
Yoonju Kim, You-Na Jang, Ji-Young Kim, Nari Kim, Seulgi Noh, Hyeyeon Kim, Bridget N. Queenan, Ryan Bellmore, Ji Young Mun, Hyungju Park, Jong Cheol Rah, Daniel T. S. Pak, Kea Joo Lee
Article
Neurosciences
Jungmin Lee, Joon Ho Choi, Jong-Cheol Rah
Article
Neurosciences
Shinwon Kang, Hyun Jong Noh, Soo Hyeon Bae, Yong-Seok Kim, Hogun Lew, Jisoo Lim, Se Joo Kim, Kyung Sue Hong, Jong-Cheol Rah, Chul Hoon Kim
Article
Medicine, Research & Experimental
Jun-Young Oh, Jeong-Ho Han, Hyoeun Lee, Young-Eun Han, Jong Cheol Rah, Hyungju Park
EXPERIMENTAL NEUROBIOLOGY
(2020)
Article
Neurosciences
Seung Wook Oh, Sook Jin Son, John A. Morris, Joon Ho Choi, Changkyu Lee, Jong-Cheol Rah
Summary: The posterior parietal cortex plays a crucial role in various higher order cognitive functions and integrates inputs from different sensory cortices and subcortical areas to facilitate the execution of functions. Comprehensive understanding of the long-range connectivity of the mouse PPC is still limited, hindering the interpretation of accumulating functional data and effective paths forward for various studies.
Article
Multidisciplinary Sciences
Eunhee Kim, Sungwoong Jeon, Hyun-Kyu An, Mehrnoosh Kianpour, Seong-Woon Yu, Jin-young Kim, Jong-Cheol Rah, Hongsoo Choi
Article
Neurosciences
Nari Kim, Sangkyu Bahn, Joon Ho Choi, Jinseop S. Kim, Jong-Cheol Rah
Summary: The synapses from POm and vM1 on the distal tuft dendrites of L5 pyramidal neurons do not show a significant branchlet preference, but they form robust spatial clusters within dendritic branches. There is a close proximity between POm and vM1 clusters, which is crucial for understanding the synaptic integration of whisker-based sensory information.
Article
Neurosciences
Yoon-Sil Yang, Joon Ho Choi, Jong-Cheol Rah
Summary: This study found that changes in potassium channel activity and voltage dependence during hypoxia and inflammation (Hypo-Inf), as well as reperfusion, affect neuronal excitability and input resistance. The results suggest that selective K-V channel modulators can potentially be used as neuroprotective drugs to reduce neuronal damage caused by hypoxia and reperfusion.
Article
Engineering, Biomedical
Seongtak Kang, Jiho Park, Kyungsoo Kim, Sung-Ho Lim, Samhwan Kim, Joon Ho Choi, Jong-Cheol Rah, Ji-Woong Choi
Summary: The proposed iterative correlation-based ROI detection (ICoRD) method robustly extracts the calcium signal of the target neuron from noisy calcium imaging series. ICoRD outperforms conventional methods in extracting calcium signals closer to ground-truth in all low SNR ranges from simulated calcium imaging data. Additionally, ICoRD demonstrated reliable extraction of activation signals in vivo from neurons with low SNR and sparse activation.
JOURNAL OF NEURAL ENGINEERING
(2022)
Review
Biochemistry & Molecular Biology
Jong-Cheol Rah, Joon Ho Choi
Summary: Understanding the microcircuitry of the brain requires resolving the anatomical and functional connectivity among neurons. Electron microscopy has been the gold standard method for microcircuit reconstruction, but it has limitations in compatibility with functional and molecular analysis. Recent advances in fluorescence microscopy techniques offer a new possibility for reliable synapse detection in large volumes of neural circuits.
MOLECULES AND CELLS
(2022)
Article
Engineering, Electrical & Electronic
Samhwan Kim, Seongtak Kang, Jinmo Kim, Doyoung Lee, Sanghee Kim, Junghyup Lee, Kyung-In Jang, Yong-Seok Oh, Jong-Cheol Rah, Man Seung Huh, Sun Ha Paek, Ji-Woong Choi
Summary: DBS is an established clinical therapy for patients with movement disorders, particularly effective in controlling symptoms in Parkinson's disease (PD). Advancements in technology have allowed for the assessment of dysfunctional brain activity and the stimulation of pathological circuitry, with the potential to develop personalized biomarkers and predict symptom progression in PD. The term neuromodulation has been considered more accurate and comprehensive, encompassing both electrical and neurochemical treatments for neurological and psychiatric disorders.
IEEE TRANSACTIONS ON MOLECULAR BIOLOGICAL AND MULTI-SCALE COMMUNICATIONS
(2021)