Article
Nanoscience & Nanotechnology
Ruslan Rohrich, A. Femius Koenderink
Summary: This article introduces a new structured illumination microscopy technique that extends the capabilities of SIM by combining ideas from illumination engineering and nanophotonics. Experimental results demonstrate the potential for resolution enhancements beyond regular SIM, validated through simulations and experiments. However, there are still obstacles to overcome in the implementation of experiments for artifact-free super-resolution imaging.
Article
Optics
Ankit Butola, Sebastian Acuna, Daniel Henry Hansen, Krishna Agarwal
Summary: We propose a novel approach to achieve super-resolution structured illumination microscopy using an alignment non-critical illumination system and a reconstruction algorithm that does not require illumination information. This method simplifies instrumentation and allows for system adaptability to different resolutions without recalibration.
Review
Optics
Xin Chen, Suyi Zhong, Yiwei Hou, Ruijie Cao, Wenyi Wang, Dong Li, Qionghai Dai, Donghyun Kim, Peng Xi
Summary: Structured illumination microscopy (SIM) has become the standard for next-generation wide-field microscopy, offering ultrahigh imaging speed, superresolution, a large field-of-view, and long-term imaging. Advanced reconstruction algorithms are necessary to unlock the full potential of SIM system hardware. This article introduces the theory and implementation modalities of two SIM algorithms, optical sectioning SIM (OS-SIM) and superresolution SIM (SR-SIM), and provides an overview of existing processing algorithms and the development of reconstruction algorithms for different SIM techniques. Comparison of off-the-shelf SIM systems and future perspectives are also discussed.
LIGHT-SCIENCE & APPLICATIONS
(2023)
Article
Optics
Guoxuan Liu, Ning Xu, Huaidong Yang, Qiaofeng Tan, Guofan Jin
Summary: Structured illumination microscopy (SIM) is an advanced microscope system with superresolution capability and fast imaging speed. However, the bulky size has limited its wider application. We developed a miniaturized SIM system that greatly simplified the experimental setup and demonstrated its important applications in bio-imaging.
PHOTONICS RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Xuesong Li, Yicong Wu, Yijun Su, Ivan Rey-Suarez, Claudia Matthaeus, Taylor B. B. Updegrove, Zhuang Wei, Lixia Zhang, Hideki Sasaki, Yue Li, Min Guo, John P. P. Giannini, Harshad D. D. Vishwasrao, Jiji Chen, Shih-Jong J. Lee, Lin Shao, Huafeng Liu, Kumaran S. S. Ramamurthi, Justin W. W. Taraska, Arpita Upadhyaya, Patrick La Riviere, Hari Shroff
Summary: Enhanced axial resolution for 3D SIM is achieved with deep learning or four-beam interference. These methods allow for higher spatial frequency content and near-isotropic imaging with resolutions of around 120 nm in both lateral and axial directions. The deep learning method can also be combined with denoising for volumetric imaging. Various cellular samples were imaged to demonstrate the potential of these advancements.
NATURE BIOTECHNOLOGY
(2023)
Article
Optics
Xiaomin Zheng, Jie Zhou, Lei Wang, Meiting Wang, Wenshuai Wu, Jiajie Chen, Junle Qu, Bruce Zhi Gao, Yonghong Shao
Summary: Structured Illumination Microscopy (SIM) has shown remarkable progress in resolution, imaging depth, and technological advancements in recent years, making it a powerful tool in biomedical research. Its flexibility allows for effective combination with other methods, offering enhanced imaging capabilities.
Article
Optics
Tristan C. Paul, Guy Hagen
Summary: A new technique called Spinning Disk Structured Illumination Microscopy (SD-SIM) was investigated, which combines Spinning Disk microscopy with Structured Illumination Microscopy to achieve better background removal and detect cellular structures that were previously undetectable with either method alone.
Article
Optics
Zhiqiang Fu, Qiang Geng, Jialong Chen, Li-An Chu, Ann-Shyn Chiang, Shih-Chi Chen
Summary: This study introduces a light sheet-based structured light illumination light field microscopy system for fast 3D imaging, utilizing a digital micromirror device to generate sinusoidal patterns rapidly. By combining deconvolution and HiLo algorithms, fast volumetric imaging with improved optical cross-sectioning capability is achieved. Imaging experiments on various samples show that this new method presents a fast 3D imaging solution with significantly enhanced optical cross-sectioning capability compared to standard light sheet-based LFM.
Article
Plant Sciences
Caiwen Xue, Wenfeng Li, Renfang Shen, Ping Lan
Summary: In Arabidopsis, iron participates in phosphate starvation-induced root hair growth by regulating reactive oxygen species generation, auxin signaling, and vesicle trafficking.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Multidisciplinary Sciences
Yanquan Mo, Fan Feng, Heng Mao, Junchao Fan, Liangyi Chen
Summary: Despite the wide application of structured illumination microscopy (SIM) in live-cell super-resolution imaging, aberrations caused by various sources remain a challenge. This study focused on investigating the impact of sample thickness on aberrations due to scattering of excitation light in SIM imaging, finding that thicker samples led to more severe aberrant interference light and degraded image reconstruction. The findings can guide future algorithm development to suppress SIM artefacts caused by scattering in thick samples.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2021)
Article
Biochemical Research Methods
Carlas S. Smith, Johan A. Slotman, Lothar Schermelleh, Nadya Chakrova, Sangeetha Hari, Yoram Vos, Cornelis W. Hagen, Marcel Mueller, Wiggert van Cappellen, Adriaan B. Houtsmuller, Jacob P. Hoogenboom, Sjoerd Stallinga
Summary: This study presents a physically realistic noise model explaining structured noise artifacts and proposes new complementary reconstruction approaches to eliminate them. By utilizing True-Wiener-filtered SIM and flat-noise SIM methods, contrast optimization and resolution maintenance are achieved while overcoming structured noise artifacts. These techniques enhance the objective representation of imaged objects without the need for adjustable parameters.
Article
Optics
Krishnendu Samanta, Anupriya Tiwari, Shereena Joseph, Joby Joseph
Summary: We propose a novel super-resolution technique called saturable absorption assisted nonlinear structured illumination microscopy (SAN-SIM), which exploits the saturable absorption property of a material. By converting the incident sinusoidal excitation into nonlinear illumination through a saturable absorbing material, the technique achieves more than two-fold resolution improvement over the diffraction limit by generating higher harmonics that fold high frequency components within the passband.
Article
Optics
Zewei Luo, Ge Wu, Mengting Kong, Zhi Chen, Zhengfei Zhuang, Junchao Fan, Tongsheng Chen
Summary: Forster resonance energy transfer (FRET) microscopy is a valuable tool for studying biological systems, but super-resolution FRET imaging in living cells is challenging. In this study, we propose a SR FRET method called SIM-FRET that combines SR structured illumination microscopy (SIM) imaging and acceptor sensitized emission FRET imaging to achieve live-cell quantitative SR FRET imaging. Our method provides enhanced spatial resolution and maintains the advantages of quantitative FRET analysis. We validate the effectiveness of SIM-FRET through simulated models and live-cell samples, and demonstrate its ability to reveal the intricate structure of FRET signals.
PHOTONICS RESEARCH
(2023)
Article
Optics
Juanjuan Zheng, Xiang Fang, Kai Wen, Jiaoyue Li, Ying Ma, Min Liu, Sha An, Jianlang Li, Zeev Zalevsky, Peng Gao
Summary: In this paper, the large-field, five-step lattice structured illumination microscopy (Lattice SIM) is introduced. It utilizes a 2D grating for lattice projection and a spatial light modulator (SLM) for phase shifting. By recording five phase-shifted intensity images, a super-resolution image is reconstructed, resulting in improved imaging speed and reduced photo-bleaching compared to conventional SIM methods. Furthermore, Lattice SIM achieves a three-fold spatial bandwidth product enhancement compared to SLM/DMD-based SIM.
Article
Chemistry, Analytical
Hyo Mi Park, Ki-Nam Joo
Summary: This study introduces a motionless polarizing structured illumination microscopy for measuring 3D surface profiles of specimens, utilizing spatial phase-shifting technique to obtain visibility of the illumination pattern and eliminating mechanical moving parts.
Article
Biochemistry & Molecular Biology
Despina Samakovli, Tereza Ticha, Tereza Vavrdova, Miroslav Ovecka, Ivan Luptovciak, Veronika Zapletalova, Anna Kucharova, Pavel Krenek, Yuliya Krasylenko, Theoni Margaritopoulou, Loukia Roka, Dimitra Milioni, George Komis, Polydefkis Hatzopoulos, Jozef Samaj
Review
Plant Sciences
Tereza Ticha, Despina Samakovli, Anna Kucharova, Tereza Vavrdova, Jozef Samaj
JOURNAL OF EXPERIMENTAL BOTANY
(2020)
Review
Plant Sciences
Miroslava Hrbackova, Petr Dvorak, Tomas Takac, Michaela Ticha, Ivan Luptovciak, Olga Samajova, Miroslav Ovecka, Jozef Samaj
FRONTIERS IN PLANT SCIENCE
(2020)
Article
Plant Sciences
Hongjiang Li, Daniel von Wangenheim, Xixi Zhang, Shutang Tan, Nasser Darwish-Miranda, Satoshi Naramoto, Krzysztof Wabnik, Riet De Rycke, Walter A. Kaufmann, Daniel Guetl, Ricardo Tejos, Peter Grones, Meiyu Ke, Xu Chen, Jan Dettmer, Jiri Friml
Summary: The study characterized PIN clusters in detail using advanced microscopy methods, revealing their preference for clustering at polar domains. It was found that PIN clusters rely on phosphoinositol pathways, cytoskeletal structures, and specific cell-wall components. This study provides insight into the maintenance of polarity in plants and other systems through different cellular processes and structures.
Article
Plant Sciences
Petr Dvorak, Yuliya Krasylenko, Miroslav Ovecka, Jasim Basheer, Veronika Zapletalova, Jozef Samaj, Tomas Takac
Summary: The study investigates the developmental expression and subcellular localization of FSD1 in Arabidopsis using microscopy techniques, revealing its importance in seed germination and lateral root development. FSD1 plays a crucial role in salt stress tolerance and lateral root formation, with a major subcellular pool located in the plastid stroma.
PLANT CELL AND ENVIRONMENT
(2021)
Article
Biochemistry & Molecular Biology
Jing Liu, Tomas Takac, Ganjun Yi, Houbin Chen, Yingying Wang, Jian Meng, Weina Yuan, Yehuan Tan, Tong Ning, Zhenting He, Jozef Samaj, Chunxiang Xu
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Biotechnology & Applied Microbiology
Miroslava Hrbackova, Ivan Luptovciak, Katerina Hlavackova, Petr Dvorak, Michaela Ticha, Olga Samajova, Dominik Novak, Hanna Bednarz, Karsten Niehaus, Miroslav Ovecka, Jozef Samaj
Summary: Transgenic manipulation of SIMK in alfalfa plants infected with Sinorhizobium meliloti showed that downregulation of both SIMKK and SIMK led to reduced root hair growth and lower capacity for infection thread and nodule formation, while overexpression of GFP-tagged SIMK promoted root hair growth and clustering of infection threads and nodules. These findings suggest that genetic manipulations affecting SIMK expression have significant impacts on root hair, nodule, and shoot formation patterns in alfalfa, indicating the biotechnological potential of this MAPK.
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Lenka Kubenova, Tomas Takac, Jozef Samaj, Miroslav Ovecka
Summary: The der1-3 mutant carrying a single-point mutation in the ACTIN2 gene shows enhanced plant growth under oxidative stress, with a more dynamic actin cytoskeleton and higher antioxidant activity. These results suggest that alterations in the actin cytoskeleton and increased capacity to decompose reactive oxygen species contribute to the mutant's enhanced tolerance against oxidative stress.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Plant Sciences
Petr Dvorak, Yuliya Krasylenko, Adam Zeiner, Jozef Samaj, Tomas Takac
Summary: Reactive oxygen species (ROS) are essential signaling molecules in plant responses to environmental stimuli and development. Antioxidant enzymes play a critical role in scavenging ROS and their regulation is influenced by both environmental conditions and transcriptional activation.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Tomas Takac, Pavel Krenek, George Komis, Pavol Vadovic, Miroslav Ovecka, Ludmila Ohnoutkova, Tibor Pechan, Petr Kasparek, Tereza Ticha, Jasim Basheer, Mark Arick, Jozef Samaj
Summary: This study demonstrates the significant role of HvMPK3 in barley's response to the bacterial elicitor flg22, with knock-out lines showing downregulation of defense-related proteins and reduced susceptibility to flg22. The differential proteomic analysis and phenotypic observations suggest a specific molecular and root hair response of barley to flg22 in HvMPK3 KO lines.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Yuliya Krasylenko, George Komis, Sofiia Hlynska, Tereza Vavrdova, Miroslav Ovecka, Tomas Pospisil, Jozef Samaj
Summary: Strigolactones regulate developmental events in roots by affecting the organization and dynamics of cortical microtubules. Chemical and genetic manipulation of strigolactone signaling impacts microtubule remodeling, especially under light conditions. The application of strigolactones in dark conditions partially alleviates cytoskeletal rearrangement, suggesting a new mechanistic connection between cytoskeletal behavior and light-dependent strigolactone signaling.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Despina Samakovli, Tereza Ticha, Tereza Vavrdova, Natalie Zavorkova, Ales Pecinka, Miroslav Ovecka, Jozef Samaj
Summary: The YODA kinase pathway is closely related to Arabidopsis embryo development control, with HSP90 proteins emerging as key regulators. Genetic interactions between HSP90 and YDA affect downstream signaling pathways, impacting basal and apical cell lineage development. Spatial-temporal expression of specific genes is altered when HSP90 or YDA function is impaired, suggesting a crucial role in cell fate determination and potential connection to auxin signaling during early embryo development.
Article
Plant Sciences
Laining Zhang, Tetyana Smertenko, Deirdre Fahy, Nuria Koteyeva, Natalia Moroz, Anna Kucharova, Dominik Novak, Eduard Manoilov, Petro Smertenko, Charitha Galva, Jozef Samaj, Alla S. Kostyukova, John C. Sedbrook, Andrei Smertenko
Summary: The study focuses on the function of formins in cytokinesis, suggesting their roles in promoting microtubule polymerization, nucleating F-actin at the cell plate, retaining dynamin-related proteins at the cell plate, and remodeling the cell plate membrane. The use of SMIFH2 has helped reveal the impact of formins on these processes.
Article
Biotechnology & Applied Microbiology
Ping-Li Liu, Xi Zhang, Jian-Feng Mao, Yan-Ming Hong, Ren-Gang Zhang, E. Yilan, Shuai Nie, Kaihua Jia, Chen-Kun Jiang, Jian He, Weiwei Shen, Qizouhong He, Wenqing Zheng, Samar Abbas, Pawan Kumar Jewaria, Xuechan Tian, Chang-jun Liu, Xiaomei Jiang, Yafang Yin, Bo Liu, Li Wang, Biao Jin, Yongpeng Ma, Zongbo Qiu, Frantisek Baluska, Jozef Samaj, Xinqiang He, Shihui Niu, Jianbo Xie, Lei Xie, Huimin Xu, Hongzhi Kong, Song Ge, Richard A. Dixon, Yuannian Jiao, Jinxing Lin
Article
Biochemistry & Molecular Biology
Despina Samakovli, Tereza Ticha, Jozef Samaj
PLANT SIGNALING & BEHAVIOR
(2020)