Article
Developmental Biology
Mostafa Aakhte, Hans-Arno J. Mueller
Summary: Light-sheet or selective plane illumination microscopy (SPIM) is suitable for in toto imaging of living specimens at high temporal-spatial resolution, but faces limitations due to light scattering in opaque specimens. The Multiview tiling SPIM (MT-SPIM) combines the strengths of Multi-view SPIM (M-SPIM) and a confined, multi-tiled light sheet, providing high-resolution, robust, and rotation-free imaging of living specimens. It improves axial resolution by a factor of two, enhancing automated segmentation of cellular structures.
Article
Cell Biology
Laura Zoe Kreplin, Senthil Arumugam
Summary: Live-cell imaging plays a crucial role in researching organelle dynamics, cytoskeletal interactions, membrane protrusions, and cell motility. In recent years, various light-sheet geometries have been developed to push the boundaries of measurements.
CURRENT OPINION IN CELL BIOLOGY
(2023)
Article
Biochemical Research Methods
Tingting Zhu, Jun Nie, Tingting Yu, Dan Zhu, Yanyi Huang, Zaozao Chen, Zhongze Gu, Jiang Tang, Dongyu LI, Peng Fei
Summary: Light sheet microscopy combined with a microchip is an emerging tool in biomedical research that improves efficiency. However, noticeable aberrations induced by the complex refractive indices in the chip limit microchip-enhanced light-sheet microscopy. This study introduces a droplet microchip with a polymer index matched to water, enabling large-scale culture of 3D spheroids and time-lapse imaging with high resolution and throughput.
BIOMEDICAL OPTICS EXPRESS
(2023)
Article
Multidisciplinary Sciences
Matteo Bernardello, Emilio J. Gualda, Pablo Loza-Alvarez
Summary: Light-sheet fluorescence microscopy is an important tool used in biological and biomedical research. However, the sample mounting procedure can be cumbersome and time-consuming. This article presents a new imaging paradigm for LSFM that offers multimodal imaging and a straightforward sample mounting strategy, enhancing the flexibility and throughput of the system.
SCIENTIFIC REPORTS
(2022)
Article
Optics
S. Crombez, P. Leclerc, C. Ray, N. Ducros
Summary: We present a computational light-sheet microscope that enables hyperspectral acquisition at high spectral resolution. By focusing the emitted fluorescence light onto the entrance slit of an imaging spectrometer using a cylindrical lens, and illuminating the specimen with a sequence of structured light patterns to capture the spatial dimension orthogonal to the slit, we demonstrate the feasibility of this method and report the initial results in vivo using hydra specimens labeled with two fluorophores.
Article
Nanoscience & Nanotechnology
Yuan Luo, Ming Lun Tseng, Sunil Vyas, Ting-Yu Hsieh, Jui-Ching Wu, Shang-Yang Chen, Hsiao-Fang Peng, Vin-Cent Su, Tzu-Ting Huang, Hsin Yu Kuo, Cheng Hung Chu, Mu Ku Chen, Jia-Wern Chen, Yu-Chun Chen, Kuang-Yuh Huang, Chieh-Hsiung Kuan, Xu Shi, Hiroaki Misawa, Din Ping Tsai
Summary: Light-sheet fluorescent microscopy (LSFM) is the leading technique for in vivo imaging in the fields of disease, medicine, and cell biology research. This study demonstrates the successful integration of a nanophotonic meta-lens as the illumination component for LSFM, addressing the challenges of high image resolution and optical sectioning. With the meta-lens, the LSFM system complexity is significantly reduced, enabling multicolor fluorescent imaging of live biological specimens with cellular resolution.
Article
Optics
N. R. Subedi, S. Yaraghi, P. S. Jung, G. Kukal, A. G. McDonald, D. N. Christodoulides, A. E. Vasdekis
Summary: Research shows that digitally scanned Airy beams can improve the throughput rates in Raman imaging by an order of magnitude compared to traditional diffraction-limited beams, achieving high contrast and 1 micron axial resolution for three-dimensional imaging of microparticles. This method also achieves orders of magnitude lower irradiation density than coherent Raman imaging schemes, with faster speed and lower phototoxicity.
Article
Physics, Applied
Kevin Keomanee-Dizon, Matt Jones, Peter Luu, Scott E. Fraser, Thai V. Truong
Summary: ExD-SPIM is an improved light-sheet microscopy strategy that solves the limitation of capturing fluorescence signals in large volumes by extending the depth of field (DOF) of high-NA detection objectives to match the thickness of the illumination light sheet. Compared to conventional light sheet imaging, ExD-SPIM improves the signal-to-noise ratio and reduces the rate of photobleaching. In whole-brain activity imaging, ExD-SPIM enhances signal sensitivity and volumetric coverage.
APPLIED PHYSICS LETTERS
(2022)
Article
Chemistry, Multidisciplinary
Pengfei Liu, Tianze Shi, Hongwei Li, Hongyu Chen, You Huang, Huizhen Ma, Tianyu Zhu, Rong Zhao, Yuan Li, Qi Xin, Ling Liu, Si Sun, Hongmei Nie, Wei Long, Hao Wang, Jiwei Wang, Xiao-Dong Zhang, Dong Ming
Summary: Near-infrared II (1000-1700 nm) three-dimensional microscopy with Airy beam-assistance improves z-direction spatial resolution and provides a large field of view for thick biological specimens. The technique achieves higher axial resolution and signal background ratio compared to traditional microscopy, allowing accurate observation of pathological conditions and progression of kidney injury and precise discrimination of damage degree in intestinal mucosal cells. It enables distortion-free three-dimensional imaging in deep tissue.
Article
Biology
Soohyun Park, Myeongsu Na, Sunghoe Chang, Ki Hean Kim
Summary: The development of high-resolution open-top axially swept LSM (HR-OTAS-LSM) enables high-throughput and high-resolution imaging in all dimensions. The method uses an aberration-corrected axially swept excitation light sheet and a high numerical aperture immersion objective lens to achieve high axial and lateral resolutions.
Article
Optics
Stephan Daetwyler, Bo-jui Chang, Bingying Chen, Fabian f. Voigt, Divya Rajendran, Felix Zhou, Reto Fiolka
Summary: Understanding the intricate interplay and inter-connectivity of biological processes across an entire organism is crucial in various fields of biology. The mesoscopic oblique plane microscope (OPM) presented here allows high-speed whole organism imaging with fine details revealed. By utilizing a microprism, the axial resolution and optical sectioning are enhanced through total internal reflection. The imaging depth is extended up to threefold while maintaining constant axial resolution through rapid refocusing of the light sheet. The mesoscopic OPM enables in vivo and in toto whole organism imaging, demonstrating quantitative mapping of blood flow dynamics in zebrafish vasculature and endothelial nuclei at a 12 Hz acquisition rate.
Article
Optics
Philip Wijesinghe, Stella Corsetti, Darren J. X. Chow, Shuzo Sakata, Kylie R. Dunning, Kishan Dholakia
Summary: In this study, a deep-learning method for deconvolution is proposed, which is trained using the known physics of the imaging system. By combining a generative adversarial network with unpaired experimental data, the method can rapidly and robustly deconvolve and super-resolve microscopy images.
LIGHT-SCIENCE & APPLICATIONS
(2022)
Article
Biochemical Research Methods
Kevin M. Dean, Tonmoy Chakraborty, Stephan Daetwyler, Jinlong Lin, Gerard Garrelts, Ons M'Saad, Hannahmariam T. Mekbib, Fabian F. Voigt, Martina Schaettin, Esther T. Stoeckli, Fritjof Helmchen, Joerg Bewersdorf, Reto Fiolka
Summary: The protocol provides detailed instructions for assembling and operating a versatile variant of light-sheet fluorescence microscopy called axially swept light-sheet microscopy (ASLM), which offers an unparalleled combination of field of view, optical resolution, and optical sectioning. It includes information on the working principle, applications, practical tips, part lists, schematics, and software for instrument control of ASLM.
Article
Biochemical Research Methods
Bumju Kim, Myeongsu Na, Soohyun Park, Kitae Kim, Jung-Hoon Park, Euiheon Chung, Sunghoe Chang, Ki Hean Kim
Summary: Open-top axially swept LSM (OTAS-LSM) was developed for high-throughput cellular imaging with improved axial resolution by sweeping a tightly focused excitation light sheet across the imaging field of view using an electro tunable lens (ETL). The effects of optical aberration were analyzed by both simulation and experiment, and the image resolutions were under 1.6 µm in all directions. The newly developed OTAS-LSM demonstrated single-cell resolution imaging of neuronal networks in optically cleared mouse brain and small intestine, showing potential for high-throughput cellular examination of optically cleared large tissues.
BIOMEDICAL OPTICS EXPRESS
(2021)
Article
Biochemical Research Methods
Petra Paie, Gianmaria Calisesi, Alessia Candeo, Andrea Comi, Federico Sala, Francesco Ceccarelli, Ada De Luigi, Pietro Veglianese, Korbinian Muhlberger, Michael Fokine, Gianluca Valentini, Roberto Osellame, Mark Neil, Andrea Bassi, Francesca Bragheri
Summary: Heterogeneity investigation at the single-cell level is crucial in clinical research. The combination of light sheet fluorescence microscopy and structured illumination microscopy in an optofluidic platform enables high throughput super-resolution imaging, allowing comprehensive evaluation of cellular heterogeneity at high resolution.
Correction
Biotechnology & Applied Microbiology
Sergei Yakneen, Sebastian M. Waszak, Michael Gertz, Jan O. Korbel, Brice Aminou, Javier Bartolome, Keith A. Boroevich, Rich Boyce, Angela N. Brooks, Alex Buchanan, Ivo Buchhalter, Adam P. Butler, Niall J. Byrne, Andy Cafferkey, Peter J. Campbell, Zhaohong Chen, Sunghoon Cho, Wan Choi, Peter Clapham, Brandi N. Davis-Dusenbery, Francisco M. De La Vega, Jonas Demeulemeester, Michelle T. Dow, Lewis Jonathan Dursi, Juergen Eils, Roland Eils, Kyle Ellrott, Claudiu Farcas, Francesco Favero, Nodirjon Fayzullaev, Vincent Ferretti, Paul Flicek, Nuno A. Fonseca, Josep Ll. Gelpi, Gad Getz, Bob Gibson, Robert L. Grossman, Olivier Harismendy, Allison P. Heath, Michael C. Heinold, Julian M. Hess, Oliver Hofmann, Jongwhi H. Hong, Thomas J. Hudson, Barbara Hutter, Carolyn M. Hutter, Daniel Hubschmann, Seiya Imoto, Sinisa Ivkovic, Seung-Hyup Jeon, Wei Jiao, Jongsun Jung, Rolf Kabbe, Andre Kahles, Jules N. A. Kerssemakers, Hyung-Lae Kim, Hyunghwan Kim, Jihoon Kim, Youngwook Kim, Kortine Kleinheinz, Michael Koscher, Antonios Koures, Milena Kovacevic, Chris Lawerenz, Ignaty Leshchiner, Jia Liu, Dimitri Livitz, George L. Mihaiescu, Sanja Mijalkovic, Ana Mijalkovic Lazic, Satoru Miyano, Naoki Miyoshi, Hardeep K. Nahal-Bose, Hidewaki Nakagawa, Mia Nastic, Steven J. Newhouse, Jonathan Nicholson, Brian D. O'Connor, David Ocana, Kazuhiro Ohi, Lucila Ohno-Machado, Larsson Omberg, B. F. Francis Ouellette, Nagarajan Paramasivam, Marc D. Perry, Todd D. Pihl, Manuel Prinz, Montserrat Puiggros, Petar Radovic, Keiran M. Raine, Esther Rheinbay, Mara Rosenberg, Romina Royo, Gunnar Ratsch, Gordon Saksena, Matthias Schlesner, Solomon I. Shorser, Charles Short, Heidi J. Sofia, Jonathan Spring, Lincoln D. Stein, Adam J. Struck, Grace Tiao, Nebojsa Tijanic, David Torrents, Peter Van Loo, Miguel Vazquez, David Vicente, Jeremiah A. Wala, Zhining Wang, Sebastian M. Waszak, Joachim Weischenfeldt, Johannes Werner, Ashley Williams, Youngchoon Woo, Adam J. Wright, Qian Xiang, Liming Yang, Denis Yuen, Christina K. Yung, Junjun Zhang, Jan O. Korbel
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Marina Laplana, Matthias Bieg, Christian Faltus, Svitlana Melnik, Olga Bogatyrova, Zuguang Gu, Thomas Muley, Michael Meister, Hendrik Dienemann, Esther Herpel, Christopher Amos, Matthias Schlesner, Roland Eils, Christoph Plass, Angela Risch
Summary: This study utilized a targeted sequencing approach to investigate DNA methylation changes in NSCLC patients, identifying differential methylation regions and confirming potential regulatory elements. The research contributes to understanding the mechanisms of lung cancer initiation and progression, and offers new potential targets for cancer treatment.
Article
Biotechnology & Applied Microbiology
J. Loske, J. Roehmel, S. Lukassen, S. Stricker, Vg Magalhaes, J. Liebig, Rl Chua, L. Thurmann, M. Messingschlager, A. Seegebarth, B. Timmermann, S. Klages, M. Ralser, B. Sawitzki, Le Sander, Vm Corman, C. Conrad, S. Laudi, M. Binder, S. Trump, R. Eils, M. A. Mall, I Lehmann
Summary: Children exhibit higher basal expression of relevant pattern recognition receptors in airway immune cells, resulting in stronger early innate antiviral responses to SARS-CoV-2 infection compared to adults. Unique immune cell subpopulations, including cytotoxic T cells and memory CD8+ T cells, predominantly occur in children.
NATURE BIOTECHNOLOGY
(2022)
Article
Immunology
Anita Balazs, Pamela Millar-Buechner, Michael Muelleder, Vadim Farztdinov, Lukasz Szyrwiel, Annalisa Addante, Aditi Kuppe, Tihomir Rubil, Marika Drescher, Kathrin Seidel, Sebastian Stricker, Roland Eils, Irina Lehmann, Birgit Sawitzki, Jobst Roehmel, Markus Ralser, Marcus A. Mall
Summary: The nasal epithelium acts as the first line of defense against inhaled pathogens, allergens, and irritants, and plays a crucial role in the development of various respiratory diseases. This study aims to investigate the age-related differences in the structure and function of the nasal epithelium. The results showed intrinsic, age-related differences in the structure and function of the nasal epithelium, which may contribute to the development of age-dependent respiratory diseases.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Genetics & Heredity
Sebastian Tiesmeyer, Shashwat Sahay, Niklas Mueller-Boetticher, Roland Eils, Sebastian D. Mackowiak, Naveed Ishaque
Summary: The combination of a cell's transcriptional profile and location defines its function in a spatial context. Spatially resolved transcriptomics (SRT) has become a popular method for characterizing cells in situ. However, the correct aggregation of mRNA molecules into cells has been a computational problem in single-molecule SRT methods. SSAM-lite is an easy-to-use graphical interface tool that enables rapid and segmentation-free cell typing of SRT data in a web browser.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Philipp Klein, Stefan M. Kallenberger, Hanna Roth, Karsten Roth, Thi Bach Nga Ly-Hartig, Vera Magg, Janez Ales, Soheil Rastgou Talemi, Yu Qiang, Steffen Wolf, Olga Oleksiuk, Roma Kurilov, Barbara Di Ventura, Ralf Bartenschlager, Roland Eils, Karl Rohr, Fred A. Hamprecht, Thomas Hoefer, Oliver T. Fackler, Georg Stoecklin, Alessia Ruggieri
Summary: This study elucidated the molecular mechanism of stress granules formation by integrating quantitative experiments and mathematical modeling. The study revealed that the stress response is controlled by a stochastic switch, with key elements including cooperative activation of PKR, ultrasensitive response of SG formation to eIF2 alpha phosphorylation, and negative feedback via GADD34. Furthermore, the study identified GADD34 mRNA levels as a molecular memory of the ISR that plays a central role in cell adaptation to acute and chronic stress.
Article
Oncology
Timo B. Trefzer, Marc A. Schneider, Katharina Jechow, Robert Lorenz Chua, Thomas Muley, Hauke Winter, Mark Kriegsmann, Michael Meister, Roland Eils, Christian Conrad
Summary: Lung cancer, the leading cause of cancer-related death worldwide, is not only highly associated with smoking status but also occurs in a significant proportion of non-smokers, particularly female non-smokers. This study used single-cell transcriptomics to analyze surgical lung adenocarcinoma (LUAD) and normal lung tissue samples from smokers and non-smokers, revealing different cell populations and immune interactions between the two groups. The findings provide important insights into lung cancer heterogeneity and immune involvement, which can guide future therapeutic strategies.
Article
Multidisciplinary Sciences
Maik Pietzner, Robert Lorenz Chua, Eleanor Wheeler, Katharina Jechow, Julian D. S. Willett, Helena Radbruch, Saskia Trump, Bettina Heidecker, Hugo Zeberg, Frank L. Heppner, Roland Eils, Marcus A. Mall, J. Brent Richards, Leif-Erik Sander, Irina Lehmann, Soeren Lukassen, Nicholas J. Wareham, Christian Conrad, Claudia Langenberg
Summary: This study integrates genomic, proteomic, and single-cell data to identify ELF5 as a candidate risk gene for severe COVID-19. ELF5 shows consistent associations with different outcome definitions and is specifically expressed in respiratory epithelial cells, which are likely targets of SARS-CoV-2.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
Sebastian Schuth, Solange Le Blanc, Teresa G. Krieger, Julia Jabs, Miriam Schenk, Nathalia A. Giese, Markus W. Buchler, Roland Eils, Christian Conrad, Oliver Strobel
Summary: This study established co-cultures of PDAC organoids and patient-matched CAFs to investigate the effect of fibroblastic compartment on sensitivity to chemotherapy. The presence of CAFs was found to enhance proliferation and reduce chemotherapy-induced cell death of PDAC organoids. Single-cell RNA sequencing analysis revealed a pro-inflammatory phenotype in CAFs and identified gene expression and receptor-ligand interactions associated with epithelial-to-mesenchymal transition (EMT), supporting the role of CAF-driven EMT in PDAC chemoresistance.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2022)
Article
Allergy
Loreen Thuermann, Matthias Kloes, Sebastian D. Mackowiak, Matthias Bieg, Tobias Bauer, Naveed Ishaque, Marey Messingschlager, Carl Herrmann, Stefan Roeder, Mario Bauer, Sascha Schaeuble, Erik Faessler, Udo Hahn, Dieter Weichenhan, Oliver Muecke, Christoph Plass, Michael Borte, Erika von Mutius, Gabriele I. Stangl, Roger Lauener, Anne M. Karvonen, Amandine Divaret-Chauveau, Josef Riedler, Joachim Heinrich, Marie Standl, Andrea von Berg, Beate Schaaf, Gunda Herberth, Michael Kabesch, Roland Eils, Saskia Trump, Irina Lehmann
Summary: This study used whole genome bisulfite sequencing to identify dysregulation of enhancer regions as a hallmark of childhood asthma. Abnormal DNA methylation was found in key immune genes and was linked to prenatal influences and genetic susceptibility.
Article
Multidisciplinary Sciences
Florent Murat, Noe Mbengue, Sofia Boeg Winge, Timo Trefzer, Evgeny Leushkin, Mari Sepp, Margarida Cardoso-Moreira, Julia Schmidt, Celine Schneider, Katharina Moessinger, Thoomke Bruening, Francesco Lamanna, Meritxell Riera Belles, Christian Conrad, Ivanela Kondova, Ronald Bontrop, Ruediger Behr, Philipp Khaitovich, Svante Paeaebo, Tomas Marques-Bonet, Frank Gruetzner, Kristian Almstrup, Mikkel Heide Schierup, Henrik Kaessmann
Summary: Through evolutionary analysis of single-nucleus transcriptome data from 11 species, it was found that the rapid evolution of the testis was driven by accelerated fixation rates of gene expression changes, amino acid substitutions, and new genes in late spermatogenic stages. The study also revealed that genes predominantly expressed in spermatogonia and Sertoli cells accumulated on X chromosomes during evolution, possibly due to male-beneficial selective forces. Additionally, it was discovered that meiotic sex-chromosome inactivation (MSCI) is an ancestral feature in mammalian sex-chromosome systems, including monotremes.
Article
Biochemical Research Methods
Daria Doncevic, Carl Herrmann
Summary: In this study, a novel VAE model called OntoVAE is designed to incorporate any ontology in its latent space and decoder part, providing pathway or phenotype activities for ontology terms. OntoVAE is demonstrated to be applicable in predictive modeling and is able to predict the effects of genetic or drug-induced perturbations using different ontologies and both bulk and single-cell transcriptomic datasets. Furthermore, a flexible framework is provided, which can be easily adapted to any ontology and dataset.
Article
Biochemistry & Molecular Biology
Philipp Georg, Rosario Astaburuaga-Garcia, Lorenzo Bonaguro, Sophia Brumhard, Laura Michalick, Lena J. Lippert, Tomislav Kostevc, Christiane Gaebel, Maria Schneider, Mathias Streitz, Vadim Demichev, Ioanna Gemuend, Matthias Barone, Pinkus Tober-Lau, Elisa T. Helbig, David Hillus, Lev Petrov, Julia Stein, Hannah-Philine Dey, Daniela Paclik, Christina Iwert, Michael Muelleder, Simran Kaur Aulakh, Sonja Djudjaj, Roman D. Buelow, Henrik E. Mei, Axel R. Schulz, Andreas Thiel, Stefan Hippenstiel, Antoine-Emmanuel Saliba, Roland Eils, Irina Lehmann, Marcus A. Mall, Sebastian Stricker, Jobst Roehmel, Victor M. Corman, Dieter Beule, Emanuel Wyler, Markus Landthaler, Benedikt Obermayer, Saskia von Stillfried, Peter Boor, Munevver Demir, Hans Wesselmann, Norbert Suttorp, Alexander Uhrig, Holger Mueller-Redetzky, Jacob Nattermann, Wolfgang M. Kuebler, Christian Meisel, Markus Ralser, Joachim L. Schultze, Anna C. Aschenbrenner, Charlotte Thibeault, Florian Kurth, Leif E. Sander, Nils Bluethgen, Birgit Sawitzki
Summary: Severe COVID-19 is associated with highly activated CD16(+) T cells that exhibit cytotoxic functions and contribute to endothelial injury. These CD16(+) T cells can degranulate and induce cytotoxicity through immune-complex-mediated mechanisms independent of the T cell receptor, which is not observed in other diseases. The presence of activated CD16(+) T cells and elevated levels of complement proteins upstream of C3a are associated with a fatal outcome of COVID-19, indicating the pathological role of enhanced cytotoxicity and complement activation in the disease.
Article
Medical Informatics
Jakob Steinfeldt, Thore Buergel, Lukas Loock, Paul Kittner, Greg Ruyoga, Julius Upmeier zu Belzen, Simon Sasse, Henrik Strangalies, Lara Christmann, Noah Hollmann, Benedict Wolf, Brian Ference, John Deanfield, Ulf Landmesser, Roland Eils
Summary: In this study, a neural network-based risk model (NeuralCVD) was developed and validated to estimate cardiovascular risk for primary prevention. The model integrates polygenic and clinical predictors and improves risk discrimination compared to established clinical scores and a Cox model. The findings highlight the importance of genetic information in identifying individuals with a high genetic predisposition for preventive interventions.
LANCET DIGITAL HEALTH
(2022)