Article
Cell Biology
Joanna W. Pylvanainen, Estibaliz Gomez-de-Mariscal, Ricardo Henriques, Guillaume Jacquemet
Summary: Live imaging, particularly when combined with fluorescence microscopy, is a powerful tool for observing cellular components in real time. However, implementing live imaging and analyzing the resulting datasets is challenging due to issues such as drift, phototoxicity, and dataset size. Recent advances in bioimage analysis, including deep learning, are revolutionizing how live imaging is performed. Important computational methods for live imaging include drift correction, denoising, super-resolution imaging, artificial labeling, tracking, and time series analysis. Self-driving microscopy has also seen recent advancements.
CURRENT OPINION IN CELL BIOLOGY
(2023)
Article
Biochemical Research Methods
Zhi Ling, Keyi Han, Wenhao Liu, Xuanwen Hua, Shu Jia
Summary: This study presents a rapid, volumetric live-cell imaging technique using high-resolution Fourier light-field microscopy to visualize autofluorescent sub-cellular structures and their dynamics. Lysosomal autofluorescence in fibroblasts and HeLa cells was observed, and multicolor imaging allowed simultaneous observation of lysosomal autofluorescence and fluorescently-labeled organelles such as lysosomes and mitochondria. Data analysis provided quantitative measurements of lysosome-mitochondria interactions. This research paves the way for future exploration of native cellular states and functions in three-dimensional environments, offering advantages of reduced photodamage and elimination of exogenous labels.
BIOMEDICAL OPTICS EXPRESS
(2023)
Review
Chemistry, Analytical
Zrinko Baricevic, Zahra Ayar, Samuel M. Leitao, Miranda Mladinic, Georg E. Fantner, Jelena Ban
Summary: Time-lapse light microscopy combined with in vitro neuronal cultures has made a significant contribution to Developmental Neuroscience. Although fluorescently labeled tags and dyes have provided advancements in cell imaging, long-term recordings remain challenging due to phototoxicity and interference with cell physiology. Hence, label-free high-resolution methods, such as scanning ion conductance microscopy (SICM) or digital holography microscopy (DHM) are proposed for studying live cell dynamics during neuronal development and regeneration.
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
Biology
Jeremy Copperman, Sean M. Gross, Young Hwan Chang, Laura M. Heiser, Daniel M. Zuckerman
Summary: Time-lapse imaging is a powerful tool to study cell dynamics, but analyzing morphological changes over time is challenging. In this study, we use trajectory embedding to analyze cellular behavior based on multiple time points simultaneously. We apply this method to study the effects of microenvironmental perturbagens on MCF10A mammary epithelial cells. Our analysis reveals ligand-specific regulation of cell state transitions and provides descriptive models of single-cell trajectories. Incorporating trajectories improves the characterization of cell states and enables better identification of phenotypes compared to snapshot-based analysis. This approach has broad applications in live-cell imaging for studying cell responses.
COMMUNICATIONS BIOLOGY
(2023)
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
Biochemical Research Methods
Keyi Han, Xuanwen Hua, Vishwa Vasani, Ge-Ah R. Kim, Wenhao Liu, Shuichi Takayama, Shu Jia
Summary: This study reports a 3D super-resolution live-cell microscopy method called rad-FLFM, which combines radiality analysis and Fourier light-field microscopy. The method enables scanning-free, high-resolution, and low photodamage live-cell imaging in three dimensions.
BIOMEDICAL OPTICS EXPRESS
(2022)
Article
Biotechnology & Applied Microbiology
Andreas Boden, Francesca Pennacchietti, Giovanna Coceano, Martina Damenti, Michael Ratz, Ilaria Testa
Summary: A new 3D pRESOLFT microscope method with sub-80-nm resolution has been developed to visualize the volumetric architecture of organelles and molecules inside whole living cells, allowing for targeted 3D confinement of fluorescence and observation of dynamic structural alterations in cells.
NATURE BIOTECHNOLOGY
(2021)
Article
Nanoscience & Nanotechnology
Alice Sandmeyer, Mario Lachetta, Hauke Sandmeyer, Wolfgang Huebner, Thomas Huser, Marcel Mueller
Summary: This paper presents a compact, cost-effective high-speed structured illumination microscope that allows for video-rate super-resolved image reconstructions. The instrument, based on a digital micromirror device and a global-shutter camera, optimizes SIM pattern contrast and enables real-time reconstruction and visualization of living cells with high sensitivity.
Review
Optics
Herbert Schneckenburger, Verena Richter
Summary: This short overview discusses 3D live cell imaging, relevant samples, challenges like optical sectioning and phototoxicity, and enhanced microscopy methods with some examples and applications. Future advancements may involve increasing microscopic resolution and utilizing molecular sensing techniques.
Article
Biochemistry & Molecular Biology
Anayat Bhat, Shuang Li, Daniel Hammler, Martin J. Winterhalder, Andreas Marx, Andreas Zumbusch
Summary: The hydrolysis of nucleotides is important for cellular energy, and the transfer of phosphates to proteins is crucial for post-translational modification. A novel fluorogenic adenosine 5'-tetraphosphate (Ap4) analog has been developed for real-time monitoring of ATP hydrolysis within live cells, with potential applications in studying cellular processes involving Ap4 hydrolysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Rajesh Ranjan, Xin Chen
Summary: This study presents a method for conducting super-resolution timelapse fluorescence live cell imaging in situ, compatible with low fluorescent intensity cells and capable of visualizing multiple subcellular structures. Special procedures in sample preparation and immobilizing specimens are necessary for this technique, but it is broadly applicable to various cell types.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Review
Chemistry, Multidisciplinary
Fan Yang, Huiting Lu, Xiangdan Meng, Haifeng Dong, Xueji Zhang
Summary: This review focuses on the application of DNA-based nanoprobes in miRNA biosensors, presenting strategies for customizing desired nanoplatforms including delivery vehicles, DNA sequence design, and advancements in imaging technologies for accurate signal output. Challenges and future directions in the field are also discussed.
Article
Nanoscience & Nanotechnology
Cynthia Richard, Erick J. Vargas-Ordaz, Victor J. Cadarso, Adrian Neild
Summary: Having a system that can capture high-resolution, quantitative, subcellular information of live cells without causing cell damage is crucial in various research fields. Optofluidic light-sheet fluorescent microscopy (LSFM) has emerged as a powerful tool that offers a low photo-toxic imaging method using microfluidics. In this study, LSFM benefits were combined with an acoustic single cell prison to enable precise single cell manipulation and 3D multi-imaging in a semi-automated manner. By trapping individual cells using standing surface acoustic waves (SSAWs), planar and cross-sectional images of the cells were obtained. The results were further processed to reconstruct 3D volumetric images and compare imaging outcomes between rounds.
MICROFLUIDICS AND NANOFLUIDICS
(2023)
Review
Plant Sciences
Maria Ada Prusicki, Martina Balboni, Kostika Sofroni, Yuki Hamamura, Arp Schnittger
Summary: Live-cell imaging is a powerful tool for understanding cellular processes, especially in meiosis where chromosomes and cellular components exhibit complex dynamics over a short period of time. Recent advances in live-cell imaging now allow real-time analysis of meiotic events in plants.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Engineering, Biomedical
Jiawei Yin, A. Agung Julius, John T. Wen, John P. Hanifin, Benjamin Warfield, George C. Brainard
Summary: This paper introduces a method for estimating sleep/wake state based on actigraphy data, as well as a method for estimating circadian phase shift using an adaptive notch filter algorithm. The study also explores the relationship between concussion detection and sleep-related features.
BIOMEDICAL SIGNAL PROCESSING AND CONTROL
(2021)
Review
Cell Biology
Alejandra Vasquez-Limeta, Jadranka Loncarek
Summary: This chapter delves into the early history of chromosome studies and the current understanding of the structure and formation of mitotic chromosomes, highlighting the central organizing region and chromosome scaffold within each chromatid. It emphasizes the essential role of condensins I and II in shaping the chromosome through loop extrusion, with a spiral staircase arrangement of condensin II and nested loops formed by condensin I.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Yuan-Chih Peng, Shuyang Chen, Devavrat Jivani, John Wason, William Lawler, Glenn Saunders, Richard J. Radke, Jeff Trinkle, Shridhar Nath, John T. Wen
Summary: This paper presents a robotic assembly methodology for the manufacturing of large segmented composite structures, which uses sensors and cameras for high-precision panel pick-up, placement, and transport. Human-assisted path planning ensures reliable motion of the robot, demonstrating the versatility of sensor-guided robotic assembly in complex tasks.
APPLIED SCIENCES-BASEL
(2021)
Article
Engineering, Electrical & Electronic
Qi Jin, John T. Wen, Shankar Narayanan
Summary: Flow boiling in microchannel evaporators offers advantages such as compact structure, high heat transfer coefficient, and better temperature uniformity, but challenges like critical heat flux, local dry-outs, and flow instabilities exist. Experimental studies can help understand the impact of evaporator design and system parameters, leading to the development of dynamic control strategies to address transient heat loads.
JOURNAL OF ELECTRONIC PACKAGING
(2021)
Article
Multidisciplinary Sciences
Jiawei Yin, A. Agung Julius, John T. Wen
Summary: The circadian rhythm, governed by Process C and Process S, regulates various biological processes such as sleep and metabolism, determining the sleep-wake cycle. This paper introduces a method of regulating Process C and Process S through light exposure and sleep scheduling, solving the optimal synchronization problem for the two-process model, with the finding that joint optimization of light and sleep times can reduce synchronization time.
Article
Engineering, Manufacturing
Qi Jin, Charles C. Okaeme, John T. Wen, Shankar Narayanan
Summary: This study quantitatively compares finite element (FE) and lumped modeling techniques for analyzing phase-change and multiphase flow in a microchannel evaporator. Results show that the one-zone model's relative errors increase with evaporator heat load, while the liquid-phase region and exit vapor quality are predicted more accurately. Overall errors using one- and two-zone lumped models were less than 30% when exit qualities do not exceed 0.5, making lumped models favorable under conditions that avoid high exit vapor qualities.
IEEE TRANSACTIONS ON COMPONENTS PACKAGING AND MANUFACTURING TECHNOLOGY
(2021)
Article
Thermodynamics
Qi Jin, John T. Wen, Shankar Narayan
Summary: This study analyzes the effect of using an oscillatory valve opening on the flow distribution and channel temperatures across a two-channel evaporator. Experiments and prediction models indicate that a specific range of valve oscillation amplitude and frequency may cause synchronization resulting in balancing the flow distribution and temperature.
APPLIED THERMAL ENGINEERING
(2022)
Article
Cell Biology
Alejandra Vasquez-Limeta, Kimberly Lukasik, Dong Kong, Catherine Sullenberger, Delgermaa Luvsanjav, Natalie Sahabandu, Raj Chari, Jadranka Loncarek
Summary: Centrioles assembly is regulated by CPAP during the cell cycle, and insufficiency of CPAP can lead to incomplete microtubule triplets and fragmentation of centrioles. These findings improve our understanding of the role of CPAP in centrosome biogenesis and its association with human diseases.
JOURNAL OF CELL BIOLOGY
(2022)
Article
Mathematics
Jiawei Yin, Agung Julius, John T. Wen, Zhen Wang, Chuanlin He, Lei Kou
Summary: This paper addresses the optimization of light exposure and sleep schedules to improve alertness, using a three-process hybrid dynamic model to simulate circadian rhythm and predict alertness. By adjusting sleep and wake times based on individual differences, the impacts of light and sleep schedules on alertness are evaluated using variational calculus, and an optimal solution is determined using a gradient descent algorithm.
Article
Robotics
David S. Carabis, John T. Wen
Summary: Space manipulator arms often have joint flexibility and limited motor torque, which can be accentuated when manipulating massive objects. Astronauts currently use visual feedback to mitigate oscillations and trajectory following issues. However, ground teleoperation is difficult due to time delays between orbit and Earth, necessitating more autonomous operations. To improve trajectory tracking performance, trajectory planning for autonomous systems should be considered. The proposed model-based trajectory generation methodology for flexible-joint space manipulators shows efficacy in simulation and physical experiments.
FRONTIERS IN ROBOTICS AND AI
(2022)
Article
Multidisciplinary Sciences
Katerina A. Turner, Luke Achinger, Dong Kong, Derek F. Kluczynski, Emily Lillian Fishman, Audrey Phillips, Barbara Saltzman, Jadranka Loncarek, Bo R. Harstine, Tomer Avidor-Reiss
Summary: This study found that evaluating sperm centriole quality can identify subfertility in cattle. The current methods are unable to detect subfertility in bulls, but fluorescence-based Ratiometric Analysis of Sperm Centrioles (FRAC) and acetylated tubulin labeling can provide insight into this novel mechanism of subfertility.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Chukwuemeka O. Ike, John T. Wen, Meeko M. K. Oishi, Lee K. Brown, A. Agung Julius
Summary: In this paper, a linear state observer is proposed as an elegant solution for continuous phase estimation in circadian rhythms. By adjusting the gains of the observer using an evolutionary optimization algorithm, the target components can be extracted from individuals' data, providing accurate phase estimates under ambulatory conditions.
Article
Chemistry, Physical
Saminathan Ramakrishnan, Jason R. Stagno, Valentin Magidson, William F. Heinz, Yun-Xing Wang
Summary: This study investigates the effect of crystal size on the uniformity of solid-solid phase transitions (SSPTs) by monitoring changes in crystal birefringence. The results show that the transition time width increases with crystal size, and medium to large crystals exhibit large variations in transition time and width depending on the region of the crystal being analyzed.
STRUCTURAL DYNAMICS-US
(2021)
Article
Engineering, Aerospace
David S. Carabis, Kimberly Oakes, John T. Wen
Summary: This paper proposes a methodology for massive object manipulation using flexible-joint manipulators in space applications. The manipulation task involves phases such as tracking, capture, path planning, trajectory execution, and berthing. Visual servoing and compliance control are utilized to track and capture the object, with motion planning accounting for various constraints to ensure successful manipulation.
JOURNAL OF GUIDANCE CONTROL AND DYNAMICS
(2021)
Article
Robotics
Shuyang Chen, John T. Wen
Summary: This paper introduces a method that combines neural networks and iterative learning controls to enhance the trajectory tracking performance of multi-axis articulated industrial robots. By training neural networks to emulate the dynamical inverse of the nonlinear inner-loop dynamics, the performance can be improved.
