Article
Biochemical Research Methods
Yu-Le Wu, Philipp Hoess, Aline Tschanz, Ulf Matti, Markus Mund, Jonas Ries
Summary: Quantitative data analysis is crucial for extracting biological insights from the coordinates of single fluorophores in a single-molecule localization microscopy (SMLM) workflow. LocMoFit, an open-source framework, is introduced to fit an arbitrary model to localization coordinates, extract meaningful parameters, and select suitable models. It enables the analysis of complex, heterogeneous, and dynamic structures, and has been demonstrated in assembling multi-protein distribution maps, calculating single-particle averages, and performing time-resolved reconstruction of dynamic processes from static snapshots. Extensive simulation and visualization routines validate the robustness of LocMoFit, and tutorials are provided to enhance users' extraction of information from SMLM data.
Article
Biochemical Research Methods
Yu-Le Wu, Philipp Hoess, Aline Tschanz, Ulf Matti, Markus Mund, Jonas Ries
Summary: This paper presents an open-source framework called LocMoFit for fitting arbitrary models to localization coordinates. The framework has significant potential for analyzing complex, heterogeneous, and dynamic structures, and can be used for assembling protein distribution maps, calculating single-particle averages, and performing time-resolved analysis of highly dynamic processes.
Article
Optics
Cheng Chen, Richard Leach, Jian Wang, Xiaojun Liu, Xiangqian Jiang, Wenlong Lu
Summary: The iteration-free approach based on a centroid algorithm with a locally adaptive threshold achieves nanometer-level peak position localization of the axial response signal in confocal microscopy. The localization accuracies are near theoretical limits, especially with a small number of sampling points within the discrete signal. The algorithm is orders of magnitude faster than fitting schemes based on maximum likelihood estimation. Simulations and experiments demonstrate the approach's localization performance.
Article
Plant Sciences
Kazusato Oikawa, Keiko Midorikawa, Yutaka Kodama, Keiji Numata
Summary: Organelles contribute to plant growth through their movements and interactions. In this study, a high-throughput method was developed to quantitatively evaluate the interactions between peroxisomes and chloroplasts in living plant cells using distance transformation algorithm and high-resolution 3D fluorescent images. The results showed that the distance between peroxisomes and chloroplasts was shorter in the light conditions.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Hari B. Krishnan, Alexander Jurkevich
Summary: This study used confocal fluorescent microscopy to examine the presence or absence of subdomains within soybean PSVs. The results showed that while complex subdomains were present in FAA-fixed seeds, fluorescence immunolabeling and other microscopy examinations failed to confirm the existence of subdomains within soybean PSVs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
David Doan, Daniel J. Echeveste, John Kulikowski, X. Wendy Gu
Summary: Optical and confocal microscopy are used to image the self-assembly of microscale colloidal particles. Machine learning is applied to improve identification speed and accuracy, achieving a mean Average Precision (mAP) of around 85%. Synthetic data generated using Blender supplements the training data, capturing key characteristics of confocal images.
Article
Multidisciplinary Sciences
Joshua D. Spitzberg, Scott Ferguson, Katherine S. Yang, Hannah M. Peterson, Jonathan C. T. Carlson, Ralph Weissleder
Summary: This study developed a technique called MASEV for multiplexed analysis of EVs, which allows the interrogation of thousands of individual EVs using multi-channel fluorescence staining. The findings reveal the presence of multiple biomarkers in single vesicles and the potential loss of rare EV subtypes through affinity purification. These findings demonstrate the importance of MASEV in uncovering the heterogeneity and biology of EVs and improving diagnostic specificity.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
George Sirinakis, Edward S. Allgeyer, Jinmei Cheng, Daniel St Johnston
Summary: When using spinning disks combined with PAINT methods for super-resolution imaging, the geometry of the spinning disk has an impact on imaging performance. Disk geometries with higher light collection efficiency perform better for PAINT-based super-resolution imaging.
BIOMEDICAL OPTICS EXPRESS
(2022)
Article
Biochemical Research Methods
Daniel J. Nieves, Jeremy A. Pike, Florian Levet, David J. Williamson, Mohammed Baragilly, Sandra Oloketuyi, Ario de Marco, Juliette Griffie, Daniel Sage, Edward A. K. Cohen, Jean-Baptiste Sibarita, Mike Heilemann, Dylan M. Owen
Summary: This study compares the performance of seven algorithms for cluster analysis of single-molecule localization microscopy data. The results provide a framework for comparing these methods and guide users to the best tools. Cluster analysis is an effective method for extracting meaningful information from single-molecule localization microscopy data, but there is no consensus framework for evaluating the performance of different algorithms. This study proposes a systematic approach and evaluation metrics based on simulated conditions to score the success of clustering algorithms.
Article
Biochemistry & Molecular Biology
Christopher Halkias, Antony Orth, Bryce N. Feltis, Theodore A. Macrides, Brant C. Gibson, Paul F. A. Wright
Summary: The in vitro human THP‐1 monocyte model of cholesterol crystallization provides an effective and efficient means of quantitating cholesterol crystallization in the pre-clinical stage of research, and allows for the screening of potentially therapeutic compounds that may be used in attenuating or preventing cholesterol crystallization.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS
(2021)
Review
Medicine, General & Internal
Eleonora Cosmo, Giulia Midena, Luisa Frizziero, Marisa Bruno, Michela Cecere, Edoardo Midena
Summary: Distal symmetric polyneuropathy (DPN) is a common complication of diabetes, and the use of corneal confocal microscopy (CCM) as a diagnostic tool can effectively detect sub-basal nerve plexus damage in diabetic patients, correlating with the severity of DPN.
JOURNAL OF CLINICAL MEDICINE
(2022)
Article
Biology
Brandon Ho, Ethan J. Sanford, Raphael Loll-Krippleber, Nikko P. Torres, Marcus B. Smolka, Grant W. Brown
Summary: The replication checkpoint plays a crucial role in maintaining genomic integrity during DNA replication and repair under genotoxic stress. In this study, the researchers investigated the regulation of subcellular localization of proteins during chemically induced DNA replication stress in yeast. They found that the checkpoint kinases Mec1 and Rad53 are responsible for regulating the subcellular localization of 159 proteins during replication stress. Surprisingly, Rad53 can regulate the localization of certain proteins independently of its known activators and mediator proteins. The study also revealed a noncanonical mode of Rad53 activation that relies partially on the retrograde signaling transcription factor Rtg3.
Article
Plant Sciences
Huai-Na Gao, Han Jiang, Xin-Yu Lian, Jian-Ying Cui, Chun-Xiang You, Yu-Jin Hao, Yuan-Yuan Li
Summary: In this study, 26 potential LTPG genes were identified in apple using bioinformatics methods, and 20 of them were confirmed as MdLTPG family members based on subcellular localization predictions. These MdLTPG genes were induced by growth conditions and one protein was shown to interact with another protein, collectively participating in wax transport during plant growth and development.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Biochemical Research Methods
Yichen Li, Mark Tingey, Andrew Ruba, Weidong Yang
Summary: SPEED microscopy offers an effective approach to achieve 3D sub-diffraction-limit information in subcellular structures and organelles with rotational symmetry. It does not rely on complex optical components and can be implemented onto a standard inverted epifluorescence microscope, providing high spatiotemporal resolution for studying individual immobile or moving fluorescent molecules inside biological channels or cavities. The complete protocol takes around 9 days to complete, including cell culture and sample preparation, SPEED imaging, and data analysis and validation through simulation.
Article
Food Science & Technology
Deepa Agarwal, Esther H-J Kim, Limei Feng, Cath Wade, Gert-Jan Moggre, Marco P. Morgenstern, Duncan Hedderley
Summary: This study investigates the impact of locust bean gum (LBG) on plant-based proteins, specifically quinoa protein (QPI) and pea protein isolates (PPI). Experimental measurements including microscopy, rheological analysis, and nuclear magnetic resonance (NMR) were conducted. The addition of LBG enhanced the viscoelastic properties and shear viscosities of the mixtures, forming more dense protein networks and coacervates. PPI-LBG interaction resulted in higher shear viscosities and decreased water mobility compared to QPI-LBG formulations, highlighting the significance of protein-polysaccharide interaction in microstructure and rheological properties.
FOOD RESEARCH INTERNATIONAL
(2023)