Background: Single-molecule localization microscopy is a super-resolution microscopy technique that allows for nanoscale determination of the localization and organization of proteins in biological samples. For biological interpretation of the data it is essential to extract quantitative information from the super-resolution data sets. Due to the complexity and size of these data sets flexible and user-friendly software is required.
Results: We developed SMoLR (Single Molecule Localization in R): a flexible framework that enables exploration and analysis of single-molecule localization data within the R programming environment. SMoLR is a package aimed at extracting, visualizing and analyzing quantitative information from localization data obtained by single-molecule microscopy. SMoLR is a platform not only to visualize nanoscale subcellular structures but additionally provides means to obtain statistical information about the distribution and localization of molecules within them. This can be done for individual images or SMoLR can be used to analyze a large set of super-resolution images at once. Additionally, we describe a method using SMoLR for image feature-based particle averaging, resulting in identification of common features among nanoscale structures.
Conclusions: Embedded in the extensive R programming environment, SMoLR allows scientists to study the nanoscale organization of biomolecules in cells by extracting and visualizing quantitative information and hence provides insight in a wide-variety of different biological processes at the single-molecule level.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6334411 | PMC |
| http://dx.doi.org/10.1186/s12859-018-2578-3 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Human Endogenous Retrovirus K in Astrocytes Is Altered in Parkinson's Disease.
Mov Disord
January 2025
Brain and Mind Centre, The University of Sydney, Sydney, New South Wales, Australia.
Background: Parkinson's disease (PD) is the most common neurodegenerative movement disease. Human endogenous retroviruses (HERVs) are proviral remnants of ancient retroviral infection of germ cells that now constitute about 8% of the human genome. Under certain disease conditions, HERV genes are activated and partake in the disease process.
View Article and Find Full Text PDFChiral and Quantum Plasmonic Sensors: New Frontiers in Selective and Ultra-Sensitive Sensing.
Small
January 2025
Department of Chemistry, Dr. Vishwanath Karad MIT World Peace University, Survey No, 124, Paud Rd, Kothrud, Pune, Maharashtra, 411038, India.
Surface Plasmon Polaritons (SPPs) and Localized Surface Plasmon Resonances (LSPRs) are fundamental phenomena in plasmonics that enable the confinement of electromagnetic waves beyond the diffraction limit. This confinement results in a significant enhancement of the electric field, making this phenomenon particularly beneficial for sensitive detection applications. However, conventional plasmonic sensors face several challenges, notably their difficulty in distinguishing chiral molecules, which are vital in drug development.
View Article and Find Full Text PDFMINFLUX Nanoscopy: A "Brilliant" Technique Promising Major Breakthrough.
Microsc Res Tech
January 2025
Dipartimento di Fisica, Università di Genova, Genova, Italy.
MINFLUX nanoscopy relies on the localization of single fluorophores with expected ~ 2 nm precision in 3D mapping, roughly one order of magnitude better than standard stimulated emission depletion microscopy or stochastic optical reconstruction microscopy. This "brilliant" technique takes advantage of specialized localization principles and algorithms that require only dim fluorescence signals with a minimum flux of photons; hence the name follows. With this level of performance, MINFLUX imaging and tracking should allow for the routine study of biological processes down to the molecular scale, revealing previously unresolved details in cell structures, such as the organization of calcium channels in muscle cells or the clustering of receptors in synapses.
View Article and Find Full Text PDFSingle-molecule microscopy reveals that importin α slides along DNA while transporting cargo molecules.
Biochem Biophys Res Commun
January 2025
Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan; Faculty of Engineering and Graduate School of Engineering, Gifu University, Yanagido 1-1, Gifu, 501-1193, Japan. Electronic address:
Importin α is a crucial player in the nucleocytoplasmic transport of nuclear localization signal (NLS)-containing cargo proteins and is suggested to bind to DNA directly. We hypothesized that importin α, after binding to DNA, may move along DNA via sliding or hopping. We investigated the movement dynamics of importin αs fused to AcGFP along DNA using single-molecule fluorescence microscopy and single-tethered DNA arrays.
View Article and Find Full Text PDFRetroviruses are responsible for significant pathology in humans and animals, including the acquired immunodeficiency syndrome and a wide range of malignancies. A crucial yet poorly understood step in the replication cycle is the recognition and selection of unspliced viral RNA (USvRNA) by the retroviral Gag protein, which binds to the psi (Ψ) packaging sequence in the 5' leader, to package it as genomic RNA (gRNA) into nascent virions. It was previously thought that Gag initially bound gRNA in the cytoplasm.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!