Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dynamic Structure of Yeast Septin by Fast Fluctuation-Enhanced Structured Illumination Microscopy.

ABSTRACT: When Saccharomyces cerevisiae divides, a structure composed of different septin proteins arranged according to a certain rule is formed at the cell division site. The structure undergoes multiple remodeling stages during the cell cycle, thus guiding the yeast cells to complete the entire division process. Although the higher-order structure of septins can be determined using electron microscopy, the septin's dynamic processes are poorly understood because of limitations in living cell super-resolution imaging technology. Herein, we describe a high lateral resolution and temporal resolution technique, known as fast fluctuation-enhanced structured illumination microscopy (fFE-SIM), which more than doubles the SIM resolution at a frame rate of 38 Hz in living cells. This allows a highly dynamic and sparse septin structure to be observed in Saccharomyces cerevisiae.

SUBMITTER: Yao L

PROVIDER: S-EPMC8620077 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Dynamic Structure of Yeast Septin by Fast Fluctuation-Enhanced Structured Illumination Microscopy.

Yao Longfang L Zhang Li L Chen Liwen L Gong Xingyu X Zhong Jiahui J Wang Baoju B Fei Yiyan Y Mi Lan L Ma Jiong J

Microorganisms 20211029 11

When <i>Saccharomyces cerevisiae</i> divides, a structure composed of different septin proteins arranged according to a certain rule is formed at the cell division site. The structure undergoes multiple remodeling stages during the cell cycle, thus guiding the yeast cells to complete the entire division process. Although the higher-order structure of septins can be determined using electron microscopy, the septin's dynamic processes are poorly understood because of limitations in living cell sup ...[more]

PMID: 34835381

Similar Datasets

Narrowband photoblinking InP/ZnSe/ZnS quantum dots for super-resolution multifocal structured illumination microscopy enhanced by optical fluctuation.

Project description:Cadmium-free quantum-dot (QD) fluorophores can bridge the gap between the macroscopic and microscopic domains in fluorescence super-resolution bioimaging. InP/ZnSe/ZnS QD photoblinking fluorescent probes can improve the performance of reactive super-resolution imaging techniques and spontaneously switch fluorophores between at least two states (open and close) without depending on intense laser light and specialized buffers for bioimaging. Multifocal structured illumination microscopy (MSIM) provides a two-fold resolution enhancement in sub-diffraction imaging, but higher resolutions are limited by the pattern frequency and signal-to-noise ratio. We exploit the synergy between MSIM and spontaneously switching InP/ZnSe/ZnS QD fluorophores to further increase the imaging resolution. We demonstrate the experimental combination of optical-fluctuation-enhanced super-resolution MSIM using ultrasonic-oscillation-assisted organic solvothermal synthesis of narrowband photoblinking InP/ZnSe/ZnS QDs. The InP/ZnSe/ZnS QDs show a monodisperse grain size of approximately 9 nm, fluorescence quantum yields close to 100%, and full width at half maximum below 30 nm. The structural, electronic, and optical properties are characterized through experiments and first-principles calculations. The enhanced MSIM imaging achieves an approximate fourfold improvement in resolution for fixed cells compared with widefield imaging. The proposed InP/ZnSe/ZnS QD fluorescent probes seem promising for super-resolution imaging using MSIM.

| S-EPMC11501639 | biostudies-literature

Multifocus structured illumination microscopy for fast volumetric super-resolution imaging.

Project description:We here report for the first time the synergistic implementation of structured illumination microscopy (SIM) and multifocus microscopy (MFM). This imaging modality is designed to alleviate the problem of insufficient volumetric acquisition speed in super-resolution biological imaging. SIM is a wide-field super-resolution technique that allows imaging with visible light beyond the classical diffraction limit. Employing multifocus diffractive optics we obtain simultaneous wide-field 3D imaging capability in the SIM acquisition sequence, improving volumetric acquisition speed by an order of magnitude. Imaging performance is demonstrated on biological specimens.

| S-EPMC5611928 | biostudies-literature

Fast reconstruction and optical-sectioning three-dimensional structured illumination microscopy.

Project description:Three-dimensional structured illumination microscopy (3DSIM) is a popular method for observing subcellular/cellular structures or animal/plant tissues with gentle phototoxicity and 3D super-resolution. However, its time-consuming reconstruction process poses challenges for high-throughput imaging and real-time observation. Moreover, traditional 3DSIM typically requires more than six z layers for successful reconstruction and is susceptible to defocused backgrounds. This poses a great gap between single-layer 2DSIM and 6-layer 3DSIM, and limits the observation of thicker samples. To address these limitations, we developed FO-3DSIM, a novel method that integrates spatial-domain reconstruction with optical-sectioning SIM. FO-3DSIM enhances reconstruction speed by up to 855.7 times with superior performance with limited z layers and under high defocused backgrounds. It retains the high-fidelity, low-photon reconstruction capabilities of our previously proposed Open-3DSIM. Utilizing fast reconstruction and optical sectioning, we achieved large field-of-view (FOV) 3D super-resolution imaging of mouse kidney actin, covering a region of 0.453 mm × 0.453 mm × 2.75 μm within 23 min of acquisition and 13 min of reconstruction. Near real-time performance was demonstrated in live actin imaging with FO-3DSIM. Our approach reduces photodamage through limited z layer reconstruction, allowing the observation of ER tubes with just three layers. We anticipate that FO-3DSIM will pave the way for near real-time, large FOV 6D imaging, encompassing xyz super-resolution, multi-color, long-term, and polarization imaging with less photodamage, removed defocused backgrounds, and reduced reconstruction time.

| S-EPMC11846033 | biostudies-literature

Three-dimensional structured illumination microscopy with enhanced axial resolution.

Project description:The axial resolution of three-dimensional structured illumination microscopy (3D SIM) is limited to ∼300 nm. Here we present two distinct, complementary methods to improve axial resolution in 3D SIM with minimal or no modification to the optical system. We show that placing a mirror directly opposite the sample enables four-beam interference with higher spatial frequency content than 3D SIM illumination, offering near-isotropic imaging with ∼120-nm lateral and 160-nm axial resolution. We also developed a deep learning method achieving ∼120-nm isotropic resolution. This method can be combined with denoising to facilitate volumetric imaging spanning dozens of timepoints. We demonstrate the potential of these advances by imaging a variety of cellular samples, delineating the nanoscale distribution of vimentin and microtubule filaments, observing the relative positions of caveolar coat proteins and lysosomal markers and visualizing cytoskeletal dynamics within T cells in the early stages of immune synapse formation.

| S-EPMC10497409 | biostudies-literature

Fast and robust phase-shift estimation in two-dimensional structured illumination microscopy.

Project description:A method of determining unknown phase-shifts between elementary images in two-dimensional Structured Illumination Microscopy (2D-SIM) is presented. The proposed method is based on the comparison of the peak intensity of spectral components. These components correspond to the inherent structured illumination spectral content and the residual component that appears from wrongly estimated phase-shifts. The estimation of the phase-shifts is carried out by finding the absolute maximum of a function defined as the normalized peak intensity difference in the Fourier domain. This task is performed by an optimization method providing a fast estimation of the phase-shift. The algorithm stability and robustness are tested for various levels of noise and contrasts of the structured illumination pattern. Furthermore, the proposed approach reduces the number of computations compared to other existing techniques. The method is supported by the theoretical calculations and validated by means of simulated and experimental results.

| S-EPMC6697343 | biostudies-literature

Machine learning assisted interferometric structured illumination microscopy for dynamic biological imaging.

Project description:Structured Illumination Microscopy, SIM, is one of the most powerful optical imaging methods available to visualize biological environments at subcellular resolution. Its limitations stem from a difficulty of imaging in multiple color channels at once, which reduces imaging speed. Furthermore, there is substantial experimental complexity in setting up SIM systems, preventing a widespread adoption. Here, we present Machine-learning Assisted, Interferometric Structured Illumination Microscopy, MAI-SIM, as an easy-to-implement method for live cell super-resolution imaging at high speed and in multiple colors. The instrument is based on an interferometer design in which illumination patterns are generated, rotated, and stepped in phase through movement of a single galvanometric mirror element. The design is robust, flexible, and works for all wavelengths. We complement the unique properties of the microscope with an open source machine-learning toolbox that permits real-time reconstructions to be performed, providing instant visualization of super-resolved images from live biological samples.

| S-EPMC9772218 | biostudies-literature

Structured line illumination Raman microscopy.

Project description:In the last couple of decades, the spatial resolution in optical microscopy has increased to unprecedented levels by exploiting the fluorescence properties of the probe. At about the same time, Raman imaging techniques have emerged as a way to image inherent chemical information in a sample without using fluorescent probes. However, in many applications, the achievable resolution is limited to about half the wavelength of excitation light. Here we report the use of structured illumination to increase the spatial resolution of label-free spontaneous Raman microscopy, generating highly detailed spatial contrast from the ensemble of molecular information in the sample. Using structured line illumination in slit-scanning Raman microscopy, we demonstrate a marked improvement in spatial resolution and show the applicability to a range of samples, including both biological and inorganic chemical component mapping. This technique is expected to contribute towards greater understanding of chemical component distributions in organic and inorganic materials.

| S-EPMC4686755 | biostudies-literature

Multifocal structured illumination optoacoustic microscopy.

Project description:Optoacoustic (OA) imaging has the capacity to effectively bridge the gap between macroscopic and microscopic realms in biological imaging. High-resolution OA microscopy has so far been performed via point-by-point scanning with a focused laser beam, thus greatly restricting the achievable imaging speed and/or field of view. Herein we introduce multifocal structured illumination OA microscopy (MSIOAM) that attains real-time 3D imaging speeds. For this purpose, the excitation laser beam is shaped to a grid of focused spots at the tissue surface by means of a beamsplitting diffraction grating and a condenser and is then scanned with an acousto-optic deflector operating at kHz rates. In both phantom and in vivo mouse experiments, a 10 mm wide volumetric field of view was imaged with 15 Hz frame rate at 28 μm spatial resolution. The proposed method is expected to greatly aid in biological investigations of dynamic functional, kinetic, and metabolic processes across multiple scales.

| S-EPMC7459102 | biostudies-literature

Deep-MSIM: Fast Image Reconstruction with Deep Learning in Multifocal Structured Illumination Microscopy.

Project description:Fast and precise reconstruction algorithm is desired for for multifocal structured illumination microscopy (MSIM) to obtain the super-resolution image. This work proposes a deep convolutional neural network (CNN) to learn a direct mapping from raw MSIM images to super-resolution image, which takes advantage of the computational advances of deep learning to accelerate the reconstruction. The method is validated on diverse biological structures and in vivo imaging of zebrafish at a depth of 100 µm. The results show that high-quality, super-resolution images can be reconstructed in one-third of the runtime consumed by conventional MSIM method, without compromising spatial resolution. Last but not least, a fourfold reduction in the number of raw images required for reconstruction is achieved by using the same network architecture, yet with different training data.

| S-EPMC10520669 | biostudies-literature

Correlative single-molecule and structured illumination microscopy of fast dynamics at the plasma membrane.

Project description:Total internal reflection fluorescence (TIRF) microscopy offers powerful means to uncover the functional organization of proteins in the plasma membrane with very high spatial and temporal resolution. Traditional TIRF illumination, however, shows a Gaussian intensity profile, which is typically deteriorated by overlaying interference fringes hampering precise quantification of intensities-an important requisite for quantitative analyses in single-molecule localization microscopy (SMLM). Here, we combine flat-field illumination by using a standard πShaper with multi-angular TIR illumination by incorporating a spatial light modulator compatible with fast super-resolution structured illumination microscopy (SIM). This distinct combination enables quantitative multi-color SMLM with a highly homogenous illumination. By using a dual camera setup with optimized image splitting optics, we achieve a versatile combination of SMLM and SIM with up to three channels. We deploy this setup for establishing robust detection of receptor stoichiometries based on single-molecule intensity analysis and single-molecule Förster resonance energy transfer (smFRET). Homogeneous illumination furthermore enables long-term tracking and localization microscopy (TALM) of cell surface receptors identifying spatial heterogeneity of mobility and accessibility in the plasma membrane. By combination of TALM and SIM, spatially and molecularly heterogenous diffusion properties can be correlated with nanoscale cytoskeletal organization and dynamics.

| S-EPMC11236984 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data