scholarly journals Combining single-molecule super-resolved localization microscopy with fluorescence polarization imaging to study cellular processes

2021 ◽  
Author(s):  
Jack W Shepherd ◽  
Alex L Payne-Dwyer ◽  
Mark C Leake
Keyword(s):  
Single Molecule ◽  
Fluorescence Polarization ◽  
Fluorescent Protein ◽  
Imaging Modality ◽  
Simultaneous Detection ◽  
Optical Resolution ◽  
Biological Processes ◽  
Localization Microscopy ◽  
Cellular Processes ◽  
Wide Range

AbstractSuper-resolution microscopy has enabled valuable insights into the subcellular, mechanistic details of many different biological processes across a wide range of cell types. Fluorescence polarization spectroscopy tools have also enabled important insights into cellular processes through identifying orientational changes of biological molecules typically at an ensemble level. Here, we combine these two biophysical methodologies in a single home-made instrument to enable the simultaneous detection of orthogonal fluorescence polarization signals from single fluorescent protein molecules used as common reporters on the localization on biomolecules in cellular processes, whose spatial location can be pinpointed to a super-resolved precision better than the diffraction-limited optical resolution. In this small innovation we have adapted a millisecond timescale “Slimfield” microscope used for single-molecule detection to enable spitting of the fluorescence polarization emissions into two separate imaging channels for s- and p- polarization signals that are imaged onto separate halves of the same high sensitivity back-illuminated CMOS camera detector. We applied this fluorescence polarization super-resolved imaging modality to a range of test fluorescent samples relevant to the study of biological processes, including purified monomeric green fluorescent protein (mGFP). Our findings are largely qualitative but demonstrate promise in showing how fluorescence polarization and Slimfield-mediated super-resolved localization microscopy can be combined on the same sample to enable new biological insights.

Enabling single-molecule localization microscopy in turbid food emulsions

2021 ◽  
Author(s):  
Abbas Jabermoradi ◽  
Suyeon Yang ◽  
Martijn Gobes ◽  
John P.M. van Duynhoven ◽  
Johannes Hohlbein
Keyword(s):  
Adaptive Optics ◽  
Single Molecule ◽  
Optical Resolution ◽  
Three Dimensions ◽  
Water Interface ◽  
Water Emulsion ◽  
Food Emulsions ◽  
Localization Microscopy ◽  
Oil Water ◽  
Single Molecule Localization Microscopy

Turbidity poses a major challenge for the microscopic characterization of many food systems. In these systems, local mismatches in refractive indices can cause reflection, absorption and scattering of incoming as well as outgoing light leading to significant image deterioration along sample depth. To mitigate the issue of turbidity and to increase the achievable optical resolution, we combined adaptive optics (AO) with single-molecule localization microscopy (SMLM). Building on our previously published open hardware microscopy framework, the miCube, we first added a deformable mirror to the detection path. This element enables both the compensation of aberrations directly from single-molecule data and, by further modulating the emission wavefront, the introduction of various point spread functions (PSFs) to enable SMLM in three dimensions. We further added a top hat beam shaper to the excitation path to obtain an even illumination profile across the field of view (FOV). As a model system for a non-transparent food colloid in which imaging in depth is challenging, we designed an oil-in-water emulsion in which phosvitin, a ferric ion binding protein present in from egg yolk, resides at the oil water interface. We targeted phosvitin with fluorescently labelled primary antibodies and used PSF engineering to obtain 2D and 3D images of phosvitin covered oil droplets with sub 100 nm resolution. Droplets with radii as low as 200 nm can be discerned, which is beyond the range of conventional confocal light microscopy. Our data indicated that in the model emulsion phosvitin is homogeneously distributed at the oil-water interface. With the possibility to obtain super-resolved images in depth of nontransparent colloids, our work paves the way for localizing biomacromolecules at colloidal interfaces in heterogeneous food emulsions.

Nanomechanochemical Delivery of Nanoparticles for Nanomechanics Inside Living Cells

2010 ◽  
Author(s):  
Kyungsuk Yum ◽  
Sungsoo Na ◽  
Yang Xiang ◽  
Ning Wang ◽  
Min-Feng Yu
Keyword(s):  
Single Molecule ◽  
Living Cells ◽  
Endocytic Pathway ◽  
Great Promise ◽  
Biological Processes ◽  
Temporal Precision ◽  
Single Molecule Level ◽  
Cellular Processes ◽  
Cellular Environment ◽  
Biological Studies

Studying biological processes and mechanics in living cells is challenging but highly rewarding. Recent advances in experimental techniques have provided numerous ways to investigate cellular processes and mechanics of living cells. However, most of existing techniques for biomechanics are limited to experiments outside or on the membrane of cells, due to the difficulties in physically accessing the interior of living cells. On the other hand, nanomaterials, such as fluorescent quantum dots (QDs) and magnetic nanoparticles, have shown great promise to overcome such limitations due to their small sizes and excellent functionalities, including bright and stable fluorescence and remote manipulability. However, except a few systems, the use of nanoparticles has been limited to the study of biological studies on cell membranes or related to endocytosis, because of the difficulty of delivering dispersed and single nanoparticles into living cells. Various strategies have been explored, but delivered nanoparticles are often trapped in the endocytic pathway or form aggregates in the cytoplasm, limiting their further use. Here we show a nanoscale direct delivery method, named nanomechanochemical delivery, where we manipulate a nanotube-based nanoneedle, carrying “cargo” (QDs in this study), to mechanically penetrate the cell membrane, access specific areas inside cells, and release the cargo [1]. We selectively delivered well-dispersed QDs into either the cytoplasm or the nucleus of living cells. We quantified the dynamics of the delivered QDs by single-molecule tracking and demonstrated the applicability of the QDs as a nanoscale probe for studying nanomechanics inside living cells (by using the biomicrorhology method), revealing the biomechanical heterogeneity of the cellular environment. This method may allow new strategies for studying biological processes and mechanics in living cells with spatial and temporal precision, potentially at the single-molecule level.

scholarly journals Single-molecule light-sheet microscopy with local nanopipette delivery

2020 ◽  
Author(s):  
B. Li ◽  
A. Ponjavic ◽  
W. H. Chen ◽  
L. Hopkins ◽  
C. Hughes ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Single Molecule ◽  
Single Molecules ◽  
Light Sheet ◽  
Local Delivery ◽  
Live Cells ◽  
Biological Processes ◽  
Light Sheet Microscopy ◽  
Wide Range

AbstractDetection of single molecules in biological systems has rapidly increased in resolution over the past decade. However, delivery of single molecules has remained a challenge. Currently there is no effective method that can both introduce a precise amount of molecules onto or into a single cell at a defined position, and then image the cellular response. Here we have combined light sheet microscopy with local delivery, using a nanopipette, to accurately deliver individual proteins to a defined position. We call this method local delivery selective plane illumination microscopy (ldSPIM). ldSPIM uses a nanopipette and the ionic feedback current at the nanopipette tip to control the position from which molecules are delivered. The number of proteins delivered can be controlled by varying the voltage applied. For single-molecule detection, we implemented single-objective SPIM using a reflective atomic force microscopy cantilever to create a 2µm thin sheet. Using this setup, we demonstrate that ldSPIM can deliver single fluorescently-labeled proteins onto the plasma membrane of HK293 cells or into the cytoplasm. Next, we deposited aggregates of amyloid-β, which causes proteotoxicity relevant to Alzheimer’s disease, onto a single macrophage stably expressing a MyDD88-eGFP fusion construct. Whole-cell imaging in 3D mode enables live detection of MyDD88 accumulation and formation of MyDDosome signaling complexes, as a result of aggregate-induced triggering of toll-like receptor 4. Overall, we demonstrate a novel multifunctional imaging system capable of precise delivery of single proteins to a specific location on the cell surface or inside the cytoplasm and high-speed 3D detection at single-molecule resolution within live cells.Statement of SignificanceThis paper describes and validates a new method to study biological processes based on the controlled local delivery of molecules onto or into the cell, combined with single molecule imaging using light sheet microscopy. we not only demonstrate the instrument’s capability of delivering controlled numbers of molecules to a defined position, down to the level of single molecules, but also its potential in study of the triggering of the innate immune response by protein aggregates, a key process in the development of neurodegenerative diseases such as Alzheimer’s disease. The same approach could be applied to a wide range of other important biological processes allowing them to be followed in live cells in real-time, hence it will be of great interest to the biophysical community.

scholarly journals CD-tagging-MS2: detecting allelic expression of endogenous mRNAs and their protein products in single cells

2017 ◽  
Vol 2 (1) ◽  
Author(s):  
Jonathan Sheinberger ◽  
Hodaya Hochberg ◽  
Erez Lavi ◽  
Itamar Kanter ◽  
Shira Avivi ◽  
...  
Keyword(s):  
Single Molecule ◽  
Fluorescent Protein ◽  
Cell Clone ◽  
Single Cells ◽  
Simultaneous Detection ◽  
Protein Product ◽  
Intact Cells ◽  
Endogenous Gene ◽  
Specific Allele ◽  
Endogenous Proteins

Abstract Discriminating between the mRNA and protein outputs of each of the alleles of an endogenous gene in intact cells, is a difficult task. To examine endogenous transcripts originating from a specific allele, we applied Central Dogma tagging (CD-tagging), which is based on a tag insertion into an endogenous gene by creation of a new exon. Previously, CD-tagging was used to tag endogenous proteins. Here we developed a CD-tagging-MS2 approach in which two tags were inserted in tandem; a fluorescent protein tag in conjunction with the mRNA MS2 tag used for tagging mRNAs in cells. A cell clone library of CD-tagged-MS2 genes was generated, and protein and mRNA distributions were examined and characterized in single cells. Taking advantage of having one allele tagged, we demonstrate how the transcriptional activity of all alleles, tagged and untagged, can be identified using single molecule RNA fluorescence in situ hybridization (smFISH). Allele-specific mRNA expression and localization were quantified under normal and stress conditions. The latter generate cytoplasmic stress granules (SGs) that can store mRNAs, and the distribution of the mRNAs within and outside of the SGs was measured. Altogether, CD-tagging-MS2 is a robust and inexpensive approach for direct simultaneous detection of an endogenous mRNA and its translated protein product in the same cell.

scholarly journals Regulation of the bovine oviductal fluid proteome

Reproduction ◽  
2016 ◽  
Vol 152 (6) ◽  
pp. 629-644 ◽  
Author(s):  
Julie Lamy ◽  
Valérie Labas ◽  
Grégoire Harichaux ◽  
Guillaume Tsikis ◽  
Pascal Mermillod ◽  
...  
Keyword(s):  
Early Embryo ◽  
Oestrous Cycle ◽  
Biological Processes ◽  
Label Free ◽  
Cellular Processes ◽  
One Stage ◽  
Wide Range ◽  
Shock Proteins ◽  
Oviductal Fluid ◽  
Differentially Abundant Proteins

Our objective was to investigate the regulation of the proteome in the bovine oviductal fluid according to the stage of the oestrous cycle, to the side relative to ovulation and to local concentrations of steroid hormones. Luminal fluid samples from both oviducts were collected at four stages of the oestrous cycle: pre-ovulatory (Pre-ov), post-ovulatory (Post-ov), and mid- and late luteal phases from adult cyclic cows (18–25 cows/stage). The proteomes were assessed by nanoLC–MS/MS and quantified by label-free method. Totally, 482 proteins were identified including a limited number of proteins specific to one stage or one side. Proportions of differentially abundant proteins fluctuated from 10 to 24% between sides at one stage and from 4 to 20% among stages in a given side of ovulation. In oviductal fluids ipsilateral to ovulation, Annexin A1 was the most abundant protein at Pre-ov compared with Post-ov while numerous heat shock proteins were more abundant at Post-ov compared with Pre-ov. Among differentially abundant proteins, seven tended to be correlated with intra-oviductal concentrations of progesterone. A wide range of biological processes was evidenced for differentially abundant proteins, of which metabolic and cellular processes were predominant. This work identifies numerous new candidate proteins potentially interacting with the oocyte, spermatozoa and embryo to modulate fertilization and early embryo development.

scholarly journals Efficient switching of mCherry fluorescence using chemical caging

2017 ◽  
Vol 114 (27) ◽  
pp. 7013-7018 ◽  
Author(s):  
Bas M. C. Cloin ◽  
Elke De Zitter ◽  
Desiree Salas ◽  
Vincent Gielen ◽  
Gert E. Folkers ◽  
...  
Keyword(s):  
Single Molecule ◽  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Functional Characterization ◽  
Fluorescence Emission ◽  
Total Recovery ◽  
X Ray Crystallography ◽  
Chemically Induced ◽  
Wide Range ◽  
Fluorescent State

Fluorophores with dynamic or controllable fluorescence emission have become essential tools for advanced imaging, such as superresolution imaging. These applications have driven the continuing development of photoactivatable or photoconvertible labels, including genetically encoded fluorescent proteins. These new probes work well but require the introduction of new labels that may interfere with the proper functioning of existing constructs and therefore require extensive functional characterization. In this work we show that the widely used red fluorescent protein mCherry can be brought to a purely chemically induced blue-fluorescent state by incubation with β-mercaptoethanol (βME). The molecules can be recovered to the red fluorescent state by washing out the βME or through irradiation with violet light, with up to 80% total recovery. We show that this can be used to perform single-molecule localization microscopy (SMLM) on cells expressing mCherry, which renders this approach applicable to a very wide range of existing constructs. We performed a detailed investigation of the mechanism underlying these dynamics, using X-ray crystallography, NMR spectroscopy, and ab initio quantum-mechanical calculations. We find that the βME-induced fluorescence quenching of mCherry occurs both via the direct addition of βME to the chromophore and through βME-mediated reduction of the chromophore. These results not only offer a strategy to expand SMLM imaging to a broad range of available biological models, but also present unique insights into the chemistry and functioning of a highly important class of fluorophores.

scholarly journals A practical method for monitoring FRET-based biosensors in living animals using two-photon microscopy

2015 ◽  
Vol 309 (11) ◽  
pp. C724-C735 ◽  
Author(s):  
Wen Tao ◽  
Michael Rubart ◽  
Jennifer Ryan ◽  
Xiao Xiao ◽  
Chunping Qiao ◽  
...  
Keyword(s):  
Cell Biology ◽  
Fluorescent Protein ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Practical Method ◽  
Two Photon Microscopy ◽  
Cellular Processes ◽  
Two Photon ◽  
Photon Excitation ◽  
Wide Range

The commercial availability of multiphoton microscope systems has nurtured the growth of intravital microscopy as a powerful technique for evaluating cell biology in the relevant context of living animals. In parallel, new fluorescent protein (FP) biosensors have become available that enable studies of the function of a wide range of proteins in living cells. Biosensor probes that exploit Förster resonance energy transfer (FRET) are among the most sensitive indicators of an array of cellular processes. However, differences between one-photon and two-photon excitation (2PE) microscopy are such that measuring FRET by 2PE in the intravital setting remains challenging. Here, we describe an approach that simplifies the use of FRET-based biosensors in intravital 2PE microscopy. Based on a systematic comparison of many different FPs, we identified the monomeric (m) FPs mTurquoise and mVenus as particularly well suited for intravital 2PE FRET studies, enabling the ratiometric measurements from linked FRET probes using a pair of experimental images collected simultaneously. The behavior of the FPs is validated by fluorescence lifetime and sensitized emission measurements of a set of FRET standards. The approach is demonstrated using a modified version of the AKAR protein kinase A biosensor, first in cells in culture, and then in hepatocytes in the liver of living mice. The approach is compatible with the most common 2PE microscope configurations and should be applicable to a variety of different FRET probes.

scholarly journals Millisecond single-molecule localization microscopy combined with convolution analysis and automated image segmentation to determine protein concentrations in complexly structured, functional cells, one cell at a time

2015 ◽  
Vol 184 ◽  
pp. 401-424 ◽  
Author(s):  
Adam J. M. Wollman ◽  
Mark C. Leake
Keyword(s):  
Signal Transduction ◽  
Image Segmentation ◽  
Cell Population ◽  
Single Molecule ◽  
Protein Concentration ◽  
Fluorescent Protein ◽  
Glucose Sensing ◽  
Localization Microscopy ◽  
A Cell ◽  
External Glucose

We present a single-molecule tool called the CoPro (concentration of proteins) method that uses millisecond imaging with convolution analysis, automated image segmentation and super-resolution localization microscopy to generate robust estimates for protein concentration in different compartments of single living cells, validated using realistic simulations of complex multiple compartment cell types. We demonstrate its utility experimentally on modelEscherichia colibacteria andSaccharomyces cerevisiaebudding yeast cells, and use it to address the biological question of how signals are transduced in cells. Cells in all domains of life dynamically sense their environment through signal transduction mechanisms, many involving gene regulation. The glucose sensing mechanism ofS. cerevisiaeis a model system for studying gene regulatory signal transduction. It uses the multi-copy expression inhibitor of the GAL gene family, Mig1, to repress unwanted genes in the presence of elevated extracellular glucose concentrations. We fluorescently labelled Mig1 molecules with green fluorescent protein (GFP)viachromosomal integration at physiological expression levels in livingS. cerevisiaecells, in addition to the RNA polymerase protein Nrd1 with the fluorescent protein reporter mCherry. Using CoPro we make quantitative estimates of Mig1 and Nrd1 protein concentrations in the cytoplasm and nucleus compartments on a cell-by-cell basis under physiological conditions. These estimates indicate a ∼4-fold shift towards higher values in the concentration of diffusive Mig1 in the nucleus if the external glucose concentration is raised, whereas equivalent levels in the cytoplasm shift to smaller values with a relative change an order of magnitude smaller. This compares with Nrd1 which is not involved directly in glucose sensing, and which is almost exclusively localized in the nucleus under high and low external glucose levels. CoPro facilitates time-resolved quantification of protein concentrations in single functional cells, and enables the distributions of concentrations across a cell population to be measured. This could be useful in investigating several cellular processes that are mediated by proteins, especially where changes in protein concentration in a single cell in response to changes in the extracellular chemical environment are subtle and rapid and may be smaller than the variability across a cell population.

scholarly journals Accurate and rapid background estimation in single-molecule localization microscopy using the deep neural network BGnet

2019 ◽  
Vol 117 (1) ◽  
pp. 60-67 ◽  
Author(s):  
Leonhard Möckl ◽  
Anish R. Roy ◽  
Petar N. Petrov ◽  
W. E. Moerner
Keyword(s):  
Neural Network ◽  
Single Molecule ◽  
Deep Neural Network ◽  
Substantial Improvement ◽  
Localization Microscopy ◽  
3 Dimensional ◽  
Background Estimation ◽  
Spatial Features ◽  
Spatial Frequencies ◽  
Wide Range

Background fluorescence, especially when it exhibits undesired spatial features, is a primary factor for reduced image quality in optical microscopy. Structured background is particularly detrimental when analyzing single-molecule images for 3-dimensional localization microscopy or single-molecule tracking. Here, we introduce BGnet, a deep neural network with a U-net-type architecture, as a general method to rapidly estimate the background underlying the image of a point source with excellent accuracy, even when point-spread function (PSF) engineering is in use to create complex PSF shapes. We trained BGnet to extract the background from images of various PSFs and show that the identification is accurate for a wide range of different interfering background structures constructed from many spatial frequencies. Furthermore, we demonstrate that the obtained background-corrected PSF images, for both simulated and experimental data, lead to a substantial improvement in localization precision. Finally, we verify that structured background estimation with BGnet results in higher quality of superresolution reconstructions of biological structures.

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