Correlative Fluorescence Microscopy Research Articles

Direct Observations of Segmental Dynamics at the Polymer–Substrate Interface Enabled by Localizing Fluorescent Probes with Polymer Brushes

We employed imaging rotational fluorescence correlation microscopy to directly observe the segmental dynamics of the polymer near the polymer–substrate interface using a probe-tethered polymer brush buried in bulk polymer films. The probe-tethered polymers grafted onto the polymer–substrate interface provide spatial selectivity to probe only the segmental dynamics of polymer near the polymer–substrate interface. The perturbation caused by the grafted polymer chains on the segmental dynamics of the polymer film near the interface was minimized by reducing the molecular weight of the polymer brush compared with the critical entanglement molecular weight of the polymer and grafted with a low grafting density (≈0.1 chains/nm²) using a “grafting-to” method, which allows precisely controlled and fully characterized polymer brush structures. In addition, the molecular weight of the brush polymer was further controlled to ≈10 kg/mol with the root-mean-square end-to-end distance of ≈5 nm to probe dynamics within 10 nm of the polymer–substrate interface. Polystyrene and poly(methyl methacrylate) films carrying rather unfavorable and similar surface energies, respectively, with the silane-modified silicon wafer substrates were investigated. The polymer dynamics near the interface characterized by the degrees of non-Arrhenius temperature dependence and nonexponential relaxation were not altered in both systems compared with those of the bulk, suggesting that the polymer dynamics is not sensitive to moderate differences in enthalpic interaction between the polymer and the substrate.

Single‐molecule Analysis to Visualize the Direct Interaction of Proteins and DNA

Biological processes performed by proteins interacting with DNA and chromatin are key to cell health and viability. Detailed insights into these processes provide essential information for understanding the pathological conditions that develop when such processes go awry and provide us with tools to alter the fate of the cells. Direct, real-time observations of individual proteins interacting with DNA are required to validate and complete the current biological models. Single-molecule technologies offer an exciting opportunity to meet these challenges and to study protein function and activity in real-time. Here, we present our efforts for further enabling discoveries in the field of DNA-protein interactions using both the combination of optical tweezers with correlative confocal fluorescence microscopy. We present several examples in which our technologies enhanced the understanding of the DNA repair mechanisms, chromatin structure and DNA editing tools. Furthermore, we show that advances in hybrid single-molecule methods can be turned into an easy-to-use and stable instrument that has the ability to open up new venues in the field of DNA-protein interactions.

EGFR Expression in HER2-Driven Breast Cancer Cells.

The epidermal growth factor receptor HER2 is overexpressed in 20% of breast cancer cases. HER2 is an orphan receptor that is activated ligand-independently by homodimerization. In addition, HER2 is able to heterodimerize with EGFR, HER3, and HER4. Heterodimerization has been proposed as a mechanism of resistance to therapy for HER2 overexpressing breast cancer. Here, a method is presented for the simultaneous detection of individual EGFR and HER2 receptors in the plasma membrane of breast cancer cells via specific labeling with quantum dot nanoparticles (QDs). Correlative fluorescence microscopy and liquid phase electron microscopy were used to analyze the plasma membrane expression levels of both receptors in individual intact cells. Fluorescent single-cell analysis of SKBR3 breast cancer cells dual-labeled for EGFR and HER2 revealed a heterogeneous expression for receptors within both the cell population as well as within individual cells. Subsequent electron microscopy of individual cells allowed the determination of individual receptors label distributions. QD-labeled EGFR was observed with a surface density of (0.5–5) × 101 QDs/µm2, whereas labeled HER2 expression was higher ranging from (2–10) × 102 QDs/µm2. Although most SKBR3 cells expressed low levels of EGFR, an enrichment was observed at large plasma membrane protrusions, and amongst a newly discovered cellular subpopulation termed EGFR-enriched cells.

Visualizing Microorganism-Mineral Interaction in the Iberian Pyrite Belt Subsurface: The Acidovorax Case.

Despite being considered an extreme environment, several studies have shown that life in the deep subsurface is abundant and diverse. Microorganisms inhabiting these systems live within the rock pores and, therefore, the geochemical and geohydrological characteristics of this matrix may influence the distribution of underground biodiversity. In this study, correlative fluorescence and Raman microscopy (Raman-FISH) was used to analyze the mineralogy associated with the presence of members of the genus Acidovorax, an iron oxidizing microorganisms, in native rock samples of the Iberian Pyrite Belt subsurface. Our results suggest a strong correlation between the presence of Acidovorax genus and pyrite, suggesting that the mineral might greatly influence its subsurface distribution.

Step-by-step guide to post-acquisition correlation of confocal and FIB/SEM volumes using Amira software.

In recent years new methodologies and workflow pipelines for acquiring correlated fluorescence microscopy and volume electron microscopy datasets have been extensively described and made accessible to users of different levels. Post-acquisition image processing, and particularly correlation of the optical and electron data in a single integrated three-dimensional framework can be key for extracting valuable information, especially when imaging large sample volumes such as whole cells or tissues. These tasks remain challenging and are often rate-limiting to most users. Here we provide a step-by-step guide to image processing and manual correlation using ImageJ and Amira software of a confocal microscopy stack and a focused ion beam/scanning electron microscopy (FIB/SEM) tomogram acquired using a correlative pipeline. These previously published datasets capture a highly transient invasion event by the bacterium Shigella flexneri infecting an epithelial cell grown in culture, and are made available here in their pre-processed form for readers who wish to gain hands-on experience in image processing and correlation using existing data. In this guide we describe a simple protocol for correlation based on internal sample features clearly visible by both fluorescence and electron microscopy, which is normally sufficient when correlating standard fluorescence microscopy stacks with FIB/SEM data. While the guide describes the treatment of specific datasets, it is applicable to a wide variety of samples and different microscopy approaches that require basic correlation and visualization of two or more datasets in a single integrated framework.

Correlated fluorescence microscopy and multi-ion beam secondary ion mass spectrometry imaging reveals phosphatidylethanolamine increases in the membrane of cancer cells over-expressing the molecular chaperone subunit CCT\u03b4

Changes in the membrane composition of sub-populations of cells can influence different properties with importance to tumour growth, metastasis and treatment efficacy. In this study, we use correlated fluorescence microscopy and ToF-SIMS with C60+ and (CO2)6k+ ion beams to identify and characterise sub-populations of cells based on successful transfection leading to over-expression of CCTδ, a component of the multi-subunit molecular chaperone named chaperonin-containing tailless complex polypeptide 1 (CCT). CCT has been linked to increased cell growth and proliferation and is known to affect cell morphology but corresponding changes in lipid composition of the membrane have not been measured until now. Multivariate analysis of the surface mass spectra from single cells, focused on the intact lipid ions, indicates an enrichment of phosphatidylethanolamine species in the transfected cells. While the lipid changes in this case are driven by the structural changes in the protein cytoskeleton, the consequence of phosphatidylethanolamine enrichment may have additional implications in cancer such as increased membrane fluidity, increased motility and an ability to adapt to a depletion of unsaturated lipids during cancer cell proliferation. This study demonstrates a successful fluorescence microscopy-guided cell by cell membrane lipid analysis with broad application to biological investigation.Graphical abstract

Internal Motion of Chromatin Fibers Is Governed by Dynamics of Uncompressed Linker Strands

Chromatin compaction and internal motion are fundamental aspects of gene expression regulation. Here, we have investigated chromatin fibers comprising recombinant histone octamers reconstituted with double-stranded bacteriophage T4-DNA. The size of the fibers approaches the typical size of genomic topologically associated domains. Atomic force and fluorescence (correlation) microscopy have been used to assess the structural organization, histone-induced compaction, and internal motion. In particular, the fibers are stretched on arrays of nanochannels, each channel with a diameter of 60 or 125 nm. Major intrafiber segregation and fast internal fluctuations are observed. Full compaction was only achieved by triggering an attractive nucleosome interaction through the addition of magnesium cations. Besides compaction, histone complexation results in a dramatic decrease in the fiber’s relaxation time. The relaxation times are similar to those of naked DNA with a comparable stretch, which indicates that internal motion is governed by the dynamics of uncompressed linker strands. Furthermore, the main reorganization process is association-dissociation of individually compacted regions. We surmise that the modulation of chromatin’s internal motion by histone complexation might have implications for transcriptional bursting.

Mitochondrial RNA granules are fluid condensates positioned by membrane dynamics.

Mitochondria contain the genetic information and expression machinery to produce essential respiratory chain proteins. Within the mitochondrial matrix, newly synthesised RNA, RNA processing proteins, and mitoribosome assembly factors form punctate sub-compartments referred to as mitochondrial RNA granules (MRGs) 1–3. Despite their proposed importance in regulating gene expression, the structural and dynamic properties of MRGs remain largely unknown. We investigated the internal architecture of MRGs using fluorescence super-resolution localisation microscopy and correlative electron microscopy, and find that MRG ultrastructure consists of compacted RNA embedded within a protein cloud. Using live-cell super-resolution structured illumination microscopy and fluorescence recovery after photobleaching, we reveal that MRGs rapidly exchange components and can undergo fusion, characteristic properties of fluid condensates 4. Furthermore, MRGs associate with the inner mitochondrial membrane and their fusion coincides with mitochondrial remodelling. Inhibition of mitochondrial fission or fusion leads to an aberrant accumulation of MRGs into concentrated pockets, where they remain as distinct individual units despite their close apposition. Together, our findings reveal that MRGs are nanoscale fluid compartments, which are dispersed along mitochondria via membrane dynamics.

Correlative fluorescence and atomic force microscopy to advance the bio-physical characterisation of co-culture of living cells

An understanding of the cell mechanical properties involved in numerous cellular processes including cell division, cell migration/invasion, and cell morphology, is crucial in developing and informing cell physiology and function. Atomic force microscopy (AFM) offers a powerful biophysical technique that facilitates the imaging of living cells under physiological buffer conditions. However, AFM in isolation cannot discriminate between different cell types within heterogeneous samples for example in a solid biopsy. The current studies demonstrate the potential of AFM in combination with correlative fluorescence optical sectioning microscopy for live cell imaging. Furthermore, this work establishes the advantage of fluorescence-AFM imaging to distinguish and analyse single-cell bio-physical properties in mixed human cell populations, in real-time. Critically, our results show that correlative fluorescence-AFM imaging allows the simultaneous co-localised detection of fluorescence coupled with nano-mechanical mapping. The findings from this work contribute to the promotion and dissemination of correlative multimodal imaging in life sciences, providing a platform for further investigations in biological and pre-clinical research.

3D Correlative Cryo-Structured Illumination Fluorescence and Soft X-ray Microscopy Elucidates Reovirus Intracellular Release Pathway

SummaryImaging of biological matter across resolution scales entails the challenge of preserving the direct and unambiguous correlation of subject features from the macroscopic to the microscopic level. Here, we present a correlative imaging platform developed specifically for imaging cells in 3D under cryogenic conditions by using X-rays and visible light. Rapid cryo-preservation of biological specimens is the current gold standard in sample preparation for ultrastructural analysis in X-ray imaging. However, cryogenic fluorescence localization methods are, in their majority, diffraction-limited and fail to deliver matching resolution. We addressed this technological gap by developing an integrated, user-friendly platform for 3D correlative imaging of cells in vitreous ice by using super-resolution structured illumination microscopy in conjunction with soft X-ray tomography. The power of this approach is demonstrated by studying the process of reovirus release from intracellular vesicles during the early stages of infection and identifying intracellular virus-induced structures.

Correlative Fluorescence- and Electron Microscopy of Whole Breast Cancer Cells Reveals Different Distribution of ErbB2 Dependent on Underlying Actin.

Epidermal growth factor receptor 2 (ErbB2) is found overexpressed in several cancers, such as gastric, and breast cancer, and is, therefore, an important therapeutic target. ErbB2 plays a central role in cancer cell invasiveness, and is associated with cytoskeletal reorganization. In order to study the spatial correlation of single ErbB2 proteins and actin filaments, we applied correlative fluorescence microscopy (FM), and scanning transmission electron microscopy (STEM) to image specifically labeled SKBR3 breast cancer cells. The breast cancer cells were grown on microchips, transformed to express an actin-green fluorescent protein (GFP) fusion protein, and labeled with quantum dot (QD) nanoparticles attached to specific anti-ErbB2 Affibodies. FM was performed to identify cellular regions with spatially correlated actin and ErbB2 expression. For STEM of the intact plasma membrane of whole cells, the cells were fixed and covered with graphene. Spatial distribution patterns of ErbB2 in the actin rich ruffled membrane regions were examined, and compared to adjacent actin-low regions of the same cell, revealing an association of putative signaling active ErbB2 homodimers with actin-rich regions. ErbB2 homodimers were found absent from actin-low membrane regions, as well as after treatment of cells with Cytochalasin D, which breaks up larger actin filaments. In both latter data sets, a significant inter-label distance of 36 nm was identified, possibly indicating an indirect attachment to helical actin filaments via the formation of heterodimers of ErbB2 with epidermal growth factor receptor (EGFR). The possible attachment to actin filaments was further explored by identifying linear QD-chains in actin-rich regions, which also showed an inter-label distance of 36 nm.

Optical tweezers and multimodality imaging: a platform for dynamic single‐molecule analysis

Utilization of single molecule technologies offer researchers the unique opportunity to perform direct real‐time observations and measurements for a plethora of biological mechanisms. Here, we present our efforts to facilitate biologically meaningful discoveries using fully integrated optical tweezers with single‐molecule fluorescence microscopy technology. Correlative fluorescence and optical tweezer microscopy (C‐trap™) is the only technology that truly integrates optical tweezers, confocal/STED microscopy and an advanced microfluidics. The C‐Trap ™ enables live, simultaneous and correlative visualization and manipulation of molecular interactions with sub‐piconewton (pN) force resolution and a kilo‐Hz (to mega‐Hz) temporal resolution, such that even the quickest cellular events can be captured. This technology can be utilized as an easy‐to‐use and stable instrument with the capacity to elucidate biologically meaningful mechanisms. Here we present applications detailing protein (un)folding and conformational changes; DNA‐protein interactions and genome modifications; effects of mechanical stress on DNA/RNA structure; motility of cytoskeletal molecular motors; and protein droplet and aggregation dynamics. These experiments demonstrate technological advances in hybrid single‐molecule methods and the potential for their use in future scientific breakthroughs.

Surface Chemistry-Dependent Evolution of the Nanomaterial Corona on TiO2 Nanomaterials Following Uptake and Sub-Cellular Localization.

Nanomaterial (NM) surface chemistry has an established and significant effect on interactions at the nano-bio interface, with important toxicological consequences for manufactured NMs, as well as potent effects on the pharmacokinetics and efficacy of nano-therapies. In this work, the effects of different surface modifications (PVP, Dispex AA4040, and Pluronic F127) on the uptake, cellular distribution, and degradation of titanium dioxide NMs (TiO2 NMs, ~10 nm core size) are assessed and correlated with the localization of fluorescently-labeled serum proteins forming their coronas. Imaging approaches with an increasing spatial resolution, including automated high throughput live cell imaging, correlative confocal fluorescence and reflectance microscopy, and dSTORM super-resolution microscopy, are used to explore the cellular fate of these NMs and their associated serum proteins. Uncoated TiO2 NMs demonstrate a rapid loss of corona proteins, while surface coating results in the retention of the corona signal after internalization for at least 24 h (varying with coating composition). Imaging with two-color super-resolution dSTORM revealed that the apparent TiO2 NM single agglomerates observed in diffraction-limited confocal microscopy are actually adjacent smaller agglomerates, and provides novel insights into the spatial arrangement of the initial and exchanged coronas adsorbed at the NM surfaces.

Replication Fork Activation is Enabled by a Single-Stranded DNA Gate in CMG Helicase

The eukaryotic replicative helicase CMG is a closed ring around double-stranded (ds)DNA at origins yet must transition to single-stranded (ss)DNA for helicase action. CMG must also handle repair intermediates, such as reversed forks that lack ssDNA. Here, using correlative single-molecule fluorescence and force microscopy, we show that CMG harbors a ssDNA gate that enables transitions between ss and dsDNA. When coupled to DNA polymerase, CMG remains on ssDNA, but when uncoupled, CMG employs this gate to traverse forked junctions onto dsDNA. Surprisingly, CMG undergoes rapid diffusion on dsDNA and can transition back onto ssDNA to nucleate a functional replisome. The gate-distinct from that between Mcm2/5 used for origin loading-is intrinsic to CMG; however, Mcm10 promotes strand passage by enhancing the affinity of CMG to DNA. This gating process may explain the dsDNA-to-ssDNA transition of CMG at origins and help preserve CMG on dsDNA during fork repair.

Genetically-Encoded Tags for Correlative Fluorescence and Electron Microscopy

Genetically-Encoded Tags for Correlative Fluorescence and Electron Microscopy

Nanoscale View of Amyloid Photodynamic Damage.

A combination of time-resolved optical spectroscopy and nanoscale imaging has been used to study the complex binding to amyloids of a photocatalyst that selectively photo-oxygenates pathogenic aggregates, as well as the consequences of its irradiation. Correlative atomic force microscopy (AFM) and fluorescence microscopy reveals topography-dependent binding of the dye to model β-lactoglobulin fibers, which may also explain the observed difference in their response to photodegradation. We provide direct evidence of the photosensitization of singlet oxygen by the photocatalyst bound to amyloid fibers by direct detection of its NIR phosphorescence. The effect of singlet oxygen at the molecular level brings about nanoscale morphological changes that can be observed with AFM at the single-fiber level. We also find differential response of two α-synuclein mutants to photodamage, which can be rationalized by the presence of amino acids susceptible to photo-oxygenation. Overall, our results help to unravel some of the complexity associated with highly heterogeneous amyloid populations and contribute to the development of improved phototherapeutic strategies for amyloid-related disorders.

Age, lipofuscin and melanin oxidation affect fundus near-infrared autofluorescence.

BackgroundFundus autofluorescence is a non-invasive imaging technique in ophthalmology. Conventionally, short-wavelength autofluorescence (SW-AF) is used for detection of lipofuscin, a byproduct of the visual cycle which accumulates with age or disease in the retinal pigment epithelium (RPE). Furthermore, near-infrared autofluorescence (NIR-AF) is used as a marker for RPE and choroidal melanin, but contribution of lipofuscin to the NIR-AF signal is unclear.MethodsWe employed fluorescence microscopy to investigate NIR-AF properties of melanosomes, lipofuscin and melanolipofuscin granules in histologic sections of wildtype and Abca4−/− mouse eyes, the latter having increased lipofuscin, as well as aged human donor eyes. Differentiation between these pigments was verified by analytical electron microscopy. To investigate the influence of oxidative and photic stress we used an in vitro model with isolated ocular melanosomes and an in vivo phototoxicity mouse model.FindingsWe show that NIR-AF is not an intrinsic property of melanin, but rather increases with age and after photic or oxidative stress in mice and isolated melanosomes. Furthermore, when lipofuscin levels are high, lipofuscin granules also show NIR-AF, as confirmed by correlative fluorescence and electron microscopy in human tissue. However, lipofuscin in albino Abca4−/− mice lacks NIR-AF signals.InterpretationWe suggest that NIR-AF is derived from melanin degradation products that accumulate with time in lipofuscin granules. These findings can help to improve the interpretation of patient fundus autofluorescence data.FundingThis work was supported by Bundesministerium für Bildung und Forschung, Deutsche Forschungsgemeinschaft and Chinese Scholarship Council. Major instrumentation used in this work was supported by Deutsche Forschungsgemeinschaft, the European Fund for Regional Development and the state of Baden-Württemberg.

How Tethered Probes Report the Dynamics of a Polymer near the Glass Transition.

How tethered probes report dynamics of host polymers near the glass transition was investigated by changing the length of the flexible linkers and the number of tethering points via imaging rotational fluorescence correlation microscopy and compared with free probes of different sizes. The results show that tethering did not alter the temperature-dependence of polymer dynamics and the shape of the correlation decay reported by the probe; however, the rotation slowed down up to ≈1 decade when both ends of the probe were restricted with short alkyl chain linkers. Upon comparison with the bigger free probe, the mechanism of the slowdown was attributed to the restricted motion upon tethering for tethered probes compared to averaging over different regions of the dynamic heterogeneity for the bigger probe. If the size of the probe was comparable to that of the dynamic heterogeneity of the system, tethered probes accurately report dynamics relevant to glass transition, regardless of tethering conditions.

Abstract 1759: Studying T-cell force activation and DNA repair dynamics at the single-molecule level with optical tweezers and correlated fluorescence microscopy

Abstract DNA repair, the collection of highly regulated mechanisms by which a cell identifies and repairs DNA damage, remains one of the most essential processes of human life. Without DNA repair mechanisms cells lose the ability to transcribe important regions of their genome, resulting in harmful mutations, which could eventually jeopardize cellular wellbeing. Sources of DNA damage include double-stranded breaks and DNA intra- and interstrand crosslinks, which can ultimately become malignant tumors, leading to cancer. To study DNA repair, single-molecule studies have proven to greatly enhance understanding at the molecular level. However, it is often challenging to obtain adequate sensitivity and resolution, as well as biological conditions mimicking in vivo environments. The C-Trap™ system allows for realtime visualization of the interaction between DNA and DNA repair proteins, under biologically relevant conditions with high spatial and temporal resolution. The C-Trap™ is the only instrument that integrates optical tweezers, confocal/STED microscopy, and an advanced microfluidics system in a truly correlated manner. It enables live, simultaneous and correlative visualization and manipulation of molecular interactions with sub-picoNewton (pN) force resolution and a kilo-Hz (to mega-Hz) temporal resolution. Previously we have presented applications in: protein (un)folding and conformational changes; DNA-protein interactions and genome modifications; effects of mechanical stress on DNA/RNA structure; motility of cytoskeletal molecular motors; and protein droplet and aggregation dynamics. By culturing or adhering cells to the surface of the flow chamber, single-molecule cell-based studies can also be performed with the C-Trap. Cell-surface bound mechano-receptors can be activated by forming tethers with an optically trapped particle and then creating a controlled tension on the molecule. Correlated fluorescent imaging can elucidate internal protein cascades and other similar reactions to the applied force. Here, we present our experiments visualizing and quantifying the mechanisms of DNA repair and the force activation of T-cells using the C-Trap system. These experiments show that the technological advances in hybrid single-molecule methods can be turned into an easy-to-use and stable instrument that opens up new venues in many research areas. Citation Format: Ali Raja, Leif Anderson, Willem Peutz, Andrea Candelli, Gerrit Sitters. Studying T-cell force activation and DNA repair dynamics at the single-molecule level with optical tweezers and correlated fluorescence microscopy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1759.

Replication Fork Activation Is Enabled by a Single-Stranded DNA Gate in CMG Helicase

The eukaryotic replicative helicase CMG is a closed ring around double-stranded (ds)DNA at origins yet must transition to single-stranded (ss)DNA for helicase action. CMG must also handle repair intermediates, such as reversed forks that lack ssDNA. Here, using correlative single-molecule fluorescence and force microscopy, we show that CMG harbors a ssDNA gate that enables transitions between ss and dsDNA. When coupled to DNA polymerase, CMG remains on ssDNA, but when uncoupled, CMG employs this gate to traverse forked junctions onto dsDNA. Surprisingly, CMG undergoes rapid diffusion on dsDNA and can transition back onto ssDNA to nucleate a functional replisome. The gate-distinct from that between Mcm2/5 used for origin loading-is intrinsic to CMG; however, Mcm10 promotes strand passage by enhancing the affinity of CMG to DNA. This gating process may explain the dsDNA-to-ssDNA transition of CMG at origins and help preserve CMG on dsDNA during fork repair.