Visualization of the nucleus and nuclear envelope in situ by SEM in tissue culture cells

Mitochondria/lysosome dual-organelle labelling esterase probe for monitoring cell viability and evaluating lung cancer drug efficiency

Monitoring of cell viability plays a key role in cancer therapy and evaluation of drug efficiency. Mitochondria and lysosomes are involved in regulating cell viability in many biological processes such as apoptosis, necrosis, autophagy, and cell proliferation. Thus, there is an emerging interest in the real-time evaluation of cell viability in both mitochondria and lysosomes. Herein, for the first time, we rationally designed and developed a mitochondria/lysosome dual-organelle labelling esterase-responsive ratiometric fluorescent probe, named TMLE-2, for dual-channel monitoring of cell viability and evaluation of lung cancer drug efficiency. TMLE-2 showed dramatic ratio fluorescence changes (about 51-fold) upon reacting with esterase. Furthermore, TMLE-2 enabled visualization of mitochondria and lysosomes with red and green emission, respectively; moreover, H2O2-induced cell damage, sorafenib-induced ferroptosis and ascorbic-acid-mediated cell protective effects were successfully assessed by dual-organelle ratiometric fluorescent imaging and flow cytometry data. More importantly, TMLE-2 was successfully used for the first time to evaluate the efficiency of lung cancer drugs at the cellular and tissue levels based on dual-organelle esterase activity assay. In summary, the newly designed TMLE-2 is expected to have enormous potential for facilitating advancements in biomedical fields related to cell viability.

Comprehensive maturity of nuclear pore complexes regulates zygotic genome activation

Nuclear pore complexes (NPCs) are channels for nucleocytoplasmic transport of proteins and RNAs. However, it remains unclear whether composition, structure, and permeability of NPCs dynamically change during the cleavage period of vertebrate embryos and affect embryonic development. Here, we report that the comprehensive NPC maturity (CNM) controls the onset of zygotic genome activation (ZGA) during zebrafish early embryogenesis. We show that more nucleoporin proteins are recruited to and assembled into NPCs with development, resulting in progressive increase of NPCs in size and complexity. Maternal transcription factors (TFs) transport into nuclei more efficiently with increasing CNM. Deficiency or dysfunction of Nup133 or Ahctf1/Elys impairs NPC assembly, maternal TFs nuclear transport, and ZGA onset, while nup133 overexpression promotes these processes. Therefore, CNM may act as a molecular timer for ZGA by controlling nuclear transport of maternal TFs that reach nuclear concentration thresholds at a given time to initiate ZGA.

Scanning Electron Microscopy (SEM) and Immuno-SEM of Nuclear Pore Complexes from Amphibian Oocytes, Mammalian Cell Cultures, Yeast, and Plants

Scanning electron microscopy (SEM) can be used to image nuclear pore complex (NPC) surface structure of from a number of organisms and model systems. With a field emission SEM , this is a medium resolution technique where details of the organization of various components can be directly imaged. Some components, such as the NPC baskets and cytoplasmic filaments, are difficult to visualize in any other way. Protein components can be identified by immunogold labeling. Any surface that can be exposed can potentially be studied by SEM . Several overlapping protocols for SEM sample preparation and immunogold labeling of NPCs are given here. Various parameters for sample preparation, fixation, immunogold labeling, drying, metal coating, and imaging are detailed which have been optimized for different types of specimens and desired endpoints.

Simultaneous label-free live imaging of cell nucleus and luminescent nanodiamonds

In recent years, fluorescent nanodiamond (fND) particles containing nitrogen-vacancy (NV) centers gained recognition as an attractive probe for nanoscale cellular imaging and quantum sensing. For these applications, precise localization of fNDs inside of a living cell is essential. Here we propose such a method by simultaneous detection of the signal from the NV centers and the spectroscopic Raman signal from the cells to visualize the nucleus of living cells. However, we show that the commonly used Raman cell signal from the fingerprint region is not suitable for organelle imaging in this case. Therefore, we develop a method for nucleus visualization exploiting the region-specific shape of C-H stretching mode and further use k-means cluster analysis to chemically distinguish the vicinity of fNDs. Our technique enables, within a single scan, to detect fNDs, distinguish by chemical localization whether they have been internalized into cell and simultaneously visualize cell nucleus without any labeling or cell-fixation. We show for the first time spectral colocalization of unmodified high-pressure high-temperature fND probes with the cell nucleus. Our methodology can be, in principle, extended to any red- and near-infrared-luminescent cell-probes and is fully compatible with quantum sensing measurements in living cells.

Dual-channel fluorescent probe bearing two-photon activity for cell viability monitoring

We developed a dual-channel two-photon fluorescence probe to monitor cell viability.

Dynamically Monitoring Cell Viability in a Dual-Color Mode: Construction of an Aggregation/Monomer-Based Probe Capable of Reversible Mitochondria-Nucleus Migration

Mitochondria and nucleus play crucial roles during cell apoptosis process. In this work, a unique fluorescent probe capable of reversible migration between mitochondria and nucleus, as well as detection of cell viability in a dual-color mode is presented. The dual-color probe targets mitochondria in healthy cells, to form aggregates with deep-red emission. It migrates into nucleus and binds to DNA to form monomers with green fluorescence during apoptosis. Interestingly, the migration is reversible dependent on cell viability, which enables the dynamic visualization of apoptosis process. With the probe, mitochondria and nucleus can be visualized in dual colors during apoptosis, and the cell viability could be monitored by the emission color and localization of the probe.

Immunogold Labeling for Scanning Electron Microscopy

Scanning electron microscopes are useful biological tools that can be used to image the surface of whole organisms, tissues, cells, cellular components, and macromolecules. Processes and structures that exist at surfaces can be imaged in pseudo, or real 3D at magnifications ranging from about 10× to 1,000,000×. Therefore a whole multicellular organism, such as a fly, or a single protein embedded in one of its cell membranes can be visualized. In order to identify that protein at high resolution, or to see and quantify its distribution at lower magnifications, samples can be labeled with antibodies. Any surface that can be exposed can potentially be studied in this way. Presented here is a generic method for immunogold labeling for scanning electron microscopy, using two examples of specimens: isolated nuclear envelopes and the cytoskeleton of mammalian culture cells. Various parameters for sample preparation, fixation, immunogold labeling, drying, metal coating, and imaging are discussed so that the best immunogold scanning electron microscopy results can be obtained from different types of specimens.

Initiation of DNA replication requires actin dynamics and formin activity

Nuclear actin regulates transcriptional programmes in a manner dependent on its levels and polymerisation state. This dynamics is determined by the balance of nucleocytoplasmic shuttling, formin- and redox-dependent filament polymerisation. Here, using Xenopus egg extracts and human somatic cells, we show that actin dynamics and formins are essential for DNA replication. In proliferating cells, formin inhibition abolishes nuclear transport and initiation of DNA replication, as well as general transcription. In replicating nuclei from transcriptionally silent Xenopus egg extracts, we identified numerous actin regulators, and disruption of actin dynamics abrogates nuclear transport, preventing NLS (nuclear localisation signal)-cargo release from RanGTP-importin complexes. Nuclear formin activity is further required to promote loading of cyclin-dependent kinase (CDK) and proliferating cell nuclear antigen (PCNA) onto chromatin, as well as initiation and elongation of DNA replication. Therefore, actin dynamics and formins control DNA replication by multiple direct and indirect mechanisms.

High-resolution scanning electron microscopy for the imaging of nuclear pore complexes and Ran-mediated transport

High-resolution scanning electron microscopy provides three-dimensional surface images of nuclear pore complexes (NPCs) embedded in the nuclear envelope. Here, we describe a method for exposing the nuclear surface in mammalian tissue culture cells for imaging by scanning electron microscopy. Hypotonic treatment is followed by low-speed centrifugation onto polylysine-coated silicon chips, without the use of detergents. This helps to preserve NPCs close to their native morphology, embedded in undamaged nuclear membranes. This method is particularly advantageous for combining high-resolution imaging of NPCs with mammalian genetic systems.

Imaging plant nuclei and membrane-associated cytoskeleton by field emission scanning electron microscopy

Scanning electron microscopy (SEM) is a powerful technique that can image exposed surfaces in 3D. Modern scanning electron microscopes, with field emission electron sources and in-lens specimen chambers, achieve resolutions of better than 0.5 nm and thus offer views of ultrastructural details of subcellular structures or even macromolecular complexes. Obtaining a reliable image is, however, dependent on sample preparation methods that robustly but accurately preserve biological structures. In plants, exposing the object of interest may be difficult due to the existence of a cell wall. This protocol shows how to isolate plant nuclei for SEM imaging of the nuclear envelope and associated structures from both sides of the nuclear envelope in cultured cells as well as in leaf or root cells. Further, it provides a method for uncovering membrane-associated cytoskeletal structures.

Imaging metazoan nuclear pore complexes by field emission scanning electron microscopy

High resolution three-dimensional surface images of nuclear pore complexes (NPCs) can be obtained by field emission scanning electron microscopy. We present a short retrospective view starting from the early roots of microscopy, through the discovery of the cell nucleus and the development of some modern techniques for sample preparation and imaging. Detailed protocols are presented for assembling anchored nuclei in a Xenopus cell-free reconstitution system and for the exposure of the nuclear surface in mammalian cell nuclei. Immunogold labeling of metazoan NPCs and a promising new technique for delicate coating with iridium are also discussed.

Revisiting HIV-1 uncoating

HIV uncoating is defined as the loss of viral capsid that occurs within the cytoplasm of infected cells before entry of the viral genome into the nucleus. It is an obligatory step of HIV-1 early infection and accompanies the transition between reverse transcription complexes (RTCs), in which reverse transcription occurs, and pre-integration complexes (PICs), which are competent to integrate into the host genome. The study of the nature and timing of HIV-1 uncoating has been paved with difficulties, particularly as a result of the vulnerability of the capsid assembly to experimental manipulation. Nevertheless, recent studies of capsid structure, retroviral restriction and mechanisms of nuclear import, as well as the recent expansion of technical advances in genome-wide studies and cell imagery approaches, have substantially changed our understanding of HIV uncoating. Although early work suggested that uncoating occurs immediately following viral entry in the cell, thus attributing a trivial role for the capsid in infected cells, recent data suggest that uncoating occurs several hours later and that capsid has an all-important role in the cell that it infects: for transport towards the nucleus, reverse transcription and nuclear import. Knowing that uncoating occurs at a later stage suggests that the viral capsid interacts extensively with the cytoskeleton and other cytoplasmic components during its transport to the nucleus, which leads to a considerable reassessment of our efforts to identify potential therapeutic targets for HIV therapy. This review discusses our current understanding of HIV uncoating, the functional interplay between infectivity and timely uncoating, as well as exposing the appropriate methods to study uncoating and addressing the many questions that remain unanswered.

Preparation of cells for assessing ultrastructural localization of nanoparticles with transmission electron microscopy

We describe the use of transmission electron microscopy (TEM) for cellular ultrastructural examination of nanoparticle (NP)-exposed biomaterials. Preparation and imaging of electron-transparent thin cell sections with TEM provides excellent spatial resolution (approximately 1 nm), which is required to track these elusive materials. This protocol provides a step-by-step method for the mass-basis dosing of cultured cells with NPs, and the process of fixing, dehydrating, staining, resin embedding, ultramicrotome sectioning and subsequently visualizing NP uptake and translocation to specific intracellular locations with TEM. In order to avoid potential artifacts, some technical challenges are addressed. Based on our results, this procedure can be used to elucidate the intracellular fate of NPs, facilitating the development of biosensors and therapeutics, and provide a critical component for understanding NP toxicity. This protocol takes approximately 1 week.

Immunogold labelling for scanning electron microscopy

Scanning electron microscopes are useful biological tools that can be used to image the surface of whole organisms, tissues, cells, cellular components and macromolecules. Processes and structures that exist at surfaces can be imaged in pseudo or real 3D at magnifications of anything from about x10 to x1,000,000. Therefore a whole multicellular organism, such as a fly, or a single protein embedded in one of its cell membranes can be visualised. In order to identify that protein at high resolution, or to see and quantify its distribution at lower magnifications, samples can be labelled with antibodies. Any surface that can be exposed can potentially be studied in this way. Presented here is a generic method for immunogold labelling for scanning electron microscopy, using two examples of specimens: isolated nuclear envelopes and the cytoskeleton of mammalian culture cells. Various parameters for sample preparation, fixation, immunogold labelling, drying, metal coating and imaging are discussed so that the best immunogold scanning electron microscopy results can be obtained from different types of specimens.

A protocol for isolating Xenopus oocyte nuclear envelope for visualization and characterization by scanning electron microscopy (SEM) or transmission electron microscopy (TEM)

This protocol details methods for the isolation of oocyte nuclear envelopes (NEs) from the African clawed toad Xenopus laevis, immunogold labeling of component proteins and subsequent visualization by field-emission scanning electron microscopy (FESEM) and transmission electron microscopy (TEM). This procedure involves the initial removal of the ovaries from mature female X. laevis, the dissection of individual oocytes, then the manual isolation of the giant nucleus and subsequent preparation for high-resolution visualization. Unlike light microscopy, and its derivative technologies, electron microscopy enables 3-5 nm resolution of nuclear structures, thereby giving unrivalled opportunities for investigation and immunological characterization in situ of nuclear structures and their structural associations. There are a number of stages where samples can be stored, although we recommend that this protocol take no longer than 2 d. Samples processed for FESEM can be stored for weeks under vacuum, allowing considerable time for image acquisition.

Generation of cell-free extracts of Xenopus eggs and demembranated sperm chromatin for the assembly and isolation of in vitro-formed nuclei for Western blotting and scanning electron microscopy (SEM)

This protocol details methods for the generation of cell-free extracts and DNA templates from the eggs and sperm chromatin, respectively, of the clawed toad Xenopus laevis. We have used this system with scanning electron microscopy (SEM), as detailed herein, to analyze the biochemical requirements and structural pathways for the biogenesis of eukaryotic nuclear envelopes (NEs) and nuclear pore complexes (NPCs). This protocol requires access to female frogs, which are induced to lay eggs, and a male frog, which is killed for preparation of the sperm chromatin. Egg extracts should be prepared in 1 d and can be stored for many months at -80 degrees C. Demembranated sperm chromatin should take only approximately 2-3 h to prepare and can be stored at -80 degrees C almost indefinitely. The time required for assembly of structurally and functionally competent nuclei in vitro depends largely on the quality of the cell-free extracts and, therefore, must be determined for each extract preparation.

Scanning electron microscopy of nuclear structure

Accessing internal structure and retaining relative three dimensional (3D) organization within the nucleus has always proved difficult in the electron microscope. This is due to the overall size and largely fibrous nature of the contents, making large scale 3D reconstructions difficult from thin sections using transmission electron microscopy. This chapter brings together a number of methods developed for visualization of nuclear structure by scanning electron microscopy (SEM). These methods utilize the easily accessed high resolution available in field emission instruments. Surface imaging has proved particularly useful to date in studies of the nuclear envelope and pore complexes, and has also shown promise for internal nuclear organization, including the dynamic and radical reorganization of structure during cell division. Consequently, surface imaging in the SEM has the potential to make a significant contribution to our understanding of nuclear structure.