Quantitative fluorescence imaging of protein diffusion and interaction in living cells

Hydrodynamics of a disk in a thin film of weakly nematic fluid subject to linear friction

To make progress towards the development of a theory on the motion of inclusions in thin structured films and membranes, we here consider as an initial step a circular disk in a two-dimensional, uniaxially anisotropic fluid layer. We assume overdamped dynamics, incompressibility of the fluid, and global alignment of the axis of anisotropy. Motion within this layer is affected by additional linear friction with the environment, for instance, a supporting substrate. We investigate the induced flows in the fluid when the disk is translated parallel or perpendicular to the direction of anisotropy. Moreover, expressions for corresponding mobilities and resistance coefficients of the disk are derived. Our results are obtained within the framework of a perturbative expansion in the parameters that quantify the anisotropy of the fluid. Good agreement is found for moderate anisotropy when compared to associated results from finite-element simulations. At pronounced anisotropy, the induced flow fields are still predicted qualitatively correctly by the perturbative theory, although quantitative deviations arise. We hope to stimulate with our investigations corresponding experimental analyses, for example, concerning fluid flows in anisotropic thin films on uniaxially rubbed supporting substrates.

Segmented fluorescence correlation spectroscopy (FCS) on a commercial laser scanning microscope

Performing accurate Fluorescence Correlation Spectroscopy (FCS) measurements in cells can be challenging due to cellular motion or other intracellular processes. In this respect, it has recently been shown that analysis of FCS data in short temporal segments (segmented FCS) can be very useful to increase the accuracy of FCS measurements inside cells. Here, we demonstrate that segmented FCS can be performed on a commercial laser scanning microscope (LSM), even in the absence of the dedicated FCS module. We show how data can be acquired on a Leica SP8 confocal microscope and then exported and processed with a custom software in MATLAB. The software performs segmentation of the data to extract an average ACF and measure the diffusion coefficient in specific subcellular regions. First of all, we measure the diffusion of fluorophores of different size in solution, to show that good-quality ACFs can be obtained in a commercial LSM. Next, we validate the method by measuring the diffusion coefficient of GFP in the nucleus of HeLa cells, exploiting variations of the intensity to distinguish between nucleoplasm and nucleolus. As expected, the measured diffusion coefficient of GFP is slower in the nucleolus relative to nucleoplasm. Finally, we apply the method to HeLa cells expressing a PARP1 chromobody to measure the diffusion coefficient of PARP1 in different subcellular regions. We find that PARP1 diffusion is slower in the nucleolus compared to the nucleoplasm.

From the beginnings to multidimensional light and electron microscopy of virus morphogenesis

Individual functional viral morphogenesis events are often dynamic, short, and infrequent and might be obscured by other pathways and dead-end products. Volumetric live cell imaging has become an essential tool for studying viral morphogenesis events. It allows following entire dynamic processes while providing functional evidence that the imaged process is involved in viral production. Moreover, it allows to capture many individual events and allows quantitative analysis. Finally, the correlation of volumetric live-cell data with volumetric electron microscopy (EM) can provide crucial insights into the ultrastructure and mechanisms of viral morphogenesis events. Here, we provide an overview and discussion of suitable imaging methods for volumetric correlative imaging of viral morphogenesis and frame them in a historical summary of their development.

Quantitative live-cell imaging of lipidated peptide transport through an epithelial cell layer

Oral drug delivery increases patient compliance and is thus the preferred administration route for most drugs. However, for biologics the intestinal barrier greatly limits the absorption and reduces their bioavailability. One strategy employed to improve on this is chemical modification of the biologic through the addition of lipid side chains. While it has been established that lipidation of peptides can increase transport, a mechanistic understanding of this effect remains largely unexplored. To pursue this mechanistic understanding, end-point detection of biopharmaceuticals transported through a monolayer of fully polarized epithelial cells is typically used. However, these methods are time-consuming and tedious. Furthermore, most established methods cannot be combined easily with high-resolution live-cell fluorescence imaging that could provide a mechanistic insight into cellular uptake and transport. Here we address this challenge by developing an axial PSF deconvolution scheme to quantify the transport of peptides through a monolayer of Caco-2 cells using single-cell analysis with live-cell confocal fluorescence microscopy. We then measure the known cross-barrier transport of several compounds in our model and compare the results with results obtained in an established microfluidic model finding similar transport phenotypes. This verifies that already after two days the Caco-2 cells in our model form a tight monolayer and constitute a functional barrier model. We then apply this assay to investigate the effects of side chain lipidation of the model peptide drug salmon calcitonin (sCT) modified with 4‑carbon and 8‑carbon-long fatty acid chains. Furthermore, we compare that with experiments performed at lower temperature and using inhibitors for some endocytotic pathways to pinpoint how lipidation length modifies the main avenues for the transport. We thus show that increasing the length of the lipid chain increases the transport of the drug significantly but also makes endocytosis the primary transport mechanism in a short-term cell culture model.

Plasmonic random laser enabled artefact-free wide-field fluorescence bioimaging: uncovering finer cellular features

Narrow bandwidth, high brightness, and spectral tunability are the unique properties of lasers that make them extremely desirable for fluorescence imaging applications. However, due to the high spatial coherence, conventional lasers are often incompatible for wide-field fluorescence imaging. The presence of parasitic artefacts under coherent illumination causes uneven excitation of fluorophores, which has a critical impact on the reliability, resolution, and efficiency of fluorescence imaging. Here, we demonstrate artefact-free wide-field fluorescence imaging with a bright and low threshold silver nanorod based plasmonic random laser, offering the capability to image finer cellular features with sub-micrometer resolution even in highly diffusive biological samples. A spatial resolution of 454 nm and up to 23% enhancement in the image contrast in comparison to conventional laser illumination are attained. Based on the results presented in this paper, random lasers, with their laser-like properties and spatial incoherence are envisioned to be the next-generation sources for developing highly efficient wide-field fluorescence imaging systems having high spatial and temporal resolution for real-time, in vivo bioimaging.

Scaling Relationship in Chromatin as a Polymer

Genomic DNA, which controls genetic information, is stored in the cell nucleus in eukaryotes. Chromatin moves dynamically in the nucleus, and this movement is closely related to the function of chromatin. However, the driving force of chromatin movement, its control mechanism, and the functional significance of movement are unclear. In addition to biochemical and genetic approaches such as identification and analysis of regulators, approaches based on the physical properties of chromatin and cell nuclei are indispensable for this understanding. In particular, the idea of polymer physics is expected to be effective. This paper introduces our efforts to combine biological experiments on chromatin kinetics with theoretical analysis based on polymer physics.

How Genomes Emerge, Function, and Evolve: Living Systems Emergence-Genotype-Phenotype-Multilism-Genome/Systems Ecology

What holds together the world in its innermost, what life is, how it emerges, functions, and evolves, has not only been an epic matter of endless romantic sunset poetry and philosophy, but also manifests explicitly in its perhaps most central organization unit-genomes. Their 3D architecture and dynamics, including the interaction networks of regulatory elements, obviously co-evolved as inseparable systems allowing the physical storage, expression, and replication of genetic information. Since we were able to fill finally the much-debated centennial gaps in their 3D architecture and dynamics, now entire new perspectives open beyond epigenetics reaching as far as a general understanding of living systems: besides the previously known DNA double helix and nucleosome structure, the latter compact into a chromatin quasi-fibre folded into stable loops forming stable multi-loop aggregates/rosettes connected by linkers, creating hence the again already known chromosome arms and entire chromosomes forming the cell nucleus. Instantly and for the first time this leads now to a consistent and cross-proven systems statistical mechanics genomics framework elucidating genome intrinsic function and regulation including various components. It balances stability/flexibility ensuring genome integrity, enabling expression/regulation of genetic information, as well as genome replication/spread. Furthermore, genotype and phenotype are multiplisticly entangled being evolutionarily the outcome of both Darwinian natural selection and Lamarckian self-referenced manipulation-all embedded in even broader genome ecology (autopoietic) i(!)n- and environmental scopes. This allows formulating new meta-level functional semantics of genomics, i.e. notions as communication of genes, genomes, and information networks, architectural and dynamic spaces for creativity and innovation, or genomes as central geno-/phenotype entanglements. Beyond and most fundamentally, the paradoxical-seeming local equilibrium substance stability in its entity though far from a universal heat-death-like equilibrium is solved, and system irreversibility, time directionality, and thus the emergence of existence are clarified. Consequently, real deep understandings of genomes, life, and complex systems in general appear in evolutionary perspectives as well as from systems analyses, via system damage/disease (its repair/cure and manipulation) as far as the understanding of extraterrestrial life, the de novo creation and thus artificial life, and even the raison d'etre.

Simulation of Different Three-Dimensional Models of Whole Interphase Nuclei Compared to Experiments - A Consistent Scale-Bridging Simulation Framework for Genome Organization

The three-dimensional architecture of chromosomes, their arrangement, and dynamics within cell nuclei are still subject of debate. Obviously, the function of genomes-the storage, replication, and transcription of genetic information-has closely coevolved with this architecture and its dynamics, and hence are closely connected. In this work a scale-bridging framework investigates how of the 30 nm chromatin fibre organizes into chromosomes including their arrangement and morphology in the simulation of whole nuclei. Therefore, mainly two different topologies were simulated with corresponding parameter variations and comparing them to experiments: The Multi-Loop-Subcompartment (MLS) model, in which (stable) small loops form (stable) rosettes, connected by chromatin linkers, and the Random-Walk/Giant-Loop (RW/GL) model, in which large loops are attached to a flexible non-protein backbone, were simulated for various loop and linker sizes. The 30 nm chromatin fibre was modelled as a polymer chain with stretching, bending and excluded volume interactions. A spherical boundary potential simulated the confinement to nuclei with different radii. Simulated annealing and Brownian Dynamics methods were applied in a four-step decondensation procedure to generate from metaphase decondensated interphase configurations at thermodynamical equilibrium. Both the MLS and the RW/GL models form chromosome territories, with different morphologies: The MLS rosettes result in distinct subchromosomal domains visible in electron and confocal laser scanning microscopic images. In contrast, the big RW/GL loops lead to a mostly homogeneous chromatin distribution. Even small changes of the model parameters induced significant rearrangements of the chromatin morphology. The low overlap of chromosomes, arms, and subchromosomal domains observed in experiments agrees only with the MLS model. The chromatin density distribution in CLSM image stacks reveals a bimodal behaviour in agreement with recent experiments. Combination of these results with a variety of (spatial distance) measurements favour an MLS like model with loops and linkers of 63 to 126 kbp. The predicted large spaces between the chromatin fibres allow typically sized biological molecules to reach nearly every location in the nucleus by moderately obstructed diffusion and is in disagreement with the much simplified assumption that defined channels between territories for molecular transport as in the Interchromosomal Domain (ICD) hypothesis exist and are necessary for transport. All this is also in agreement with recent selective high-resolution chromosome interaction capture (T2C) experiments, the scaling behaviour of the DNA sequence, the dynamics of the chromatin fibre, the diffusion of molecules, and other measurements. Also all other chromosome topologies can in principle be excluded. In summary, polymer simulations of whole nuclei compared to experimental data not only clearly favour only a stable loop aggregate/rosette like genome architecture whose local topology is tightly connected to the global morphology and dynamics of the cell nucleus and hence can be used for understanding genome organization also in respect to diagnosis and treatment. This is in agreement with and also leads to a general novel framework of genome emergence, function, and evolution.

A survey of physical methods for studying nuclear mechanics and mechanobiology

It is increasingly appreciated that the cell nucleus is not only a home for DNA but also a complex material that resists physical deformations and dynamically responds to external mechanical cues. The molecules that confer mechanical properties to nuclei certainly contribute to laminopathies and possibly contribute to cellular mechanotransduction and physical processes in cancer such as metastasis. Studying nuclear mechanics and the downstream biochemical consequences or their modulation requires a suite of complex assays for applying, measuring, and visualizing mechanical forces across diverse length, time, and force scales. Here, we review the current methods in nuclear mechanics and mechanobiology, placing specific emphasis on each of their unique advantages and limitations. Furthermore, we explore important considerations in selecting a new methodology as are demonstrated by recent examples from the literature. We conclude by providing an outlook on the development of new methods and the judicious use of the current techniques for continued exploration into the role of nuclear mechanobiology.

Application of quantitative cell imaging using label-free optical diffraction tomography

The cell is three-dimensionally and dynamically organized into cellular compartments, including the endoplasmic reticulum, mitochondria, vesicles, and nucleus, which have high relative molecular density. The structure and functions of these compartments and organelles may be deduced from the diffusion and interaction of related biomolecules. Among these cellular components, various protein molecules can freely access the nucleolus or mitotic chromosome through Brownian diffusion, even though they have a densely packed structure. However, physicochemical properties of the nucleolus and chromosomes, such as molecular density and volume, are not yet fully understood under changing cellular conditions. Many studies have been conducted based on high-resolution imaging and analysis techniques using fluorescence. However, there are limitations in imaging only fluorescently labeled molecules, and cytotoxicity occurs during three-dimensional imaging. Alternatively, the recently developed label-free three-dimensional optical diffraction tomography (ODT) imaging technique can divide various organelles in cells into volumes and analyze them by refractive index, although specific molecules cannot be observed. A previous study established an analytical method that provides comprehensive insights into the physical properties of the nucleolus and mitotic chromosome by utilizing the advantages of ODT and fluorescence techniques, such as fluorescence correlation spectroscopy and confocal laser scanning microscopy. This review article summarizes a recent study and discusses the future aspects of the ODT for cellular compartments.

Nanowaveguide-illuminated fluorescence correlation spectroscopy for single molecule studies

Fluorescence Correlation Spectroscopy (FCS) is a method of investigating concentration fluctuations of fluorescent particles typically in the nM range as a result of its femtoliter-sized sample volume. However, biological processes on cell membranes that involve molecules in the μM concentration range require sample volumes well below the conventional FCS limit as well as nanoscale confinement in the longitudinal direction. In this study, we show that an effective measurement volume down to the zeptoliter range can be achieved via the introduction of a nanowire waveguide, resulting in an illumination spot of about 50 nm in lateral dimensions and a longitudinal confinement of around 20 nm just above the waveguide exit surface. Using illumination profiles obtained from finite element method simulations of dielectric nanowaveguides, we perform Monte Carlo simulations of fluorescence fluctuations for two scenarios of fluorophore movement: fluorophores freely diffusing in the three-dimensional (3D) space above the nanowaveguide and fluorophores moving in a two-dimensional (2D) membrane situated directly above the nanowaveguide exit surface. We have developed analytical functions to fit the simulation results and found that an effective illumination size of about 150 zl and 4 × 10-3 µm2 can be obtained for the 3D and 2D scenarios, respectively. Given the flat surface geometry and the deep-subwavelength confinement of its illumination spot, this nanowaveguide-illuminated fluorescence correlation spectroscopy technique may be well suited for studying the concentration and dynamics of densely distributed protein molecules on cell membranes.

Degradation of Drug Delivery Nanocarriers and Payload Release: A Review of Physical Methods for Tracing Nanocarrier Biological Fate

Nanoformulations offer multiple advantages over conventional drug delivery, enhancing solubility, biocompatibility, and bioavailability of drugs. Nanocarriers can be engineered with targeting ligands for reaching specific tissue or cells, thus reducing the side effects of payloads. Following systemic delivery, nanocarriers must deliver encapsulated drugs, usually through nanocarrier degradation. A premature degradation, or the loss of the nanocarrier coating, may prevent the drug's delivery to the targeted tissue. Despite their importance, stability and degradation of nanocarriers in biological environments are largely not studied in the literature. Here we review techniques for tracing the fate of nanocarriers, focusing on nanocarrier degradation and drug release both intracellularly and in vivo. Intracellularly, we will discuss different fluorescence techniques: confocal laser scanning microscopy, fluorescence correlation spectroscopy, lifetime imaging, flow cytometry, etc. We also consider confocal Raman microscopy as a label-free technique to trace colocalization of nanocarriers and drugs. In vivo we will consider fluorescence and nuclear imaging for tracing nanocarriers. Positron emission tomography and single-photon emission computed tomography are used for a quantitative assessment of nanocarrier and payload biodistribution. Strategies for dual radiolabelling of the nanocarriers and the payload for tracing carrier degradation, as well as the efficacy of the payload delivery in vivo, are also discussed.

Quantifying Nanoscale Viscosity and Structures of Living Cells Nucleus from Mobility Measurements

Understanding the mobility of nano-objects in the eukaryotic cell nucleus, at multiple length-scales, is essential for dissecting nuclear structure-function relationships both in space and in time. Here, we demonstrate, using single-molecule fluorescent correlation spectroscopies, that motion of inert probes (proteins, polymers, or nanoparticles) with diameters ranging from 2.6 to 150 nm is mostly unobstructed in a nucleus. Supported by the analysis of electron tomography images, these results advocate the ∼150 nm-wide interchromosomal channels filled with the aqueous diluted protein solution. The nucleus is percolated by these channels to allow various cargos to migrate freely at the nanoscale. We determined the volume of interchromosomal channels in the HeLa cell nucleus to 237 ± 61 fL, which constitutes 34% of the cell nucleus volume. The volume fraction of mobile proteins in channels equals 16% ± 4%, and the concentration is 1 mM.

Confocal Laser Scanning Microscopy and Fluorescence Correlation Methods for the Evaluation of Molecular Interactions

Confocal laser scanning microscopy (CLSM) and related microscopic techniques allow a unique and versatile approach to image and analyze living cells due to their specificity and high sensitivity. Among confocal related techniques, fluorescence correlation methods, such as fluorescence correlation spectroscopy (FCS) and dual-color fluorescence cross-correlation spectroscopy (FCCS), are highly sensitive biophysical methods for analyzing the complex dynamic events of molecular diffusion and interaction change in live cells as well as in solution by exploiting the characteristics of fluorescence signals. Analytical and quantitative information from FCS and FCCS coupled with fluorescence images obtained from CLSM can now be applied in convergence science such as drug delivery and nanomedicine, as well as in basic cell biology. In this chapter, a brief introduction into the physical parameters that can be obtained from FCS and FCCS is first provided. Secondly, experimental examples of the methods for evaluating the parameters is presented. Finally, two potential FCS and FCCS applications for convergence science are introduced in more detail.

Of numbers and movement - understanding transcription factor pathogenesis by advanced microscopy

Transcription factors (TFs) are life-sustaining and, therefore, the subject of intensive research. By regulating gene expression, TFs control a plethora of developmental and physiological processes, and their abnormal function commonly leads to various developmental defects and diseases in humans. Normal TF function often depends on gene dosage, which can be altered by copy-number variation or loss-of-function mutations. This explains why TF haploinsufficiency (HI) can lead to disease. Since aberrant TF numbers frequently result in pathogenic abnormalities of gene expression, quantitative analyses of TFs are a priority in the field. In vitro single-molecule methodologies have significantly aided the identification of links between TF gene dosage and transcriptional outcomes. Additionally, advances in quantitative microscopy have contributed mechanistic insights into normal and aberrant TF function. However, to understand TF biology, TF-chromatin interactions must be characterised in vivo, in a tissue-specific manner and in the context of both normal and altered TF numbers. Here, we summarise the advanced microscopy methodologies most frequently used to link TF abundance to function and dissect the molecular mechanisms underlying TF HIs. Increased application of advanced single-molecule and super-resolution microscopy modalities will improve our understanding of how TF HIs drive disease.

Fast Diffusion of the Unassembled PetC1-GFP Protein in the Cyanobacterial Thylakoid Membrane

Biological membranes were originally described as a fluid mosaic with uniform distribution of proteins and lipids. Later, heterogeneous membrane areas were found in many membrane systems including cyanobacterial thylakoids. In fact, cyanobacterial pigment-protein complexes (photosystems, phycobilisomes) form a heterogeneous mosaic of thylakoid membrane microdomains (MDs) restricting protein mobility. The trafficking of membrane proteins is one of the key factors for long-term survival under stress conditions, for instance during exposure to photoinhibitory light conditions. However, the mobility of unbound 'free' proteins in thylakoid membrane is poorly characterized. In this work, we assessed the maximal diffusional ability of a small, unbound thylakoid membrane protein by semi-single molecule FCS (fluorescence correlation spectroscopy) method in the cyanobacterium Synechocystis sp. PCC6803. We utilized a GFP-tagged variant of the cytochrome b₆f subunit PetC1 (PetC1-GFP), which was not assembled in the b₆f complex due to the presence of the tag. Subsequent FCS measurements have identified a very fast diffusion of the PetC1-GFP protein in the thylakoid membrane (D = 0.14 - 2.95 µm²s^-1). This means that the mobility of PetC1-GFP was comparable with that of free lipids and was 50-500 times higher in comparison to the mobility of proteins (e.g., IsiA, LHCII-light-harvesting complexes of PSII) naturally associated with larger thylakoid membrane complexes like photosystems. Our results thus demonstrate the ability of free thylakoid-membrane proteins to move very fast, revealing the crucial role of protein-protein interactions in the mobility restrictions for large thylakoid protein complexes.

In situ exploring Chidamide, a histone deacetylase inhibitor, induces molecular changes of leukemic T-lymphocyte apoptosis using Raman spectroscopy

Though it has been demonstrated that Chidamide (CS055/HBI-8000), a novel benzamide class of histone deacetylase (HDAC) subtype-selectively inhibitor, reveals better anticancer effect in acute leukemia, but it remains unknown about the precise mechanism of Chidamide-induced acute leukemia cell apoptosis due to the lack of in situ molecular changes information. Based on Raman spectral analysis, we find that the action of Chidamide on Jurkat cell will lead to an addition of an acetyl group to a specific lysine residue at the end of histone amino acid, and greatly enhance the acetylation of histones H1, H2A, H2B, H3, and H4, and then destroy the electrostatic force between the alkaline terminal of the positive charged arginine side chain and the negative charged DNA of phosphate group, finally cause the depolymerization of DNA and histone octamer in chromatin nucleosome depolymerization and the relaxation of chromatin. Accordingly, the accumulation of reactive oxygen species (ROS) and the decreasing of mitochondrial membrane potential (MMP) are observed. For comparison, we also present the corresponding results of suberoylanilide hydroxamic acid (SAHA) and MS-275 inhibitors. The achieved results show that proliferation of Chidamide-treated Jurkat cells is low relative to MS-275 or SAHA, and the action of Chidamide or MS-275 on Jurkat cells lead to obvious increasing in histones H1, H2A, H2B, H3, and H4, whereas the action effect of SAHA is mainly observed in histones H1, H2A, H2B, H3 but weak in histone H4. Moreover, it is found that Chidamide-induced histone H3 acetylation in Jurkat cells is stronger than MS-275 and SAHA. Collectively, by Raman spectral analysis, we achieve the dynamic behavior of biochemical components, molecular conformation and morphological changes of HDAC inhibitors-treated Jurkat cells. Importantly, our research is the first to demonstrate that the action site of HDAC inhibitors on Jurkat cell is located in the DNA minor groove. Most importantly, the application of Raman spectrum in exploring in-situ molecular changes information, histone acetylation modification in epigenetics, drug action sites and cell cycle affected by HDAC inhibitors will supply new idea and reference for the design and modification of HDAC inhibitors.

Phase separation at the nanoscale quantified by dcFCCS

Liquid–liquid phase separation causes formation of membraneless condensates containing concentrated biomolecules, which play essential roles in diverse cellular processes. Currently, micrometer-scale phase-separated condensates are examined routinely to elucidate their functions and mechanisms in details. However, limited by current commonly used methods, the transition process from miscible individual molecules to micrometer-scale condensates is mostly unknown. Herein, we captured formation of nanoscale condensates, whose size, growth rate, molecular stoichiometry, and binding affinity to recruit client molecules were all quantified. To achieve this, we developed a dual-color fluorescence cross-correlation spectroscopy (dcFCCS) method, and we expect that dcFCCS can be widely applied to investigate phase separation of other biomolecules at the nanoscale.

Liquid–liquid phase separation, driven by multivalent macromolecular interactions, causes formation of membraneless compartments, which are biomolecular condensates containing concentrated macromolecules. These condensates are essential in diverse cellular processes. Formation and dynamics of micrometer-scale phase-separated condensates are examined routinely. However, limited by commonly used methods which cannot capture small-sized free-diffusing condensates, the transition process from miscible individual molecules to micrometer-scale condensates is mostly unknown. Herein, with a dual-color fluorescence cross-correlation spectroscopy (dcFCCS) method, we captured formation of nanoscale condensates beyond the detection limit of conventional fluorescence microscopy. In addition, dcFCCS is able to quantify size and growth rate of condensates as well as molecular stoichiometry and binding affinity of client molecules within condensates. The critical concentration to form nanoscale condensates, identified by our experimental measurements and Monte Carlo simulations, is at least several fold lower than the detection limit of conventional fluorescence microscopy. Our results emphasize that, in addition to micrometer-scale condensates, nanoscale condensates are likely to play important roles in various cellular processes and dcFCCS is a simple and powerful quantitative tool to examine them in detail.

Combined Selective Plane Illumination Microscopy and FRAP Maps Intranuclear Diffusion of NLS-GFP

Since its initial development in 1976, fluorescence recovery after photobleaching (FRAP) has been one of the most popular tools for studying diffusion and protein dynamics in living cells. Its popularity is derived from the widespread availability of confocal microscopes and the relative ease of the experiment and analysis. FRAP, however, is limited in its ability to resolve spatial heterogeneity. Here, we combine selective plane illumination microscopy (SPIM) and FRAP to create SPIM-FRAP, wherein we use a sheet of light to bleach a two-dimensional (2D) plane and subsequently image the recovery of the same image plane. This provides simultaneous quantification of diffusion or protein recovery for every pixel in a given 2D slice, thus moving FRAP measurements beyond these previous limitations. We demonstrate this technique by mapping both intranuclear diffusion of NLS-GFP and recovery of 53BP1-mCherry, a marker for DNA damage, in live MDA-MB-231 cells. SPIM-FRAP proves to be an order of magnitude faster than fluorescence-correlation-spectroscopy-based techniques for such measurements. We observe large length-scale (>∼500 nm) heterogeneity in the recovery times of NLS-GFP, which is validated against simulated data sets. 2D maps of NLS-GFP recovery times showed no pixel-by-pixel correlation with histone density, although slower diffusion was observed in nucleoli. Additionally, recovery of 53BP1-mCherry was observed to be slowed at sites of DNA damage. We finally developed a diffusion simulation for our SPIM-FRAP experiments to compare across techniques. Our measured diffusion coefficients are on the order of previously reported results, thus validating the quantitative accuracy of SPIM-FRAP relative to well-established methods. With the recent rise of accessibility of SPIM systems, SPIM-FRAP is set to provide a straightforward means of quantifying the spatial distribution of protein recovery or diffusion in living cells.

Fluorescence strategies for mapping cell membrane dynamics and structures

Fluorescence spectroscopy has been a cornerstone of research in membrane dynamics and organization. Technological advances in fluorescence spectroscopy went hand in hand with discovery of various physicochemical properties of membranes at nanometric spatial and microsecond timescales. In this perspective, we discuss the various challenges associated with quantification of physicochemical properties of membranes and how various modes of fluorescence spectroscopy have overcome these challenges to shed light on the structure and organization of membranes. Finally, we discuss newer measurement strategies and data analysis tools to investigate the structure, dynamics, and organization of membranes.

Light-Sheet Microscopy for Surface Topography Measurements and Quantitative Analysis

A novel light-sheet microscopy (LSM) system that uses the laser triangulation method to quantitatively calculate and analyze the surface topography of opaque samples is discussed. A spatial resolution of at least 10 μm in z-direction, 10 μm in x-direction and 25 μm in y-direction with a large field-of-view (FOV) is achieved. A set of sample measurements that verify the system′s functionality in various applications are presented. The system has a simple mechanical structure, such that the spatial resolution is easily improved by replacement of the objective, and a linear calibration formula, which enables convenient system calibration. As implemented, the system has strong potential for, e.g., industrial sample line inspections, however, since the method utilizes reflected/scattered light, it also has the potential for three-dimensional analysis of translucent and layered structures.

Profiling epigenetic changes in human cell line induced by atrazine exposure

How environmental chemicals can affect and exert their toxic effect at a molecular level has gained significant interest in recent years, not only for understanding their immediate health implications over exposed individuals, but also for their subsequent progeny. Atrazine (ATZ) is a commonly used herbicide in the U.S. and a long-suspected endocrine disrupting chemical. The molecular mechanism conferring long-term adverse health outcomes, however, remain elusive. Here, we explored changes in epigenetic marks that arise after exposure to ATZ at selected doses using image-based analysis coupled with data clustering. Significant decreases in methylated CpG (^meCpG) and histone 3 lysine 9 tri-methylated (H3K9me3) were observed in the selected human cell line with a clear spatial preference. Treating cells with ATZ leads to the loss of a subpopulation of cells with high ^meCpG levels as identified in our clustering and histogram analysis. A similar trend was observed in H3K9me3 potentially attributing to the cross-talking between ^meCpG and H3K9me3. Changes in ^meCpG are likely to be associated with alterations in epigenetic enzyme expression levels regulating ^meCpG and persist after the removal of ATZ source which collectively provide a plausible mechanism for long-term ATZ-induced toxicity.

Simultaneous Mapping of Molecular Proximity and Comobility Reveals Agonist-Enhanced Dimerization and DNA Binding of Nuclear Receptors

Single Plane Illumination Microscopy (SPIM) revolutionized time lapse imaging of live cells and organisms due to its high speed and reduced photodamage. Quantitative mapping of molecular (co)mobility by fluorescence (cross-)correlation spectroscopy (F(C)CS) in a SPIM has been introduced to reveal molecular diffusion and binding. A complementary aspect of interactions is proximity, which can be studied by Förster resonance energy transfer (FRET). Here, we extend SPIM-FCCS by alternating laser excitation, which reduces false positive cross-correlation and facilitates comapping of FRET. Thus, different aspects of interacting systems can be studied simultaneously, and molecular subpopulations can be discriminated by multiparameter analysis. After demonstrating the benefits of the method on the AP-1 transcription factor, the dimerization and DNA binding behavior of retinoic acid receptor (RAR) and retinoid X receptor (RXR) is revealed, and an extension of the molecular switch model of the nuclear receptor action is proposed. Our data imply that RAR agonist enhances RAR-RXR heterodimerization, and chromatin binding/dimerization are positively correlated. We also propose a ligand induced conformational change bringing the N-termini of RAR and RXR closer together. The RXR agonist increased homodimerization of RXR suggesting that RXR may act as an autonomous transcription factor.

Dynamic Imaging of Transferrin Receptor Molecules on Single Live Cell with Bridge Gaps-Enhanced Raman Tags

A metal nanoparticles-based surface-enhanced Raman scattering (SERS) technique has been developed for biosensing and bioimaging due to its advantages in ultra-narrow line width for multiplexing, ultra-high sensitivity and excellent photostability. However, the "hotspots" effect between nanoparticles usually leads to unstable and nonuniform Raman enhancement, and this will greatly reduce the quality of SERS imaging. In this study, we employ the bridge gaps-enhanced Raman tags (BGERTs) to perform SERS imaging, in which BGERTs can not only reduce the influence of the "hotspots" effect between nanoparticles on Raman signal intensity but provide a great Raman enhancement when the Gold (Au) shell is thick enough. Based on BGERTs and its conjugation with the thiol-terminated polyethylene glycol (PEG) and transferrin, we construct a targeted Transferrin (TF)-PEG-BGERTs SERS nanoprobe and achieve the dynamic imaging of transferrin receptor (TfR) molecules on a single live cell, in which the role of transferrin-conjugated PEG-BGERT is for targeting TfR molecules located in cellular membrane surface. Importantly, this BGERTs-based SERS imaging could potentially provide a useful tool for studying the precise mechanism during the receptor-mediated nanoparticles endocytosis or cell proliferation, apoptosis, and other complicated molecular events.

Functional Fluorescence Microscopy Imaging: Quantitative Scanning-Free Confocal Fluorescence Microscopy for the Characterization of Fast Dynamic Processes in Live Cells

Functional fluorescence microscopy imaging (fFMI), a time-resolved (21 μs/frame) confocal fluorescence microscopy imaging technique without scanning, is developed for quantitative characterization of fast reaction-transport processes in solution and in live cells. The method is based on massively parallel fluorescence correlation spectroscopy (FCS). Simultaneous excitation of fluorescent molecules in multiple spots in the focal plane is achieved using a diffractive optical element (DOE). Fluorescence from the DOE-generated 1024 illuminated spots is detected in a confocal arrangement by a matching matrix detector comprising 32 × 32 single-photon avalanche photodiodes (SPADs). Software for data acquisition and fast auto- and cross-correlation analysis by parallel signal processing using a graphic processing unit (GPU) allows temporal autocorrelation across all pixels in the image frame in 4 s and cross-correlation between first- and second-order neighbor pixels in 45 s. We present here this quantitative, time-resolved imaging method with single-molecule sensitivity and demonstrate its usefulness for mapping in live cell location-specific differences in the concentration and translational diffusion of molecules in different subcellular compartments. In particular, we show that molecules without a specific biological function, e.g., the enhanced green fluorescent protein (eGFP), exhibit uniform diffusion. In contrast, molecules that perform specialized biological functions and bind specifically to their molecular targets show location-specific differences in their concentration and diffusion, exemplified here for two transcription factor molecules, the glucocorticoid receptor (GR) before and after nuclear translocation and the Sex combs reduced (Scr) transcription factor in the salivary gland of Drosophila ex vivo.

Measuring Mobility in Chromatin by Intensity-Sorted FCS

The architectural organization of chromatin can play an important role in genome regulation by affecting the mobility of molecules within its surroundings via binding interactions and molecular crowding. The diffusion of molecules at specific locations in the nucleus can be studied by fluorescence correlation spectroscopy (FCS), a well-established technique based on the analysis of fluorescence intensity fluctuations detected in a confocal observation volume. However, detecting subtle variations of mobility between different chromatin regions remains challenging with currently available FCS methods. Here, we introduce a method that samples multiple positions by slowly scanning the FCS observation volume across the nucleus. Analyzing the data in short time segments, we preserve the high temporal resolution of single-point FCS while probing different nuclear regions in the same cell. Using the intensity level of the probe (or a DNA marker) as a reference, we efficiently sort the FCS segments into different populations and obtain average correlation functions that are associated to different chromatin regions. This sorting and averaging strategy renders the method statistically robust while preserving the observation of intranuclear variations of mobility. Using this approach, we quantified diffusion of monomeric GFP in high versus low chromatin density regions. We found that GFP mobility was reduced in heterochromatin, especially within perinucleolar heterochromatin. Moreover, we found that modulation of chromatin compaction by ATP depletion, or treatment with solutions of different osmolarity, differentially affected the ratio of diffusion in both regions. Then, we used the approach to probe the mobility of estrogen receptor-α in the vicinity of an integrated multicopy prolactin gene array. Finally, we discussed the coupling of this method with stimulated emission depletion FCS for performing FCS at subdiffraction spatial scales.

Modulation of Membrane Fluidity Performed on Model Phospholipid Membrane and Live Cell Membrane: Revealing through Spatiotemporal Approaches of FLIM, FAIM, and TRFS

We have elucidated the role of unsaturated fatty acid in the in vitro model phospholipid membrane and in vivo live cell membrane. Fluorescence microscopy and time-resolved fluorescence spectroscopy have been employed to uncover how modulation of vesicle bilayer fluidity persuades structural transformation. This unsaturation induced structural transformation due to packing disorder in bilayer has been delineated through spatially resolved fluorescence lifetime imaging microscopy (FLIM) and fluorescence polarization or anisotropy imaging microscopy (FPIM/FAIM). Structure-function relationship of phospholipid vesicle is also investigated by monitoring intervesicular water dynamics behavior, which has been demonstrated by temporally resolved fluorescence spectroscopy (TRFS) techniques. Nevertheless, it has also been manifested from this study that loss of rigidity in bilayer breaks down the strong hydrogen bond (H-bond) network around the charged lipid head groups. The disruption of this H-bond network increases the bilayer elasticity, which helps to evolve various kinds of vesicular structure. Furthermore, the significant influence of unsaturated fatty acid on membrane bilayer has been ratified through in vivo live cell imaging.

Fluorescence Correlation Spectroscopy to Examine Protein-Lipid Interactions in Membranes

Fluorescence correlation spectroscopy (FCS) is a versatile technique to study membrane dynamics and protein-lipid interactions. It can provide information about diffusion coefficients, concentrations, and molecular interactions of proteins and lipids in the membrane. These parameters allow for the determination of protein partitioning into different lipid environments, the identification of lipid domains, and the detection of lipid-protein complexes on the membrane. During the last decades, FCS studies were successfully performed on model membrane systems as also on living cells, to characterize protein-lipid interactions. Recent developments of the method described here improved quantitative measurements on membranes and decreased the number of potential artifacts. The aim of this chapter is to provide the reader with the necessary information and some practical guidelines to perform FCS studies on artificial and cellular membranes.

Comprehensive correlation analysis for super-resolution dynamic fingerprinting of cellular compartments using the Zeiss Airyscan detector

The availability of the Airyscan detector in the Zeiss LSM 880 has made possible the development of a new concept in fluctuation correlation spectroscopy using super-resolution. The Airyscan unit acquires data simultaneously on 32 detectors arranged in a hexagonal array. This detector opens up the possibility to use fluctuation methods based on time correlation at single points or at a number of points simultaneously, as well as methods based on spatial correlation in the area covered by the detector. Given the frame rate of this detector, millions of frames can be acquired in seconds, providing a robust statistical basis for fluctuation data. We apply the comprehensive analysis to the molecular fluctuations of free GFP diffusing in live cells at different subcellular compartments to show that at the nanoscale different cell environments can be distinguished by the comprehensive fluctuation analysis.

A Guided Protocol for Array Based T2C: A High-Quality Selective High-Resolution High-Throughput Chromosome Interaction Capture

After now more than 170 years of research the dynamic three-dimensional chromatin architecture of genomes and the co-evolved interaction networks of regulatory elements which create genome function - i.e. the storage, expression, and finally replication of genetic information - involves ever more investigative efforts in respect to not only the pure understanding of living organisms, but also diagnosis, treatment, and even future genome engineering. To study genomic interactions, we developed a novel and superior high-quality selective high-resolution, high-throughput chromosome interaction capture method - T2C (targeted chromatin capture) - which allows to arbitrarily balance resolution, frequency range of interactions, and the investigated general genetic region or single interactions in a highly cost-effective manner in respect to the obtainable result and compared to other techniques. Beyond, T2C has such a high signal-to-noise ratio at high resolution that the "genomic" statistical mechanics level can be reached. With the guided T2C protocol described here, we were already able to finally determine the chromatin quasi-fiber conformation and its folding into stable multi-loop aggregates/rosettes connected by a linker. Actually, this guided T2C protocol provides the means for architectural genome sequencing from the level of the single base pair to the entire cell nucleus and thus to analyze genetic interactions in respect to genome function in a systems biological manner in general as well as in settings ranging from basic research, via diagnostics and treatment, to genome engineering. © 2018 by John Wiley & Sons, Inc.

Multiscale imaging of plant development by light-sheet fluorescence microscopy

Light-sheet fluorescence microscopy (LSFM) methods collectively represent the major breakthrough in developmental bio-imaging of living multicellular organisms. They are becoming a mainstream approach through the development of both commercial and custom-made LSFM platforms that are adjusted to diverse biological applications. Based on high-speed acquisition rates under conditions of low light exposure and minimal photo-damage of the biological sample, these methods provide ideal means for long-term and in-depth data acquisition during organ imaging at single-cell resolution. The introduction of LSFM methods into biology extended our understanding of pattern formation and developmental progress of multicellular organisms from embryogenesis to adult body. Moreover, LSFM imaging allowed the dynamic visualization of biological processes under almost natural conditions. Here, we review the most important, recent biological applications of LSFM methods in developmental studies of established and emerging plant model species, together with up-to-date methods of data editing and evaluation for modelling of complex biological processes. Recent applications in animal models push LSFM into the forefront of current bio-imaging approaches. Since LSFM is now the single most effective method for fast imaging of multicellular organisms, allowing quantitative analyses of their long-term development, its broader use in plant developmental biology will likely bring new insights.

Simulation of different three-dimensional polymer models of interphase chromosomes compared to experiments-an evaluation and review framework of the 3D genome organization

Despite all the efforts the three-dimensional higher-order architecture and dynamics in the cell nucleus are still debated. The regulation of genes, their transcription, replication, as well as differentiation in Eukarya is, however, closely connected to this architecture and dynamics. Here, an evaluation and review framework is setup to investigate the folding of a 30 nm chromatin fibre into chromosome territories by comparing computer simulations of two different chromatin topologies to experiments: The Multi-Loop-Subcompartment (MLS) model, in which small loops form rosettes connected by chromatin linkers, and the Random-Walk/Giant-Loop (RW/GL) model, in which large loops are attached to a flexible non-protein backbone, were simulated for various loop, rosette, and linker sizes. The 30 nm chromatin fibre was modelled as a polymer chain with stretching, bending, and excluded volume interactions. A spherical boundary potential simulated the confinement by other chromosomes and the nuclear envelope. Monte Carlo and Brownian Dynamics methods were applied to generate chain configurations at thermodynamic equilibrium. Both the MLS and the RW/GL models form chromosome territories, with different morphologies: The MLS rosettes form distinct subchromosomal domains, compatible in size as those from light microscopic observations. In contrast, the big RW/GL loops lead to a more homogeneous chromatin distribution. Only the MLS model agrees with the low overlap of chromosomes, their arms, and subchromosomal domains found experimentally. A review of experimental spatial distance measurements between genomic markers labelled by FISH as a function of their genomic separation from different publications and comparison to simulated spatial distances also favours an MLS-like model with loops and linkers of 63 to 126 kbp. The chromatin folding topology also reduces the apparent persistence length of the chromatin fibre to a value significantly lower than the free solution persistence length, explaining the low persistence lengths found various experiments. The predicted large spaces between the chromatin fibres allow typically sized biological molecules to reach nearly every location in the nucleus by moderately obstructed diffusion and disagrees with the much simplified assumption that defined channels between territories for molecular transport as in the Interchromosomal Domain (ICD) hypothesis exist. All this is also in agreement with recent selective high-resolution chromosome interaction capture (T2C) experiments, the scaling behaviour of the DNA sequence, the dynamics of the chromatin fibre, the nuclear diffusion of molecules, as well as other experiments. In summary, this polymer simulation framework compared to experimental data clearly favours only a quasi-chromatin fibre forming a stable multi-loop aggregate/rosette like genome organization and dynamics whose local topology is tightly connected to the global morphology and dynamics of the cell nucleus.

Recent Progress in Light Sheet Microscopy for Biological Applications

The introduction of light sheet fluorescence microscopy (LSFM) has overcome the challenges in conventional optical microscopy. Among the recent breakthroughs in fluorescence microscopy, LSFM had been proven to provide a high three-dimensional spatial resolution, high signal-to-noise ratio, fast imaging acquisition rate, and minuscule levels of phototoxic and photodamage effects. The aforementioned auspicious properties are crucial in the biomedical and clinical research fields, covering a broad range of applications: from the super-resolution imaging of intracellular dynamics in a single cell to the high spatiotemporal resolution imaging of developmental dynamics in an entirely large organism. In this review, we provided a systematic outline of the historical development of LSFM, detailed discussion on the variants and improvements of LSFM, and delineation on the most recent technological advancements of LSFM and its potential applications in single molecule/particle detection, single-molecule super-resolution imaging, imaging intracellular dynamics of a single cell, multicellular imaging: cell-cell and cell-matrix interactions, plant developmental biology, and brain imaging and developmental biology.

Quantitative mapping of fluorescently tagged cellular proteins using FCS-calibrated four-dimensional imaging

The ability to tag a protein at its endogenous locus with a fluorescent protein (FP) enables quantitative understanding of protein dynamics at the physiological level. Genome-editing technology has now made this powerful approach routinely applicable to mammalian cells and many other model systems, thereby opening up the possibility to systematically and quantitatively map the cellular proteome in four dimensions. 3D time-lapse confocal microscopy (4D imaging) is an essential tool for investigating spatial and temporal protein dynamics; however, it lacks the required quantitative power to make the kind of absolute and comparable measurements required for systems analysis. In contrast, fluorescence correlation spectroscopy (FCS) provides quantitative proteomic and biophysical parameters such as protein concentration, hydrodynamic radius, and oligomerization but lacks the capability for high-throughput application in 4D spatial and temporal imaging. Here we present an automated experimental and computational workflow that integrates both methods and delivers quantitative 4D imaging data in high throughput. These data are processed to yield a calibration curve relating the fluorescence intensities (FIs) of image voxels to the absolute protein abundance. The calibration curve allows the conversion of the arbitrary FIs to protein amounts for all voxels of 4D imaging stacks. Using our workflow, users can acquire and analyze hundreds of FCS-calibrated image series to map their proteins of interest in four dimensions. Compared with other protocols, the current protocol does not require additional calibration standards and provides an automated acquisition pipeline for FCS and imaging data. The protocol can be completed in 1 d.

Random Motion of Chromatin Is Influenced by Lamin A Interconnections

Using fluorescence correlation spectroscopy in single-plane illumination microscopy, we investigated the dynamics of chromatin in interphase mouse adult fibroblast cell nuclei under the influence of the intermediate filament protein lamin A. We find that 1) lamin A-eGFP and histone H2A-mRFP show significant comobility, indicating that their motions are clearly interconnected in the nucleus, and 2) that the random motion of histones H2A within the chromatin network is subdiffusive, i.e., the effective diffusion coefficient decreases for slow timescales. Knocking out lamin A changes the diffusion back to normal. Thus, lamin A influences the dynamics of the entire chromatin network. Our conclusion is that lamin A plays a central role in determining the viscoelasticity of the chromatin network and helping to maintain local ordering of interphase chromosomes.

FCS Analysis of Protein Mobility on Lipid Monolayers

In vitro membrane model systems are used to dissect complex biological phenomena under controlled unadulterated conditions. In this context, lipid monolayers are a powerful tool to particularly study the influence of lipid packing on the behavior of membrane proteins. Here, monolayers deposited in miniaturized fixed area-chambers, which require only minute amounts of protein, were used and shown to faithfully reproduce the characteristics of Langmuir monolayers. This assay is ideally suited to be combined with single-molecule sensitive fluorescence correlation spectroscopy (FCS) to characterize diffusion dynamics. Our results confirm the influence of lipid packing on lipid mobility and validate the use of FCS as an alternative to conventional surface pressure measurements for characterizing the monolayer. Furthermore, we demonstrate the effect of lipid density on the diffusional behavior of membrane-bound components. We exploit the sensitivity of FCS to characterize protein interactions with the lipid monolayer in a regime in which the monolayer physical properties are not altered. To demonstrate the potential of our approach, we analyzed the diffusion behavior of objects of different nature, ranging from a small peptide to a large DNA-based nanostructure. Moreover, in this work we quantify the surface viscosity of lipid monolayers. We present a detailed strategy for the conduction of point FCS experiments on lipid monolayers, which is the first step toward extensive studies of protein-monolayer interactions.

Local raster image correlation spectroscopy generates high-resolution intracellular diffusion maps

Raster image correlation spectroscopy (RICS) is a powerful method for measuring molecular diffusion in live cells directly from images acquired on a laser scanning microscope. However, RICS only provides single average diffusion coefficients from regions with a lateral size on the order of few micrometers, which means that its spatial resolution is mainly limited to the cellular level. Here we introduce the local RICS (L-RICS), an easy-to-use tool that generates high resolution maps of diffusion coefficients from images acquired on a laser scanning microscope. As an application we show diffusion maps of a green fluorescent protein (GFP) within the nucleus and within the nucleolus of live cells at an effective spatial resolution of 500 nm. We find not only that diffusion in the nucleolus is slowed down compared to diffusion in the nucleoplasm, but also that diffusion in the nucleolus is highly heterogeneous.

Lorenzo Scipioni et al. present Local Raster Image Correlation Spectroscopy (L-RICS), a method for generating sub-micrometer diffusion maps. They apply L-RICS to GFP in live cells and find that diffusion coefficients differ between the nucleus and nucleolus and are highly heterogeneous within compartments.

Visualization of barriers and obstacles to molecular diffusion in live cells by spatial pair-cross-correlation in two dimensions

Despite recent advances in optical super-resolution, we lack a method that can visualize the path followed by diffusing molecules in the cytoplasm or in the nucleus of cells. Fluorescence correlation spectroscopy (FCS) provides molecular dynamics at the single molecule level by averaging the behavior of many molecules over time at a single spot, thus achieving very good statistics but at only one point in the cell. Earlier image-based methods including raster-scan and spatiotemporal image correlation need spatial averaging over relatively large areas, thus compromising spatial resolution. Here, we use spatial pair-cross-correlation in two dimensions (2D-pCF) to obtain relatively high resolution images of molecular diffusion dynamics and transport in live cells. The 2D-pCF method measures the time for a particle to go from one location to another by cross-correlating the intensity fluctuations at specific points in an image. Hence, a visual map of the average path followed by molecules is created.

The hitchhiker's guide to quantitative diffusion measurements

Quantitative comparison of three widely used techniques for diffusion measurements, implemented on a light sheet microscope.

The Next Frontier: Quantitative Biochemistry in Living Cells

Researchers striving to convert biology into an exact science foremost rely on structural biology and biochemical reconstitution approaches to obtain quantitative data. However, cell biological research is moving at an ever-accelerating speed into areas where these approaches lose much of their edge. Intrinsically unstructured proteins and biochemical interaction networks composed of interchangeable, multivalent, and unspecific interactions pose unique challenges to quantitative biology, as do processes that occur in discrete cellular microenvironments. Here we argue that a conceptual change in our way of conducting biochemical experiments is required to take on these new challenges. We propose that reconstitution of cellular processes in vitro should be much more focused on mimicking the cellular environment in vivo, an approach that requires detailed knowledge of the material properties of cellular compartments, essentially requiring a material science of the cell. In a similar vein, we suggest that quantitative biochemical experiments in vitro should be accompanied by corresponding experiments in vivo, as many newly relevant cellular processes are highly context-dependent. In essence, this constitutes a call for chemical biologists to convert their discipline from a proof-of-principle science to an area that could rightfully be called quantitative biochemistry in living cells. In this essay, we discuss novel techniques and experimental strategies with regard to their potential to fulfill such ambitious aims.

Molecular simulations of cellular processes

It is, nowadays, possible to simulate biological processes in conditions that mimic the different cellular compartments. Several groups have performed these calculations using molecular models that vary in performance and accuracy. In many cases, the atomistic degrees of freedom have been eliminated, sacrificing both structural complexity and chemical specificity to be able to explore slow processes. In this review, we will discuss the insights gained from computer simulations on macromolecule diffusion, nuclear body formation, and processes involving the genetic material inside cell-mimicking spaces. We will also discuss the challenges to generate new models suitable for the simulations of biological processes on a cell scale and for cell-cycle-long times, including non-equilibrium events such as the co-translational folding, misfolding, and aggregation of proteins. A prominent role will be played by the wise choice of the structural simplifications and, simultaneously, of a relatively complex energetic description. These challenging tasks will rely on the integration of experimental and computational methods, achieved through the application of efficient algorithms. Graphical abstract.

Single plane illumination microscopy as a tool for studying nucleome dynamics

Single plane illumination microscopy (SPIM) is a new optical method that has become extremely important in recent years. It is based on the formation of a "light slice" in the specimen in which fluorescently tagged molecules are observed. The spatial resolution is close to that of confocal optics, but without the disadvantages inherent to scanning or high laser irradiation doses. A recent development is light sheet fluctuation microscopy, which exploits the dynamic information contained in the fluorescence intensity fluctuations of each image pixel. Here we review the principles of this method and show some recent applications to the dynamics of transcription factors and chromatin. We show that the dimerization of Fos and Jun proteins is directly linked to their binding to DNA; that nuclear receptor activation changes their intranuclear dynamics; and that the viscoelastic behavior of interphase chromatin strongly depends on the presence of lamin A.

3D Protein Dynamics in the Cell Nucleus

The three-dimensional (3D) architecture of the cell nucleus plays an important role in protein dynamics and in regulating gene expression. However, protein dynamics within the 3D nucleus are poorly understood. Here, we present, to our knowledge, a novel combination of 1) single-objective based light-sheet microscopy, 2) photoconvertible proteins, and 3) fluorescence correlation microscopy, to quantitatively measure 3D protein dynamics in the nucleus. We are able to acquire >3400 autocorrelation functions at multiple spatial positions within a nucleus, without significant photobleaching, allowing us to make reliable estimates of diffusion dynamics. Using this tool, we demonstrate spatial heterogeneity in Polymerase II dynamics in live U2OS cells. Further, we provide detailed measurements of human-Yes-associated protein diffusion dynamics in a human gastric cancer epithelial cell line.

Single-Cell and Single-Molecule Analysis of Gene Expression Regulation

Recent advancements in single-cell and single-molecule imaging technologies have resolved biological processes in time and space that are fundamental to understanding the regulation of gene expression. Observations of single-molecule events in their cellular context have revealed highly dynamic aspects of transcriptional and post-transcriptional control in eukaryotic cells. This approach can relate transcription with mRNA abundance and lifetimes. Another key aspect of single-cell analysis is the cell-to-cell variability among populations of cells. Definition of heterogeneity has revealed stochastic processes, determined characteristics of under-represented cell types or transitional states, and integrated cellular behaviors in the context of multicellular organisms. In this review, we discuss novel aspects of gene expression of eukaryotic cells and multicellular organisms revealed by the latest advances in single-cell and single-molecule imaging technology.

Measuring macromolecular crowding in cells through fluorescence anisotropy imaging with an AIE fluorogen

We report a new strategy that allows spatiotemporal visualization of the macromolecular crowding effect in cells.

The detailed 3D multi-loop aggregate/rosette chromatin architecture and functional dynamic organization of the human and mouse genomes

BACKGROUND

The dynamic three-dimensional chromatin architecture of genomes and its co-evolutionary connection to its function-the storage, expression, and replication of genetic information-is still one of the central issues in biology. Here, we describe the much debated 3D architecture of the human and mouse genomes from the nucleosomal to the megabase pair level by a novel approach combining selective high-throughput high-resolution chromosomal interaction capture (T2C), polymer simulations, and scaling analysis of the 3D architecture and the DNA sequence.

RESULTS

The genome is compacted into a chromatin quasi-fibre with ~5 ± 1 nucleosomes/11 nm, folded into stable ~30-100 kbp loops forming stable loop aggregates/rosettes connected by similar sized linkers. Minor but significant variations in the architecture are seen between cell types and functional states. The architecture and the DNA sequence show very similar fine-structured multi-scaling behaviour confirming their co-evolution and the above.

CONCLUSIONS

This architecture, its dynamics, and accessibility, balance stability and flexibility ensuring genome integrity and variation enabling gene expression/regulation by self-organization of (in)active units already in proximity. Our results agree with the heuristics of the field and allow "architectural sequencing" at a genome mechanics level to understand the inseparable systems genomic properties.