Texture analysis of fluorescence lifetime images of nuclear DNA with effect of fluorescence resonance energy transfer

Method to Detect the Cellular Source of Over-Activated NADPH Oxidases Using NAD(P)H Fluorescence Lifetime Imaging

Fluorescence-lifetime imaging microscopy (FLIM) is a technique to generate images, in which the contrast is obtained by the excited-state lifetime of fluorescent molecules instead of their intensity and emission spectrum. The ubiquitous coenzymes NADH and NADPH, hereafter NAD(P)H, in cells show a short fluorescence lifetime ≈400 psec in the free-state and a longer fluorescence lifetime when bound to enzymes. The fluorescence lifetime of NAD(P)H in this state depends on the binding-site on the specific enzyme. In the case of NADPH bound to members of the NADPH oxidases family we measured a fluorescence lifetime of 3650 psec as compared to enzymes typically active in cells, in which case fluorescence lifetimes of ∼2000 psec are measured. Here we present a robust protocol based on NAD(P)H fluorescence lifetime imaging in isolated cells to distinguish between normally active enzymes and NADPH oxidases, mainly responsible for oxidative stress. © 2017 by John Wiley & Sons, Inc.

Tracking CNS and systemic sources of oxidative stress during the course of chronic neuroinflammation

The functional dynamics and cellular sources of oxidative stress are central to understanding MS pathogenesis but remain elusive, due to the lack of appropriate detection methods. Here we employ NAD(P)H fluorescence lifetime imaging to detect functional NADPH oxidases (NOX enzymes) in vivo to identify inflammatory monocytes, activated microglia, and astrocytes expressing NOX1 as major cellular sources of oxidative stress in the central nervous system of mice affected by experimental autoimmune encephalomyelitis (EAE). This directly affects neuronal function in vivo, indicated by sustained elevated neuronal calcium. The systemic involvement of oxidative stress is mirrored by overactivation of NOX enzymes in peripheral CD11b⁺ cells in later phases of both MS and EAE. This effect is antagonized by systemic intake of the NOX inhibitor and anti-oxidant epigallocatechin-3-gallate. Together, this persistent hyper-activation of oxidative enzymes suggests an “oxidative stress memory” both in the periphery and CNS compartments, in chronic neuroinflammation.

Fluorescent protein-based biosensors and their clinical applications

Green fluorescent protein and its relatives have shed their light on a wide range of biological problems. To date, with a color palette consisting of fluorescent proteins with different spectra, researchers can "paint" living cells as they desire. Moreover, sophisticated biosensors engineered to contain single or multiple fluorescent proteins, including FRET-based biosensors, spatiotemporally unveil molecular mechanisms underlying physiological processes. Although such molecules have contributed considerably to basic research, their abilities to be used in applied life sciences have yet to be fully explored. Here, we review the molecular bases of fluorescent proteins and fluorescent protein-based biosensors and focus on approaches aimed at applying such proteins to the clinic.

The Use of texture analysis in the morpho-functional characterization of mast cell degranulation in rainbow trout (Onchorhynchus mykiss)

Degranulation of intestinal mast cells in rainbow trout was studied ex vivo by means of texture analysis and related to the maximal intestinal contraction elicited by degranulation itself. Two strips from the same intestinal segment from ten trout were sampled, processed for light microscopy and stained with Giemsa solution. One of the two strips was exposed to an incremental dose of compound 48/80 in an isolated organ bath before processing. Gray-level RGB channel equivalent and 8-bit gray-level images of five granular cytoplasm areas of mast cells for each section were analyzed for texture features and to evaluate discrimination possibility between treatment groups by means of linear discriminant analysis according to feature selection methods and RGB stacks. Differential mean values (after-before compound 48/80) of the green (r 2 = 0.84, p < 0.01) and blue (r 2 = 0.83, p < 0.01) RGB channels and 8-bit grayscale (r 2 = 0.76, p < 0.05) image correlated significantly with the respective value of maximal intestinal contraction. A possible acidic (anionic) nature for the putative pro-contractile basophil agonist can be inferred.

Global analysis of microscopic fluorescence lifetime images using spectral segmentation and a digital micromirror spatial illuminator

Fluorescence lifetime imaging (FLIM) is very demanding from a technical and computational perspective, and the output is usually a compromise between acquisition/processing time and data accuracy and precision. We present a new approach to acquisition, analysis, and reconstruction of microscopic FLIM images by employing a digital micromirror device (DMD) as a spatial illuminator. In the first step, the whole field fluorescence image is collected by a color charge-coupled device (CCD) camera. Further qualitative spectral analysis and sample segmentation are performed to spatially distinguish between spectrally different regions on the sample. Next, the fluorescence of the sample is excited segment by segment, and fluorescence lifetimes are acquired with a photon counting technique. FLIM image reconstruction is performed by either raster scanning the sample or by directly accessing specific regions of interest. The unique features of the DMD illuminator allow the rapid on-line measurement of global good initial parameters (GIP), which are supplied to the first iteration of the fitting algorithm. As a consequence, a decrease of the computation time required to obtain a satisfactory quality-of-fit is achieved without compromising the accuracy and precision of the lifetime measurements.

Intravital two-photon microscopy: focus on speed and time resolved imaging modalities

Initially used mainly in the neurosciences, two-photon microscopy has become a powerful tool for the analysis of immunological processes. Here, we describe currently available two-photon microscopy techniques with a focus on novel approaches that allow very high image acquisition rates compared with state-of-the-art systems. This improvement is achieved through a parallelization of the excitation process: multiple beams scan the sample simultaneously, and the fluorescence is collected with sensitive charge-coupled device (CCD)-based line or field detectors. The new technique's performance is compared with conventional single beam laser-scanning systems that detect signals by means of photomultipliers. We also discuss the use of time- and polarization-resolved fluorescence detection, especially fluorescence lifetime imaging (FLIM), which goes beyond simple detection of cells and tissue structures and allows insight into cellular physiology. We focus on the analysis of endogenous fluorophores such as NAD(P)H as a way to analyze the redox status in cells with subcellular resolution. Here, high-speed imaging setups in combination with novel ways of data analysis allow the generation of FLIM data sets almost in real time. The implications of this technology for the analysis of immune reactions and other cellular processes are discussed.

Conservation and alteration of chromosome territory arrangements in thyroid carcinoma cell nuclei

Chromosome territories (CTs) are intranuclear subregions occupied by individual chromosomes in an interphase cell. In this study, we investigated intranuclear CT positionings of chromosomes 10 (CS10), 18 (CS18), and 19 (CS19) in epithelial cells from four normal thyroid tissue (NT), four adenomatous goiters (AGs), six papillary carcinomas (PCs), and two undifferentiated carcinomas (UCs) using the multicolor fluorescence in situ hybridization method. In the NT and AGs, the radial positionings of CS10 and CS18 were detected at the periphery of nuclei in more than 60% and 80% of cells, respectively, whereas the radial positioning of CS19 was in the central region of the nuclei in more than 80% of cells. In the PCs, radial positioning pattern of CS10 and CS18 were similar to that in the NT. The nuclei with centrally located CS19 in PCs were less frequent than those in NT cells (p < 0.01). On the other hand, UCs with cells having DNA amplification demonstrated the locational abnormalities of the CS10, CS18, and CS19 radial positions. These findings indicate that alteration of CT positioning could be related to DNA amplification and, morphologically, may explain the nuclear atypia that accompanies the abnormal chromatin feature.

Cytometric assessment of DNA damage in relation to cell cycle phase and apoptosis

Reviewed are the methods aimed to detect DNA damage in individual cells, estimate its extent and relate it to cell cycle phase and induction of apoptosis. They include the assays that reveal DNA fragmentation during apoptosis, as well as DNA damage induced by genotoxic agents. DNA fragmentation that occurs in the course of apoptosis is detected by selective extraction of degraded DNA. DNA in chromatin of apoptotic cells shows also increased propensity to undergo denaturation. The most common assay of DNA fragmentation relies on labelling DNA strand breaks with fluorochrome-tagged deoxynucleotides. The induction of double-strand DNA breaks (DSBs) by genotoxic agents provides a signal for histone H2AX phosphorylation on Ser139; the phosphorylated H2AX is named gammaH2AX. Also, ATM-kinase is activated through its autophosphorylation on Ser1981. Immunocytochemical detection of gammaH2AX and/or ATM-Ser1981(P) are sensitive probes to reveal induction of DSBs. When used concurrently with analysis of cellular DNA content and caspase-3 activation, they allow one to correlate the extent of DNA damage with the cell cycle phase and with activation of the apoptotic pathway. The presented data reveal cell cycle phase-specific patterns of H2AX phosphorylation and ATM autophosphorylation in response to induction of DSBs by ionizing radiation, topoisomerase I and II inhibitors and carcinogens. Detection of DNA damage in tumour cells during radio- or chemotherapy may provide an early marker predictive of response to treatment.

Cytometric assessment of DNA damage in relation to cell cycle phase and apoptosis

Reviewed are the methods aimed to detect DNA damage in individual cells, estimate its extent and relate it to cell cycle phase and induction of apoptosis. They include the assays that reveal DNA fragmentation during apoptosis, as well as DNA damage induced by genotoxic agents. DNA fragmentation that occurs in the course of apoptosis is detected by selective extraction of degraded DNA. DNA in chromatin of apoptotic cells shows also increased propensity to undergo denaturation. The most common assay of DNA fragmentation relies on labelling DNA strand breaks with fluorochrome-tagged deoxynucleotides. The induction of double-strand DNA breaks (DSBs) by genotoxic agents provides a signal for histone H2AX phosphorylation on Ser139; the phosphorylated H2AX is named gammaH2AX. Also, ATM-kinase is activated through its autophosphorylation on Ser1981. Immunocytochemical detection of gammaH2AX and/or ATM-Ser1981(P) are sensitive probes to reveal induction of DSBs. When used concurrently with analysis of cellular DNA content and caspase-3 activation, they allow one to correlate the extent of DNA damage with the cell cycle phase and with activation of the apoptotic pathway. The presented data reveal cell cycle phase-specific patterns of H2AX phosphorylation and ATM autophosphorylation in response to induction of DSBs by ionizing radiation, topoisomerase I and II inhibitors and carcinogens. Detection of DNA damage in tumour cells during radio- or chemotherapy may provide an early marker predictive of response to treatment.

3D-resolved investigation of the pH gradient in artificial skin constructs by means of fluorescence lifetime imaging

PURPOSE

The development of substitutes for the human skin, e.g., artificial skin constructs (ASCs), is of particular importance for pharmaceutical and dermatologic research because they represent economical test samples for the validation of new drugs. In this regard, it is essential for the skin substitutes to be reliable models of the genuine skin, i.e., to have similar morphology and functionality. Particularly important is the barrier function, i.e., the selective permeability of the skin, which is strongly related to the epidermal pH gradient. Because the pH significantly influences the permeation profile of ionizable drugs such as nonsteroidal anti-inflammatory drugs, it is of major importance to quantitatively measure the epidermal pH gradient of the ASC and compare it to that of genuine skin.

METHODS

Using three-dimensional fluorescence lifetime imaging combined with two-photon scanning microscopy, we measured with submicron resolution the three-dimensional pH gradient in the epidermis of ASCs stained with 2',7'-bis-(2-carboxyethyl)-5/6-carboxyfluorescein.

RESULTS

Similar to genuine skin, the surface of the artificial epidermis has an acidic character (pH 5.9), whereas in the deeper layers the pH increases up to 7.0. Moreover, the pH gradient differs in the cell interior (maximally 7.2) and in the intercellular matrix (maximally 6.6). Apart from the similitude of the pH distribution, the genuine and the artificial skin prove to have similar morphologies and to be characterized by similar distributions of the refractive index.

CONCLUSIONS

Artificial skin is a reliable model of genuine human skin, e.g., in permeability studies, because it is characterized by a similar pH gradient, a similar morphology, and a similar distribution of the refractive index to that of genuine skin.

Application of microscopic Forster resonance energy transfer to cytological diagnosis of the thyroid tumors

We propose a novel application of microscopic Forster resonance energy transfer (FRET) to clinical cytological diagnosis based on sensitive measurements of distance changes between fluorescently labeled deoxyribose nucleic acid (DNA) molecules. We have employed the microscopic FRET imaging for investigation of six papillary carcinomas and eight benign cases. In each case the FRET images of 20 cells stained by the AT-specific donor Hoechst 33258 and the GC-specific acceptor 7-aminoactinomycin D were acquired and analyzed by texture analysis. We have not found significant difference of the mean FRET efficiency between the benign and malignant groups. On the other hand, the texture analysis revealed a significant difference of the intranuclear spatial distribution of FRET efficiencies between the benign and malignant groups. The results indicate that despite the similar average distance between the AT- and the GC-rich DNA segments in the papillary carcinomas and the benign cases, the former has more heterogeneous distribution of the AT- and the GC-rich DNA segments in nuclei compared to the benign groups. We have demonstrated that the FRET imaging is a helpful tool for the medical cytological diagnosis of human tumors by giving information on the chromatin topology on the scale below the resolution of conventional optical microscopes. (c) 2005 Society of Photo-Optical Instrumentation Engineers.

Identification of plasma membrane macro- and microdomains from wavelet analysis of FRET microscopy

In this study, we sought to characterize functional signaling domains by applying the multiresolution properties of the continuous wavelet transform to fluorescence resonance energy transfer (FRET) microscopic images of plasma membranes. A genetically encoded FRET reporter of protein kinase C (PKC)-dependent phosphorylation was expressed in COS1 cells. Differences between wavelet coefficient matrices revealed several heterogeneous domains (typically ranging from 1 to 5 microm), reflecting the dynamic balance between PKC and phosphatase activity during stimulation with phorbol-12,13-dibutyrate or acetylcholine. The balance in these domains was not necessarily reflected in the overall plasma membrane changes, and observed heterogeneity was absent when cells were exposed to a phosphatase or PKC inhibitor. Prolonged exposure to phorbol-12,13-dibutyrate and acetylcholine yielded more homogeneous FRET distribution in plasma membranes. The proposed wavelet-based image analysis provides, for the first time, a basis and a means of detecting and quantifying dynamic changes in functional signaling domains, and may find broader application in studying fine aspects of cellular signaling by various imaging reporters.

Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli

By exploring global gene expression of Escherichia coli growing on six different carbon sources, we discovered a striking genome transcription pattern: as carbon substrate quality declines, cells systematically increase the number of genes expressed. Gene induction occurs in a hierarchical manner and includes many factors for uptake and metabolism of better but currently unavailable carbon sources. Concomitantly, cells also increase their motility. Thus, as the growth potential of the environment decreases, cells appear to devote progressively more energy on the mere possibility of improving conditions. This adaptation is not what would be predicated by classic regulatory models alone. We also observe an inverse correlation between gene activation and rRNA synthesis suggesting that reapportioning RNA polymerase (RNAP) contributes to the expanded genome activation. Significant differences in RNAP distribution in vivo, monitored using an RNAP-green fluorescent protein fusion, from energy-rich and energy-poor carbon source cultures support this hypothesis. Together, these findings represent the integration of both substrate-specific and global regulatory systems, and may be a bacterial approximation to metazoan risk-prone foraging behavior.

A survey on histological image analysis-based assessment of three major biological factors influencing radiotherapy: proliferation, hypoxia and vasculature

Image analysis is a rapidly evolving field with growing applications in science and engineering. In cancer research, it has played a key role in advancing techniques of major diagnostic importance, minimising human intervention and providing vital clinical information. Especially in the field of tissue microscopy, the use of computers for the automated analysis of histological sections is becoming increasingly important. This paper presents an overview of various image analysis methodologies and summarises developments in this field, with great emphasis given on the assessment of three major biological factors known to influence the outcome of radiotherapy: proliferation, vasculature and hypoxia. A brief introduction followed by a survey is provided in each of these areas.

The distribution of RNA polymerase in Escherichia coli is dynamic and sensitive to environmental cues

Despite extensive genetic, biochemical and structural studies on Escherichia coli RNA polymerase (RNAP), little is known about its location and distribution in response to environmental changes. To visualize the RNAP by fluorescence microscopy in E. coli under different physiological conditions, we constructed a functional rpoC-gfp gene fusion on the chromosome. We show that, although RNAP is located in the nucleoid and at its periphery, the distribution of RNAP is dynamic and dramatically influenced by cell growth conditions, nutrient starvation and overall transcription activity inside the cell. Moreover, mutational analysis suggests that the stable RNA synthesis plays an important role in nucleoid condensation.

Morphological abstraction of thyroid tumor cell nuclei using morphometry with factor analysis

Various morphonuclear studies by digital image analysis have successfully been applied to quantify the nuclear morphology, including chromatin distribution pattern, in cytology of various organs; however, the majority of past reports have not shown correlation between the quantitative data by digital image analysis and cytological findings in practical diagnosis. In this report, we present the usefulness of morphological abstraction to combine the objective data and subjective observation in cytological diagnosis. Randomly selected, 100 cells in each Papanicolaou-stained ABC smear samples of 39 benign and malignant thyroid tumor cases were studied. Gray-level image data provided seven parameters for nuclear size, four parameters for nuclear shape, and 16 parameters showing the nuclear chromatin patterns from high-dimensional texture analysis of using co-occurrence and run-length matrices. To statistically abstract nuclear morphology, factor analysis was used. Factor analysis classified morphological nuclear characters as abstraction parameter into five abstract parameters composed of nuclear size, shape, heterogeneity, and contrast and homogeneity of chromatin pattern. The nuclei of papillary carcinoma showed larger size, more irregular shape, and higher contrast of chromatin pattern than those of the benign group. The follicular carcinomas have larger nucleus in each cell and more monotonous chromatin pattern among cells in each case than those of the benign group. Morphological abstraction by morphometry with factor analysis may provide a practical approach to the detection of the underlying characteristics of nuclear morphology in aspiration biopsy cytology.

Spatial distribution analysis of AT- and GC-rich regions in nuclei using corrected fluorescence resonance energy transfer

We employed microscopic intensity-based fluorescence resonance energy transfer (FRET) images with correction by donor and acceptor concentrations to obtain unbiased maps of spatial distribution of the AT- and GC-rich DNA regions in nuclei. FRET images of 137 bovine aortic endothelial cells stained by the AT-specific donor Hoechst 33258 and the GC-specific acceptor 7-aminoactinomycin D were acquired and corrected for the donor and acceptor concentrations by the Gordon's method based on the three fluorescence filter sets. The corrected FRET images were quantitatively analyzed by texture analysis to correlate the spatial distribution of the AT- and GC-rich DNA regions with different phases of the cell cycle. Both visual observation and quantitative texture analysis revealed an increased number and size of the low FRET efficiency centers for cells in the G(2)/M-phases, compared to the G(1)-phase cells. We have detected cell cycle-dependent changes of the spatial organization and separation of the AT- and GC-rich DNA regions. Using the corrected FRET (cFRET) technique, we were able to detect early DNA separation stages in late interphase nuclei.

Detection of underlying characteristics of nuclear chromatin patterns of thyroid tumor cells using texture and factor analyses

BACKGROUND

Aspiration biopsy cytology of thyroid tumors has been used more frequently in recent times to differentiate between malignant and benign lesions. Chromatin patterns of the tumor cell nuclei are one of most important factors for cytologic diagnosis. The interpretation of nuclear chromatin patterns is subjective and more difficult than that of nuclear size or shape. In the present report, we investigated how to detect underlying chromatin characteristics of benign and malignant thyroid tumor cells by means of texture and factor analyses.

METHODS

We employed a computer-aided system in which light microscopy was combined with an image processor and monochrome camera. Using this system, 100 randomly selected cells in a Papanicolaou stained, aspiration biopsy cytologic smear in each case of 39 benign and malignant thyroid tumor cases were digitized. We applied two-dimensional and higher texture analyses with the use of co-occurrence and run-length matrices to analyze the chromatin patterns. Factor analysis was used to determine whether a large number of independent variables actually measured one or more underlying common variables.

RESULTS

According to parameters with high factor-loading values, the morphologic chromatin characters were classified into three categories according to heterogeneity, contrast, and homogeneity of chromatin patterns. On the basis of analyses with these morphologic categories, nuclei of papillary carcinoma showed higher contrast of chromatin patterns than did those of the benign group. Moreover, there was a variety of contrasting chromatin patterns among cells in each papillary carcinoma case in comparison with the benign group. In contrast, follicular carcinomas showed a significant difference in the standard deviation of factor 3, which indicated more monotonous chromatin patterns among cells in each follicular carcinoma case than in each benign case.

CONCLUSION

We believe that this technique, using texture and factor analyses, is useful in the detection of underlying characteristics of nuclear chromatin patterns in aspiration biopsy cytology.

Diheteroarylethenes as thermally stable photoswitchable acceptors in photochromic fluorescence resonance energy transfer (pcFRET)

We have employed diheteroarylethenes as acceptors for photochromic FRET (pcFRET), a technique introduced for the quantitative determination of fluorescence resonance energy transfer (FRET). In pcFRET, the fluorescent emission of the donor is modulated by cyclical transformations of a photochromic acceptor. Light induces a reversible change in the structure and, concomitantly, in the absorption properties of the acceptor. Only the closed forms of the selected diheteroarylethenes 2a and 2b have an absorption band overlapping the emission band of the donor, 1. The corresponding variation in the overlap integral (and thus critical transfer distance R(o)) between the two states provides the means for reversibly switching the process of FRET on and off, allowing direct and repeated evaluation of the relative changes in the donor fluorescence quantum yield. The diheteroarylethenes demonstrate excellent stability in aqueous media, an absence of thermal back reactions, and negligible fatigue. The equilibration of these systems after exposure to near-UV or visible light follows simple monoexponential kinetics. We developed a general conceptual scheme for such coupled photochromic-FRET reactions, allowing quantitative interpretations of the photostationary and kinetic data, from which the quantum yields for the cyclization and cycloreversion reactions of the photochromic acceptor were calculated.

Texture analysis of fluorescence lifetime images of AT- and GC-rich regions in nuclei

We used intensity and fluorescence lifetime microscopy (FLIM) of 3T3 nuclei to investigate the existence of AT-rich and GC-rich regions of the nuclear DNA. Hoechst 33258 (Ho) and 7-aminoactinomycin D (7-AAD) were used as fluorescence probes specific for AT and GC base pairs, respectively. YOYO-1 (Yo) was used as a dye that displays distinct fluorescence lifetimes when bound to AT or GC base pairs. We combined fluorescence imaging of Ho and 7-AAD with time-resolved measurements of Yo and took advantage of an additional information content of the time-resolved fluorescence. Because a single nucleus could not be stained and measured with all three dyes, we used texture analysis to compare the spatial distribution of AT-rich and GC-rich DNA in 100 nuclei in different phases of the cell cycle. The fluorescence intensity-based analysis of Ho- or 7-AAD-stained images indicates increased number and larger size of the DNA condensation centers in the G2/M-phases compared to G0/1-phases. The lifetime-based study of Yo-stained images suggests spatial separation of the AT- or GC-rich DNA regions in the G2/M-phase. Texture analysis of fluorescence intensity and lifetime images was used to quantitatively study the spatial change of condensation and separation of AT- and GC-rich DNA during the cell cycle.