carbocyanines and cyanine-dye-2

Hypochlorite anion, one of the biologically important reactive oxygen species, plays an essential role in diverse normal biochemical functions and abnormal pathological processes. Herein, an efficient high-resolution mitochondria-targeting ratiometric fluorescent probe for hypochlorous acid detection has been designed, synthesized and characterized. It is easily synthesized by the condensation reaction (CC) of a 2-(2-hydroxyphenyl) quinazolin-4(3H)-one fluorophore and a cyanine group (mitochondria-targeting), which made the whole molecular a large Stokes shift (210nm) and the two well-resolved emission peaks separated by 140nm. As a result, it is considered as a good candidate for high resolution hypochlorous acid imaging in live cells. The ratiometric fluorescent probe exhibited outstanding features of high sensitivity, high selectivity, rapid response time (within 50s), and excellent mitochondria-targeting ability. Moreover, the probe can also be successfully applied to imaging endogenously hypochlorous acid in the mitochondria of living cells with low cytotoxicity, and high resolution.

Topics: Carbocyanines; Cell Line; Fluorescent Dyes; Humans; Hypochlorous Acid; Microscopy, Fluorescence; Mitochondria; Optical Imaging; Quinazolinones; Spectrometry, Fluorescence

The difficulty in developing a diagnostic assay for Creutzfeldt - Jakob disease (CJD) and other transmissible spongiform encephalopathies (TSEs) stems in part from the fact that the infectious agent is an aberrantly folded form of an endogenous cellular protein. This precludes the use of the powerful gene based technologies currently applied to the direct detection of other infectious agents. To circumvent this problem our research objective has been to identify a set of proteins exhibiting characteristic differential abundance in response to TSE infection. The objective of the present study was to assess the disease specificity of differentially abundant urine proteins able to identify scrapie infected mice. Two-dimensional differential gel electrophoresis was used to analyze longitudinal collections of urine samples from both prion-infected mice and a transgenic mouse model of Alzheimer's disease. The introduction of fluorescent dyes, that allow multiple samples to be co-resolved and visualized on one two dimensional gel, have increased the accuracy of this methodology for the discovery of robust protein biomarkers for disease. The accuracy of a small panel of differentially abundant proteins to correctly classify an independent naïve sample set was determined. The results demonstrated that at the time of clinical presentation the differential abundance of urine proteins were capable of identifying the prion infected mice with 87% sensitivity and 93% specificity. The identity of the diagnostic differentially abundant proteins was investigated by mass spectrometry.

Topics: Algorithms; Alzheimer Disease; Animals; Biomarkers; Carbocyanines; Diagnosis, Differential; Disease Models, Animal; Electrophoresis, Gel, Two-Dimensional; Female; Mass Spectrometry; Mice; Mice, Inbred C57BL; Mice, Transgenic; Principal Component Analysis; Proteins; Proteome; Reproducibility of Results; Scrapie

A new dye, PTZ-Cy2, based on a hybrid cyanine–phenothiazine platform, is described. Oxidation by highly reactive oxygen species (hROS) involves attack at the thiazine sulfur atom and destruction of the p conjugation of the cyaninemoiety. Dual fluorescence emissions are enhanced dramatically at λ(em) 470 nm and 595 nm, and PTZ-Cy2 thus serves both as an absorbance ratiometric and a fluorescent "off-on" sensor for detecting hROS. Moreover PTZ-Cy2 shows selectivity for hROS over other oxidants, and gives a highly sensitive response to such endogenous species within the mitochondria of living cells.

Topics: Carbocyanines; Fluorescent Dyes; HeLa Cells; Humans; Microscopy, Confocal; Mitochondria; Phenothiazines; Reactive Oxygen Species; Spectrophotometry, Ultraviolet

Free flow electrophoresis (FFE) has been applied in numerous studies as a protein separation technique due to its multiple advantages such as fast and efficient sample recovery, high resolving power, high reproducibility, and wide applicability to protein classes. As a stand-alone platform however, its utility in comparative proteomic analysis is limited as protein samples must be run sequentially rather than simultaneously which introduces inherent variability when attempting to perform quantitative analysis. Here we describe an approach combining fluorescent CyDye technology (DIGE) with FFE to simultaneously separate and identify differentially expressed proteins in a model cell system.

Topics: Buffers; Carbocyanines; Cell Extracts; Denaturing Gradient Gel Electrophoresis; Densitometry; Fluorescent Dyes; HT29 Cells; Humans; Hydrogen-Ion Concentration; Image Processing, Computer-Assisted; Isoelectric Point; Proteins; Staining and Labeling

Implantation of tissue engineering constructs is a promising technique to reconstruct injured tissue. However, after implantation the nutrition of the constructs is predominantly restricted to vascularization. Since cells possess distinct angiogenic potency, we herein assessed whether scaffold vitalization with different cell types improves scaffold vascularization. 32 male balb/c mice received a dorsal skinfold chamber. Angiogenesis, microhemodynamics, leukocyte-endothelial cell interaction and microvascular permeability induced in the host tissue after implantation of either collagen coated poly (L-lactide-co-glycolide) (PLGA) scaffolds (group 4), additionally seeded with osteoblast-like cells (OLCs, group 1), bone marrow mesenchymal stem cells (bmMSCs, group 2) or a combination of OLCs and bmMSCs (group 3) were analyzed repetitively over 14 days using intravital fluorescence microscopy. Apart from a weak inflammatory response in all groups, vascularization was found distinctly accelerated in vitalized scaffolds, indicated by a significantly increased microvascular density (day 6, group 1: 202+/-15 cm/cm(2), group 2: 202+/-12 cm/cm(2), group 3: 194+/-8 cm/cm(2)), when compared with controls (group 4: 72+/-5 cm/cm(2)). This acceleration was independent from the seeded cell type. Immunohistochemistry revealed in vivo VEGF expression in close vicinity to the seeded OLCs and bmMSCs. Therefore, the observed lack of cell type confined differences in the vascularization process suggests that the accelerated vascularization of vitalized scaffolds is VEGF-related rather than dependent on the potential of bmMSCs to differentiate into specific vascular cells.

Topics: Alkaline Phosphatase; Animals; Biocompatible Materials; Bone Marrow Cells; Carbocyanines; Cells, Cultured; Collagen; Femur; Fluorescent Antibody Technique, Indirect; Fluorescent Dyes; Immunohistochemistry; Indoles; Lactic Acid; Male; Mesenchymal Stem Cells; Mice; Mice, Inbred BALB C; Neovascularization, Pathologic; Osteoblasts; Polyglycolic Acid; Polylactic Acid-Polyglycolic Acid Copolymer; Tibia; Tissue Engineering; Tissue Scaffolds

Difference in-gel electrophoresis (DIGE)-based protein expression analysis allows assessing the relative expression of proteins in two biological samples differently labeled (Cy5, Cy3 CyDyes). In the same gel, a reference sample is also used (Cy2 CyDye) for spot matching during image analysis and volume normalization. The standard statistical techniques to identify differentially expressed (DE) proteins are the calculation of fold-changes and the comparison of treatment means by the t-test. The analyses rarely accounts for other experimental effects, such as CyDye and gel effects, which could be important sources of noise while detecting treatment effects.. We propose to identify DIGE DE proteins using a two-stage linear mixed model. The proposal consists of splitting the overall model for the measured intensity into two interconnected models. First, we fit a normalization model that accounts for the general experimental effects, such as gel and CyDye effects as well as for the features of the associated random term distributions. Second, we fit a model that uses the residuals from the first step to account for differences between treatments in protein-by-protein basis. The modeling strategy was evaluated using data from a melanoma cell study. We found that a heteroskedastic model in the first stage, which also account for CyDye and gel effects, best normalized the data, while allowing for an efficient estimation of the treatment effects. The Cy2 reference channel was used as a covariate in the normalization model to avoid skewness of the residual distribution. Its inclusion improved the detection of DE proteins in the second stage.

Topics: Carbocyanines; Cell Line, Tumor; Computational Biology; Electrophoresis, Gel, Two-Dimensional; Fluorescent Dyes; Humans; Image Processing, Computer-Assisted; Linear Models; Melanoma; Proteome; Proteomics

Differential in-gel electrophoresis (DIGE) experiments allow three protein samples to be run per gel. The three samples are labeled with the spectrally resolvable fluorescent dyes, Cy2, Cy3, and Cy5, respectively. Here, we show that protein-specific dye effects exist, and we present a linear mixed model for analysis of DIGE data which takes dye effects into account. A Java implementation of the model, called DIGEanalyzer, is freely available at http://bioinfo.thep.lu.se/digeanalyzer.html. Three DIGE experiments from our laboratory, with 173, 64, and 24 gels, respectively, were used to quantify and verify the dye effects. DeCyder 5.0 and 6.5 were used for spot detection and matching. The fractions of proteins with a statistically significant (0.001 level) dye effect were 19, 34, and 23%, respectively. The fractions of proteins with a dye effect above 1.4-fold change were 1, 4, and 6%, respectively. The median magnitude of the dye effect was 1.07-fold change for Cy5 versus Cy3 and 1.16-fold change for Cy3 versus Cy2. The maximal dye effect was a seven-fold change. The dye effects of spots corresponding to the same protein tend to be similar within each of the three experiments, and to a smaller degree across experiments.

Topics: Algorithms; Animals; Brain Chemistry; Breast Neoplasms; Carbocyanines; Computational Biology; Electrophoresis, Gel, Two-Dimensional; Female; Fluorescent Dyes; Humans; Image Processing, Computer-Assisted; Internet; Linear Models; Ovarian Neoplasms; Proteins; Proteomics; Rats; Software; Tandem Mass Spectrometry

Two-dimensional difference gel electrophoresis (DIGE) is a tool for measuring changes in protein expression between samples involving pre-electrophoretic labeling with cyanine dyes. Here we assess a common method to analyze DIGE data using the DeCyder software system. Experimental error was studied by a series of same sample comparisons. Aliquots of sample were labeled with N-hydroxyl succinimidyl ester-derivatives of Cy2, Cy3, and Cy5 dyes and run together on one gel. This allowed assessment of how experimental error influenced differential expression analysis. Bias in the log volume ratios was observed, which could be explained by differences in dye background. Further complications are caused by significant gel-to-gel variation in the spot volume ratio distributions. Using DeCyder alone results in an inability to define ratio thresholds for 90 or 95% confidence. An alternative normalization method was thus applied which resulted in improved data distribution and allowed greater sensitivity in analysis. When combined with a standardizing function, this allowed gel-independent thresholds for 90% confidence. The new approach, detailed here, represents a method to greatly improve the success of DIGE data analysis.

Topics: Bacterial Proteins; Bias; Carbocyanines; Confidence Intervals; Electrophoresis, Gel, Two-Dimensional; Erwinia; Fluorescent Dyes; Proteins; Reproducibility of Results; Sensitivity and Specificity; Software; Staining and Labeling

Fluorescence (auto)correlation spectroscopy (FCS) has developed into a widely used method for investigating molecular dynamics and mobility of molecules in vitro and in vivo. Dual-color cross-correlation, an extension of this technique, also assesses the concomitant movement of two spectrally distinguishable fluorescent molecules and has therefore proven superior to autocorrelation analysis to study interactions between different molecular species in solution. Here we explore the benefits of cross-correlation analysis when applied to live cells, by demonstrating its potential in analyzing endocytic processes. Bacterial cholera toxin (CTX) was labeled with Cy2 and Cy5 dyes on different subunits of the same holotoxin. Along the endocytic pathway, positive cross-correlation between the A and B subunits was first preserved, later followed by a loss in cross-correlation upon their separation in the Golgi. Furthermore, endocytosis of a mixture of only Cy2- and only Cy5-labeled holotoxins also gave rise to cross-correlation. Our results suggest that cross-correlation may be used to recognize whether different cargoes use the same endocytic pathway. Additionally, we show that cross-correlation is applicable to two-dimensional membrane diffusion. CTX bound to GM1-containing artificial giant unilamellar vesicles was diffusible, whereas CTX bound to the plasma membrane was immobile on the FCS time-scale, possibly because of raft-association of GM1.

Topics: Animals; Biophysical Phenomena; Biophysics; Carbocyanines; Cell Membrane; Chlorocebus aethiops; Cholera Toxin; Endocytosis; Endosomes; Fluorescent Dyes; Golgi Apparatus; Membrane Microdomains; Models, Statistical; Protein Structure, Tertiary; Spectrometry, Fluorescence; Time Factors; Vero Cells

An immunohistochemical technique was developed to visualize nitric oxide synthase (NOS)-immunopositive neurons in fresh-frozen tissue sections of rat brain for laser capture microdissection (LCM) and mRNA analysis. The effect of tissue fixation and the choice of fluorophore were investigated. Here we describe a rapid immunofluorescence protocol that allows the processing of fresh-frozen tissue sections within eight minutes and subsequent mRNA extraction and real-time PCR from pools of 20 NOS-immunopositive LCM neurons. The cellular complement of a subset of ionotropic glutamate receptors, specifically N-methyl-D-aspartate receptor subunit mRNAs, was examined because these receptor complexes are thought to mediate the effects of fast and slow glutamate excitotoxicity. Real-time PCR data revealed that striatal NOS interneurons express the mRNAs encoding NR1, NR2A, NR2B, and NR2D but not NR2C. These LCM mRNA data are consistent with previous in situ hybridization studies and demonstrate the utility of rapid immuno-LCM with real-time quantitative PCR for the study of mRNA abundance in discrete populations of neurons within the mammalian brain.

Topics: Animals; Carbocyanines; Cell Separation; Computer Systems; Corpus Striatum; Fluorescent Antibody Technique, Indirect; Fluorescent Dyes; Frozen Sections; Hydrazines; Interneurons; Isoenzymes; Lasers; Nerve Tissue Proteins; Nitric Oxide Synthase; Nitric Oxide Synthase Type I; Polymerase Chain Reaction; Rats; Rats, Sprague-Dawley; Receptors, N-Methyl-D-Aspartate; Rhodamines; RNA, Messenger; Specimen Handling; Time Factors

The processes of nonradiative deactivation of electronic excitation energy in cyanine dyes determine their quantum yield. Because of that, the study of the influence of cyanines binding to DNA on these processes can provide information on the causes leading to the cyanines fluorescence intensity enhancement in the presence of DNA. In the presented paper, the activation energies of nonradiative degradation of electronic excitation, quantum yields and rate constants of nonradiative transitions of several cyanines in free state and in the presence of DNA were established and compared. The mechanisms of nonradiative deactivation of dye excitation energy were discussed.

Topics: Carbocyanines; Coloring Agents; DNA; Electrons; Energy Transfer; Molecular Structure; Spectrometry, Fluorescence; Spectrophotometry, Atomic

Fluorescein isothiocyanate (FITC) is largely used in immunofluorescence methods. We propose to analyse the quality of some recent fluorochromes using image analysis. Fluorochromes tested include FITC and dichlorotriazinylaminofluorescein (DTAF), dipyrrometheneboron difluoride (BODIPY), Rhodol Green and cyanine 2. RAMOS cells were immunolabelled against the proliferating cell nuclear antigen (PCNA) revealed by the biotin-streptavidin technique. Slides were mounted in anhydrous glycerol or in buffered glycerol (pH 7.0 or pH 8.5). No antifading medium was added. Cell fluorescence emission intensity and bleaching characteristics were measured. Rhodol Green exhibited the highest fluorescence intensity and the best photobleaching resistance. Although BODIPY also resisted well during the photobleaching assay, its fluorescence intensity was weak. FITC, DTAF and cyanine 2 showed intermediate fluorescence intensity and a fast decay of fluorescence. Among the green emitting fluorochromes tested, Rhodol Green appeared to be the best.

Topics: Bacterial Proteins; Boron Compounds; Carbocyanines; Evaluation Studies as Topic; Fluorescein-5-isothiocyanate; Fluoresceins; Fluorescent Antibody Technique; Fluorescent Dyes; Humans; Microscopy, Fluorescence; Proliferating Cell Nuclear Antigen; Spectrometry, Fluorescence; Streptavidin; Tumor Cells, Cultured