Reconstruction of firing rate changes across neuronal populations by temporally deconvolved Ca2+ imaging

Methods to record action potential (AP) firing in many individual neurons are essential to unravel the function of complex neuronal circuits in the brain. A promising approach is bolus loading of Ca(2+) indicators combined with multiphoton microscopy. Currently, however, this technique lacks cell-type specificity, has low temporal resolution and cannot resolve complex temporal firing patterns. Here we present simple solutions to these problems. We identified neuron types by colocalizing Ca(2+) signals of a red-fluorescing indicator with genetically encoded markers. We reconstructed firing rate changes from Ca(2+) signals by temporal deconvolution. This technique is efficient, dramatically enhances temporal resolution, facilitates data interpretation and permits analysis of odor-response patterns across thousands of neurons in the zebrafish olfactory bulb. Hence, temporally deconvolved Ca(2+) imaging (TDCa imaging) resolves limitations of current optical recording techniques and is likely to be widely applicable because of its simplicity, robustness and generic principle.

Multicolor Fluorescence Detection on an Electrophoretic Microdevice Using an Acoustooptic Tunable Filter

An acoustooptic tunable filter (AOTF) is used to detect multiple fluorescent signals on a fluidic microdevice. A confocal laser-induced fluorescence detection setup is used to excite fluorescent dyes in glass microchannels, presenting a streamlined and robust detection system consisting of the narrow-bandwidth AO filter and a single photodetector. The flexibility of the filter is demonstrated by alternating between wavelengths for precise microchannel alignment and sweeping through a range of wavelengths for preliminary spectral characterization of subnanoliter probe volumes of target analytes. The AOTF is also coupled with an electrophoretic separation for the multicolor detection of PCR-amplified DNA against a labeled sizing standard, the discrimination of multiple amplicons overlapped in time, and the identification of amplified biowarfare agents in a fluorescent spiking experiment. Finally, to demonstrate the multicolor capability of the system, 19-wavelength detection is performed during the separation of a three-dye sample mixture.

Cell sorting but not serum starvation is effective for SV40 human corneal epithelial cell cycle synchronization

SV40 human corneal epithelial cell (HCEC) populations are readily used as a substitute for primary corneal epithelial cells that are difficult to maintain in vitro. To initiate cell-cycle experiments with the SV40-HCEC cells, two separate methods of cell synchronization were compared including serum starvation and sterile cell sorting. We hypothesized that SV40 cells are synchronized at higher efficiencies into each cell cycle phase (G1, S, G2M) when cell sorting is performed when compared to alternative methods of synchronization. SV40 cells were synchronized by deprivation of serum over 96 h or labeled with Höechst 33342 dye and sorted based on DNA content. Cells were synchronized using both methods and harvested at time points up to 72 h after release. To define more precisely the nature of sorted fractions, cells were pulsed with BrdU prior to sorting. SV40-HCEC cells exhibit a well-defined cell cycle profile. Serum deprivation up to 96 h was ineffective for cell synchronization of SV40-HCECs. In comparison, we achieved efficient synchronization of the SV40-HCECs with sterile cell sorting. SV40-HCEC cells gated into G1, S and G2M were synchronized up to 85% following the sort and maintained synchronization up to 24 h. Our findings indicate that serum starvation is not effective for synchronization of the SV40-HCEC cell line. We present a more effective approach, the use of cell sorting for cell synchronization of the SV40-HCEC cells.

[Fluorescence spectral characteristics of human blood and its endogenous fluorophores]

The three-dimensional fluorescence spectra and excitation-emission matrix of human blood were measured, and an attempt was made to exploit the endogenous fluorophores of major peaks in the UV and visible. The result indicates that the absorption peaks of human blood appear at 274, 345, 415, 541 and 576 nm. Based on the analysis of fluorescence excitation-emission matrix, the major emission peaks of human blood occur at excitation-emission wavelength pairs of 260-630, 280-340, 340-460 and 450-520 nm, which are attributed to endogenous porphyrins, tryptophan, reduced nicotinamide adenine dinucleotide (NADH) or reduced nicotinamide adenine dinucleotide phosphate (NADPH), and flavin adenine dinucleotide (FAD), respectively. These results can be used to analyze and explain the effect of blood on the distortion of fluorescence signal of human tissues for optical diagnosis.

[Application of L-cysteine-capped nano-ZnS as a fluorescence probe to the determination of proteins in human serum]

Nanometer-sized L-cysteine-capped ZnS particles as a fluorescence probe were synthesized, and the effect of proteins on the fluorescence intensity has been investigated. With deltalambda = 190 nm, the maximum and constant synchronous fluorescence enhancement was produced at 268.0 nm and pH 5.12 in the presence of proteins. A highly sensitive synchronous fluorescence method for the rapid determination of proteins was developed. Under optimum conditions, the calibration curve was linear over the range 0.05-6.0 microg x mL(-1) for human serum albumin (HSA), and 0.05-8.0 microg x mL(-1) for gamma-globulin (gamma-G), respectively. The relative standard deviations of seven measurements were 1.90% for 1.0 microg x mL(-1) HSA, and 1.65% for 1.0 microg mL(-1) gamma-G.

Fluorescence in situ hybridization and spectral imaging of coral-associated bacterial communities

Microbial communities play important roles in the functioning of coral reef communities. However, extensive autofluorescence of coral tissues and endosymbionts limits the application of standard fluorescence in situ hybridization (FISH) techniques for the identification of the coral-associated bacterial communities. This study overcomes these limitations by combining FISH and spectral imaging.

One-step analysis of protein complexes in microliters of cell lysate using indirect immunolabeling & fluorescence cross-correlation spectroscopy

This protocol describes a 'mix-and-measure' procedure for the analysis of interactions of endogenous proteins in microliters of crude cell lysates. The proteins of interest are labeled by indirect immunofluorescence through simple addition of all primary and secondary antibodies to the lysate. Detection is based on fluorescence cross-correlation spectroscopy. Due to the minimal number of handling steps for sample preparation and the need of only microliters of sample, the approach enables the parallel and miniaturized analysis of protein-protein interactions. No heterologous expression of proteins with detection tags is required. For this reason, the cellular processes leading to protein-protein interactions are not skewed by overexpression of individual components. This makes the approach particularly suitable for the parallel monitoring of interactions in signaling networks. Additionally, the approach enables the screening and titration of compounds interfering with interactions, especially for those interactions based on signaling-dependent post-translational modifications. This protocol can be completed in approximately 22 h, including a 16-h incubation phase.

A novel tool to characterize paracellular transport: the APTS-dextran ladder

PURPOSE

The aim of this work was to develop an easy, manageable, and precise analytic tool to describe the tightness of cell layers by a molecular weight ladder.

METHODS

Dextrans were labeled by reductive amination with fluorescent 8-aminopyrene-1,3,6-trisulfonate (APTS). This mixture, including the internal standard diazepam, was used for transport studies in Transwell models using Caco-2, ECV304, and PBMEC/C1-2 cell lines. Samples were analyzed by fluorimetry, capillary electrophoresis, and reverse-phase high-performance liquid chromatography.

RESULTS

Following this approach, a logarithm correlation of R2 = 0.8958 between transepithelial electrical resistance (TEER) and APTS-dextran permeability was shown. In addition, a TEER-dependent permeability pattern could be observed including each single fraction from free APTS, APTS-glucose up to APTS-dextran consisting of 35 glucose units. The TEER-independent permeability coefficients of diazepam and confocal laser scanning microscopy images confirmed the paracellular transport of APTS-dextran.

CONCLUSIONS

All in all, the developed APTS-dextran ladder is a useful tool to characterize cell layer tightness and especially to describe paracellular transport ways and the extent of leakiness of cell layers (for blood-brain barrier or intestinal studies) over time--applying a wide array from smaller to larger molecules at the same time to refine TEER, sucrose, or Evans blue measurements.

Development of a microsphere-based p38alpha MAP kinase no-wash assay

A nonradioactive, microsphere-based, no-wash assay for the measurement of p38alpha mitogen-activated protein (MAP) kinase activity was established. In this assay, a glutathione-S-transferase activating transcription factor 2 (amino acids 19-96) fusion protein (GST-ATF-2) was used as substrate for p38alpha MAP kinase. The assay involves immobilization of GST-ATF-2 on glutathione-microspheres (GSH-microspheres), addition of test solution containing p38alpha MAP kinase and test compounds, and measurement of the respective substrate phosphorylation with the aid of a bi-phospho-specific antibody. The optimization of test conditions is described in this article. With an optimized standard protocol, p38alpha MAP kinase inhibitors were investigated and IC50 values were compared to those derived using known assays. This assay might be useful in testing drug candidates.

Raman spectroscopy for tablet coating thickness quantification and coating characterization in the presence of strong fluorescent interference

We report a novel approach to the measurement of colored tablet coating thickness, which employs Raman spectroscopy with univariate and multivariate data analysis. Our results suggest that Raman sensing can serve as a viable non-invasive means to quantify tablet coating thickness in the presence of a fluorescent ingredient in the coating formulation (food colorant Alphazurine FG or D&C Blue No. 4). This study comparatively tests the advantage of several data transformation approaches, including mean centering, standard normal variate, and Savitzky-Golay smoothed second derivative as means of improving predictive models in the presence of fluorescence. By application of the partial least squares (PLS) calibration algorithm to establish optimum covariance between transformed spectral data and measured tablet coating thicknesses, we have been able to create predictive models with calibration errors as small as 4 microm for a training set that spans colored coating thicknesses from 50 to 151 microm.

The presence of ABCG2-dependent side population cells in human periodontal ligaments

Periodontal ligament (PDL) is capable of regenerating several types of periodontal tissues. However, the stem cells in PDL have been less well characterized. Recently, it has been represented that stem cells have a potent ability to exclude Hoechst dye, and cells possessing this phenotype are termed "side population (SP)." In addition, it is suggested that the SP cells are ubiquitously present in adult tissues, therefore, we investigated the presence of SP cells in PDL. Hoechst dye efflux assay showed that PDL cells include 3.9% SP cells. This SP profile disappeared in the presence of verapamil or reserpine. Only ABCG2-expressing cells were detected in PDL cells by flow cytometric analysis. Furthermore, RT-PCR demonstrated that ABCG2 mRNA expression remarkably correlated with PDL SP phenotype. Our findings demonstrate that PDL contains ABCG2-dependent SP cells. Hence, it is possible that this population could contribute to periodontal tissue regeneration as PDL stem cells.

Novel fluorescent probe for detecting hydroperoxides with strong emission in the visible range

A novel fluorescent probe, a swallow-tailed perylene derivative for detecting hydroperoxides (Spy-HP), containing perylene 3,4,9,10-tetracarboxyl bisimide as the main skeleton in the structure, was developed. Spy-HP reacted rapidly with hydroperoxides such as m-chloroperbenzoic acid (MCPBA) and cumene hydroperoxide to form its oxidized derivative, Spy-HPOx, and emitted an extremely strong fluorescence (phi approximately 1) in the visible range (lambda(ex) = 524 nm and lambda(em) = 535 nm), as the result of canceling the photoinduced electron transfer (PET) effect. The reaction between Spy-HP and hydroperoxides proceeded quantitatively in strict stoichiometry, without being affected by autoxidation or photobleaching. Because of these prominent properties, Spy-HP is expected to be a novel and useful fluorescent probe to 'spy' on hydroperoxides in biosamples.

Influence of Fluorescence Anisotropy on Fluorescence Intensity and Lifetime Measurement: Theory, Simulations and Experiments

The significance of fluorescence anisotropy in fluorescence intensity and lifetime measurements, and erroneous measurements and interpretations resulting from its disregard, are thoroughly discussed, formulated and quantified. In all fluorescence-related measurements--including excitation and emission spectra, relative fluorescence intensity (FI), fluorescenc life time (FLT), fluorescence resonance energy transfer (FRET), etc., with the exception of fluorescence polarization and anisotropy--it is generally true that the higher the fluorescence anisotropy, the greater the distortion of fluorescence measurements. Quantifiable distortions occur when fluorescence measurements are conducted without considering the influence of fluorescence anisotropy. Here, this influence is described by numerous newly developed mathematical expressions which are simulated and experimentally confirmed utilizing single and binary fluorescent solutions of fluorophores with different spectroscopic characteristics. A marked agreement is shown between the theory and experimental data, clearly indicating the legitimacy of the physical suppositions and the mathematical expressions presented in this paper. Practical and instructive implications are discussed. The following findings are of special applicative importance: 1) the existence of an infinite number of couples of Magic Angles; 2) the deviation between two equally fluorescing particles having different fluorescence anisotropies; 3) the relation between the detected fluorescence intensity and anisotropy when measured under various setups of emission and excitation polarizers; 4) the dependence of the artificial normalized steady-state weight of a single-exponentially decaying fluorophore on its fluorescence anisotropy.

Highly sensitive spectrofluorimetric determination of trace amounts of lecithin using a norfloxacin–terbium probe

BACKGROUND

Lecithin is found throughout biological systems. A new spectrofluorimetric method was developed for the determination of trace amounts of lecithin.

METHODS

Optimum conditions for the determination of lecithin were investigated.

RESULTS

Using norfloxacin (NF)-terbium ion (Tb3+) as a fluorescent probe, in a buffer solution at pH=6.80, lecithin reduced the fluorescence intensity of the NF-Tb3+ complex at lambda=545 nm; the reduced fluorescence intensity of the Tb3+ ion is proportional to the concentration of lecithin. The linear range and detection limit for the determination of lecithin were 1.08 x 10(-6)-3.02 x 10(-5) mol/l and 2.54 x 10(-7) mol/l.

CONCLUSION

This method is simple, practical and relatively free of interference from coexisting substances, and can be successfully applied to assess lecithin in serum samples.

Tryptophan-BODIPY: a versatile donor-acceptor pair for probing generic changes of intraprotein distances

We demonstrate that Tryptophan (Trp) and N-(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-yl)methyl iodoacetamide (BODIPY) is a suitable donor-acceptor (D-A) pair for intraprotein distance measurements, applicable to the study of protein folding. The suitability of the Trp-BODIPY electronic energy transfer is exemplified on the extensively-characterised two-state protein, S6, from Thermus thermophilus. This protein has proved to be useful for the elucidation of folding cooperativity and nucleation, as well as the changes upon induction of structural transitions. For a comprehensive structural coverage, BODIPY molecules were anchored by Cys insertions at four different positions on the S6 surface. Trp residues at position 33 or 62 acted as donors of electronic energy to the BODIPY groups. None of the D-A pairs show any detectable difference in the folding kinetics (or protein stability), which supports the notion that the two-state transition of S6 is a highly concerted process. Similar results are obtained for mutants affecting the N- and C-terminus. The kinetic analyses indicate that changes of the transition state occur through local unfolding of the native state, rather than by a decrease of the folding cooperativity. The distances obtained from the analysis of the time-resolved fluorescence experiments in the native state were compared to those calculated from X-ray structure. As an additional measure, molecular dynamics simulations of the different protein constructs were performed to account for variability in the BODIPY location on the protein surface. The agreement between fluorescence and X-ray data is quite convincing, and shows that energy transfer measurements between Trp and BODIPY can probe distances between ca. 17 to 34 A, with an error better than 10%.

Actin polymerisation at the cytoplasmic face of eukaryotic nuclei

Background

There exists abundant molecular and ultra-structural evidence to suggest that cytoplasmic actin can physically interact with the nuclear envelope (NE) membrane system. However, this interaction has yet to be characterised in living interphase cells.

Results

Using a fluorescent conjugate of the actin binding drug cytochalasin D (CD-BODIPY) we provide evidence that polymerising actin accumulates in vicinity to the NE. In addition, both transiently expressed fluorescent actin and cytoplasmic micro-injection of fluorescent actin resulted in accumulation of actin at the NE-membrane. Consistent with the idea that the cytoplasmic phase of NE-membranes can support this novel pool of perinuclear actin polymerisation we show that isolated, intact, differentiated primary hepatocyte nuclei support actin polymerisation in vitro. Further this phenomenon was inhibited by treatments hindering steric access to outer-nuclear-membrane proteins (e.g. wheat germ agglutinin, anti-nesprin and anti-nucleoporin antibodies).

Conclusion

We conclude that actin polymerisation occurs around interphase nuclei of living cells at the cytoplasmic phase of NE-membranes.

Second messenger pas de deux: the coordinated dance between calcium and cAMP

Dynamic calcium signaling is a well-established precept in biology. Different cell types exhibit spontaneous as well as stimulus-triggered transient changes in the concentration of intracellular calcium. Does this behavior extend to other second messengers? Optical dissection of various signal transduction pathways with fluorescent reporter molecules that enable visualization of changes in concentration of other second messengers is well under way. Recent research using technologically refined probes provides improved temporal and spatial resolution of adenosine 3',5'-monophosphate (cAMP) dynamics to generate insights into the bidirectional interplay between intracellular fluctuations of cAMP and calcium. cAMP oscillations are generated in response to hormones, and cells can recognize and differentially respond to transient versus sustained changes in this second messenger. Second messenger reporters are now available to track multiple players and so provide a dynamic picture of signaling networks.

Validation of dye-binding/high-resolution thermal denaturation for the identification of mutations in the SLC22A5 gene

Primary carnitine deficiency is an autosomal recessive disorder of fatty acid oxidation resulting from defective carnitine transport. This disease is caused by mutations in the OCTN2 carnitine transporter encoded by the SLC22A5 gene. Here we validate dye-binding/high-resolution thermal denaturation as a screening procedure to identify novel mutations in this gene. This procedure is based on the amplification of DNA by PCR in capillaries with the dsDNA binding dye LCGreen I. The PCR reaction is then analyzed in the same capillary by high-resolution thermal denaturation. Samples with abnormal melting profiles are sequenced. This technique correctly identified all known patients who were compound heterozygotes for different mutations in the carnitine transporter gene and about 30% of homozygous patients. The remaining 70% of homozygous patients were identified by a second amplification, in which the patient's DNA was mixed with the DNA of a normal control. This screening system correctly identified eight novel mutations and both abnormal alleles in six new families with primary carnitine deficiency. The causative role of the missense mutations identified (c.3G>T/p.M1I, c.695C>T/p.T232M, and c.1403 C>G/p.T468R) was confirmed by expression in Chinese hamster ovary (CHO) cells. These results expand the mutational spectrum in primary carnitine deficiency and indicate dye-binding/high-resolution thermal denaturation as an ideal system to screen for mutations in diseases with no prevalent molecular alteration.

Solvent relaxation in phospholipid bilayers: principles and recent applications

Although there exist a number of methods, such as NMR, X-ray, e.g., which explore the hydration of phospholipid bilayers, the solvent relaxation (SR) method has the advantage of simple instrumentation, easy data treatment and possibility of measuring fully hydrated samples. The main information gained from SR by the analysis of recorded "time-resolved emission spectra" (TRES) is micro-viscosity and micro-polarity of the dye microenvironment. Based on these parameters, one can draw conclusions about water structure in the bilayer. In this review, we focus on physical background of this method, on all the procedures that are needed in order to obtain relevant parameters, and on the requirements on the fluorescence dyes. Furthermore, a few recent applications (the effect of curvature, binding of antibacterial peptides and phase transition) illustrating the versatility of this method are mentioned. Moreover, limitations and potential problems are discussed.

Side population (SP) cells isolated from fetal rat calvaria are enriched for bone, cartilage, adipose tissue and neural progenitors

In some tissues, stem cells are enriched within the side population (SP) cells characterized by the efficient efflux of Hoechst 33342, but few data are yet available to address whether such is the case in bone tissue. When we Hoechst-stained and FACS-analyzed freshly isolated 20- or 21-day fetal rat calvaria (RC) cells, a small fraction of cells (0.15 +/- 0.05%) comprised of a distinct SP. When SP, non-SP and total/unfractionated (Total) RC cells were plated at a density of 30 cells per microtiter well, the percentage of wells containing bone-forming progenitors (CFU-O) was significantly higher in the SP compared to the non-SP or Total populations (13 +/- 4% vs. 1.8 +/- 0.4% and 0.7 +/- 0.4% respectively). The SP was also highly enriched for CFU-alkaline phosphatase (CFU-ALP) and CFU-fibroblast (CFU-F). While Dex increased the recruitment of CFU-O and CFU-F in the SP, it did not increase the frequency of CFU-ALP. Limiting dilution analysis showed a non-linear relationship between cell densities (1, 5, 10, 20 and 30 cells/microtiter well) and the frequency of readout CFU-O, CFU-ALP and CFU-F in all populations, suggesting a cell non-autonomous component to proliferation-differentiation of these progenitor types. When the developmental potential of SP cells for chondrocyte, adipocyte and neural lineages was assessed, SP cells were also found to be enriched for progenitors of all three lineages. These data demonstrate that Hoechst staining and SP sorting by flow cytometry are a useful strategy for the enrichment of CFU-O and possibly other precursors present in RC cell populations.

A simple light-emitted diode-induced fluorescence detector using optical fibers and a charged coupled device for direct and indirect capillary electrophoresis methods

We constructed a simple fluorescence detector for both direct and indirect CE methods using a blue light-emitted diode (470 nm) as excitation source, a bifurcated optical fiber as a waveguide, and a CCD camera as a detector. The connection of all the components is fairly easy even for nonexperts and the use of a CCD camera improves the applicability of this detector compared to the others using PMTs because it permits the recording of 2-D electropherograms or phosphorescence measurements. This detector provides a compact, low cost, and rapid system for the determination of native fluorescence compounds which have high quantum yields by CE with direct fluorescence detection, showing an LOD of 2.6 x 10(-6) M for fluorescein; the determination of fluorescence derivative compounds by CE with direct fluorescence detection, showing an LOD of 1.6 x 10(-7) M for FITC-labeled 1,6-diaminohexane; and nonfluorescence compounds by CE with indirect fluorescence detection with an LOD of 2.7 x 10(-6) M for gallic acid.

Multiple nucleolus organizer regions in Leptodactylus mystacinus (Amphibia, Anura) and comments on its systematic position in the L. fuscus group based on cytogenetic and molecular analyses

Specimens of Leptodactylus mystacinus from Brazil were karyotyped with conventional and differential staining. The 2n = 22 karyotype is similar to that found for the majority of the Leptodactylus, the karyotypic conservatism also confirmed by the similarity of the replication banding patterns with those previously described. L. mystacinus has a small amount of C-banded heterochromatin, located mainly at the centromeres, although telomeric or interstitial bands have also been noticed. With DA/CMA(3) some chromosome regions showed slightly bright fluorescence, and with DA/DAPI, no particular AT-rich repetitive region was observed. Silver staining showed an extensive inter- and intraindividual variation in the number and position of Ag-positive regions, in 1p, 4p, 8p, 8q, and 11p. Nevertheless, FISH using rDNA probes confirmed only the signals on the short arms of chromosomes 4 and 8 as true NORs. The remaining silver stained regions are probably due to the heterochromatin with some affinity to the Ag-staining. Phylogenetic analysis based on partial cytochrome b sequence revealed that L. mystacinus forms a basal branch, so that the presence of multiple NORs in pairs 4 and 8 in this species indicates an autapomorphy.

High-Throughput Screening for the Discovery of Inhibitors of Fatty Acid Amide Hydrolase Using a Microsome-Based Fluorescent Assay

Fatty acid amide hydrolase (FAAH) is a membrane-associated enzyme that catalyzes the hydrolysis of several endogenous bioactive lipids, including anandamide (AEA), N-palmitoylethanolamine (PEA), oleamide, and N-oleoylethanolamine (OEA). These fatty acid amides participate in many physiological activities such as analgesia, anxiety, sleep modulation, anti inflammatory responses, and appetite suppression. Because FAAH plays an essential role in controlling the tone and activity of these endogenous bioactive lipids, this enzyme has been implicated to be a drug target for the therapeutic management of pain, anxiety, and other disorders. In an effort to discover FAAH inhibitors, the authors have previously reported the development of a novel fluorescent assay using purified FAAH microsomes as an enzyme source and a fluorogenic substrate, arachidonyl 7-amino, 4-methyl coumarin amide (AAMCA). Herein, the authors have adapted this assay to a high-throughput format and have screened a large library of small organic compounds, identifying a number of novel FAAH inhibitors. These data further verify that this fluorescent assay is sufficiently robust, efficient, and low-cost for the identification of FAAH inhibitory molecules and open this class of enzymes for therapeutic exploration.