Carbocyanine Dye Research Articles

Diffusion tensor magnetic resonance imaging and tract-tracing analysis of Probst bundle structure in Netrin1- and DCC-deficient mice.

In many cases of callosal dysgenesis in both human patients and mouse models, misguided fibers from the cortex form abnormal bilateral, barrel-shaped structures known as Probst bundles. Because little is known about how axons are arranged within these anomalous fiber bundles, understanding this arrangement may provide structural and molecular insights into how axons behave when they are misguided in vivo. Previous studies described these bundles as longitudinal swirls of axons that fail to cross the midline (Ozaki et al., 1987). However, recent studies on human acallosal patients using diffusion tensor magnetic resonance imaging (DTMRI) technology suggest that axons project in an anteroposterior direction within the Probst bundle (Lee et al., 2004; Tovar-Moll et al., 2007). This led us to ask the question, is DTMRI an accurate method for analyzing axonal tracts in regions of high axon overlap and disorganization, or is our current perception of axon arrangement within these bundles inaccurate? Using DTMRI, immunohistochemistry, and carbocyanine dye tract-tracing studies, we analyzed the Probst bundles in both Netrin1 and deleted in colorectal cancer (DCC) mutant mice. Our findings indicate that DTMRI can accurately demonstrate fiber tract orientation and morphology where axons are in ordered arrays such as in the dorsal part of the bundle. In ventral areas, where the axons are disorganized, no coordinated diffusion is apparent via DTMRI. In these regions, a higher-resolution approach such as tract tracing is required. We conclude that in DCC and Netrin1 mutant mice, guidance mechanisms remain in the dorsal part of the tract but are lost ventrally.

Regenerating optic axons restore topography after incomplete optic nerve injury

Following complete optic nerve injury in a lizard, Ctenophorus ornatus, retinal ganglion cell (RGC) axons regenerate but fail to restore retinotectal topography unless animals are trained on a visual task (Beazley et al. [ 1997] J Comp Neurol 370:105-120, [2003] J Neurotrauma 20:1263-1270). Here we show that incomplete injury, which leaves some RGC axons intact, restores normal topography. Strict RGC axon topography allowed us to preserve RGC axons on one side of the nerve (projecting to medial tectum) while lesioning those on the other side (projecting to lateral tectum). Topography and response properties for both RGC axon populations were assessed electrophysiologically. The majority of intact RGC axons retained appropriate topography in medial tectum and had normal, consistently brisk, reliable responses. Regenerate RGC axons fell into two classes: those that projected topographically to lateral tectum with responses that tended to habituate and those that lacked topography, responded weakly, and habituated rapidly. Axon tracing by localized retinal application of carbocyanine dyes supported the electrophysiological data. RGC soma counts were normal in both intact and axotomized RGC populations, contrasting with the 30% RGC loss after complete injury. Unlike incomplete optic nerve injury in mammals, where RGC axon regeneration fails and secondary cell death removes many intact RGC somata, lizards experience a "win-win" situation: intact RGC axons favorably influence the functional outcome for regenerating ones and RGCs do not succumb to either primary or secondary cell death.

Early segregation of layered projections from the lateral superior olivary nucleus to the central nucleus of the inferior colliculus in the neonatal cat

The central nucleus of the inferior colliculus (IC) is a laminated structure that receives multiple converging afferent projections. These projections terminate in a layered arrangement and are aligned with dendritic arbors of the predominant disc-shaped neurons, forming fibrodendritic laminae. Within this structural framework, inputs terminate in a precise manner, establishing a mosaic of partially overlapping domains that likely define functional compartments. Although several of these patterned inputs have been described in the adult, relatively little is known about their organization prior to hearing onset. The present study used the lipophilic carbocyanine dyes DiI and DiD to examine the ipsilateral and contralateral projections from the lateral superior olivary (LSO) nucleus to the IC in a developmental series of paraformaldehyde-fixed kitten tissue. By birth, the crossed and uncrossed projections had reached the IC and were distributed across the frequency axis of the central nucleus. At this earliest postnatal stage, projections already exhibited a characteristic banded arrangement similar to that described in the adult. The heaviest terminal fields of the two inputs were always complementary in nature, with the ipsilateral input appearing slightly denser. This early arrangement of interdigitating ipsilateral and contralateral LSO axonal bands that occupy adjacent sublayers supports the idea that the initial establishment of this highly organized mosaic of inputs that defines distinct synaptic domains within the IC occurs largely in the absence of auditory experience. Potential developmental mechanisms that may shape these highly ordered inputs prior to hearing onset are discussed.

Spectral and kinetic investigation of interaction of 3,3′-diethyl-9-chlorothiacarbocyanine perchlorate with DNA

Interaction of the meso-substituted carbocyanine dye 3,3′-diethyl-9-chlorothiacarbocyanine (DCTC) perchlorate with DNA in phosphate buffer solutions (pH 7) was studied by spectral and kinetic methods. It was shown that the dye mainly exists in the cis-isomer form in water and aqueous-alcoholic solutions. The interaction with DNA leads to the formation of a trans-DCTC complex, which gradually (over a few tens of minutes) converts into the complex of the dye cis-isomer. It was revealed that the reactant concentration and ionic strength of solution have a considerable effect on the kinetic characteristics of trans-cis-reorganization of DCTC complexes, thus indicating a complex character of the process.

Development of banded afferent compartments in the inferior colliculus before onset of hearing in ferrets

Axonal projections from the lateral superior olivary nuclei (LSO), as well as from the dorsal cochlear nucleus (DCN) and dorsal nucleus of the lateral lemniscus (DNLL), converge in frequency-ordered layers in the central nucleus of the inferior colliculus (IC) where they distribute among different synaptic compartments. A carbocyanine dye, 1,1′-dioctadecyl-3,3,3′,3′-tetramethylindocarbocyanine perchlorate (DiI), was used as a tracer to study the postnatal development of axonal projections in the ferret IC. The results indicated that projections from all three nuclei are present at birth, but are not segregated into bands. During the postnatal week between approximately postnatal days 4 and 12 (P4–P12), axons from LSO proliferate in IC, become more branched, and segregate into a series of bands composed of densely packed fibers and endings. LSO projections in these afferent bands course parallel to IC layers and are separated by intervening regions with few endings. A modest fit of a sine curve ( R 2>0.15) to the pattern of spacing of LSO projections in IC indicated that regularly spaced bands are forming by P7. Similarly, banded patterns of DCN and DNLL projections to IC have developed by the end of the first postnatal week. Thus, well before hearing onset in ferret (P28–30), three different afferent projections have segregated into banded compartments along layers in the central nucleus of the ferret IC. Possible mechanisms in circuit development are discussed.

Labeling of dendritic spines with the carbocyanine dye DiI for confocal microscopic imaging in lightly fixed cortical slices

Visualization of dendritic spines is an important tool for researches on structural synaptic plasticity. Fluorescent labeling of the dendrites and spines followed by confocal microscopy permits imaging a large population of dendritic spines with a higher resolution. We sought to establish an optimal protocol to label neurons in cortical slices with the carbocyanine dye DiI for confocal microscopic imaging of dendritic spines. DiI finely labeled dendrites and spines in slices prefixed (by cardiac perfusion) with 1.5% paraformaldehyde to the similar extent that could be achieved in live preparation. In contrast, fixation with 4% paraformaldehyde severely compromised dye diffusion. Confocal microscopy showed that structural integrity of dendrites and spines was preserved much better in lightly (1.5%) fixed slices than those prepared without fixation. Quantitative measurement revealed that spine density was lower in live slices than that counted in lightly fixed slices, suggesting that fixation is necessary for an adequate evaluation of spine density. The quality of confocal microscopic images obtained from lightly fixed slices allowed us to observe distinctive morphologies such as branched spines and dendritic filopodium, which may be indicative of structural changes at synapses. This method will thus be useful for studying structural synaptic plasticity.

Modification of the Nanoscale Structure of the J-Aggregate of a Sulfonate-Substituted Amphiphilic Carbocyanine Dye through Incorporation of Surface-Active Additives

The amphiphilic dye 3,3'-bis(2-sulfopropyl)-5,5',6,6'-tetrachloro-1,1'-dioctylbenzimidacarbocyanine (C8S3) self-aggregates in aqueous solution to form tubular J-aggregates with a diameter of 17.0 +/- 0.5 nm, a wall thickness of approximately 4 nm, and a length exceeding several hundred nanometers. The absorption spectrum shows the typical features expected for tubular J-aggregates with several sharp and red-shifted absorption bands. Morphological investigations using cryo-transmission electron microscopy (cryo-TEM) and spectroscopic investigations reveal a high stability of the tubular morphology but a tendency of the aggregates to assemble into ropelike bundles after several weeks of storage. It is found that aggregation in solutions containing additives such as alcohols or surfactants results in the formation of new types of aggregates. A second type of tubular aggregate with a diameter of 13.0 +/- 0.5 nm is observed when the solutions contain more than 10 wt % MeOH. On the time scale of days these tubular aggregates transform into ribbonlike structures characterized by a new absorption spectrum, and they convert after several weeks into giant tubes with diameters of up to 500 nm.

DiS-C 3(3) monitoring of in vivo mitochondrial membrane potential in C. elegans

The mitochondrial respiratory chain plays a crucial role in cellular and organismal health. In addition to being the major source of energy for most cells, mitochondrial respiratory chain function regulates or modulates redox and metabolite homeostasis, apoptosis and the generation of reactive oxygen species. In order to measure the relative in vivo mitochondrial membrane potential of different strains of the nematode, Caenorhabditis elegans, we have developed a fluorescence assay using the cationic, lipophilic carbocyanine dye, diS-C 3(3). We demonstrate that two complex I-deficient mutants have significantly lower mitochondrial membrane potentials in vivo than wild type animals. Our fluorescence assay will enable us to better dissect and understand the complex phenotypic consequences of mitochondrial dysfunction.

Anterograde labeling of the corticospinal tract in jimpy mutant mice by Di I injection into the motor cortex

Carbocyanine fluorescent dye, DiI, is an excellent anterograde/retrograde neural tracer, but its efficacy for the anterograde labeling of neural circuits in the adult brain tends to decrease with ages. The present study shows that an injection of DiI into the motor cortex of the young adult jimpy mutant mice (Plp1(jp)/+) resulted in successful anterograde labeling of corticospinal tract fibers. Furthermore, an injection of Fast Blue into the lumbar spinal cord of the mutant mice resulted in retrograde labeling of layer 5 corticospinal tract neurons within the motor cortex. Since no abnormality except for myelin deficiency is known in the long descending and ascending tracts of jimpy mutant mouse, this mutant is suitable for neural tracing studies of long axonal trajectories with the use of carbocyanine dye, DiI, although these males die between 20 and 40 days of age.

Prenatal carbocyanine dye tracing of septo-hypothalamic connections

This is the first study of the prenatal development of septal projections to the hypothalamus in rats, using carbocyanine dyes (DiI and DiA) as retrograde tracers. First septal neurons send axons to the preoptic area and anterior hypothalamus on embryonic day 14,5 (E14,5) and on E15 numerous labeled neurons are visualized in the septum after DiI insertion into the preoptic region. On E18 and E20 these neurons develop numerous spiny dendrites that occupy all rostrocaudal extension of the septum with concentration in the ventral part of the septum. Only a few septal neurons send their axons to the mediobasal hypothalamus at E15 confirmed by double-labeling (DiI + DiA) experiments on E20–E21. All septo-hypothalamic connections are unilateral and the number of the neurons revealed in the septum correlates with the place and size of the DiI insertion in the hypothalamus: more lateral and anterior hypothalamic marker insertions always resulted in significant neuronal labeling in the septum. No septal connections with the posterior hypothalamus specifically, the mammillary bodies are formed prenatally. We have demonstrated that the development of septal projections to various rostrocaudal regions of the hypothalamus take place during different stages of development. Prominent parts of the septal projections are to the preoptic area and anterior hypothalamus while few connections with the mediobasal hypothalamus are formed prenatally. These data provide basic knowledge of early steps of the development of the septo-hypothalamic connections.

Postnatal Development of Entorhinodentate Projection of the Reeler Mutant Mouse

We anterogradely labeled entorhinodentate axons by the injection of biotin dextran amine into the entorhinal cortex of adult wildtype and reeler mice to clarify whether the course and terminal endings of the reeler entorhinal projection are normal or not. We found that in the reeler mouse, biotin dextran amine-labeled entorhinodentate fibers arising from the entorhinal cortex curved around the hippocampal fissure instead of crossing it, whereas in the wildtype mouse, they crossed the fissure as a perforant pathway. Next, we examined carbocyanine dye (DiI) labeling of the immature entorhinodentate projection and the developmental changes of the hippocampal fissure during early postnatal days based on the laminin and glial fibrillary acidic protein (GFAP) immunohistochemistry. Injection of DiI into the entorhinal area of the wildtype and reeler mice at postnatal day 1 resulted in anterograde labeling of pioneer axons passing through the hippocampal fissure. However, follower axons could not penetrate through the hippocampal fissure in reeler mice, whereas in the normal controls, many DiI-labeled axons continued to pass through the fissure. GFAP immunohistochemistry demonstrated that GFAP-immunopositive astrocytes were abundant along the hippocampal fissure both in the wildtype and reeler mice at birth. In the wildtype mouse, GFAP-positive neurons nearby the fissure were decreasing in number during the early postnatal days, whereas in the reeler mouse, many GFAP-positive astrocytes were continuing to accumulate there. This barrier made of astrocytes in the reeler mouse may obstruct the ingrowth of the follower axons arising from the entorhinal cortex through the hippocampal fissure, resulting in the abnormal course of the entorhinodentate axons in this mutant.

The axis of polarity of the mouse blastocyst is specified before blastulation and independently of the zona pellucida

Rather than being prepatterned, orientation of the embryonic-abembryonic (Em-Ab) axis of the mouse blastocyst has been claimed to depend on the conceptus being constrained by its zona pellucida (ZP) during blastulation. This hypothesis merited closer scrutiny, because it seemed at variance with observations on living conceptuses. Two-cell conceptuses with an oil drop injected into the lesser diameter (LD) of the ZP at the first cleavage plane were cultured until shortly before blastulation when the blastomere underlying the drop was labelled with carbocyanine dye. After removing the ZP, conceptuses were re-cultured to the blastocyst stage for recording the position along the axis of the centres of the patches of labelled cells. These centres showed significant bias towards the equatorial (Eq) region of the axis compared with those resulting from labelling a blastomere at random, even following softening of the ZP at the 2-cell stage. This was also true if conceptuses were denuded at the 2-cell stage and the blastomere underlying an intact second polar body (PB) labelled in morulae. These findings further support the view that the Em-Ab axis of the mouse blastocyst is normally prepatterned and provide no evidence of a role for the ZP in its specification.

Harvesting Photons in the Infrared. Electron Injection from Excited Tricarbocyanine Dye (IR-125) into TiO2 and Ag@TiO2 Core−Shell Nanoparticles

TiO2 and Ag@TiO2 core shell nanoparticles have been modified with a carbocyanine dye (IR-125) to extend the photoresponse in the near-infrared. Upon binding dye molecules to TiO2, we observe a sharp decrease in the fluorescence yield. The electron injection into TiO2 was found to dominate the deactivation of the excited singlet state. The rate constant for the charge injection process as determined from the decay of the excited singlet is ∼1011 s-1. In the case of Ag@TiO2, the electrons injected into the TiO2 layer are quickly transferred to the Ag core. The metal core in Ag@TiO2 did not alter the forward charge-transfer kinetics, but it influenced the back electron transfer. The regeneration of the dye involving the reaction between the oxidized dye and injected electron was a factor of 2 slower for Ag@TiO2 than the TiO2 system. Use of composite nanoparticles comprised of a metal core semiconductor shell may provide new ways to modulate charge recombination processes in dye-sensitized solar cells.

Unilateral cochlear ablation before hearing onset disrupts the maintenance of dorsal nucleus of the lateral lemniscus projection patterns in the rat inferior colliculus

During postnatal development, ascending and descending auditory inputs converge to form fibrodendritic layers within the central nucleus of the inferior colliculus (IC). Before the onset of hearing, specific combinations of inputs segregate into bands separated by interband spaces. These bands may define functional zones within the IC. Previous studies in our laboratory have shown that unilateral or bilateral cochlear ablation at postnatal day 2 (P2) disrupts the development of afferent bands from the dorsal nucleus of the lateral lemniscus (DNLL) to the IC. These results suggest that spontaneous activity propagated from the cochlea is required for the segregation of afferent bands within the developing IC. To test if spontaneous activity from the cochlea also may be required to maintain segregated bands of DNLL input, we performed cochlear ablations in rat pups at P9, after DNLL bands already are established. All animals were killed at P12 and glass pins coated with carbocyanine dye, DiI (1,1′-dioctodecyl-3,3,3′,3′-tetramethylindocarbocyanine perchlorate), subsequently were placed in the commissure of Probst to label the crossed projections from both DNLLs. When compared with surgical controls, experimental results showed a similar pattern of DNLL bands in the IC contralateral to the ablated cochlea, but a disruption of DNLL bands in the IC ipsilateral to the cochlear ablation. The present results suggest that cochlear ablation after DNLL bands have formed may affect the maintenance of banded DNLL projections within the central nucleus of the IC.

Confocal laser scanning microscopy using dialkylcarbocyanine dyes for cell tracing in hard and soft biomaterials

The aim of this work was to study, in vitro, cell colonization of two biomaterials currently used for bone and cartilage repair, this step being important to understand the function of engineered tissues. Current methods that use histological approaches are not always suited to tissue-engineering analysis. We, therefore, set up a protocol to assess cell distribution, utilizing noninvasive confocal microscopy and fluorescent labels with a far red emission wavelength to optimize scaffold transparency and minimize light scattering. Hard (ceramic substitute) and soft (collagen sponge) biomaterials were seeded respectively, on one side of the scaffold, with human fibroblasts and bovine chondrocytes labelled with carbocyanine dyes (DiD and DiR). The mean penetration depth for DiR labelled fibroblasts and chondrocytes in the two scaffolds, around 270 m, was greater than for DiD (136-218 microm) labelled cells. These depths were independent of cell origin but were influenced by the nature of the scaffolds. Collagen sponge is transparent in contrast to ceramic substitutes where measurements could only be made in opened macropores. Besides the limits of the equipment, the limits of the supports were diffusion for collagen sponges and transmission for ceramic substitutes. Confocal microscopy techniques could thus be used to address the question of cell colonization of porous biomaterials in a noninvasive manner.

Characterization of a Single Molecule DNA Switch in Free Solution

We have studied a donor-acceptor fluorophore-labeled DNA switch where the acceptor is Alexa-647, a carbocyanine dye, in solution at the single molecule level to elucidate the fluorescence switching mechanism. The acceptor, which is in an initial high fluorescence trans state, undergoes a photoisomerization reaction resulting in two additional states during its sub-millisecond transit across the probe volume. These two states are assigned to a nonfluorescent triplet trans state that strongly quenches the donor emission and a singlet cis state that blocks the fluorescence resonance energy transfer (FRET) pathway and gives rise to donor-only fluorescence. The formation of these states is faster than the transit time, so that all three states are approximately equally populated under our experimental conditions. The acceptor dye can stick to the DNA in all these states, with the rate of unsticking determining the rate of isomerization into the other states. Measurement of the rate of change of the FRET signal therefore provides information about the fluorophore-DNA intramolecular dynamics. These results explain the large zero peak in the proximity ratio, often seen in single molecule FRET experiments, and suggest that photoinduced effects may be important in single molecule FRET experiments using carbocyanine dyes. They also suggest that for fast photoinduced switching the interactions of the acceptor dye with the DNA and other surfaces should be prevented.

Harvesting Infrared Photons with Tricarbocyanine Dye Clusters

The absorption of 4,5-benzoindotricarbocyanine dye (IR125) in the infrared can be tuned by controlling the type of aggregation in different media. Molecular clusters of this dye formed in a mixed solvent show broad absorption in the 550-950 nm region as compared to the absorption bands of J- and H-type aggregates. The molecular clusters of the carbocyanine dye are electrophoretically deposited as thin film on optically transparent electrodes using a dc electric field. These tricarbocyanine dye cluster films are photoactive in the infrared region and produce cathodic current when employed as photocathode in a photoelectrochemical cell. Transient absorption spectroscopy of the molecular clusters show short-lived singlet state in the picosecond time scale (lifetime 6 ps) and a charge separated state in the nanosecond time scale. Implication of such dye cluster films for harvesting infrared photons in a photoelectrochemical cell is discussed.

Diolistic labeling of neuronal cultures and intact tissue using a hand-held gene gun

Diolistic labeling is a highly efficient method for introducing dyes into cells using biolistic techniques. The use of lipophilic carbocyanine dyes, combined with particle-mediated biolistic delivery using a hand-held gene gun, allows non-toxic labeling of multiple cells in both living and fixed tissue. The technique is rapid (labeled cells can be visualized in minutes) and technically undemanding. Here, we provide a detailed protocol for diolistic labeling of cultured human embryonic kidney 293 cells and whole brain using a hand-held gene gun. There are four major steps: (i) coating gold microcarriers with one or more dyes; (ii) transferring the microcarriers into a cartridge to make a bullet; (iii) preparation of cells or intact tissue; and (iv) firing the microcarriers into cells or tissue. The method can be readily adapted to other cell types and tissues. This protocol can be completed in less than 1 h.

Pathological changes in human retinal ganglion cells associated with diabetic and hypertensive retinopathy

To examine whether systemic diseases like diabetes and arterial hypertension, which frequently cause retinopathies leading to blindness effect the morphology of retinal ganglion cells (RGC). Histological retina material with a history of being untreated, or laser-coagulated (LC) diabetic retinopathy (DR), or arterial hypertensive retinopathy (AHR) was used. The RGC were labeled by introducing crystals of the fluorescent carbocyanine dye DiI into the nerve fiber layer, which contains ganglion cell axons. The typical silhouettes of both major types of RGC, parasol and midget cells, were identified. The axons in DR and AHR retinas showed morphology changes such as irregular swelling and beading. Dendritic field sizes were significantly reduced in RGC of both the hypertonic and diabetic retinas. A significant reduction in branching frequency was evident in both the diabetic and hypertonic retinas, in both the midget and the parasol cells. In LC retinas, both parasol and midget RGC were observed within the LC spots, although their numbers were dramatically decreased compared with normal retinas. The data suggest that diabetes and arterial hypertonia have similar effects on the morphology of RGC, in addition to causing microvascular alterations and bleeding. Therefore, therapeutic measures and prognostic outcomes in diabetic and hypertensive retinopathy should also consider regressive changes in retinal neurons.

Role of p35/Cdk5 in Preplate Splitting in the Developing Cerebral Cortex

The earliest generated cells of the mammalian cerebral cortex form the preplate layer (PPL). The subsequently born cortical plate (CP) cells split this layer into the superficial layer I (LI) and the deep subplate (SP). The cellular and molecular mechanisms that underlie this event are unclear. To investigate the role of the cyclin-dependent kinase 5 (Cdk5) and its activator p35 in preplate splitting, we used Nissl staining, carbocyanine dye tracing, cell birthdating, and immunohistochemistry for calretinin (CalR) in p35 and Cdk5 knockout mice. Our data demonstrated changes in early cortical lamination and aberrant thalamic axon trajectories in these mice. Specifically, LI was thicker, and cell-dense and thalamic axons did not accumulate in the SP layer before invading the CP. Instead, they grew past the SP and more superficial cortical layers and coursed obliquely toward the pial surface. This behavior has been previously observed in reeler mice and suggests a defect in PPL splitting. CalR immunohistochemistry and bromo-deoxyuridine birthdating confirmed the abnormality in position of the earliest generated cortical cells of mutants. These observations suggest that the p35/Cdk5 pathway plays a role in preplate splitting in addition to regulating layer formation.