Activation of human RNA lariat debranching enzyme Dbr1 by binding protein TTDN1 occurs though an intrinsically disordered C-terminal domain.

In eukaryotic cells, the introns are excised from pre-mRNA by the spliceosome. These introns typically have a lariat configuration due to the 2'-5' phosphodiester bond between an internal branched residue and the 5' terminus of the RNA. The only enzyme known to selectively hydrolyze the 2'-5' linkage of these lariats is the RNA lariat debranching enzyme Dbr1. In humans, Dbr1 is involved in processes such as class-switch recombination of immunoglobulin genes, and its dysfunction is implicated in viral encephalitis, HIV, ALS, and cancer. However, mechanistic details of precisely how Dbr1 affects these processes are missing. Here we show that human Dbr1 contains a disordered C-terminal domain through sequence analysis and nuclear magnetic resonance. This domain stabilizes Dbr1 in vitro by reducing aggregation but is dispensable for debranching activity. We establish that Dbr1 requires Fe2+ for efficient catalysis and demonstrate that the noncatalytic protein Drn1 and the uncharacterized protein trichothiodystrophy nonphotosensitive 1 directly bind to Dbr1. We demonstrate addition of trichothiodystrophy nonphotosensitive 1 to in vitro debranching reactions increases the catalytic efficiency of human Dbr1 19-fold but has no effect on the activity of Dbr1 from the amoeba Entamoeba histolytica, which lacks a disordered C-terminal domain. Finally, we systematically examine how the identity of the branchpoint nucleotide affects debranching rates. These findings describe new aspects of Dbr1 function in humans and further clarify how Dbr1 contributes to human health and disease.

Effect of laser pulse shaping on photoacoustic dosimetry in retinal models.

Photoacoustic sensing can be a powerful technique to obtain real-time feedback of laser energy dose in treatments of biological tissue. However, when laser therapy uses pulses with microsecond duration, they are not optimal for photoacoustic pressure wave generation. This study examines a programmable fiber laser technique using pulse modulation in order to optimize the photoacoustic feedback signal to noise ratio (SNR) in a context where longer laser pulses are employed, such as in selective retinal therapy. We have demonstrated with a homogeneous tissue phantom that this method can yield a greater than seven-fold improvement in SNR over non-modulated square pulses of the same duration and pulse energy. This technique was further investigated for assessment of treatment outcomes in leporine retinal explants by photoacoustic mapping around the cavitation-induced frequency band.

Effect of liposomal confinement on photothermal and photo-oximetric fluorescence lifetimes of photosensitizers with varying hydrophilicity.

The time-resolved fluorescence of photosensitizers (PSs) of varying hydrophobicities, di-and tetrasulfonated Al phthalocyanines (Al-2 and Al-4), and Photochlor (HPPH), was investigated in liposomes used as cell-mimetic models. Using frequency-and time-domain apparatus, the fluorescence lifetime, tau(fluo), was compared for PSs free in aqueous solution and in a liposome-associated state at varied temperatures (25 to 78 degrees C) and oxygen concentrations (0-190 microM). The analysis of tau(fluo) revealed different decay behaviors for the free-solution and liposome-confined PSs, most significantly for the lipophilic HPPH. Hydrophilic PS drugs (Al-4, Al-2) were less affected by the liposomal confinement, depending on the relative hydrophilicity of the compound and the consequent localization in liposomes. Changes in the emission decay due to confinement were detected as differences in the lifetime between the bulk solution and the liposome-localized PS in response to heating and deoxygenation. Specifically, hydrophilic Al-4 produced an identical lifetime trend as a function of temperature both in solu and in a liposome-confined state. Hydrophobic HPPH exhibited a fundamental transformation in its fluorescence decay kinetics, transitioning from a multiexponential (in free solution) to single-exponential (in liposome) decay. Deoxygenation resulted in a ubiquitous tau(fluo) increase for all PSs in free solution, while the opposite, a tau(fluo) decrease, occurred in all liposomal PSs.

Effect of liposomal confinement on photochemical properties of photosensitizers with varying hydrophilicity.

Preferential tumor localization and the aggregation state of photosensitizers (PSs) can depend on the hydrophilic/hydrophobic nature of the molecule and affect their phototoxicity. In this study, three PSs of different hydrophilicity are introduced in liposomes to understand the structure-photochemistry relationship of PSs in this cellular model system. Absorbance and fluorescence spectra of amphiphilic aluminum (III) phthalocyanine disulfonate chloride adjacent isomer (Al-2), hydrophilic aluminum (III) phthalocyanine chloride tetrasulfonic acid (Al-4), and lipophilic 2-(1-hexyloxyethyl)-2-devinyl pyropheophorbide (HPPH) are compared in a liposomal confined state with free PS in bulk solution. For fluorescence measurements, a broad range of concentrations of both bulk and liposomal confined PSs are examined to track the transition from monomers to dimers or higher order aggregates. Epifluorescence microscopy, absorbance, and fluorescence measurements all confirm different localization of the PSs in liposomes, depending on their hydrophilicity. In turn, the localization affects the aggregation of molecules inside the liposome cell model. Data obtained with such cellular models could be useful in optimizing the photochemical properties of photosensitizing drugs based on their structure-dependent interactions with cellular media and subcellular organelles.

Cy5.5-DTPA-galactosyl-dextran: a fluorescent probe for in vivo measurement of receptor biochemistry.

The high sensitivity of fluorescent reporters offers an opportunity to analytically probe the biochemistry of in vivo receptor systems with low target tissue concentration. We investigated the ability of an optical imaging system to acquire adequate signal for in vivo measurement of receptor biochemistry. The imaging system consisted of a small animal optical imager operating in the time domain (TD) and a fluorescent-labeled diagnostic probe of known receptor-binding properties. Optical imaging of mice (n = 4) using the targeted probe, Cy5.5-DTPA-galactosyl-dextran (2.2 Cy5.5, 4 DTPA, 68 galactose units per dextran, 124 kDa, 24 nmol/kg), demonstrated blood clearance and hepatic uptake. The mean and standard deviation for the time to reach 90% of the peak liver intensity were 15.4 +/- 1.6 min. Typical fluorescent intensities within a 10-pixel region-of-interest from a 30-s image acquired 30 min postinjection were in excess of 2.5 million counts. The nontargeted agent (Cy5.5-DTPA-dextran) did not demonstrate (n = 4) hepatic uptake. This uptake pattern was duplicated by nuclear imaging of rabbits using (99m)Tc-labeled Cy5.5-DTPA-galactosyl-dextran and Cy5.5-DTPA-dextran. This study demonstrated the feasibility of optically labeling a receptor-binding diagnostic probe and imaging in the TD with sufficient sensitivity and temporal resolution for pharmacokinetic analysis.

Towards a bimodal proximity sensor for in situ neurovascular bundle detection during dental implant surgery.

Proof of concept results are presented towards an in situ bimodal proximity sensor for neurovascular bundle detection during dental implant surgery using combined near infrared absorption (NIR) and optical coherence tomography (OCT) techniques. These modalities are shown to have different sensitivity to the proximity of optical contrast from neurovascular bundles. NIR AC and DC signals from the pulsing of an artery enable qualitative ranging of the bundle in the millimeter range, with best sensitivity around 0.5-3mm distance in a custom phantom setup. OCT provides structural mapping of the neurovascular bundle at sub-millimeter distances in an ex vivo human jaw bone. Combining the two techniques suggests a novel ranging system for the surgeon that could be implemented in a "smart drill." The proximity to the neurovascular bundle can be tracked in real time in the range of a few millimeters with NIR signals, after which higher resolution imaging OCT to provide finer ranging in the sub-millimeter distances.

Molecular imaging of the translocator protein (TSPO) in a pre-clinical model of breast cancer.

PURPOSE: To quantitatively evaluate the utility of a translocator protein (TSPO)-targeted near-infrared (NIR) probe (NIR-conPK11195) for in vivo molecular imaging of TSPO in breast cancer. PROCEDURES: NIR-conPK11195 uptake and TSPO-specificity were validated in TSPO-expressing human breast adenocarcinoma cells (MDA-MB-231). In vivo NIR-conPK11195 biodistribution and accumulation were quantitatively evaluated in athymic nude mice bearing MDA-MB-231 xenografts. RESULTS: Fluorescence micrographs illustrated intracellular labeling of MDA-MB-231 cells by NIR-conPK11195. Quantitative uptake and competition assays demonstrated dose-dependent (p < 0.001) and TSPO-specific (p < 0.001) NIR-conPK11195 uptake. In vivo, NIR-conPK11195 preferentially labeled MDA-MB-231 tumors with an 11-fold (p < 0.001) and 7-fold (p < 0.001) contrast enhancement over normal tissue and unconjugated NIR dye, respectively. CONCLUSIONS: NIR-conPK11195 appears to be a promising TSPO-targeted molecular imaging agent for visualization and quantification of breast cancer cells in vivo. This research represents the first study to demonstrate the feasibility of TSPO imaging as an alternative breast cancer imaging approach.

Sensitivity characterization of a time-domain fluorescence imager: eXplore Optix.

A key issue in the practical application of fluorescence imaging is the presence of a background signal detected during data acquisition when no target fluorescent material is present. Regardless of the technology employed, background signals cannot be completely eliminated, which limits the detection sensitivity of fluorescence imaging systems, especially for in vivo applications. We present a methodology to characterize the sensitivity of fluorescence imaging devices by taking the background effect into account through the fluorescent signal-to-background ratio (SBR). In an initial application of the methodology, tissuelike liquid phantoms with Cy5.5 fluorescent inclusions were investigated experimentally over a wide range of varying parameters, such as tissue absorption coefficient, scattering coefficient, fluorophore concentration, and inclusion location. By defining detectable and quantifiable SBR thresholds, empirical relations are established, and the sensitivity performance of Advanced Research Technologies's eXplore Optix using Cy5.5 is characterized.

Comparison of simplified Monte Carlo simulation and diffusion approximation for the fluorescence signal from phantoms with typical mouse tissue optical properties.

A simplified approach is proposed to simulate the fluorescence signal from a fluorophore submerged inside a turbid medium using the Monte Carlo method. Based on the reversibility of photon propagation, the fluorescence signal can be obtained from a single Monte Carlo simulation of the excitation light. This is computationally less expensive and also allows for the direct use of well-validated nonfluorescence photon migration Monte Carlo codes. Fluorescence signals from a mouse tissuelike phantom were computed using both the simplified Monte Carlo simulation and the diffusion approximation. The relative difference of signal intensity was found to be at most 30% for a fluorophore placed in the medium at various depths and horizontally midway between a source-detector pair separated by 3 mm. The difference in time characteristics of the signal is also examined.

In vivo optical imaging of acute myeloid leukemia by green fluorescent protein: time-domain autofluorescence decoupling, fluorophore quantification, and localization.

Human xenografts of acute myeloid leukemia (AML) in nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice result in disease states of diffuse, nonpalpable tissue infiltrates exhibiting a variable disease course, with some animals not developing a disease phenotype. Thus, disease staging and, more critically, quantification of preclinical therapeutic effect in these models are particularly difficult. In this study, we present the generation of a green fluorescent protein (GFP)-labeled human leukemic cell line, NB4, and validate the potential of a time-domain imager fitted with a 470 nm picosecond pulsed laser diode to decouple GFP fluorescence from autofluorescence on the basis of fluorescence lifetime and thus determine the depth and relative concentration of GFP inclusions in phantoms of homogeneous and heterogeneous optical properties. Subsequently, we developed an optical imageable human xenograft model of NB4-GFP AML and illustrate early disease detection, depth discrimination of leukemic infiltrates, and longitudinal monitoring of disease course employing time-domain optical imaging. We conclude that early disease detection through use of time-domain imaging in this initially slowly progressing AML xenograft model permits accurate disease staging and should aid in future preclinical development of therapeutics for AML.