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Under nutrient-rich conditions, stochasticity of transcription drives protein expression noise. However, by shifting the environment to amino acid-limited conditions, we identified in E. coli a source of noise whose strength is dictated by translational processes. Specifically, we discovered that cell-to-cell variations in fluorescent protein expression depend on codon choice, with codons yielding lower mean expression after amino acid downshift also resulting in greater noise. We propose that ultra-sensitivity in the tRNA charging/discharging cycle shapes the strength of the observed noise by amplifying fluctuations in global intracellular parameters, such as the concentrations of amino acid, synthetase, and tRNA. We hypothesize that this codon-dependent noise may allow bacteria to selectively optimize cell-to-cell variability in poor environments without relying on low molecular numbers.

The spectral linewidth of an ensemble of fluorescent emitters is dictated by a combination of the single emitter linewidths and sample inhomogeneities. For semiconductor nanocrystals, efforts to tune ensemble linewidths for optical applications have focused primarily on eliminating sample inhomogeneities because conventional single-molecule methods cannot reliably build accurate ensemble-level statistics for single-particle linewidths. Photon-correlation Fourier spectroscopy in solution (S-PCFS) offers a unique approach to investigating single-nanocrystal spectra with large sample statistics, without user selection bias, with high signal-to-noise ratios, and at fast timescales. With S-PCFS, we directly and quantitatively deconstruct the ensemble linewidth into contributions from the average single-particle linewidth and from sample inhomogeneity. We demonstrate that single-particle linewidths vary significantly from batch to batch and can be synthetically controlled. These findings crystallize our understanding of the synthetic challenges facing underdeveloped nanomaterials such as InP and InAs core/shell particles and introduce new avenues for the synthetic optimization of fluorescent nanoparticles.

BACKGROUND: The goal of limb-sparing surgery for a soft tissue sarcoma of the extremity is to remove all malignant cells while preserving limb function. After initial surgery, microscopic residual disease in the tumor bed will cause a local recurrence in approximately 33% of patients with sarcoma. To help identify these patients, the authors developed an in vivo imaging system to investigate the suitability of molecular imaging for intraoperative visualization. METHODS: A primary mouse model of soft tissue sarcoma and a wide field-of-view imaging device were used to investigate a series of exogenously administered, near-infrared (NIR) fluorescent probes activated by cathepsin proteases for real-time intraoperative imaging. RESULTS: The authors demonstrated that exogenously administered cathepsin-activated probes can be used for image-guided surgery to identify microscopic residual NIR fluorescence in the tumor beds of mice. The presence of residual NIR fluorescence was correlated with microscopic residual sarcoma and local recurrence. The removal of residual NIR fluorescence improved local control. CONCLUSIONS: The authors concluded that their technique has the potential to be used for intraoperative image-guided surgery to identify microscopic residual disease in patients with cancer. Cancer 2012. © 2012 American Cancer Society.

The Kennard–Stepanov relation connects the optical emission and absorption spectra of materials. It has proved useful in assessing the extent of equilibration of excited states of fluorescent systems. We propose a generalization of the theory that may help characterize the approach to equilibrium and we illustrate the method in model systems.

We describe a method to generate monovalent quantum dots (QDs) using agarose gel electrophoresis. We passivated QDs with a carboxy-terminated polyethylene-glycol ligand, yielding particles with half the diameter of commercial QDs, which we conjugated to a single copy of a high-affinity targeting moiety (monovalent streptavidin or antibody to carcinoembryonic antigen) to label cell-surface proteins. The small size improved access of QD-labeled glutamate receptors to neuronal synapses, and monovalency prevented EphA3 tyrosine kinase activation.

We measure the anomalous spectral diffusion of single colloidal quantum dots over eight temporal decades simultaneously by combining single-molecule spectroscopy and photon-correlation Fourier spectroscopy. Our technique distinguishes between discrete and continuous dynamics and directly reveals that the quasicontinuous spectral diffusion observed using conventional spectroscopy is composed of rapid, discrete spectral jumps. Despite their multiple time scales, these dynamics can be captured by a single mechanism whose parameters vary widely between dots and over time in individual dots.

Fluorescence spectroscopy of single chromophores immobilized on a substrate has provided much fundamental insight, yet the spectral line shapes and dynamics of single chromophores freely diffusing in solution have remained difficult or impossible to measure with conventional linear spectroscopies. Here, we demonstrate an interferometric technique for extracting time dependent single chromophore spectral correlations from intensity correlations in the interference pattern of an ensemble fluorescence spectrum. We apply our technique to solutions of colloidal quantum dots and explore the spectrum of single particles on short time scales not feasible with conventional fluorescence measurements.

We present a new class of polymeric ligands for quantum dot (QD) water solubilization to yield biocompatible and derivatizable QDs with compact size (approximately 10-12 nm diameter), high quantum yields (50%), excellent stability across a large pH range (pH 5-10.5), and low nonspecific binding. To address the fundamental problem of thiol instability in traditional ligand exchange systems, the polymers here employ a stable multidentate imidazole binding motif to the QD surface. The polymers are synthesized via reversible addition-fragmentation chain transfer-mediated polymerization to produce molecular weight controlled monodisperse random copolymers from three types of monomers that feature imidazole groups for QD binding, polyethylene glycol (PEG) groups for water solubilization, and either primary amines or biotin groups for derivatization. The polymer architecture can be tuned by the monomer ratios to yield aqueous QDs with targeted surface functionalities. By incorporating amino-PEG monomers, we demonstrate covalent conjugation of a dye to form a highly efficient QD-dye energy transfer pair as well as covalent conjugation to streptavidin for high-affinity single molecule imaging of biotinylated receptors on live cells with minimal nonspecific binding. The small size and low serum binding of these polymer-coated QDs also allow us to demonstrate their utility for in vivo imaging of the tumor microenvironment in live mice.

A fluorescence-based imaging system has been developed for real-time, in vivo tumor margin assessment with microscopic sensitivity. Intra-operative imaging results have matched post-surgical histo-pahtological margin assessment in all the sarcoma mice cases tested so far.

We report narrow-band absorption enhancement of semiconductor nanocrystals via Forster resonance energy transfer from cyanine J-aggregates. These J-aggregated dyes associate electrostatically with short quantum-dot (QD) surface ligands in solution. Energy transfer efficiencies approach unity for this light sensitization and result in a 5-fold enhancement in the QD excitation near the J-aggregate absorption maximum. Because a thin layer of J-aggregates attenuates the same amount of light (at peak absorbance) as a far thicker film of monomer dye, these absorption-enhanced materials may have applications in light-sensitizing applications such as photodetection and optical down-conversion.

We show that the single emitter linewidth underlying a broadened ensemble emission spectrum can be extracted from correlations among the stochastic intensity fluctuations in the ensemble spectrum. Spectral correlations can be observed at high temporal and spectral resolutions with a cross-correlated pair of avalanche photodiodes placed at the outputs of a scanning Michelson interferometer. As illustrated with simulations in conjunction with Fluorescence Correlation Spectroscopy, our approach overcomes ensemble and temporal inhomogeneous broadening to provide single emitter linewidths, even for emitters under weak, continuous, broadband excitation., 9 pages, 5 figures

We investigate the temperature dependence of exciton fluorescence, absorption, and Stokes shift for five sizes of high quality $\mathrm{Cd}\mathrm{Se}∕\mathrm{Zn}\mathrm{S}$ nanocrystals from the perspective of the fine structure model and exciton-acoustic phonon coupling. The Stokes shift is found to have a weak temperature dependence for all sizes. Within the fine structure model, we use the temperature dependence of the Stokes shift to infer the upper level energy and oscillator strength. We also interpret our ensemble measurements using an exciton-acoustic phonon scattering model. We find that neither the fine structure nor exciton-acoustic phonon scattering is able to adequately explain our data in isolation and conclude that a comprehensive theory which includes the physics of both models on an equal footing is required.

Limb-sparing surgery for extremity soft tissue sarcoma removes all cancer cells at the primary tumor site in the majority of patients. However, without radiation therapy, microscopic residual sarcoma cells left behind in the tumor bed will cause a tumor recurrence in approximately one-third of patients. Therefore, adjuvant radiation therapy is delivered to most patients, even when the tumor bed lacks residual cancer. Here, we present an imaging system for residual cancer assessment, consisting of a novel wide field-of-view imaging device and a protease-activated fluorescent probe. We demonstrate that this system directly images microscopic residual sarcoma cells in the tumor bed of mice when primary soft tissue sarcomas are resected. Moreover, this system can detect single tumor cells that have activated the fluorescent probe in vivo. This technology has the potential to be used as an intra-operative tool to identify microscopic residual disease for soft tissue sarcoma and other cancers with the goal of reducing rates of local recurrence, re-operation for positive margins, and adjuvant radiation therapy to tumor beds that lack residual cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4316.