Biomedical subjects

Ji Yu

Publications and source records attributed to Ji Yu.

7 recordsLinked to original sources

PubMed2006

Living cells as test tubes.

The combination of specific probes and advanced optical microscopy now allows quantitative probing of biochemical reactions in living cells. On selected systems, one can detect and track a particular protein with single-molecule sensitivity, nanometer spatial precision, and millisecond time resolution. Metabolites, usually difficult to detect, can be imaged and monitored in living cells with coherent anti-Stokes Raman scattering microscopy. Here, we describe the application of these techniques in studying gene expression, active transport, and lipid metabolism.

Animals↗

PubMed2006

Probing gene expression in live cells, one protein molecule at a time.

We directly observed real-time production of single protein molecules in individual Escherichia coli cells. A fusion protein of a fast-maturing yellow fluorescent protein (YFP) and a membrane-targeting peptide was expressed under a repressed condition. The membrane-localized YFP can be detected with single-molecule sensitivity. We found that the protein molecules are produced in bursts, with each burst originating from a stochastically transcribed single messenger RNA molecule, and that protein copy numbers in the bursts follow a geometric distribution. The quantitative study of low-level gene expression demonstrates the potential of single-molecule experiments in elucidating the workings of fundamental biological processes in living cells.

Bacterial Proteins↗

PubMed2005

Single molecule modulation spectroscopy of conjugated polymers.

This paper describes a new single molecule spectroscopy approach for the investigation of triplet-triplet and singlet-triplet interactions in conjugated polymers. The technique involves the irradiation of isolated single, mulitchromophoric, conjugated polymer molecules by a repetitive sequence of variable-intensity microsecond time scale excitation pulses. The fluorescence intensity is synchronously time-averaged for thousands of cycles of the pulse sequence to yield a high signal-to-noise fluorescence transient on the microsecond time scale. The transient can be analyzed with kinetic models to obtain quantitative information about the kinetics of triplet-triplet exciton annihilation and the quenching of singlet excitons by triplet excitons in conjugated polymers.

Journal Article↗

PubMed2005

Singlet-triplet and triplet-triplet interactions in conjugated polymer single molecules.

Single molecule fluorescence correlation spectroscopy has been used to investigate the photodynamics of isolated single multichromophoric polymer chains of the conjugated polymers MEH-PPV and F8BT on the microsecond to millisecond time scale. The experimental results (and associated kinetic modeling) demonstrate that (i) triplet exciton pairs undergo efficient triplet-triplet annihilation on the <<30 micros time scale, (ii) triplet-triplet annihilation is the dominant mechanism for triplet decay at incident excitation powers > or =50 W/cm(2), and (iii) singlet excitons are quenched by triplet excitons with an efficiency on the order of (1)/(2). The high efficiency of this latter process ensures that single molecule fluorescence spectroscopy can be effectively used to indirectly monitor triplet exciton population dynamics in conjugated polymers. Finally, correlation spectroscopy of MEH-PPV molecules in a multilayer device environment reveals that triplet excitons are efficiently quenched by hole polarons.

Journal Article↗

PubMed2005

Nonequilibrium steady state of a nanometric biochemical system: determining the thermodynamic driving force from single enzyme turnover time traces.

A single enzyme molecule in a living cell is a nanometric system that catalyzes biochemical reactions in a nonequilibrium steady-state condition. The chemical driving force, Deltamu, is an important thermodynamic quantity that determines the extent to which the reaction system is away from equilibrium. Here we show that Deltamu for an enzymatic reaction in situ can be determined from the nonequilibrium time traces for enzymatic turnovers of individual enzyme molecules, which can now be recorded experimentally by single-molecule techniques. Three different Deltamu estimators are presented from principles of nonequilibrium statistical mechanics: fluctuation theorem, Kawasaki identity, and fluctuation dissipation theorem, respectively. In particular, a maximum likelihood estimation method of Deltamu has been derived based on fluctuation theorem. The statistical precisions of these three Deltamu estimators are analyzed and compared for experimental time traces with finite lengths.

Computer Simulation↗

PubMed2004

Charge injection and photooxidation of single conjugated polymer molecules.

The complex, coupled mechanisms of charge transfer and oxidative damage in organic electronic devices (such as organic light-emitting diodes (OLED), solar cells, etc.) have been elucidated by a new technique that combines single-molecule spectroscopy with charge injection from a metal electrode. The experiments employed a sandwich device architecture (Au/TPD/MEH-PPV:PMMA/SiO2/ITO), essentially a modified OLED with a charge-blocking layer (SiO2) to suppress charge injection at the ITO electrode. The fluorescence (photoluminescence) of isolated MEH-PPV conjugated polymer molecules imbedded in the device was observed to exhibit diverse time- and electrical bias-dependent effects. These include: (i) fluorescence quenching due to interactions between MEH-PPV and holes in the TPD hole-transport layer; (ii) fluorescence quenching, or "photobleaching", due to chemical defects at MEH-PPV generated by photooxidation; and (iii) a novel process, reductive "repair" of the oxidative chemical defects by externally injected carriers. These results demonstrate a very different mechanism for photobleaching of organic conjugated materials than is generally assumed to operate and, furthermore, suggest an intimate relationship among photobleaching, charge transport, and persistent photoconductivity in organic materials.

Journal Article↗

PubMed2003

20-hydroxyeicosatetraenoic acid (20-HETE): structural determinants for renal vasoconstriction.

The effects of natural and synthetic eicosanoids on the diameter of rat interlobular arteries studied in vitro were compared to that of the potent, endogenous vasoconstrictor 20-HETE. Vasoconstrictor activity was optimum for chain lengths of 20-22 carbons with at least one olefin or epoxide between located between C(13)-C(15) and an oxygen substituent at C(20)-C(22). The presence of delta (Zou et al. Am. J. Physiol. 1996, 270, R228; Gebremedhin, D. et al. Am. J. Physiol. 1998, 507, 771)-, delta (Carroll et al. Am. J. Physiol. 1996, 271, R863; Vazquez et al. Life Sci. 1995, 56, 1455)-, or delta (Imig et al. Hypertension 2000, 35, 307; Lopez et al. Amer. J. Physiol. 2001, 281, F420)-olefins had no influence on the vasoconstrictor response whereas the introduction of a C(7)-thiomethylene enhanced potency. A sulfonamide or alcohol, but not a lactone, could replace the C(1)-carboxylate. These data were used to construct a putative binding domain map of the 20-HETE receptor consisting of: (i) a comparatively open, hydrophilic binding site accommodating the C(1)-functionality; (ii) a hydrophobic trough spanning the olefins; (iii) a shallow pocket containing a critical pi-pi binding site in the vicinity of the pi (Ito et al. Am. J. Physiol. 1998, 274, F395; Quigley, R.; Baum, M.; Reddy, K. M.; Griener, J. C.; Falck, J. R. Am. J. Physiol. 2000, 278, F949)-olefin; and (iv) an oxyphilic binding site proximate to the omega-terminus.

Animals↗