Rapid and direct microRNA quantification by an enzymatic luminescence assay

A quantitative bioluminescence assay for rapid and sensitive microRNA (miRNA) expression analysis was developed. The assay uses miRNA directly as a primer for binding to a circular single-stranded DNA template, followed by rolling circle amplification. The detection of inorganic pyrophosphate (PPi) molecules released during the DNA polymerization and amplification process is performed by a multi-enzyme system. PPi is converted to ATP by ATP-sulfurylase, which provides energy for luciferase to oxidize luciferin and produce light. Experimental results show that the assay has a dynamic range exceeding three orders of magnitude and the ability to discriminate miRNAs with high-homology sequences. Quantification of nine miRNAs in human heart tissues demonstrated high cross-platform consistency between this assay and the TaqMan real-time polymerase chain reaction (PCR) assay with R(2)=0.941. The assay requires fewer reagents, can be performed at an isothermal condition without thermal cycling, and is capable of detecting miRNAs in less than 1h. Compared with the real-time PCR and microarray-based detection methods, this assay provides a simpler, faster, and less expensive platform for miRNA quantification in life science research, drug discovery, and clinical diagnosis.     

Bioluminescent system for dynamic imaging of cell and animal behavior

The current utility of bioluminescence imaging is constrained by a low photon yield that limits temporal sensitivity. Here, we describe an imaging method that uses a chemiluminescent/fluorescent protein, ffLuc-cp156, which consists of a yellow variant of Aequorea GFP and firefly luciferase. We report an improvement in photon yield by over three orders of magnitude over current bioluminescent systems. We imaged cellular movement at high resolution including neuronal growth cones and microglial cell protrusions. Transgenic ffLuc-cp156 mice enabled video-rate bioluminescence imaging of freely moving animals, which may provide a reliable assay for drug distribution in behaving animals for pre-clinical studies.     

Single photon counting imagery

Advent of the multichannel plate and position sensitive detector has made possible true single photon counting imaging tubes. We have investigated the application of these detectors in studies of the ultraweak light emission of biological materials. Initially, we focussed our efforts on two objectives: (1) obtaining single photon counting images of living tissues using only the light (chemiluminescence) emitted by the specimen and (2) developing means of obtaining well-resolved spectra of weakly emitting sources. We have obtained a variety of images. One striking result of this work is the first observation of tissue specific localization of photon emission in situ. Using this detector we have also obtained the first well-resolved spectra of some important ultraweak emission processes. These results illustrate the potential use of single photon imaging in bioluminescence and chemiluminescence research.     

A sensitive bioluminescence assay for myo-inositol

A specific, sensitive bioluminescence assay for myo-inositol is described employing myo-inositol dehydrogenase linked to a commercial NADH bioluminescence kit. Optimum conditions providing a linear response over 4 orders of magnitude are presented with reproducibility of 6% CV and a sensitivity of 1 pmol. The assay is suitable for the measurement of inositol at low concentrations or in small volumes.     

Forced Detection Monte Carlo Algorithms for Accelerated Blood Vessel Image Simulations

Two forced detection (FD) variance reduction Monte Carlo algorithms for image simulations of tissue‐embedded objects with matched refractive index are presented. The principle of the algorithms is to force a fraction of the photon weight to the detector at each and every scattering event. The fractional weight is given by the probability for the photon to reach the detector without further interactions. Two imaging setups are applied to a tissue model including blood vessels, where the FD algorithms produce identical results as traditional brute force simulations, while being accelerated with two orders of magnitude. Extending the methods to include refraction mismatches is discussed. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Disposable bioluminescence-based biosensor for detection of bacterial count in food

A biosensor for rapid detection of bacterial count based on adenosine 5′-triphosphate (ATP) bioluminescence has been developed. The biosensor is composed of a key sensitive element and a photomultiplier tube used as a detector element. The disposable sensitive element consists of a sampler, a cartridge where intracellular ATP is chemically extracted from bacteria, and a microtube where the extracted ATP reacts with the luciferin–luciferase reagent to produce bioluminescence. The bioluminescence signal is transformed into relevant electrical signal by the detector and further measured with a homemade luminometer. Parameters affecting the amount of the extracted ATP, including the types of ATP extractants, the concentrations of ATP extractant, and the relevant neutralizing reagent, were optimized. Under the optimal experimental conditions, the biosensor showed a linear response to standard bacteria in a concentration range from 10³ to 10⁸ colony-forming units (CFU) per milliliter with a correlation coefficient of 0.925 (n = 22) within 5 min. Moreover, the bacterial count of real food samples obtained by the biosensor correlated well with those by the conventional plate count method. The proposed biosensor, with characteristics of low cost, easy operation, and fast response, provides potential application to rapid evaluation of bacterial contamination in the food industry, environment monitoring, and other fields.     

Attenuation in very narrow photon beams

When one measures the half-value layer (HVL) or the attenuation coefficient (mu) in a high-energy photon beam, it is necessary to use a narrow beam to eliminate the scattered photons produced in the attenuator. However, lateral electron equilibrium will be compromised if the beam is too small. If the HVL and mu are based on measurements of absorbed dose, the results will then depend on field size for a polyenergetic photon spectrum. The measured values also become sensitive to detector properties. This has been examined by experiments and Monte Carlo calculations. The field size should be sufficient for lateral electron equilibrium to prevent ambiguities in the resulting HVL or mu, which are of the order of 10% for 6-MV X rays.     

Information bounds and optimal analysis of dynamic single molecule measurements

Time-resolved single molecule fluorescence measurements may be used to probe the conformational dynamics of biological macromolecules. The best time resolution in such techniques will only be achieved by measuring the arrival times of individual photons at the detector. A general approach to the estimation of molecular parameters based on individual photon arrival times is presented. The amount of information present in a data set is quantified by the Fisher information, thereby providing a guide to deriving the basic equations relating measurement uncertainties and time resolution. Based on these information-theoretical considerations, a data analysis algorithm is presented that details the optimal analysis of single-molecule data. This method natively accounts and corrects for background photons and cross talk, and can scale to an arbitrary number of channels. By construction, and with corroboration from computer simulations, we show that this algorithm reaches the theoretical limit, extracting the maximal information out of the data. The bias inherent in the algorithm is considered and its implications for experimental design are discussed. The ideas underlying this approach are general and are expected to be applicable to any information-limited measurement.     

生物超微弱发光的两维探测

本文介绍了自行研制的二套系统及其应用。1．高灵敏荧光显微镜系统,该系统探测灵敏度达到10－6lx量级,比普通CCD系统提高了104倍,系统用宽量程照度计对微弱光成象性能进行了标定,在给出细胞荧光图象的同时,可以给出每一象元的发光强度,并可给出视觉更易分辨的光强的三维显示和伪彩色图象。在该系统上得到了分红菌甲素在Hela细胞中的分布图象,Hela细胞加入竹红菌甲素后的光照损伤及抗氧化剂维生素E等对细胞的保护图象。2．光子计数成象系统,该系统灵敏度达10-8lx量级,可探测到单个光子及其分布,在其上得到了绿豆芽,树叶,昆明鼠,人手及手指的超微弱发光的光子图象,并用统计理论进行了信号检验。     

Reversible inactivation of rat liver inorganic pyrophosphatase by substrate and its analogs.

Dissociation of Mg2+ from one of the two metal-binding sites whose occupancy is absolutely required for catalysis by rat liver inorganic pyrophosphatase is a slow reaction (tau 1/2 = 3 h). Polycarboxylic Mg2+ complexons markedly accelerate this process due to their binding with Mg2+ on the enzyme. PPi, ATP and a number of diphosphonate analogs of PPi also bind with Mg2+ on the enzyme with concomitant decrease in enzyme activity by 75% but do not release the bound Mg2+. The resulting ternary complex rapidly (tau 1/2 of several seconds) dissociates upon dilution into substrate-free medium. PPi and imidodiphosphate, which are substrates for pyrophosphatase, decrease the rate of reactivation by at least two orders of magnitude. The results can be explained by existence of two interconvertible forms of the enzyme, of which one is inactive and is stabilized by substrate or its analogs.     

Modeling and measurement of a whole-cell bioluminescent biosensor based on a single photon avalanche diode

Whole-cell biosensors are potential candidates for on-line and in situ environmental monitoring. In this work we present a new design of a whole-cell bioluminescence biosensor for water toxicity detection, based on genetically engineered Escherichia coli bacteria, carrying a recA::luxCDABE promoter-reporter fusion. Sensitive optical detection is achieved using a single photon avalanche photodiode (SPAD) working in the Geiger mode. The present work describes a simple mathematical model for the kinetic process of the bioluminescence based SOS toxin response of E. coli bacteria. We find that initially the bioluminescence signal depends on the time square and we show that the spectral intensity of the bioluminescence signal is inverse proportional to the frequency. We get excellent agreement between the theoretical model and the measured light signal. Furthermore, we present experimental results of the bioluminescent signal measurement using a SPAD and a photomultiplier, and demonstrate improvement of the measurement by applying a matched digital filter. Low intensity bioluminescence signals were measured after the whole-cell sensors were exposed to various toxicant concentrations (5, 15 and 20ppm).     

The water-water cycle as alternative photon and electron sinks

The water-water cycle in chloroplasts is the photoreduction of dioxygen to water in photosystem I (PS I) by the electrons generated in photosystem II (PS II) from water. In the water-water cycle, the rate of photoreduction of dioxygen in PS I is several orders of magnitude lower than those of the disproportionation of superoxide catalysed by superoxide dismutase, the reduction of hydrogen peroxide to water catalysed by ascorbate peroxidase, and the reduction of the resulting oxidized forms of ascorbate by reduced ferredoxin or catalysed by either dehydroascorbate reductase or monodehydroascorbate reductase. The water-water cycle therefore effectively shortens the lifetimes of photoproduced superoxide and hydrogen peroxide to suppress the production of hydroxyl radicals, their interactions with the target molecules in chloroplasts, and resulting photoinhibition. When leaves are exposed to photon intensities of sunlight in excess of that required to support the fixation of CO2, the intersystem electron carriers are over-reduced, resulting in photoinhibition. Under such conditions, the water-water cycle not only scavenges active oxygens, but also safely dissipates excess photon energy and electrons, in addition to downregulation of PS II and photorespiration. The dual functions of the water-water cycle for protection from photoinhibition under photon excess stress are discussed, along with its functional evolution.     

A single-photon imaging system for the simultaneous quantitation of luminescent emissions from multiple samples

A combination of a two-dimensional photon detector (double-microchannel plate) with single-photon sensitivity and an optical projection system that allows space-resolved quantitation of luminescent emissions from spatially extended objects is described. A "luminescent image" of the object focused onto the detector is accumulated over a preset time and stored in a digital frame memory from which photon counts over areas of interest can be read. In this study, the object consisted of a microtiter plate containing luminescent samples which was placed below a projecting lens (2.0/21 mm, 36 X 24-mm format camera lens) at a distance of 38.5 cm. Although geometry substantially limited photon collection, the sensitivity achieved was only 10X less than that obtained with a dedicated photon-counting luminometer. A slightly diminished photon collection from peripheral wells was apparently caused by the projection system and could be corrected arithmetically. Both chemically generated luminescence (ATP bioluminescence) and cell-derived, superoxide-dependent luminescence (with lucigenin as chemilumigenic probe) were detected with excellent spatial resolution and linearity of response over a wide range.     

Enhancement of imaging depth in turbid media using a wide area detector

The depth of two‐photon fluorescence imaging in turbid media can be significantly enhanced by the use of the here described fluorescence detection method that allows to efficiently collect scattered fluorescence photons from a wide area of the turbid sample. By using this detector we were able to perform imaging of turbid samples, simulating brain tissue, at depths up to 3 mm, where the two‐photon induced fluorescence signal is too weak to be detected by means used in conventional two‐photon microscopy. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Comparative kinetic studies of Mg2+-activated hydrolysis of tripolyphosphate and pyrophosphate by inorganic pyrophosphatase]

Computer analysis of P3 and pyrophosphate conversion rate dependence on substrate and metal-activator concentrations reveals the identity of kinetic patterns. Dissociation and catalytical constants for the enzyme combinations with two types of metal-substrates complexes, MS and M2S, at pH 9.0 are by one to two orders of magnitude "poorer" for P3 as compared to PPi. Optimal pH value for the hydrolysis of P3 is by 2 units higher than this for the hydrolysis of PPi. pH profiles for the kinetic parameters in the pH range 8.0--9.5 differ considerably for the two substrates, presumably due to the existence of additional catalitically important ionisations in the reaction with P3.     

Investigation of the role of the substrate metal ion in the yeast inorganic pyrophosphatase reaction

The substrate activities of a series of tripositive metal ion-pyrophosphate complexes with yeast inorganic pyrophosphatase were examined. While the Michaelis constants for these complexes were shown to be between one and two orders of magnitude greater than that of the natural substrate, [Mg(H2O)4PPi]2-, the turnover numbers were in general comparable to that of [Mg(H2O)4PPi]2-. These data suggest that the nature of the metal ion cofactor effects substrate binding but in most cases not catalysis. Thus, the role of the metal ion in catalysis is probably restricted to that of an electron sink.     

Lightsheet fluorescence lifetime imaging microscopy with wide‐field time‐correlated single photon counting

We report on wide‐field time‐correlated single photon counting (TCSPC)‐based fluorescence lifetime imaging microscopy (FLIM) with lightsheet illumination. A pulsed diode laser is used for excitation, and a crossed delay line anode image intensifier, effectively a single‐photon sensitive camera, is used to record the position and arrival time of the photons with picosecond time resolution, combining low illumination intensity of microwatts with wide‐field data collection. We pair this detector with the lightsheet illumination technique, and apply it to 3D FLIM imaging of dye gradients in human cancer cell spheroids, and C. elegans.     

Non-invasive bioluminescence imaging for monitoring herpes simplex virus type 1 hematogenous infection

Traditional studies on viral neuroinvasiveness and pathogenesis have generally relied on murine models that require the sacrifice of infected animals to determine viral distributions and titers. The present paper reports the use of in vivo bioluminescence imaging to monitor the replication and tropism of KOS strain HSV-1 viruses expressing the firefly luciferase reporter protein in hematogenously infected mice. Following intraperitoneal injection, a comparison was made between real-time PCR determinations of HSV-1 DNA concentrations (requiring the sacrifice of the experimental animals) and in vivo bioluminescence emissions in living animals. For further comparison, in vitro light emission was also measured in the ovaries and adrenal glands of sacrificed mice. After infection, HSV-1 spread preferentially to the ovaries and adrenal glands (these organs showed the highest virus levels). Both the PCR and bioluminescence methods detected low viral loads in the nervous system, where the virus was restricted to the spinal cord. The concentrations of viral DNA measured correlated with the magnitude of bioluminescence in vivo, and with the photon flux determined by the in vitro luciferase enzyme assay. The results show that bioluminescence imaging can be used for non-invasive, real-time monitoring of HSV-1 hematogenous infection in living mice, but that coupling this methodology with conventional techniques aids in the characterization of the infection.     

In situ gamma-spectrometry several years after deposition of radiocesium

A new method is introduced for deriving radiocesium soil contaminations and kerma rates in air from in situ gamma-ray spectrometric measurements. The approach makes use of additional information about gamma-ray attenuation given by the peak-to-valley ratio, which is the ratio of the count rates for primary and forward scattered photons. In situ measurements are evaluated by comparing the experimental data with the results of Monte Carlo simulations of photon transport and detector response. The influence of photons emitted by natural radionuclides on the calculation of the peak-to-valley ratio is carefully analysed. The new method has been applied to several post-Chernobyl measurements and the results agreed well with those of soil sampling.     

Interferometric Backward Third Harmonic Generation Microscopy for Axial Imaging with Accuracy Beyond the Diffraction Limit

A new nonlinear microscopy technique based on interference of backward-reflected third harmonic generation (I-THG) from multiple interfaces is presented. The technique is used to measure height variations or changes of a layer thickness with an accuracy of up to 5 nm. Height variations of a patterned glass surface and thickness variations of fibroblasts are visualized with the interferometric epi-THG microscope with an accuracy at least two orders of magnitude better than diffraction limit. The microscopy technique can be broadly applied for measuring distance variations between membranes or multilayer structures inside biological tissue and for surface height variation imaging.