Optical bio-sniffer for ethanol vapor using an oxygen-sensitive optical fiber

An optical bio-sniffer for ethanol was constructed by immobilizing alcohol oxidase (AOD) onto a tip of a fiber optic oxygen sensor with a tube-ring, using an oxygen sensitive ruthenium organic complex (excitation, 470 nm; fluorescent, 600 nm). A reaction unit for circulating buffer solution was applied to the tip of the device. After the experiment in the liquid phase, the sniffer-device was applied for gas analysis using a gas flow measurement system with a gas generator. The optical device was applied to detect the oxygen consumption induced by AOD enzymatic reaction with alcohol application. The sensor in the liquid phase was used to measure ethanol solution from 0.50 to 9.09 mmol/l. Then, the bio-sniffer was calibrated against ethanol vapor from 0.71 to 51.49 ppm with good gas-selectivity based on the AOD substrate specificity. The bio-sniffer with the reaction unit was also used to monitor the concentration change of gaseous ethanol by rinsing and cleaning the fiber tip and the enzyme membrane with buffer solution.     

Direct comparison of kinematic data collected using an electromagnetic tracking system versus a digital optical system

The purpose of this study was to quantify the dynamic accuracy of kinematics measured by a digital optical motion analysis system in a gait analysis laboratory (capture volume approximately 20m(3)) compared to a standard range direct-current electromagnetic (EM) tracking device (capture volume approximately 1m(3)). This is a subset of a larger effort to establish an appropriate marker set for the optical system to quantify upperlimb kinematics simultaneously with gait, in comparison to previous studies of isolated upperlimb movements that have employed EM tracking devices. Rigid clusters of spherical reflective markers and EM sensors were attached to a mechanical articulator that mimicked three-dimensional joint rotations, similar to the elbow. As the articulator was moved through known ranges of motion (i.e. gold standard), kinematic data were collected simultaneously using both tracking systems. Both systems were tended to underestimate the range of motion; however, the application of post hoc smoothing and least-squares correction algorithms reduced these effects. When smoothing and correction algorithms were used, the magnitude of the mean difference between the gold standard and either the EM or optical system did not exceed 2 degrees for any of the compound motions performed. This level of agreement suggests that the measurements obtained from either system are clinically comparable, provided appropriate smoothing and correction algorithms are employed.     

Photoinduced transformations in bacteriorhodopsin membrane monitored with optical microcavities

Photoinduced molecular transformations in a self-assembled bacteriorhodopsin (bR) monolayer are monitored by observing shifts in the near-infrared resonant wavelengths of linearly polarized modes circulating in a microsphere cavity. We quantify the molecular polarizability change upon all-trans to 13-cis isomerization and deprotonation of the chromophore retinal ( approximately -57 A(3)) and determine its orientation relative to the bR membrane ( approximately 61 degrees ). Our observations establish optical microcavities as a sensitive off-resonant spectroscopic tool for probing conformations and orientations of molecular self-assemblies and for measuring changes of molecular polarizability at optical frequencies. We provide a general estimate of the sensitivity of the technique and discuss possible applications.     

A computer system for the storage and retrieval of clinical pharmacokinetic data

A computer system is described which stores patient data relating to clinical pharmacokinetic assessments made by clinical pharmacists, who are participating in a clinical pharmacokinetics service. The system was developed to assist in the documentation of service activities and storage of patients' pharmacokinetic data. An additional component of the system is the ability for retrospective review of the stored data. Applications of this system to the derivation of new information on drug pharmacokinetics and drug efficacy/toxicity in various patient groups is discussed. The implications for Phase IV drug studies and toxicity screening studies is also described.     

Optical picosecond studies of bacteriorhodopsin containing a sterically fixed retinal

The photochemical behaviour of an analogous bacteriorhodopsin (9,12-Ph-BR) which contains the sterically fixed 9,12-phenylretinal has been investigated with picosecond spectroscopy. The following results have been obtained. No ground-state intermediate photoproduct is found in agreement with the previous observation that 9,12-Ph-BR does not exhibit proton pumping under illumination. The excited singlet state has a lifetime of τ_S = 10 ± 2 ps. This lifetime agrees favourably with the value calculated from the radiative lifetime τ_rad = 6.2 ns and the fluorescence quantum efficiency of 1.2·10⁻³. Excited-state absorption occurs which results in fluorescence in the ultraviolet region. These various observations differ drastically from the corresponding findings on bacteriorhodopsin. Most important for an understanding of the differences is the fact that 9,12-phenylretinal does not isomerize in the protein's binding site in contrast to retinal. Our data therefore suggest that the formation of the intermediate K observed in bacteriorhodopsin is accompanied by the all-trans to 13-cis isomerization.     

Automating data manipulation for genetic analysis using a data base management system

Inefficient coding and manipulation of pedigree data have often hindered the progress of genetic studies. In this paper we present the methodology for interfacing a data base management system (DBMS) called MEGADATS with a linkage analysis program called LIPED. Two families that segregate a dominant trait and one test marker were used in a simulated exercise to demonstrate how a DBMS can be used to automate tedious clerical steps and improve the efficiency of a genetic analysis. The merits of this approach to data management are discussed. We conclude that a standardized format for genetic analysis programs would greatly facilitate data analysis.     

Simultaneous measurements of fast optical and proton current kinetics in the bacteriorhodopsin photocycle using an enhanced spectrophotometer

A one-of-a-kind high speed optical multichannel spectrometer was designed and built at NIH and described in this journal in 1997 [J.W. Cole, R.W. Hendler, P.D. Smith, H.A. Fredrickson, T.J. Pohida, W.S. Friauf. A high speed optical multichannel analyzer. J Biochem Biophys Methods 1997;35:16–174.]. The most unique aspect of this instrument was the ability to follow an entire time course from a single activation using a single sample. The instrument has been used to study rapid kinetic processes in the photon-driven bacteriorhodopsin photocycle and electron transport from cytochrome c to cytochrome aa₃ and from cytochrome aa₃ to oxygen. The present paper describes a second generation instrument with a number of important enhancements which significantly improve its capabilities for multichannel kinetic studies. An example application is presented in which the kinetics of photon-induced proton flow across the biological membrane is measured simultaneously with the individual steps of the photocycle determined optically. Matching the time constants for the two processes indicates which molecular transformations are associated with major proton movements.     

An efficient system for the synthesis of bacteriorhodopsin in Halobacterium halobium

The mechanism by which bacteriorhodopsin (BR) transports protons across the cell membrane of Halobacterium halobium is actively studied in many laboratories. Currently available systems for the synthesis of mutant proteins obtained by site-directed mutagenesis of the gene encoding BR (bop) require reconstitution of the denatured polypeptide after its synthesis Escherichia coli or yeast; this approach is technically difficult and labor intensive, and raises questions about possible differences between in vivo and in vitro folding. Using a newly described transformation system and a halobacterial plasmid vector, we show that it is possible to reintroduce the bop gene into BR- strains of H. halobium. The bop-carrying plasmid expresses native BR in amounts similar to those obtained in several wild type strains. This system allows facile site-directed mutagenesis in halophilic archaebacteria.     

Optical lock-in detection of FRET using synthetic and genetically encoded optical switches

The Förster resonance energy transfer (FRET) technique is widely used for studying protein interactions within live cells. The effectiveness and sensitivity of determining FRET, however, can be reduced by photobleaching, cross talk, autofluorescence, and unlabeled, endogenous proteins. We present a FRET imaging method using an optical switch probe, Nitrobenzospiropyran (NitroBIPS), which substantially improves the sensitivity of detection to <1% FRET efficiency. Through orthogonal optical control of the colorful merocyanine and colorless spiro states of the NitroBIPS acceptor, donor fluorescence can be measured both in the absence and presence of FRET in the same FRET pair in the same cell. A SNAP-tag approach is used to generate a green fluorescent protein-alkylguaninetransferase fusion protein (GFP-AGT) that is labeled with benzylguanine-NitroBIPS. In vivo imaging studies on this green fluorescent protein-alkylguaninetransferase (GFP-AGT) (NitroBIPS) complex, employing optical lock-in detection of FRET, allow unambiguous resolution of FRET efficiencies below 1%, equivalent to a few percent of donor-tagged proteins in complexes with acceptor-tagged proteins.     

Determination of the number of water molecules in the proton pathway of bacteriorhodopsin using neutron diffraction data

It has been shown that water molecules participate in the proton pathway of bacteriorhodopsin. Large efforts have been made to determine with various biophysical methods the number of water molecules involved. Neutron diffraction H2O/D2O exchange experiments have been often used to reveal the position of water even with low-resolution diffraction data. With this technique, care must be taken with the limitations of the difference Fourier method which are commonly applied to analyze the data. In this paper we compare the results of the difference Fourier method applied to measured diffraction data (not presented here) and models with those from alternative methods introduced here: (1) a computer model calculation procedure to determine a label's scattering length density based on a comparison of intensity differences derived from models and intensity differences from our measurements; (2) a method based on the Parseval formula. Both alternative methods have been evaluated and tested using results of neutron diffraction experiments on purple membranes (Hauss et al. 1994). Our findings indicate that the difference Fourier method applied to low-resolution diffraction data can successfully determine the position of localized water molecules but underestimates their integrated scattering length density in the presence of labels in other positions. Furthermore, we present the results of neutron diffraction experiments on purple membranes performed to determine the number of water molecules in the projected area of the Schiff base at 86%, 75% and 57% relative humidity (r.h.). We found 19 +/- 2 exchangeable protons at 75% r.h., which means at least 8-9 water molecules are indispensable for normal pump function.     

Energy storage in the primary step of the photocycle of bacteriorhodopsin.

A pulsed-dye laser low temperature photocalorimeter is used to study the enthalpy differences between light-adapted bacteriorhodopsin (bR568) and its primary photoproduct (K) at 77 K. A key feature of our experimental method is the use of the laser-induced photostationary state as an internal reference. Analyses of the forward (bR leads to K), reverse (K leads to bR), and mixed (bR in equilibrium K) photoreactions were carried out to measure delta H12 = EK - EbR. All three experiments yielded identical values of delta H12 within experimental error (delta Have12 = 15.8 +/- 2.5 kcal mol-1). Accordingly, the primary event in the photocycle of light-adapted bacteriorhodopsin stores approximately 30% of the absorbed photon energy at the 568-nm absorption maximum. We observe that the quantum yields phi f1(bR leads to K) and phi r2(K leads to bR) add up to unity within experimental error: phi f1 + phi r2 = 1.02 +/- 0.19 for phi f1 in the range 0.28-0.33. A theoretical analysis of energy storage in K suggests that at least one-half of the enthalpy difference between K and bR is associated with charge separation accompanying chromophore isomerization.     

Nanoscale storage encryption: data storage in synthetic DNA using a cryptosystem with a neural network

<正>Dear Editor,Synthetic DNA is emerging as a new data storage medium with high density and durable preservation capability potential(Ceze et al., 2019; Yazdi et al., 2015), thus enhancing the security of data stored in DNA is particularly important(Cherian et al., 2013; El-Zoghabi et al., 2013; Kalsi et al.,2018).     

Impulse data processing system using personal computer

I developed an online impulse data processing system using a personal computer. This system may be useful for studies on any kind of unit activity.     

Individualized mating system estimation using genomic data

The estimation of outcrossing rates in hermaphroditic species has been a major focus in the evolutionary study of reproductive strategies, and is also essential for plant breeding and conservation. Surprisingly, genomics has thus far minimally influenced outcrossing rate studies. In this article, we generalize a Bayesian inference method (BORICE) to accommodate genomic data from multiple subpopulations of a species. As an empirical demonstration, BORICE is applied to 115 maternal families of Mimulus guttatus. The analysis shows that low‐level whole genome sequencing of parents and offspring is sufficient for individualized mating system estimation: 208 offspring (88.5%) were definitively called as outcrossed, 23 (9.8%) as selfed. After mating system parameters are established (each offspring as outcrossed or selfed and the inbreeding level of maternal plants), BORICE outputs posterior genotype probabilities for each SNP genomewide. Individual SNP calls are often burdened with considerable uncertainty and distilling information from closely linked sites (within genomic windows) can be a useful strategy. For the Mimulus data, principal components based on window statistics were sufficient to diagnose inversion polymorphisms and estimate their effects on spatial structure, phenotypic and fitness measures. More generally, mating system estimation with BORICE can set the stage for population and quantitative genomic analyses, particularly researchers collect phenotypic or fitness data from maternal individuals.     

New coupled model used inversely for reconstructing past terrestrial carbon storage from pollen data: validation of model using modern data

The knowledge of potential impacts of climate change on terrestrial vegetation is crucial to understand long-term global carbon cycle development. Discrepancy in data has long existed between past carbon storage reconstructions since the Last Glacial Maximum by way of pollen, carbon isotopes, and general circulation model (GCM) analysis. This may be due to the fact that these methods do not synthetically take into account significant differences in climate distribution between modern and past conditions, as well as the effects of atmospheric CO₂ concentrations on vegetation. In this study, a new method to estimate past biospheric carbon stocks is reported, utilizing a new integrated ecosystem model (PCM) built on a physiological process vegetation model (BIOME4) coupled with a process-based biospheric carbon model (DEMETER). The PCM was constrained to fit pollen data to obtain realistic estimates. It was estimated that the probability distribution of climatic parameters, as simulated by BIOME4 in an inverse process, was compatible with pollen data while DEMETER successfully simulated carbon storage values with corresponding outputs of BIOME4. The carbon model was validated with present-day observations of vegetation biomes and soil carbon, and the inversion scheme was tested against 1491 surface pollen spectra sample sites procured in Africa and Eurasia. Results show that this method can successfully simulate biomes and related climates at most selected pollen sites, providing a coefficient of determination ( R ) of 0.83–0.97 between the observed and reconstructed climates, while also showing a consensus with an R -value of 0.90–0.96 between the simulated biome average terrestrial carbon variables and the available observations. The results demonstrate the reliability and feasibility of the climate reconstruction method and its potential efficiency in reconstructing past terrestrial carbon storage.