A user''s guide for avoiding errors in absorbance image cytometry: a review with original experimental observations

Summary The sources of errors which may occur when cytophotometric analysis is performed with video microscopy using a charged-coupled device (CCD) camera and image analysis are reviewed. The importance of these errors in practice has been tested, and ways of minimizing or avoiding them are described. Many of these sources of error are known from scanning and integrating cytophotometry; they include the use of white instead of monochromatic light, the distribution error, glare, diffraction, shading distortion, and inadequate depth of field. Sources of errors specifically linked with video microscopy or image analysis are highlighted as well; these errors include blooming, limited dynamic range of grey levels, non-linear responses of the camera, contrast transfer, photon noise, dark current, read-out noise, fixed scene noise and spatial calibration. Glare, contrast transfer, fixed scene noise, depth of field and spatial calibration seem to be the most serious sources of errors when measurements are not carried out correctly. We include a table summarizing all the errors discussed in this review and procedures for avoiding them. It can be concluded that if accurate calibration steps are performed and proper guidelines followed, image cytometry can be applied safely for quantifying amounts of chromophore per cell or per unit volume of tissue in sections, even when relatively simple and inexpensive instrumentation is being used.     

Dichroism of transient absorbance changes in the red spectral region using oriented chloroplasts. II. P-700 absorbance changes

The light induced transient absorbance changes associated with the trap of photosystem I have been studied using magnetically oriented spinach chloroplasts and a polarized measuring beam. The ΔA spectra for the two polarizations parallel and perpendicular to the plane of the photosynthetic membranes have been recorded in the spectral range 630–850 nm.A dichroic ratio greater than two is observed both in the main band around 700 nm and in the radical cation band around 810 nm, leading to the conclusion that the far-red transition moment of the P-700 dimeric species is lying almost parallel to the membrane plane.Dichroic ratios smaller than one are reported in the 650–670 nm band of the ΔA spectrum. The possible attribution of this band to excitonic interactions in the dimer favors the hypothesis of a tilting out of the membrane plane of this transition. This finding ruled out an orientation parallel to the membrane plane of the two chlorophyll molecules constituting the P-700 phototrap.A small residual transient absorbance change is observed in the absence of artificial electron acceptor. Its spectrum shows significant differences as compared to the normal P-700 spectrum: the magnitude of the signal at 700 nm is only 15–25% of the normal signal, the half-band width of the band around 700 nm is nearly twice as large and the dichroic ratio in the band is only 1.5±0.1. In the presence of ferricyanide, this signal is still observed both for intact and osmotically broken chloroplasts, suggesting a heterogeneity in the population of traps in Photosystem I.     

Dichroism of transient absorbance changes in the red spectral region using oriented chloroplasts. I. Field indicating absorbance changes

The light-induced transient absorbance changes which are affected by valinomycin have been studied using magnetically oriented spinach chloroplasts and a polarized measuring beam. The ΔA spectra for the two polarizations parallel and perpendicular to the plane of the photosynthetic membranes have been recorded in the spectral range 630–750 nm. Large polarization effects are found in all the bands of the ΔA spectrum, shifts in the position of the extrema are observed and the two spectra cross each other at various wavelengths. A comparison of these spectral features with available data on the dichroism of the Stark effect on monomolecular films of chlorophyll a and b indicates similarities favoring the already well documented hypothesis of the electrochromic nature of these absorbance changes in vivo.The data on this electrochromic effect can be correlated with the linear dichroism of oriented chloroplasts and the ΔA_∥?ΔA_⊥ spectrum in the 645–655 nm region gives further evidence of the orientation out of the membrane plane of the red transition moment of chlorophyll b.     

Possible errors in assay for beta-glycosidase activity.

Cecal homogenates were assayed for the enzymes beta-glucosidase, beta-glucuronidase, and beta-galactosidase. Anaerobic incubation with the addition of excess 3,4-dichloronitrobenzene, a substrate for nitroreductase, significantly increased the detection of the beta-glycosidase enzymes' activities.     

Molar absorbance of tRNA

Examination of some published values suggests that the concentration of most tRNAs can be evaluated on the basis of ?₂₆₀ = 7200/base, in magnesium buffer.     

Stochastic errors vs. modeling errors in distance based phylogenetic reconstructions

ABSTRACT: BACKGROUND: Distance-based phylogenetic reconstruction methods use evolutionary distances between species in order to reconstruct the phylogenetic tree spanning them. There are many different methods for estimating distances from sequence data. These methods assume different substitution models and have different statistical properties. Since the true substitution model is typically unknown, it is important to consider the effect of model misspecification on the performance of a distance estimation method. RESULTS: This paper continues the line of research which attempts to adjust to each given set of input sequences a distance function which maximizes the expected topological accuracy of the reconstructed tree. We focus here on the effect of systematic error caused by assuming an inadequate model, but consider also the stochastic error caused by using short sequences. We introduce a theoretical framework for analyzing both sources of error based on the notion of deviation from additivity, which quantifies the contribution of model misspecification to the estimation error. We demonstrate this framework by studying the behavior of the Jukes-Cantor distance function when applied to data generated according to Kimura's two-parameter model with a transition-transversion bias. We provide both a theoretical derivation for this case, and a detailed simulation study on quartet trees. CONCLUSIONS: We demonstrate both analytically and experimentally that by deliberately assuming an oversimplified evolutionary model, it is possible to increase the topological accuracy of reconstruction. Our theoretical framework provides new insights into the mechanisms that enables statistically inconsistent reconstruction methods to outperform consistent methods.     

A device for the semiautomatic determination of oxygen-radical absorbance capacity

The oxygen-radical absorbance capacity (ORAC) assay has become a standard method to quantify the antioxidative properties of phytonutrients in fruit and vegetable extracts. However, it is usually not possible to determine directly the contribution of specific phytonutrients to the total ORAC value. Separation of the components in the plant extracts by HPLC followed by ORAC analyses of the column fractions might permit the determination of free radical-scavenging profiles. The accurate determination of ORAC values may require 1 to 2 h/sample. Considering the number of samples that would be generated by a single HPLC separation, a device was constructed which permits up to 45 simultaneous ORAC analyses. Varying degrees of automation were included in the design. Furthermore, since the assay has a Q(10) for peroxyl radical-scavenging of about 3, elevation of the assay temperature from the standard 37 to 47 degrees C significantly reduced the assay times. Relatively simple modifications would allow the apparatus to be used in a variety of time-dependent fluorescence and absorbance assays.     

An ultraviolet absorbance method for determining acetylsalicylic acid hydrolase activity

An ultraviolet absorbance method for quantitation of acetylsalicylic acid esterase (hydrolase) activity has been developed and validated. The sensitivity of the method was found to be 2.8 nmol/ml-min in the assay cuvette. Linearity of the reaction with enzyme concentration and time has been demonstrated. The product of the enzymatic reaction, salicylic acid, has been identified by thin-layer chromatography using acetyl-[¹⁴C]salicylic acid. The quantities of salicylic acid produced in 5, 10, and 15 min of incubation were equal when assayed by the spectrophotometric method and by the acetyl-[¹⁴C]salicylic acid thin-layer chromatographic method. The time required for assay by ultraviolet absorbance is approximately 3 min/sample.