New automatic quantification method of immunofluorescence and histochemistry in whole histological sections

Immunofluorescent staining is a widespread tool in basic science to understand organ morphology and (patho-) physiology. The analysis of imaging data is often performed manually, limiting throughput and introducing human bias. Quantitative analysis is particularly challenging for organs with complex structure such as the kidney. In this study we present an approach for automatic quantification of fluorescent markers and histochemical stainings in whole organ sections using open source software. We validate our novel method in multiple typical challenges of basic kidney research and demonstrate its general relevance and applicability to other complex solid organs for a variety of different markers and stainings. Our newly developed software tool “AQUISTO”, applied as a standard in primary data analysis, facilitates efficient large scale evaluation of cellular populations in various types of histological samples. Thereby it contributes to the characterization and understanding of (patho-) physiological processes.     

Measurement of sulfobromophthalein uptake in isolated rat hepatocytes by a direct spectrophotometric method

A spectrophotometric technique is described for the continuous recording of sulfobromophthalein uptake by isolated hepatocytes. The technique is based on the principle that sulfobromophthalein behaves as a pH-indicator and may be followed photometrically when moving from the medium at pH 7.8 into the interior of the cell. Data show that upon addition of cells to a sulfobromophthalein solution, an absorbance change can be recorded. The kinetics of the process is biphasic and the initial rate is linearly related to the amount of cells added. By this technique it was confirmed that the substrate dependence of the initial velocity of transport is a compound function including a saturable portion with an apparent Km in the mu molar region. Experiments carried out either in the presence of valinomycin or of high concentrations of potassium chloride indicate that the presence of a membrane potential opposes the entry of sulfobromophthalein into isolated hepatocytes. This finding is in agreement with previous observations in isolated plasma membrane vesicles and in liposomes reconstituted with purified bilitranslocase which indicate a rheogenic type of transport for the dye. Low concentrations of nicotinate (1.6 microM) efficiently inhibit the saturable transport. It is suggested, in addition, that the sensitivity of the transport to valinomycin could be used as an early indication of the functional integrity of cell preparations.     

Measurement of k(L)a by dynamic pressure method in pilot-plant fermentor

The dynamic pressure method (DPM) is used for measurement of k(L)a in a 1-m(3) pilot scale fermentor in coalescing (distilled water) and noncoalescing (0.3 M Na(2)SO(4) aqueous solution) batches. The method consists in recording oxygen concentration in a batch after a small pressure change (20 kPa) in the fermentor. The upward pressure change is brought about by temporary closing and subsequent throttling of outlet gas stream and the downward change by full reopening of the gas outlet. Absorption of pure oxygen yields the same k(L)a values as absorption of air. In noncoalescing batch, the downward k(L)a values are always higher than the upward values owing to spontaneous nucleation of bubbles. The experiments performed in a stirred cell confirm this behavior. Thus, only upward pressure change should be used for measurement. The correlation of k(L)a data measured in small (18-L) and large (1000-L) vessels based on power dissipated and superficial gas velocity are in a good agreement. Unlike the DPM, the classical dynamic methods yield, under the same conditions, excessively low values of k(L)a (the dynamic startup method) or fail to produce data at all (the dynamic method with interchange of air for N(2)). (c) 1994 John Wiley & Sons, Inc.     

Analysis of high-quality pharmaceutical grade water by a direct epifluorescent filter technique microcolony method

A modified direct epifluorescent filter technique (DEFT) was used to assess the microbial quality of water. Sterile, pharmaceutical grade water was inoculated with Pseudomonas cepacia. Microcolonies were grown and counted with a Bio-Foss System 3 DEFT apparatus. In this way it was possible to achieve a sensitivity of 10 cfu per 100 ml. Results were obtained within 1 working day.     

Measurement of energy expenditure in humans by doubly labeled water method

The utility of the doubly labeled water method for the determination of energy expenditure and water output was investigated in humans. Approximately 10 g of 18O and 0.5 g of 2H as water was orally administered to four healthy adults. Total body water was determined from the isotope dilution, and the ensuing 18O and 2H disappearance rates from body water were determined for 13 days by mass spectrometric isotope ratio analysis of the urinary water. During this period, subjects were maintained on a measured diet to determine energy and water intake. The energy expenditure from the doubly labeled water method differed from dietary intake plus change in body composition by an average of 2%, with a coefficient of variation of 6%. The water outputs determined by the two methods differed by 1%, with a coefficient of variation of 7%. The doubly labeled water method is noninvasive, and the subjects could maintain their daily activities without restriction.     

Monoamine-containing structures in the intestines of bivalve molluscs and a polychaete annelid revealed by fluorescence histochemistry

Summary Monoamine-containing elements in the intestines of Bivalvia and Polychaeta species have been found by use of histochemical fluorescence methods according to Falck and Furness. Catecholamine-containing perikarya and fibers are seen within the epithelium and subepithelial layers of the midgut of the bivalves Mytilus edulis, Mya arenaria, Arctica islandica, as well as the polychaete Harmothoe imbricata. In addition, intraepithelial cell bodies and fibers containing serotonin-like substance are present in Mytilus edulis. Results obtained with the Furness method, applied earlier to vertebrates, correlate with those obtained with the Falck method.     

Glycoconjugate distribution in gastric fundic mucosa of Umbrina cirrosa L. revealed by lectin histochemistry

The stomach of adult shi drum Umbrina cirrosa was investigated using a battery of nine horseradish peroxidase‐conjugated lectins combined with enzymatic treatment, in order to distinguish glycoconjugate sugar residues. Epithelial cells showed the presence of galactosyl(β1→4)N‐acetylglucosamine, mannose, N‐acetylgalactosamine, N‐acetylglucosamine, fucose and sialic acid‐galactosyl(β1→3)N‐acetylgalactosamine residues. Gastric pits had similar sugar residues with the exception of N‐acetylgalactosamine which was less diffused. Gastric glands were characterized by the presence of glycoconjugates containing galactosyl(β1→3)N‐acetylgalactosamine, N‐acetylglucosamine, galactosyl(β1→4) N‐acetylglucosamine, N‐acetylgalactosamine and a small amount of sialic acid linked to N‐acetylgalactosamine.     

Studies in lipid histochemistry. XIII. The OPA (osmiumtetroxide-periodic acid-alpha-naphthylamine) method for the detection of apolar lipids.

A new procedure for the detection of apolar lipids is described. It is a modification of the OTAN method (Adams, 1959) using periodic acid which oxidatively removes lower osmium derivatives from polar sites only, leaving those in apolar lipids intact and demonstrable with alpha-naphthylamine. Control steps for the exclusion of the possible interference of some less polar complex lipids and of lipopigments are described. The described technic is superior to the conventionally used sudan dyes due partly to the fact that only aqueous solutions are employed thus excluding any extraction of lipids, partly to the more distinct coloration.     

Testing for bacterial resistance to arsenic in monitoring well water by the direct viable counting method.

Direct viable counting of metal-resistant bacteria (DVCMR) has been found to be useful in both enumerating and differentiating metal-resistant and metal-sensitive strains of bacteria. The DVCMR bioassay was used to detect effects of low and high concentrations of arsenic and arsenicals on bacterial populations in groundwater. The level of resistance of the bacterial populations to arsenate was determined by the DVCMR bioassay, and the results showed a linear correlation with the total arsenic concentrations in the monitoring well water samples; no correlation was observed by culture methods with the methods employed. Bacteria resistant to 2,000 micrograms of arsenate per ml were isolated from all monitoring well water samples studied. Strains showed similar antibiotic and heavy-metal profiles, suggesting that the arsenic was not a highly selective pressure for arsenic alone. The monitoring well water samples were amended with arsenate and nutrients to determine the biotransformation mechanisms involved. Preliminary results suggest that bacteria indigenous to the monitoring well water samples did not directly transform, i.e., precipitate or volatilize, dissolved arsenic. It was concluded that arsenic contamination of the groundwater can be monitored by the DVCMR bioassay.     

Identification of side-chain clusters in protein structures by a graph spectral method.

This paper presents a novel method to detect side-chain clusters in protein three-dimensional structures using a graph spectral approach. Protein side-chain interactions are represented by a labeled graph in which the nodes of the graph represent the Cbeta atoms and the edges represent the distance between the Cbeta atoms. The distance information and the non-bonded connectivity of the residues are represented in the form of a matrix called the Laplacian matrix. The constructed matrix is diagonalized and clustering information is obtained from the vector components associated with the second lowest eigenvalue and cluster centers are obtained from the vector components associated with the top eigenvalues. The method uses global information for clustering and a single numeric computation is required to detect clusters of interest. The approach has been adopted here to detect a variety of side-chain clusters and identify the residue which makes the largest number of interactions among the residues forming the cluster (cluster centers). Detecting such clusters and cluster centers are important from a protein structure and folding point of view. The crucial residues which are important in the folding pathway as determined by PhiF values (which is a measure of the effect of a mutation on the stability of the transition state of folding) as obtained from protein engineering methods, can be identified from the vector components corresponding to the top eigenvalues. Expanded clusters are detected near the active and binding site of the protein, supporting the nucleation condensation hypothesis for folding. The method is also shown to detect domains in protein structures and conserved side-chain clusters in topologically similar proteins.