Fission yeast gene structure and recognition.

A database of 210 Schizosaccharomyces pombe DNA sequences (524,794 bp) was extracted from GenBank (release number 81.0) and examined by a number of methods in order to characterize statistical features of these sequences that might serve as signals or constraints for messenger RNA splicing. The statistical information compiled includes splicing signal (donor, acceptor and branch site) profiles, translational initiation start profile, exon/intron length distributions, ORF distribution, CDS size distribution, codon usage table, and 6-tuple distribution. The information content of the various signals are also presented. A rule-based interactive computer program for finding introns called INTRON.PLOT has been developed and was used to successfully analyze 7 newly sequenced genes.     

Computerized interactive morphometry as an aid in the diagnosis of pleural effusions

A morphometric study of cytologic preparations from patients with benign and malignant (mesothelioma and carcinoma) pleural effusions is reported. The routine cytologic smears from these specimens were studied with a new system of video-based computerized interactive morphometry (CIM) that allows the measurements of real-time images of cell profiles by the simple procedure of touching the two extreme points of a diameter of interest on a touch-sensitive screen. For each cell, the nuclear profile diameter (NPD) and the cytoplasmic profile diameter (CPD) are measured and categorized into classes with 2-microns intervals; the NPD/CPD ratio is also calculated. The mean NPD is calculated for the specimen after measurement of 100 cells. The data were interpreted by two independent methods: a statistical method of discriminant analysis that classifies the lesions as benign, carcinoma or mesothelioma and provides a probability statement of membership in a particular diagnostic class and an ad-hoc algorithm that categorizes the effusions as benign or malignant based on hierarchic analysis. A data base derived from study of the first 24 cases was constructed and utilized for the test classification of the second 24 cases, which were treated as specimens of unknown diagnosis. The discriminant analysis correctly classified 21 of the 24 test cases into their proper diagnostic groups. The algorithm for a computer-generated pathologic diagnosis correctly identified 47 of the 48 cases as benign or malignant. The technical advantages of video-based CIM over the existing morphometric methods are discussed.     

Cellular automaton simulation of tumour growth -- equivocal relationships between simulation parameters and morphologic pattern features.

OBJECTIVE: To develop an interpretation procedure which estimates simulation parameters (tumour cell motility, tumour cell adhesion, autocrine and paracrine growth control, stroma destruction) of simulated patterns solely based on morphometric features of the morphologic pattern. METHODS: A cellular automaton computer simulation program was developed which produces morphologic patterns by growth of a seed of tumour cells. At the beginning of each simulation run certain simulation parameters are assigned to the tumour cells. After the run has been completed, the resulting pattern is evaluated by a set of morphometric features. Simulation parameters and resulting morphometric features of 27,800 simulations were stored in a database and were used for the evaluation of potential relationships. RESULTS: Correlation analysis showed highly significant correlations between morphometric features on the one hand and the preset simulation parameters (tumour cell motility, tumour cell adhesion, autocrine and paracrine growth control, stroma destruction) on the other. Correlation coefficients, however, varied from 0.72 to 0.99. When only one simulation parameter varied while all others were kept constant, morphometric features yielded a highly reliable estimate of the particular simulation parameter. When variability was extended to 4 simulation parameters, morphometric features were less effective in estimating the setting of the parameters. Though in all patterns tested several possible simulation parameter constellations could be ruled out, morphometric features were usually compatible with more than one set of simulation parameters thus preventing a straightforward interpretation. CONCLUSIONS: Though simulation parameters significantly and reproducibly influence the resulting morphologic pattern as characterized by morphometric features, estimates of the simulation parameters based on morphometric features yield equivocal results.     

Structure of the wall of the renal artery during limitation of motor activity

The structure of the renal artery wall has been studied in histological preparations at various time of a restricted motor activity using some morphometric methods. The revealed morphological changes of wave-like character present a respond of certain compensatory processes in the vascular wall to changes of the blood stream in the kidney which is connected with the change of the organ's function.     

Sperm head morphometry in ejaculates of adult marmosets (Callithrix jacchus): A model for studying sperm subpopulations and among-donor variations

In humans and other mammals, sperm morphology has been considered one of the most important predictive parameters of fertility. The objective was to determine the presence and distribution of sperm head morphometric subpopulations in a nonhuman primate model (Callithrix jacchus), using an objective computer analysis system and principal component analysis (PCA) methods to establish the relationship between the subpopulation distribution observed and among-donor variation. The PCA method revealed a stable number of principal components in all donors studied, that represented more than 85% of the cumulative variance in all cases. After cluster analysis, a variable number (from three to seven) sperm morphometric subpopulations were identified with defined sperm dimensions and shapes. There were differences in the distribution of the sperm morphometric subpopulations (P < 0.001) in all ejaculates among the four donors analyzed. In conclusion, in this study, computerized sperm analysis methods combined with PCA cluster analyses were useful to identify, classify, and characterize various head sperm morphometric subpopulations in nonhuman primates, yielding considerable biological information. In addition, because all individuals were kept in the same conditions, differences in the distribution of these subpopulations were not attributed to external or management factors. Finally, the substantial information derived from subpopulation analyses provided new and relevant biological knowledge which may have a practical use for future studies in human and nonhuman primate ejaculates, including identifying individuals more suitable for assisted reproductive technologies.     

Phenotypical characterization of indigenous freshwater crayfish populations

The morphology of an animal is known to reflect both genetic variation and adaptation to the environment. Thus, phenotypic criteria have been used to characterize indigenous crayfish populations. Twenty-one morphometric parameters were measured on crayfish from 25 waterbodies in the Austrian and Italian parts of Tyrol. They were analysed with hierarchical cluster analysis to obtain the population structure based on morphological similarity between and within the freshwater crayfish species Astacus astacus (noble crayfish), Austropotamobius torrentium (stone crayfish) and Austropotamobius pallipes (white-clawed crayfish). Furthermore, a stepwise discriminant analysis was applied to the morphometric data to test their differentiating power between populations. Both analyses resulted in a clear differentiation of species and populations, and reflected geographic separations. Thus, the developed morphometric methods were shown to be applicable to characterize the phenotype in freshwater crayfish and seem appropriate to be used for stock identification and the effective characterization of management units in decapod crustaceans.     

The principles and advances of quantitative pathology

This article gives an overview of the quantitative pathologic techniques used today, with special emphasis on interactive morphometry and its application in the clinical setting. At present, stereologic calculations may be necessary, but in a diagnostic setting have only rarely proved to be essential. The reproducibility of the measurements is discussed in relation to the definition of the particles and staining methods. A number of technical factors that cause random errors are mentioned, such as quality of the slides, magnification, definition of the particles to be measured and measuring protocol. Large-scale experiments have revealed that the means of nuclear morphometric and certain stereologic features are reproducible, such as in the volume percentage of epithelium, the surface densities of glands and the mitotic activity index. The diagnostic applications of the standard deviation and shape factors of nuclear quantitative features require additional precautions, however. Having quantified cell and tissue features, multivariate analysis may result in a better discrimination of two or more groups under study. The quantitative pathologic examination of cells and tissues can provide important diagnostic and prognostic information. Quantitation in pathology is especially useful in so-called continuous lesions, in which interobserver and intraobserver disagreement is considerable. An important requirement of diagnostic morphometry is object selection by a skilled pathologist; the use of morphometry as a black box can result in dramatic errors. The criteria used for a morphometric classification rule that can be used for clinical applications are summarized. Quality control of the whole measuring system is essential. Application of these techniques for more than six years in diagnostic pathology has repeatedly corrected previous qualitative diagnoses.(ABSTRACT TRUNCATED AT 250 WORDS)     

Application of automatic image analysis for morphometric studies of peroxisomes stained cytochemically for catalase

Summary The feasibility of the application of an electronic image analyzer, the Texture Analysis System (TAS) (Leitz Wetzlar, FRG), for fast automatic ultrastructural morphometric studies of hepatic peroxisomes has been investigated. Rat liver peroxisomes were stained selectively with the alkaline DAB procedure for localization of catalase in order to obtain sufficient contrast for automatic detection by TAS. Electron micrographs of ultrathin sections from this material were analyzed both automatically by TAS and manually by using a digitizer tablet connected with an Apple IIe microcomputer. The results showed negligible differences. As far as the speed of the operation is concerned, the image analysis was 4–5 times faster than the manual technique. In further studies, the importance of using DAB-stained sections for accurate morphometric studies of peroxisomes was demonstrated by comparing the results of such DAB-stained preparations with unstained material. This revealed that the numerical density was lower and the average profile diameter higher in unstained sections. The value for volume density was also affected, being about 30% lower in such preparations. It is likely that in unstained preparations small peroxisomes without crystalline nucleoids were frequently not identified as such and were not taken into account in morphometric calculations.These observations establish that computer-controlled electronic image analysis in conjunction with selective cytochemical staining of peroxisomes for catalase provides a fast, accurate and reliable method for ultrastructural morphometric studies of this organelle in rat liver.     

Reassessment of morphological characteristics in freshwater eels (genus Anguilla, Anguillidae) shows congruence with molecular phylogeny estimates

The morphology-based phylogeny of freshwater eels, proposed by V. Ege in 1939, has been accepted as the basis of eel classification since that time. However, this has been called into question by recent molecular studies. Most of the morphological characteristics recognized by Ege are morphometric. Since methods for the application of morphometric data to phylogeny construction have not been fully established, it is unclear whether the observed discrepancies between morphological and molecular data arise from intrinsic differences or from flawed analyses. Here, we have used two methods to assemble evolutionary trees from distance matrices constructed according to Ege's data, the neighbor-joining (NJ) method and the minimum network (MinNet) method; the latter is based on an evolutionary algorithm. After reanalysing Ege's morphological data, we found that both methods gave results consistent with those based on molecular data, although not with Ege's original classification. Therefore, we speculate that some morphological features Ege used to subdivide the eel groups may not be synapomorphic as he proposed, but symplesiomorphic or convergent . The method developed here may prove useful for constructing phylogeny for taxon groups where only continuous morphometric characteristics are recognized, such as the freshwater eels.     

Morphology-Based Prediction of Osteogenic Differentiation Potential of Human Mesenchymal Stem Cells

Human bone marrow mesenchymal stem cells (hBMSCs) are widely used cell source for clinical bone regeneration. Achieving the greatest therapeutic effect is dependent on the osteogenic differentiation potential of the stem cells to be implanted. However, there are still no practical methods to characterize such potential non-invasively or previously. Monitoring cellular morphology is a practical and non-invasive approach for evaluating osteogenic potential. Unfortunately, such image-based approaches had been historically qualitative and requiring experienced interpretation. By combining the non-invasive attributes of microscopy with the latest technology allowing higher throughput and quantitative imaging metrics, we studied the applicability of morphometric features to quantitatively predict cellular osteogenic potential. We applied computational machine learning, combining cell morphology features with their corresponding biochemical osteogenic assay results, to develop prediction model of osteogenic differentiation. Using a dataset of 9,990 images automatically acquired by BioStation CT during osteogenic differentiation culture of hBMSCs, 666 morphometric features were extracted as parameters. Two commonly used osteogenic markers, alkaline phosphatase (ALP) activity and calcium deposition were measured experimentally, and used as the true biological differentiation status to validate the prediction accuracy. Using time-course morphological features throughout differentiation culture, the prediction results highly correlated with the experimentally defined differentiation marker values (R>0.89 for both marker predictions). The clinical applicability of our morphology-based prediction was further examined with two scenarios: one using only historical cell images and the other using both historical images together with the patient''s own cell images to predict a new patient''s cellular potential. The prediction accuracy was found to be greatly enhanced by incorporation of patients'' own cell features in the modeling, indicating the practical strategy for clinical usage. Consequently, our results provide strong evidence for the feasibility of using a quantitative time series of phase-contrast cellular morphology for non-invasive cell quality prediction in regenerative medicine.     

Determination of intraparticle immobilized enzyme distribution in porous support by confocal scanning microscopy

Summary A method for determining the distribution of immobilized protein within a porous support has been developed. The method is based on confocal microscopy of polyacrylamide gel beads coupled to fluorescein isothiocyanate labelled enzyme. It is applied to immobilized soybean lipoxygenase. This technique allows the quantitative and qualitative analysis of protein distribution profile in intact polymer beads without splitting or cutting the carrier.     

Early endocervical glandular neoplasia. II. Morphometric analysis of the cells

A morphometric analysis was performed on the cells of early endocervical glandular neoplasia, including adenocarcinoma in situ and microinvasive adenocarcinoma, in cytologic preparations. The measurements were compared with those of cells from the normal endocervix and cells from other lesions that enter into the differential diagnosis. The morphometric profile developed for the cells of early glandular neoplasia proved to be useful, reliable and reproducible. Not only could the cells of normal endocervical samples be distinguished from those of early endocervical glandular neoplasia, but the measurements also seemed capable of making the visually difficult distinction between adenocarcinoma in situ and microinvasive adenocarcinoma. The latter point requires further confirmation since only a few cases of microinvasive adenocarcinoma were available for study.     

The molecular heterogeneity of Shigella sonnei lipopolysaccharide based on polyacrylamide gel electrophoretic data

The molecular heterogeneity of S. sonnei lipopolysaccharide (LPS), reflecting the size of lateral O-specific polysaccharide chains, has been established by the method of electrophoresis in acrylamide gel in the presence of sodium dodecyl sulfate and urea. The dominating components fall into three types, viz. those with 0-3, 10-16 and 35-40 repeating structures, the remaining components being minor ones. The electrophoretic profile of S. sonnei LPS considerably differs from the profiles of Escherichia coli and S. flexneri LPS, but coincides with the LPS profiles of other strains with different virulence. The preparations of LPS obtained by extraction with trichloroacetic acid have the same electrophoretic profiles as LPS obtained by the method of aqueous phenol extraction. The domination of certain molecular variants reflects, seemingly, specific features of the biosynthesis of LPS, characteristic of a given strain. The mechanisms of the preferable synthesis of lateral O-specific chains of the definite size and the importance of the molecular parameters of lateral chains for the biological properties of LPS require further study.     

Taxonomy of the microangiological changes in the ocular conjunctiva]

By means of biomicroscopical investigations of bulbar conjunctiva in healthy persons of different age certain characteristics on normal microcirculatory bed have been obtained. Morphometric analysis of the vital microscopical observations has revealed some age peculiarities in microcirculation of the conjunctiva. As a result of clinical examination of the persons, it has been stated that the phenomena noticed at biomicroscopy which characterize certain anomalies of microcirculatory parameters correlate with latent pathology, closely related diseases or developmental anomalies. Therefore, it is possible to consider the method of biomicroscopical investigation of the conjunctiva with a subsequent morphometric analysis of the data obtained as suitable for application not only for clinical but also for prophylactic examination of healthy persons.     

Biomarker metabolites capturing the metabolite variance present in a rice plant developmental period

Background  

This study analyzes metabolomic data from a rice tillering (branching) developmental profile to define a set of biomarker metabolites that reliably captures the metabolite variance of this plant developmental event, and which has potential as a basis for rapid comparative screening of metabolite profiles in relation to change in development, environment, or genotype. Changes in metabolism, and in metabolite profile, occur as a part of, and in response to, developmental events. These changes are influenced by the developmental program, as well as external factors impinging on it. Many samples are needed, however, to characterize quantitative aspects of developmental variation. A biomarker metabolite set could benefit screening of quantitative plant developmental variation by providing some of the advantages of both comprehensive metabolomic studies and focused studies of particular metabolites or pathways.     

Quantitative ultrastructural study of nuclei from exfoliated benign and malignant mesothelial cells and metastatic adenocarcinoma cells

Various approaches, including morphometric image analysis, are currently being used to improve the distinction between diffuse mesothelioma and metastatic adenocarcinoma of the serous membranes. Since exfoliated cells of malignant mesotheliomas were thought to have nuclear profile contours with greater irregularity than the similar profiles in metastatic adenocarcinoma cells in pleural effusions, this and other nuclear parameters were measured in ultrastructurally examined preparations from three cases of reactive mesothelial hyperplasia, seven examples of diffuse mesothelioma and three cases of metastatic adenocarcinoma (with primaries in the ovary, esophagus and prostate). Contrary to the subjective impression, the nuclei in metastatic adenocarcinomas actually had a mean nuclear contour index greater than that found in diffuse mesotheliomas; statistically, the difference was not significant. Likewise, such other nuclear parameters as nuclear area, condensed chromatin area and contour index, percentage of condensed chromatin and number of condensed chromatin clumps per nuclear profile did not discriminate between malignant mesotheliomas and adenocarcinomas metastatic to pleural surfaces. These morphometric results quantitate the similarities in nuclear size, nuclear shape and condensed chromatin arrangement in these two types of tumor and explain why the cytopathologist has such great difficulty in distinguishing between exfoliated mesothelioma and adenocarcinoma cells in most cases.     

Recent progress in quantitative glycoproteomics

Protein glycosylation is acknowledged as one of the major posttranslational modifications that elicit significant effects on protein folding, conformation, distribution, stability, and activity. The changes in glycoprotein abundance, glycosylation degree, and glycan structure are associated with a variety of diseases. Therefore, the quantitative study of glycoproteomics has become a new and popular research topic, and is quickly emerging as an important technique for biomarker discovery. Mass spectrometry-based protein quantification technologies provide a powerful tool for the systematic and quantitative assessment of the quantitative differences in the protein profiles of different samples. Combined with various glycoprotein/glycopeptide enrichment strategies and other glycoprotein analysis methods, these techniques have been further developed for application in quantitative glycoproteomics. A comprehensive quantitative analysis of the glycoproteome in a complex biological sample remains challenging because of the enormous complexity of biological samples, intrinsic characteristics of glycoproteins, and lack of universal quantitative technology. In this review, recently developed technologies in quantitative glycoproteome, especially those focused on two of the most common types of glycosylation (N-linked and O-linked glycoproteome), were summarized. The strengths and weaknesses of the various approaches were also discussed.