Histochemical visualization of oxidant stress

Free radicals induce oxidative modification in distinct components of the living matter (lipid, proteins, and DNA). For qualitative and quantitative determination of free radical-induced modifications, different, more or less sensitive biochemical methods are available. Because of the high reactivity and short life of free radicals, ongoing oxidative damage is generally analyzed by measurement of secondary products-such as H(2)O(2), oxidized proteins, peroxidized lipids, and their breakdown products, oxidized DNA-or by fluorographic analysis in combination with fluorescent dyes such as dichlorofluorescin (DCFH). In addition, the determination of free radical-related oxidation products is usually carried out in plasma, urine, or, less frequently, in bioptic material. Consequently, biochemical data seldom reflect the effects of free radical insults in situ. The histochemical visualization of selected molecular markers of oxidative damage can often provide more valuable information concerning the in vivo distribution of oxidative processes. This review summarizes the methods currently available for histochemical detection and indirect visualization of free radical-induced alterations in tissues and isolated cells.     

Steady state analysis of metabolic pathways using Petri nets

Computer assisted analysis and simulation of biochemical pathways can improve the understanding of the structure and the dynamics of cell processes considerably. The construction and quantitative analysis of kinetic models is often impeded by the lack of reliable data. However, as the topological structure of biochemical systems can be regarded to remain constant in time, a qualitative analysis of a pathway model was shown to be quite promising as it can render a lot of useful knowledge, e. g., about its structural invariants. The topic of this paper are pathways whose substances have reached a dynamic concentration equilibrium (steady state). It is argued that appreciated tools from biochemistry and also low-level Petri nets can yield only part of the desired results, whereas executable high-level net models lead to a number of valuable additional insights by combining symbolic analysis and simulation.     

Variation in the self-incompatibility response within and among populations of the tropical shrub Witheringia solanacea (Solanaceae)

Breakdown of genetically enforced self-incompatibility (SI), an extremely common and important evolutionary transition in plants, has conventionally been conceived as a qualitative rather than a quantitative change. We evaluated qualitative and quantitative variation in SI for four populations of Witheringia solanacea in Costa Rica, examining growth of self-pollen tubes in pollinations of buds and mature flowers. We also measured levels of RNase production in styles to determine whether enzyme production was correlated with differences in self-rejection. The two small populations contained both self-compatible (SC) individuals and obligate outcrossers (female or SI). Plants in the two large populations were uniformly SI as revealed by pollen tube growth, although several of these individuals sporadically set seed autogamously. Stylar RNase activity did not differ significantly between bud and mature flowers, but self-pollen tube growth did differ, suggesting that a gene product in addition to S-RNase is responsible for developmental onset of SI. Population-level differences in RNase activity were consistent with differences in the strength of the rejection response in bud pollinations, suggesting that a threshold level of S-RNase, in combination with other factors, is necessary for SI. Our results support a growing body of evidence that not only qualitative variation in SI, but also quantitative variation may be functionally significant.     

An overall assessment of Life Cycle Inventory quality

A qualitative, quantitative, and overall quality assessment of life cycle inventory is suggested. The method is composed of five indicators which are set up at three levels of the inventory quality: flows, processes, and the system. The method allows one to assess the reliability of the method generating inventory data (justness of data, completeness of data, representativity of processes, repeatability of system definition) and at the same time to quantify the uncertainty of the resulting data made under the data generation method. LCA practitioners can finally decide the overall inventory quality through the information for the acceptability of the inventory result comparing the objective of quality and the cost necessary to improve the quality. The operation of the method was verified in the application to the production of polyethylene bottles. The proposed method was also found applicable for the validation of data in the ISO’s LCA data documentation format.     

Effect of carbon disulphide on the cardiovascular system

Biochemical, histological and electron-microscopic examinations of the heart and the aorta of albino rats exposed to carbon disulphide in concentrations of 10, 50, 100 and 200 mg . m-3 were carried out. Changes in the metabolic and energetic processes in the myocardium and in the quantitative and qualitative characteristics of the connective tissue of the aortal vessel wall were observed. The established disorders follow the dose-effect dependence. The authors studied the effect of carbon disulphide in concentrations of 10 and 50 mg . m-3 on the electrophoretic spectrum of serum proteins, the quantitative and qualitative characteristics of fibrous structures in the myocardium and the aorta of albino rats fed on atherogenic diet (cholesterol, cholic acid and vitamin D2). The combination of carbon disulphide with the atherogenic factor leads to intensification of changes in the cardiovascular system and in serum proteins, observed after independent exposure to either of the factors. The combination of atherogenic diet and 10 mg . m-3 carbon disulphide induced symptoms of intoxication, decreased survival of the animals, and the developing sclerotic process was found to be more severe and to progress more rapidly than in animals subject to atherogenic diet alone. The obtained results testify to cardiovascular effect of carbon disulphide. The observed atherogenic effect of carbon disulphide in low concentrations is most probably connected with its direct effect on the myocardium and the vessels.     

Design and implementation of a qualitative simulation model of lambda phage infection

MOTIVATION: Molecular biology databases hold a large number of empirical facts about many different aspects of biological entities. That data is static in the sense that one cannot ask a database 'What effect has protein A on gene B?' or 'Do gene A and gene B interact, and if so, how?'. Those questions require an explicit model of the target organism. Traditionally, biochemical systems are modelled using kinetics and differential equations in a quantitative simulator. For many biological processes however, detailed quantitative information is not available, only qualitative or fuzzy statements about the nature of interactions. RESULTS: We designed and implemented a qualitative simulation model of lambda phage growth control in Escherichia coli based on the existing simulation environment QSim. Qualitative reasoning can serve as the basis for automatic transformation of contents of genomic databases into interactive modelling systems that can reason about the relations and interactions of biological entities.      

Overnutrition in Prenatal and Neonatal Life: A Problem?

In most areas of the world nutritional problems are related to quantitative and qualitative deficiencies. However, in North America the possible harmful effects of overnutrition deserve careful consideration.Little information is available concerning overnutrition during prenatal and neonatal life. The author draws attention to this possibility by outlining clinical and biochemical disorders occurring in the newborn which are related to excessive ingestion of calories, fat, protein, vitamins and minerals before and after birth. Particular reference is made to the ingestion of nutritional substances during pregnancy in amounts that are relatively innocuous to the mother but may be harmful to the infant in utero.Further research in this interesting field is needed in an attempt to assess the effect on the fetus of qualitative overnutrition during pregnancy.     

Microbial anhydrobiosis

The loss of cellular water (desiccation) and the resulting low cytosolic water activity are major stress factors for life. Numerous prokaryotic and eukaryotic taxa have evolved molecular and physiological adaptions to periods of low water availability or water-limited environments that occur across the terrestrial Earth. The changes within cells during the processes of desiccation and rehydration, from the activation (and inactivation) of biosynthetic pathways to the accumulation of compatible solutes, have been studied in considerable detail. However, relatively little is known on the metabolic status of organisms in the desiccated state; that is, in the sometimes extended periods between the drying and rewetting phases. During these periods, which can extend beyond decades and which we term ‘anhydrobiosis’, organismal survival could be dependent on a continued supply of energy to maintain the basal metabolic processes necessary for critical functions such as macromolecular repair. Here, we review the state of knowledge relating to the function of microorganisms during the anhydrobiotic state, highlighting substantial gaps in our understanding of qualitative and quantitative aspects of molecular and biochemical processes in desiccated cells.     

Proteomics-based dissection of stress-responsive pathways in plants

Abiotic stress has an ability to alter the levels of a number of proteins, which may be soluble or structural in nature or which may exist before and after folding in the plant cell. The most crucial function of plant cell is to respond to stress by developing defence mechanisms. This defence is brought about by alteration in the pattern of gene expression. This leads to modulation of certain metabolic and defensive pathways. Owing to gene expression altered under stress, qualitative and quantitative changes in proteins are obvious. These proteins might play a role in signal transduction, antioxidative defence, antifreezing, heat shock, metal binding, antipathogenesis or osmolyte synthesis. A significant part of the literature shows the quantitative and qualitative changes in proteins, mainly employing western analysis, enzymatic kinetics, fraction isolation, one-dimensional SDS-PAGE electrophoresis, etc. Fortunately, recent developments in sensitivity and accuracy for proteome analysis have provided new dimensions to assess the changes in protein types and their expression levels under stress. The novel aim of this review is to do a side-by-side comparison of the proteins that are induced or overexpressed under abiotic stress, examining those from biochemical literature and the ones observed, sequenced and identified using the advanced proteomics and bioinformatic techniques.     

Patients' direct experiences as central elements of placebo analgesia

Placebo analgesic effects appear to be related to patients' perception of the therapeutic intervention. In this paper, we review quantitative findings of how the relationship with the physician and the verbal suggestions given for relief may influence patients' perception of a treatment and how patients' expectations and emotional feelings may affect treatment outcome. We also present qualitative data from interviews with patients who have experienced pain relief following a placebo or an active treatment. A special focus is given to the temporal development of placebo analgesia at psychological and neurophysiological levels. Finally, we discuss the extent to which the quantitative and qualitative findings supplement or contrast with each other, and we touch upon possible implications of patients' direct experience as central for placebo analgesia.     

1H NMR observation of redox potential in liver.

1H NMR spectral editing techniques can select the distinct signals of lactate, pyruvate, beta-hydroxybutyrate, and acetoacetate and provide a unique way to monitor the biochemical processes in vivo. These metabolite levels reflect the near-equilibrium dehydrogenase activity and therefore the cellular redox state. The quantitative comparison between the 1H NMR and biochemical assay data is in excellent agreement. Lactate/pyruvate and beta-hydroxybutyrate/acetoacetate ratios, obtained from normalized 1H NMR spectra, respond directly to changes in the cytosolic and mitochondrial redox states. Because NMR is noninvasive, our results set the groundwork for implementing these techniques to observe tissue redox states in vivo.     

An Information Gap in DNA Evidence Interpretation

Forensic DNA evidence often contains mixtures of multiple contributors, or is present in low template amounts. The resulting data signals may appear to be relatively uninformative when interpreted using qualitative inclusion-based methods. However, these same data can yield greater identification information when interpreted by computer using quantitative data-modeling methods. This study applies both qualitative and quantitative interpretation methods to a well-characterized DNA mixture and dilution data set, and compares the inferred match information. The results show that qualitative interpretation loses identification power at low culprit DNA quantities (below 100 pg), but that quantitative methods produce useful information down into the 10 pg range. Thus there is a ten-fold information gap that separates the qualitative and quantitative DNA mixture interpretation approaches. With low quantities of culprit DNA (10 pg to 100 pg), computer-based quantitative interpretation provides greater match sensitivity.     

Genetik intermediärer Phänotypen

The development of complex diseases such as coronary heart disease and diabetes mellitus is influenced by numerous genes. However, the contribution of a single gene is relatively small. The identification of genetic variants associated with complex diseases therefore requires large efforts and well-characterized groups of patients and controls. Alternatively, investigation of intermediate phenotypes instead of these complex endpoints seems to be more promising. An intermediate phenotype is usually already well known to be associated with the investigated disease, is heritable, and represents one aspect among others in the pathogenesis of the complex disease. This results in an accentuation of the phenotype and reduction of genetic heterogeneity. Investigating the genetics of the intermediate phenotype instead of the genetics of the end phenotype allows elucidation of this aspect of the disease. Optimal intermediate phenotypes are quantitative, easy-to-measure biochemical parameters. This results in an increased statistical power in contrast to qualitative phenotypes.     

Individual cell-based models of the spatial-temporal organization of multicellular systems--achievements and limitations.

Computational approaches of multicellular assemblies have reached a stage where they may contribute to unveil the processes that underlie the organization of tissues and multicellular aggregates. In this article, we briefly review and present some new results on a number of 3D lattice free individual cell-based mathematical models of epithelial cell populations. The models we consider here are parameterized by bio-physical and cell-biological quantities on the level of an individual cell. Eventually, they aim at predicting the dynamics of the biological processes on the tissue level. We focus on a number of systems, the growth of cell populations in vitro, and the spatial-temporal organization of regenerative tissues. For selected examples we compare different model approaches and show that the qualitative results are robust with respect to many model details. Hence, for the qualitative features and largely for the quantitative features many model details do not matter as long as characteristic biological features and mechanisms are correctly represented. For a quantitative prediction, the control of the bio-physical and cell-biological parameters on the molecular scale has to be known. At this point, slide-based cytometry may contribute. It permits to track the fate of cells and other tissue subunits in time and validated the organization processes predicted by the mathematical models.     

Age-related changes of monoaminooxidases in rat cerebellar cortex

Age-related changes of the monoaminoxidases, evaluated by enzymatic staining, quantitative analysis of images, biochemical assay and statistical analysis of data were studied in cerebellar cortex of young (3-month-old) and aged (26-month-old) male Sprague-Dawley rats. The enzymatic staining shows the presence of monoamino-oxidases within the molecular and granular layers as well as within the Purkinje neurons of the cerebellum of young and aged animals. In molecular layer, and in Purkinje neurons the levels of monoaminooxidases were strongly increased in old rats. The granular layer showed, on the contrary, an age-dependent loss of enzymatic staining. These morphological findings were confirmed by biochemical results. The possibility that age-related changes in monoaminooxidase levels may be due to impaired energy production mechanisms and/or represent the consequence of reduced energetic needs is discussed.     

Disorders of the deamination of nitrogenous compounds in the heart muscle in experimental atherosclerosis

The development of alimentary hypercholesterolemia in rabbits (confirmed by morphometric, electrophysiological and biochemical data) was accompanied by a decrease of the serotonin, benzylamine and tyramine deamination rates in heart muscle mitochondria. At the same time a qualitatively new reaction of cadaverine deamination could be seen in the mitochondria. The data obtained suggest that impairment of deamination of the nitrogenous compounds in atherosclerosis may be due to reversible qualitative modification (transformation) of mitochondrial monoamine oxidase activity. Some of the drugs which decrease the level of lipids in blood serum of hypercholesterolemic rabbits abolished and prevented the impairment of deamination of nitrogenous compounds.     

Modularization of biochemical networks based on classification of Petri net t-invariants

Background  

Structural analysis of biochemical networks is a growing field in bioinformatics and systems biology. The availability of an increasing amount of biological data from molecular biological networks promises a deeper understanding but confronts researchers with the problem of combinatorial explosion. The amount of qualitative network data is growing much faster than the amount of quantitative data, such as enzyme kinetics. In many cases it is even impossible to measure quantitative data because of limitations of experimental methods, or for ethical reasons. Thus, a huge amount of qualitative data, such as interaction data, is available, but it was not sufficiently used for modeling purposes, until now. New approaches have been developed, but the complexity of data often limits the application of many of the methods. Biochemical Petri nets make it possible to explore static and dynamic qualitative system properties. One Petri net approach is model validation based on the computation of the system's invariant properties, focusing on t-invariants. T-invariants correspond to subnetworks, which describe the basic system behavior.     

Life-Cycle Assessment: Constraints on Moving from Inventory to Impact Assessment

Life-cycle assessment (LCA) is a technique for systematically analyzing a product from cradle-to-grave, that is, from resource extraction through manufacture and use to disposal. LCA is a mixed or hybrid analytical system. An inventory phase analyzes system inputs of energy and materials along with outputs of emissions and wastes throughout life cycle, usually as quantitative mass loadings. An impact assessment phase then examines these loadings in light of potential environmental issues using a mixed spectrum of qualitative and quantitative methods. The constraints imposed by inventory's loss of spatial, temporal, dose-response, and threshold information raise concerns about the accuracy of impact assessment. The degree of constraint varies widely according to the environmental issue in question and models used to extrapolate the inventory data. LCA results may have limited value in two areas: (I) local and/ortransient biophysical processes and (2) issues involving biological parameters, such as biodiversity, habitat alteration, and toxicity. The end result is that impact assessment does not measure actual effects or impacts, nor does it calculate the likelihood of an effect or risk Rather, LCA impact assessment results are largely directional environmental indicaton. The accuracy and usefulness of indicators need to be assessed individually and in a circumstance-specific manner prior to decision making. This limits LCAs usefulness as the sole basis for comprehensive assessments and the comparisons of alternatives. In conclusion, LCA may identify potential issues from a systemwide perspective, but more-focused assessments using other analytical techniques are often necessary to resolve the issues.     

Stress Proteins and Isozymology of Acid Phosphatase, Esterase, and Peroxidase in Phaseolus vulgaris Following Peanut Mottle Virus Infection

The present work was undertaken to study soluble protein changes and enzyme alterations in "Topcrop" bean ( Phaseolus vulgaris L.) primary leaves following inoculation with peanut mottle virus (PMV) in an attempt to elucidate the biochemical basis of the hypersensitive reaction in this host virus combination. Using the discontinuous polyacrylamide gel electrophoresis (disc-PAGE) technique, at least four apparently "novel" protein bands at Rf values of 0.80, 0.77, 0.74 and 0.68 were observed in infected tissue. The band at Rf 0.76 seems to be injury related and is shown here to be an isozyme of acid phosphatase. It is believed that these proteins are neither the cause nor the product of necrosis and may thus play a role in the active defense mechanism of the plant. In this virus host combination it was found that heating soluble protein fractions at 55 °C for 10 min before electrophoresis dramatically reduced the background and improved resolution on gels. While the biological function(s) of these proteins needs further investigations it is almost certain that none of them is an isozyme of alkaline phosphatase, acid phosphatase, esterase, or peroxidase. Zymogram analysis has additionally revealed the absence of alkaline phosphatase activity in untreated, abraded and PMV-infected primary leaves and no qualitative or quantitative changes in esterase isozymes have been observed in primary leaf tissues following abrasion or PMV–infection. By contrast, qualitative alterations in acid phosphatase after PMV-infection and both qualitative and quantitative changes in peroxidase after mechanical abrasion and PMV-infection have also been demonstrated.