Concepts and approaches towards understanding the cellular redox proteome

The physiological activity of a significant subset of cell proteins is modified by the redox state of regulatory thiols. The cellular redox homeostasis depends on the balance between oxidation of thiols through oxygen and reactive oxygen species and reduction by thiol-disulfide transfer reactions. Novel and improved methodology has been designed during recent years to address the level of thiol/disulfide regulation on a genome-wide scale. The approaches are either based on gel electrophoresis or on chromatographic techniques coupled to high end mass spectrometry. The review addresses diagonal 2D-SDS-PAGE, targeted identification of specific redox-interactions, affinity chromatography with thioredoxins and glutaredoxins, gel-based and non-gel based labelling techniques with fluorophores (such as Cy3, Cy5, ICy), radioisotopes, or with isotope-coded affinity tags (ICAT), differential gel electrophoresis (DIGE) and combined fractional diagonal chromatography (COFRADIC). The extended methodological repertoire promises fast and new insight into the intricate regulation network of the redox proteome of animals, bacteria, and plants.     

The general physiological mechanisms of glutamate influence on the central nervous system

The L-Glutamate, is dicarboxilic amino acid which plays the important role in maintenance of normal functioning of the central nervous system (CNS) in invertebrate and vertebrate animals. It carrying out functions of amphibolic intermediate in biosynthesis and degradation of amino acids and some nitrogenous substances. Besides, L-Glutamate acid possesses a significant role in the regulation of the bioenergetics processes that proceeding in nervous system, due to direct or indirect participations in the reactions of glycolysis, gluconeogenesis, synthesis of ketone bodies and formation of glycogen. Also, L-Glutamate accepts direct participation in realization of a citrate cycle reactions, a respiratory circuit; in conversion of ammonia and it excretion from an organism. However the most important function of the L-Glutamate--its participation in the processes of nervous regulation as excitatory neuromediator in the CNS of invertebrate and vertebrate animals.     

Elucidating the molecular mechanisms underlying cellular response to biophysical cues using synthetic biology approaches

ABSTRACT

The use of synthetic surfaces and materials to influence and study cell behavior has vastly progressed our understanding of the underlying molecular mechanisms involved in cellular response to physicochemical and biophysical cues. Reconstituting cytoskeletal proteins and interfacing them with a defined microenvironment has also garnered deep insight into the engineering mechanisms existing within the cell. This review presents recent experimental findings on the influence of several parameters of the extracellular environment on cell behavior and fate, such as substrate topography, stiffness, chemistry and charge. In addition, the use of synthetic environments to measure physical properties of the reconstituted cytoskeleton and their interaction with intracellular proteins such as molecular motors is discussed, which is relevant for understanding cell migration, division and structural integrity, as well as intracellular transport. Insight is provided regarding the next steps to be taken in this interdisciplinary field, in order to achieve the global aim of artificially directing cellular response.     

Natural patterns of neural activity: how physiological mechanisms are orchestrated to cope with real life

Physiological mechanisms of neuronal information processing have been shaped during evolution by a continual interplay between organisms and their sensory surroundings. Thus, when asking for the functional significance of such mechanisms, the natural conditions under which they operate must be considered. This has been done successfully in several studies that employ sensory stimulation under in vivo conditions. These studies address the question of how physiological mechanisms within neurons are properly adjusted to the characteristics of natural stimuli and to the demands imposed on the system being studied. Results from diverse animal models show how neurons exploit natural stimulus statistics efficiently by utilizing specific filtering capacities. Mechanisms that allow neurons to adapt to the currently relevant range from an often immense stimulus spectrum are outlined, and examples are provided that suggest that information transfer between neurons is shaped by the system-specific computational tasks in the behavioral context.     

Insights into the mechanisms of CMV-mediated interference with cellular apoptosis

Apoptosis has the potential to function as a defence mechanism during viral infection. Identification of CMV mutants that cause the apoptotic death of infected cells confirmed that viral infection activates apoptotic pathways and that this process is counteracted by CMV to ensure efficient viral replication. The recent identification of CMV-encoded proteins that suppress cell death has greatly enhanced our understanding of the mechanisms used by this family of viruses to prevent apoptosis. CMV do not encode homologues of known death-suppressing proteins, suggesting that the CMV family has evolved novel, more sophisticated strategies for the inhibition of apoptosis. The identification and characterization of the human CMV (HCMV)-encoded antiapoptotic proteins UL36 (viral inhibitor of caspase-8 activation [vICA]) and UL37 (viral mitochondria-localized inhibitor of apoptosis [vMIA]) have confirmed that CMV target unique apoptotic control points. For example, vMIA inhibits apoptosis by binding Bax and sequestering it at the mitochondrial membrane as an inactive oligomer. This knowledge not only provides a more complete understanding of the CMV replication process but also allows the identification of previously unrecognized apoptotic checkpoints. Because HCMV is an important cause of birth defects and an increasingly important opportunistic pathogen, a firm grasp of the mechanisms by which it affects cellular apoptosis may provide avenues for the design of improved therapeutic strategies. Here, we review the recent progress made in understanding the role of CMV-encoded proteins in the inhibition of apoptosis.     

Linking the computational structure of variance adaptation to biophysical mechanisms

In multiple sensory systems, adaptation to the variance of a sensory input changes the sensitivity, kinetics, and average response over timescales ranging from < 100 ms to tens of seconds. Here, we present a simple, biophysically relevant model of retinal contrast adaptation that accurately captures both the membrane potential response and all adaptive properties. The adaptive component of this model is a first-order kinetic process of the type used to describe ion channel gating and synaptic transmission. From the model, we conclude that all adaptive dynamics can be accounted for by depletion of a signaling mechanism, and that variance adaptation can be explained as adaptation to the mean of a rectified signal. The model parameters show strong similarity to known properties of bipolar cell synaptic vesicle pools. Diverse types of adaptive properties that implement theoretical principles of efficient coding can be generated by a single type of molecule or synapse with just a few microscopic states.     

New approaches to the problem of generating coherent,reproducible phenotypes

Fundamental, unresolved questions in biology include how a bacterium generates coherent phenotypes, how a population of bacteria generates a coherent set of such phenotypes, how the cell cycle is regulated and how life arose. To try to help answer these questions, we have developed the concepts of hyperstructures, competitive coherence and life on the scales of equilibria. Hyperstructures are large assemblies of macromolecules that perform functions. Competitive coherence describes the way in which organisations such as cells select a subset of their constituents to be active in determining their behaviour; this selection results from a competition between a process that is responsible for a historical coherence and another process responsible for coherence with the current environment. Life on the scales of equilibria describes how bacteria depend on the cell cycle to negotiate phenotype space and, in particular, to satisfy the conflicting constraints of having to grow in favourable conditions so as to reproduce yet not grow in hostile conditions so as to survive. Both competitive coherence and life on the scales deal with the problem of reconciling conflicting constraints. Here, we bring together these concepts in the common framework of hyperstructures and make predictions that may be tested using a learning program, Coco, and secondary ion mass spectrometry.     

Chemical approaches to the investigation of cellular systems

Biochemistry in the context of a living cell or organism is complicated by many variables such as supramolecular organization, cytoplasmic viscosity, and substrate heterogeneity. While these variables are easily excluded or avoided in reconstituted systems, they must be dealt with in cellular environments. New developments have allowed researchers to begin probing the inner workings of the cell to gain new insight into cell function and metabolism. Advances in cellular imaging and in small molecule-controlled gene expression, signal transduction and cell surface modification are discussed in this review. These techniques have permitted the study of molecular components within the context of living cells.     

Neural mechanisms underlying the evolvability of behaviour

The complexity of nervous systems alters the evolvability of behaviour. Complex nervous systems are phylogenetically constrained; nevertheless particular species-specific behaviours have repeatedly evolved, suggesting a predisposition towards those behaviours. Independently evolved behaviours in animals that share a common neural architecture are generally produced by homologous neural structures, homologous neural pathways and even in the case of some invertebrates, homologous identified neurons. Such parallel evolution has been documented in the chromatic sensitivity of visual systems, motor behaviours and complex social behaviours such as pair-bonding. The appearance of homoplasious behaviours produced by homologous neural substrates suggests that there might be features of these nervous systems that favoured the repeated evolution of particular behaviours. Neuromodulation may be one such feature because it allows anatomically defined neural circuitry to be re-purposed. The developmental, genetic and physiological mechanisms that contribute to nervous system complexity may also bias the evolution of behaviour, thereby affecting the evolvability of species-specific behaviour.     

Understanding the chemical mechanisms of life

Understanding the biological, medical and ecological pathways of complex transformations will be greatly aided by the chemist's molecular approach. The 2nd European Conference on Chemistry for Life Sciences brought together these diverse disciplines to consider where we are and where we will go.     

Quality of life in people with physical disabilities

The aim of this study was to examine the possible differences in self-reported quality of life of people with physical disabilities with regard to both socio-demographic and disability-related characteristics. Testing was conducted on 153 respondents with physical disabilities, residents of the City of Zagreb. Positive correlations were found between the quality of life and income satisfaction, residence size (per capita floor area) and level of residence equipment. Multivariate analysis of variance showed statistically significant differences in quality of life among respondents with regard to the marital status, work status and home ownership. Statistically significant differences in the quality of life were found among the participants depending on their level of physical mobility and type of physical disability. The level of physical mobility is associated with general satisfaction with the accomplishment of goals, aspirations and hopes. The type of physical disability is related to the satisfaction with leisure activities, with the material status, expectations to achieve in the future what has not formerly been achieved. There was also a significant relation between the type of physical disability and general satisfaction with life in the past year. Positive correlations between duration of disability and quality of life were found. Membership in associations of persons with physical disability and related benefits were shown to contribute to the quality of life.     

A fluorescein-labeled derivative of estradiol with binding affinity towards cellular receptors

1,3,5,[10]-Estratriene-3,17β-diol-6-iminooxyacetic acid (I) and fluorescein amine condense in the presence of dicyclohexylcarbodiimide to give a fluorescent derivative of estradiol: 9{p-(1′,3′,5′[10′]-Estratriene-3′,17′β-diol-6′-iminooxyacetylamino) o-carboxyphenyl}-6-hydroxy-3-isoxanthenone (II). (II) can be prepared and isolated on a micro scale by thin layer chromatography. The results show that (II) is useful as a probe for estrogen interaction with cellular receptors and with antibody to estradiol.     

Model-fitting approaches to the analysis of human behaviour.

Model-fitting methods are now prominent in the analysis of human behavioural variation. Various ways of specifying models have been proposed. These are identical in their simplest form but differ in the emphasis given to more subtle sources of variation. The biometrical genetical approach allows flexibility in the specification of non-additive factors. Given additivity, the approach of path analysis may be used to specify several environmental models in the presence of assortative mating. In many cases the methods should yield identical conclusions. Several statistical methods have been proposed for parameter estimation and hypothesis testing. The most suitable rely on the method of maximum likelihood for the estimation of variance and covariance components. Any multifactorial model can be formulated in these terms. The choice of method will depend chiefly on the design of the experiment and the ease with which a data summary can be obtained without significant loss of information. Examples are given in which the causes of variation show different degrees of detectable complexity. A variety of experimental designs yield behavioural data which illustrate the contribution of additive and non-additive genetical effects, the mating system, sibling and cultural effects, the interaction of genetical effects with age and sex. The discrimination between alternative hypotheses is often difficult. The extension of the approach to the analysis of multiple measurements and discontinuous traits is considered.     

Unhealthy lifestyles during the life course: association with physical decline in late life

This study aimed to examine the association between unhealthy lifestyle in young age, midlife and/or old age and physical decline in old age, and to examine the association between chronic exposure to an unhealthy lifestyle throughout life and physical decline in old age. The study sample included 1297 respondents of the Longitudinal Aging Study Amsterdam (LASA). Lifestyle in old age (55-85 y) was assessed at baseline, while lifestyle in young age (around 25 y) and midlife (around 40 y) were assessed retrospectively. Lifestyle factors included physical activity, body mass index (BMI), number of alcohol drinks per week and smoking. Physical decline was calculated as change in physical performance score between baseline and six-year follow-up. Of the lifestyle factors present in old age, a BMI of 25-29 vs. BMI <25 kg/m2 (odds ratio (OR) 1.6; 95% confidence interval (CI) 1.1-2.2) and a BMI of > or =30 vs. BMI <25 kg/m2 (OR 1.8; 95% CI 1.2-2.7) were associated with physical decline in old age. Being physically inactive in old age was not significantly associated with an increased risk of physical decline, however, being physically inactive both in midlife and in old age increased the odds of physical decline in old age to 1.6 (95% CI 1.1-2.4) as compared to respondents who were physically inactive in midlife and physically active in old age. Being overweight in both age periods was associated with an OR of 1.5 (95% CI 1.1-2.2). These data suggest that overweight in old age, and chronic exposure to physical inactivity or overweight throughout life increases the risk of physical decline in old age. Therefore, physical activity and prevention of overweight at all ages should be stimulated to prevent physical decline in old age.     

Linking the kinome and phosphorylome--a comprehensive review of approaches to find kinase targets

Protein phosphorylation is associated with most cell signaling and developmental processes in eukaryotes. Despite the vast extent of the phosphoproteome within the cell, connecting specific kinases with relevant targets remains a significant experimental frontier. The challenge of linking kinases and their substrates reflects the complexity of kinase function. For example, kinases tend to exert their biological effects through supernumerary, redundant phosphorylation, often on multiple protein complex components. Although these types of phosphorylation events are biologically significant, those kinases responsible are often difficult to identify. Recent methods for global analysis of protein phosphorylation promise to substantially accelerate efforts to map the dynamic phosphorylome. Here, we review both conventional methods to identify kinase targets and more comprehensive genomic and proteomic approaches to connect the kinome and phosphorylome.     

Methodological differences of the physical and computational model approaches

General principles of modeling, the problem of adequency of models, and the similarity and differences between physical and computational models are discussed.     

The quest for the mechanisms of life

The genomic revolution, manifested by the sequencing of the complete genome of many organisms, along with technological advances, such as DNA microarrays and developments in high-throughput analysis of proteins, metabolites, and isotopic tracer distribution patterns, challenged the conventional ways in which questions are approached in the biological sciences: (a) rather than examining a small number of genes and/or reactions at any one time;, we can now analyze gene expression and protein activity in the context of systems of interacting genes and gene products; (b) comprehensive analysis of biological systems requires the integration of all cellular fingerprints: genome sequence, maps of gene expression, protein expression, metabolic output, and in vivo enzymatic activity; and (c) collecting, managing, and analyzing comparable data from various cellular profiles requires expertise from several fields that transcend traditional discipline boundaries. While researchers in systems biology have still to address difficult challenges in both experimental and computational arenas, they possess, for the first time, the opportunity to unravel the mechanisms of life. The enormous impact of these discoveries in diverse areas, such as metabolic engineering, strain selection, drug screening and development, bioprocess development, disease prognosis and diagnosis, gene and other medical therapies, is an obvious motivation for pursuing integrated analyses of cellular systems.     

Molecular genetic approaches to the study of cellular senescence.

Normal cells in culture exhibit limited division potential, which is used as a model for cellular aging. In contrast, tumor-derived, carcinogen- or virus-transformed cells are capable of dividing indefinitely (immortal). Fusion of normal with immortal human cells yielded hybrids having limited life span, indicating that cellular senescence is a dominant phenotype and that immortality is recessive. Fusions of various immortal human cell lines with each other led to the identification of four complementation groups for indefinite division. In order to identify the chromosomes and genes involved in growth regulation, that had been modified in immortal cells, we used the technique of microcell fusion to introduce either a normal human chromosome 11 or 4 into cell lines representative of the different complementation groups. Chromosome 11 had no effect on the in vitro life span of the different immortal human tumor lines. However, when a normal human chromosome 4 was introduced into cell lines assigned to complementation group B, the cells lost the immortal phenotype. No effect on the proliferation potential of cell lines representative of the other complementation groups was observed. These results suggest that a gene(s) on human chromosome 4 has been modified in immortal cell lines assigned to complementation group B, to allow escape from senescence. They also provide evidence for a genetic basis for cellular aging.