Oxidases and peroxidases in cardiovascular and lung disease: new concepts in reactive oxygen species signaling

Reactive oxygen species (ROS) are involved in numerous physiological and pathophysiological responses. Increasing evidence implicates ROS as signaling molecules involved in the propagation of cellular pathways. The NADPH oxidase (Nox) family of enzymes is a major source of ROS in the cell and has been related to the progression of many diseases and even environmental toxicity. The complexity of this family's effects on cellular processes stems from the fact that there are seven members, each with unique tissue distribution, cellular localization, and expression. Nox proteins also differ in activation mechanisms and the major ROS detected as their product. To add to this complexity, mounting evidence suggests that other cellular oxidases or their products may be involved in Nox regulation. The overall redox and metabolic status of the cell, specifically the mitochondria, also has implications on ROS signaling. Signaling of such molecules as electrophilic fatty acids has an impact on many redox-sensitive pathologies and thus, as anti-inflammatory molecules, contributes to the complexity of ROS regulation. This review is based on the proceedings of a recent international Oxidase Signaling Symposium at the University of Pittsburgh's Vascular Medicine Institute and Department of Pharmacology and Chemical Biology and encompasses further interaction and discussion among the presenters.     

Towards Visual Proteomics at High Resolution

Traditionally, structural biologists approach the complexity of cellular proteomes in a reductionist manner. Proteomes are fractionated, their molecular components purified and studied one-by-one using the experimental methods for structure determination at their disposal. Visual proteomics aims at obtaining a holistic picture of cellular proteomes by studying them in situ, ideally in unperturbed cellular environments. The method that enables doing this at highest resolution is cryo-electron tomography. It allows to visualize cellular landscapes with molecular resolution generating maps or atlases revealing the interaction networks which underlie cellular functions in health and in disease states. Current implementations of cryo ET do not yet realize the full potential of the method in terms of resolution and interpretability. To this end, further improvements in technology and methodology are needed. This review describes the state of the art as well as measures which we expect will help overcoming current limitations.     

Behavioral,neural and cellular components underlying olfactory learning in the honeybee

A top-down approach as applied to learning and memory in honeybees provides the opportunity of relating different levels of complexity to each other, and of analyzing the rules and mechanisms from the viewpoint of the respective next higher level. Olfactory conditioning of harnessed bees exemplifies essential elements of associative learning and, in general, forms a bridge between the systems and the cellular levels of analysis. Intracellular recordings of identified neurons during olfactory conditioning play a key role in this effort. They allow testing of the assumptions made by modern behavioral theories of associative learning and provide access to cellular and molecular studies, owing to the identification of their transmitters and the peculiarities of the connectivities. Analysis at this intermediate level of complexity is particularly profitable in the bee, because essential neural elements of the associative network are known and can be tested during ongoing learning behavior. In this respect, the honeybee offers unique properties for the building of bridges between the molecular, cellular neuronal, network and behavioral levels of associative learning.     

Modulating Notch signaling by pathway-intrinsic and pathway-extrinsic mechanisms

Despite a relatively simple core-signaling transduction machinery, Notch signaling controls cell differentiation in many different tissues and at multiple stages in a given cell lineage. To understand how Notch generates this multitude of cellular responses, it is important to learn how the Notch-signaling output is modulated at various levels. Pathway-intrinsic as well as pathway-extrinsic mechanisms, including cross-talk between Notch and other major signaling mechanisms, modulate Notch signaling, contributing to the versatile output. In this review, we discuss how Notch signaling is altered in tumors and illustrate the complexity in signaling pathway cross-talk with examples of how Notch synergizes with NF-kappaB signaling and the cellular response to lowered oxygen (hypoxia).     

SINDBIS病毒对宿主细胞基因表达的影响

Sindbis病毒(SBV)的感染能迅速地抑制宿主细胞的基因表达(mRNA合成与蛋白质合成),但细胞rRNA的合成水平与正常细胞接近.同时SBV还诱导产生一种细胞特异的核基质结合蛋白P105.用放线菌素D处理细胞,导致感染细胞中病毒结构蛋白的合成量及有感染力的子代病毒产量明显下降.实验结果不仅显示了SBV对宿主细胞基因表达的复杂调控关系,而且还表明SBV的非结构蛋白nsP2和衣壳蛋白C可能直接参与这一过程.     

Integration of omics data: how well does it work for bacteria?

In the current omics era, innovative high-throughput technologies allow measuring temporal and conditional changes at various cellular levels. Although individual analysis of each of these omics data undoubtedly results into interesting findings, it is only by integrating them that gaining a global insight into cellular behaviour can be aimed at. A systems approach thus is predicated on data integration. However, because of the complexity of biological systems and the specificities of the data-generating technologies (noisiness, heterogeneity, etc.), integrating omics data in an attempt to reconstruct signalling networks is not trivial. Developing its methodologies constitutes a major research challenge. Besides for their intrinsic value towards health care, environment and industry, prokaryotes are ideal model systems to further develop these methods because of their lower regulatory complexity compared with eukaryotes, and the ease with which they can be manipulated. Several successful examples outlined in this review already show the potential of the systems approach for both fundamental and industrial applications, which would be time-consuming or impossible to develop solely through traditional reductionist approaches.     

Robustness of cellular functions

Robustness, the ability to maintain performance in the face of perturbations and uncertainty, is a long-recognized key property of living systems. Owing to intimate links to cellular complexity, however, its molecular and cellular basis has only recently begun to be understood. Theoretical approaches to complex engineered systems can provide guidelines for investigating cellular robustness because biology and engineering employ a common set of basic mechanisms in different combinations. Robustness may be a key to understanding cellular complexity, elucidating design principles, and fostering closer interactions between experimentation and theory.     

Evolution of living organisms as a multilevel process

There is inherent capacity to increase the degree of aggregation within each of the levels of structural organization of living matter. At the macromolecular level (MML), this is an increase in the gene number in the genomes of evolving organisms; at the cellular level (CL), an increase in cell size; and at the multicellular level (MCL), an increase in the number of cells in the multicellular aggregate. However, the increase in the degree of aggregation causes gene incompatibility in case of genome evolution and instability in case of large cells and multicellular aggregates with simple structure. Gene incompatibility may be neutralized by spacio-temporal disconnection of the products of incompatible genes at the cellular and multicellular levels. The larger cells and multicellular aggregates are stabilized by increased structural complexity which is a consequence of the origin of new genes. There is a feedback between the processes of evolution at different levels MML→CL→ MCL.The processes of evolutionary development at different levels of structural organization are also relatively independent. The coincidence of these processes gives rise to stable organisms of higher complexity, which are then subjected to natural selection and population processes to establish a new step in progressive biological evolution. In all of the normal organisms of newly evolved species there is a correspondence between the different levels of structural organization, i.e. in their degree of aggregation, their complexity and functional organization. The form of correspondence for multicellular organisms is presented.     

Ancestry-Tracking of Stress Response GPCR Clades: A Conceptual Path to Treating Depression

The environmental complexity in which living organisms found themselves throughout evolution, most likely resulted in various encounters that would continuously challenge the organisms' ability to survive. Coping with this stress can prove energetically demanding and might require the proper coupling between mechanisms aimed at sensing external stimuli and cellular strategies geared at producing energy. In this issue of BioEssays, Lovejoy and Hogg hypothesize that preservation of this bifaceted coupling can be detected by the maintenance and evolution of stress response mechanisms at the genomic, molecular and cellular levels. Through ancestry-tracking, they identify a group of related G protein-coupled receptor systems with intersecting stress-modulating properties which might represent an essential part of a complex organism's coping mechanisms to stress, an attribute that they suspect may be affected in individuals suffering from mood disorders such as depression.     

Complexity of calcium signaling in synaptic spines

Long-term potentiation and long-term depression are thought to be cellular mechanisms contributing to learning and memory. Although the physiological phenomena have been well characterized, little consensus of their underlying molecular mechanisms has emerged. One reason for this may be the under-appreciated complexity of the signaling pathways that can arise if key signaling molecules are discretely localized within the synapse. Recent findings suggest an unanticipated degree of structural organization at the synapse, and improved methods in cellular imaging of living tissue have provided much-needed information about the intracellular dynamics of Ca(2+), thought to be critical for both LTP and LTD. In this review, we briefly summarize some of these developments, and show that a more complete understanding of cellular signaling depends on the successful integration of traditional biochemistry and molecular biology with the spatial and temporal details of synaptic ultrastructure. Biophysically realistic computer simulations can have an important role in bridging these disciplines.     

How a neutral evolutionary ratchet can build cellular complexity

Complex cellular machines and processes are commonly believed to be products of selection, and it is typically understood to be the job of evolutionary biologists to show how selective advantage can account for each step in their origin and subsequent growth in complexity. Here, we describe how complex machines might instead evolve in the absence of positive selection through a process of "presuppression," first termed constructive neutral evolution (CNE) more than a decade ago. If an autonomously functioning cellular component acquires mutations that make it dependent for function on another, pre-existing component or process, and if there are multiple ways in which such dependence may arise, then dependence inevitably will arise and reversal to independence is unlikely. Thus, CNE is a unidirectional evolutionary ratchet leading to complexity, if complexity is equated with the number of components or steps necessary to carry out a cellular process. CNE can explain "functions" that seem to make little sense in terms of cellular economy, like RNA editing or splicing, but it may also contribute to the complexity of machines with clear benefit to the cell, like the ribosome, and to organismal complexity overall. We suggest that CNE-based evolutionary scenarios are in these and other cases less forced than the selectionist or adaptationist narratives that are generally told.     

In-cell NMR: From target structure and dynamics to drug screening

The cellular environment can affect the structure and function of pharmacological targets and the interaction with potential drugs. Such complexity is often overlooked in the first steps of drug design, where compounds are screened and optimized in vitro, leading to high failure rates in the pre-clinical and clinical tests. In-cell NMR spectroscopy has the potential to fill this gap, as it allows structural studies of proteins and nucleic acids directly in living cells, from bacteria to human-derived, providing a unique way to investigate the structure and dynamics of ligand–target interactions in the native cellular context. When applied to drug screening, in-cell NMR provides insights on binding kinetics and affinity toward a cellular target, offering a powerful tool for improving drug potency at an early stage of drug development.     

Fungal evolution: cellular,genomic and metabolic complexity

The question of how phenotypic and genomic complexity are inter‐related and how they are shaped through evolution is a central question in biology that historically has been approached from the perspective of animals and plants. In recent years, however, fungi have emerged as a promising alternative system to address such questions. Key to their ecological success, fungi present a broad and diverse range of phenotypic traits. Fungal cells can adopt many different shapes, often within a single species, providing them with great adaptive potential. Fungal cellular organizations span from unicellular forms to complex, macroscopic multicellularity, with multiple transitions to higher or lower levels of cellular complexity occurring throughout the evolutionary history of fungi. Similarly, fungal genomes are very diverse in their architecture. Deep changes in genome organization can occur very quickly, and these phenomena are known to mediate rapid adaptations to environmental changes. Finally, the biochemical complexity of fungi is huge, particularly with regard to their secondary metabolites, chemical products that mediate many aspects of fungal biology, including ecological interactions. Herein, we explore how the interplay of these cellular, genomic and metabolic traits mediates the emergence of complex phenotypes, and how this complexity is shaped throughout the evolutionary history of Fungi.     

Fine structure of somatotrophs and mammotrophs in the pituitary pars distalis of the little (lit) mutant mouse

The cellular pathology and postnatal differentiation of somatotrophs and mammotrophs in the pars distalis of little (lit/lit) and normal (+/+; lit/+) mice were studied by means of electron microscopy. The results indicate that in little the pituitary at birth contains recognizable somatotrophs and mammotrophs; however, between 14 and 24 days of age a contrast between little and normal becomes conspicuous with respect to the somatotrophs. Little somatotrophs are less heavily populated with granules, have granules of smaller size, and show less developed organelles than do normal somatotrophs at comparable stages. Beyond 24 days the little somatotrophs become more difficult to locate, and those that do occur show a minimal increase in complexity from that present at 14 days. In contrast, the mammotrophs in little are similar in appearance to normal mammotrophs and show increasing complexity as development proceeds, often sending forth cellular processes between neighboring cells, as do normal mammotrophs.     

Exploiting biological complexity for strain improvement through systems biology

Cellular complexity makes it difficult to build a complete understanding of cellular function but also offers innumerable possibilities for modifying the cellular machinery to achieve a specific purpose. The exploitation of cellular complexity for strain improvement has been a challenging goal for applied biological research because it requires the coordinated understanding of multiple cellular processes. It is therefore pursued most efficiently in the framework of systems biology. Progress in strain improvement will depend not only on advances in technologies for high-throughput measurements but, more importantly, on the development of theoretical methods that increase the information content of these measurements and, as such, facilitate the elucidation of mechanisms and the identification of genetic targets for modification.     

The cellular computer DNA: Program or data

The classical metaphor of the genetic program written in the DNA nucleotidic sequences is reconsidered. Recent works on algorithmic complexity and logical properties of computer programs and data are used to question the explanatory value of that metaphor. Structural properties of strings are looked for which would be necessary to apply to DNA sequences if the metaphor is to be taken literally. The notion of sophistication is used to quantify meaningful complexity and to distinguish it from classical computational complexity. In this context, the distinction between program and data becomes relevant and an alternative metaphor of DNA as data to a parallel computing network embedded in the global geometrical and biochemical structure of the cell is discussed. An intermediate picture of an evolving network emerges as the most likely where the output of the cellular computing network can produce, at a different time scale, changes in the structure of the network itself by means of changes in the DNA activity patterns.     

Innovation at the intersection of synthetic and systems biology

The promises of modern biotechnology hinge upon the hope that we can understand microscopic cellular complexity and in doing so create novel function. In this regard, the fields of systems and synthetic biology are important for accelerating both our understanding of biological systems and our ability to quantitatively engineer cells. At the nexus of these two fields is a unique synergy that can help attain these goals. Thus, the next greatest advances in biology and biotechnology are arising at the intersection of the top-down systems approach and the bottom-up synthetic approach. Collectively, these developments enable the precise control of cellular state for systems studies and the discovery of novel parts, control strategies, and interactions for the design of robust synthetic function. This review seeks to highlight this activity as well as provide a perspective for future directions. Combining these efforts can provide novel insights into cellular function and lead to robust, novel synthetic design.