Modeling cellular processes in 3D

Recent advances in photonic imaging and fluorescent protein technology offer unprecedented views of molecular space-time dynamics in living cells. At the same time, advances in computing hardware and software enable modeling of ever more complex systems, from global climate to cell division. As modeling and experiment become more closely integrated we must address the issue of modeling cellular processes in 3D. Here, we highlight recent advances related to 3D modeling in cell biology. While some processes require full 3D analysis, we suggest that others are more naturally described in 2D or 1D. Keeping the dimensionality as low as possible reduces computational time and makes models more intuitively comprehensible; however, the ability to test full 3D models will build greater confidence in models generally and remains an important emerging area of cell biological modeling.     

Temporal organization of the cellular reproduction processes in Ehrlich ascites tumor

Experiments were made on randombred male mice weighing 18-20 g maintained on the light regimen L:D-12:12. The animals were given a single injection i. p. of a hypotetraploid subline of Ehrlich's ascites tumor. Fluctuations in the number of mitotic cells and no changes in the number of DNA-synthesizing cells were established. This indicates that synchronization of tumor cells under these conditions occurs mainly in the G2 phase. The results of the present experiments confirm those obtained during previous investigations, showing the lack of the dependence of the cell proliferation pattern on the cell ploidy. The disturbance of the chronobiological organization of tumor cell proliferation that is manifested by upset synchronization of cell division and DNA synthesis is common to all Ehrlich's ascites tumor sublines under study.     

An allometric interpretation of the spatio-temporal organization of molecular and cellular processes

Summary Different levels of organization distinguished by characteristics spatial dimensions, E_c, and relaxation times, T_r, of biological processes ranging from electron transport in energy transduction to growth of microbial and plant cells, are shown to be related through a relation that may be interpreted as allometric and characterized by two different slopes. Processes, at levels of organization occurring in spatial dimensions of micrometers and relaxing in the order of minutes, delimit a transition point between the two curves, that we interpret as a limit for the emergence of macroscopic coherence. The characteristic spatial dimension, E_c, and the relaxation time, T_r, contain dynamical information about the processes occurring at a given level of organization. When a steady state of a biological process at a certain level of organization becomes unstable, the system undergoes a transition to another level of organization. To exemplify the appearance of macroscopic order at levels of organization further from the transition point we present in this report various experimental systems involving many levels of organization allometrically related that exhibit different kinds of self-organized behavior, i.e. bistability, oscillations, changes in (a)symmetry.     

Comparative analysis of topological organization in Metazoa

Topological patterns in Metazoa, using previously elaborated methodology with employment of the genus of the surface (p) as topological invariant are considered. The term "density of the genus of the surface" is introduced. In sponges and in a lesser degree among Cnidaria and, Ctenophoria an increase of genus p up to indefinite high values and the shaping of topologically complicated quasifractal systems (irrigation system in sponges and gastro-vascular system in Radiata) are evident. In most Bilateria a stable topological pattern with open digestive tube is formed and subsequent topological complications of other systems may occur. Complicated topological patterns increasing the genus of the surface are evolved on the base of quasifractal systems: gut pockets in turbellaria, tracheal system in arthropods, bronchial system in birds, gills in bivalve mollusks, etc. Peculiarities of ordered and disordered topological patterns as well as topological origin of the increase of the genus of the surface are considered.     

Building synthetic cellular organization

The elaborate spatial organization of cells enhances, restricts, and regulates protein–protein interactions. However, the biological significance of this organization has been difficult to study without ways of directly perturbing it. We highlight synthetic biology tools for engineering novel cellular organization, describing how they have been, and can be, used to advance cell biology.     

Beyond the sequence: cellular organization of genome function

Genomes are more than linear sequences. In vivo they exist as elaborate physical structures, and their functional properties are strongly determined by their cellular organization. I discuss here the functional relevance of spatial and temporal genome organization at three hierarchical levels: the organization of nuclear processes, the higher-order organization of the chromatin fiber, and the spatial arrangement of genomes within the cell nucleus. Recent insights into the cell biology of genomes have overturned long-held dogmas and have led to new models for many essential cellular processes, including gene expression and genome stability.     

Aminergic cellular organization in the gills of Aplysia species

The constituent elements of the gills of Aplysia kurodai and A. juliana were examined for the presence of biogenic amines using histochemical, immunocytochemical, and HPLC techniques. Aminergic elements were revealed by glyoxylic acid-induced fluorescence in the branchial nerve, branchial ganglion, branchial vessels, and pinnules in both species. Three types of fluorescent cells were found in the neural plexus of the gill in each species. Two of them might be sensory neurons. Although HPLC analysis showed the presence of serotonin and dopamine in all gill structures including fluorescent neural elements, there were regional differences in concentrations of the monoamines. It was noted in the pinnules that there was a much higher concentration of dopamine than serotonin. Serotonin immunocytochemistry revealed neural processes which were immunoreactive to antiserotonin antibody, but serotonin immunoreactivity could not be found in a population of branchioganglionic neuron (BGN) somata. Serotonergic elements in the ganglion may be processes of the central ganglion, while dopaminergic elements may be processes of neurons in the neural plexus, located beyond the branchial ganglion. BGNs were activated by bath-applied dopamine and serotonin. These results suggest that dopaminergic sensory inputs from the neural plexus and serotonergic descending inputs from the abdominal ganglion may be among the inputs received by BGNs. It was found that serotonin depressed excitatory junctional potentials in muscle cells of the efferent branchial vessel, which were induced by an identified neuron of the abdominal ganglion. The aminergic cellular organization of the gill may involve serotonergic presynaptic-inhibitory fibers arising from the abdominal ganglion.     

Structural-functional organization of cellular signal transduction systems

The review summarizes recent data and current opinions of the structural and functional organization of the known signalling systems and their functional elements. A possible role of adenylate cyclase, phosphoinositide, guanylate cyclase, tyrosine kinase systems and also of arachidonic acid, its oxygenated derivatives and of other fatty acids in intracellular signalling processes is discussed.     

Ubiquitin crosstalk connecting cellular processes

Cullin 4 (Cul4), a member of the evolutionally conserved cullin protein family, serves as a scaffold to assemble multisubunit ubiquitin E3 ligase complexes. Cul4 interacts with the Ring finger-containing protein ROC1 through its C-terminal cullin domain and with substrate recruiting subunit(s) through its N-terminus. Previous studies have demonstrated that Cul4 E3 ligase ubiquitylates key regulators in cell cycle control and mediates their degradation through the proteasomal pathway, thus contributing to genome stability. Recent studies from several groups have revealed that Cul4 E3 ligase can target histones for ubiquitylation, and importantly, ubiquitylation of histones may facilitate the cellular response to DNA damage. Therefore, histone ubiquitylation by Cul4 E3 ligase constitutes a novel mechanism through which Cul4 regulates chromatin function and maintains genomic integrity. We outline these studies and suggest that histone ubiquitylation might play important roles in Cul4-regualted chromatin function including the cellular response to DNA damage and heterochromatin gene silencing.     

Localised interventions in cellular processes

The once linear view of cell regulatory processes is now changing as we begin to overlay spatial and temporal characteristics onto signalling pathways and dynamic membranous events. To better understand the properties of these spatially restricted processes we must refine our targeting of these events with acute localised manipulations. We review here the diverse application of a dimerisation system, which exploits immunosuppressor/immunophilin biology to provide a route to drug-inducible subdomain interventions. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases (2012).     

Patterns in the cellular organization of ovule growth in the pine, Pinus silvestris L. I. Growth processes in endosperm

The dynamics of growth processes was studied in the endosperm of Pinus silvestris during the year of fertilization. The growth of endosperm is described by an diauxic curve where the period of delay corresponds, by time, to fertilization. The growth of tissue proceeds, mainly, at the expense of cell proliferation. The mitotic activity is preserved in the endosperm till the beginning of formation of reserve substances in the cells; cell division and elongation occur simultaneously. The unfavourable environmental conditions influence the mitotic activity of cells only. The size of fully grown cells is relatively constant and somewhat decreases later, during maturation. One can distinguish rather early those regions in the endosperm where the cell size is 2-3 times less than in the rest tissue; the size of cells and nuclei in these regions suffers only insignificant changes during the growth. The large nuclei are observed in the beginning of the cell endosperm formation and, then, their size decreases 1.5-2 times; the second increase in nuclear size in the endosperm is observed during the period prior to the formation of reserve substances.     

Cbl--a polyfunctional regulator of cellular processes

C-Cb1 protein is a protooncogene product that was initially identified as part of a murine retrovirus transforming protein. C-Cb1 is ubiquitously expressed in cells of different origin. A number of isoforms subsequently identified in vertebrates and invertebrates allows to consider the existence of a family of Cb1 proteins. These proteins contain a set of sequences providing interactions with a wide range of receptor and nonreceptor tyrosine kinases and signaling proteins with SH2- and SH3-domains (for example, EGF and PDGF receptors, Src-kinases, PI-3-kinase p85, Crk, GRB2, Vav, etc.). Cb1 proteins possess also multiple tyrosine, residues, which undergo phosphorylation upon stimulation of several surface receptors. These properties permit Cb1 to take part in many protein-protein interactions as an adaptor, which forms multimolecular signaling complexes, and coordinates the activity of its components. C-Cb1 and its mutant transforming forms can act as both positive and negative regulators of many signaling pathways. Negative action of C-Cb1 on signals stimulated by receptor tyrosine kinases is thought to result from accelerated receptor degradation caused by Cb1. This ability is attributed mostly to ubiquitin-ligase activity of Cb1 proteins, since the latest research evidence suggests that ubiquitination may be a signal of not only proteasomal, but also lysosomal degradation. Thus, Cb1 manifests itself as a many-sided protein working both as an adaptor and a regulator of endocytic trafficking. In spite of numerous studies in this area, the regulation of Cb1 functions, interrelations between these functions, physiological significance of Cb1-mediated interactions, and the place of Cb1 proteins in signaling coordinating still remain obscure. In the present review, an attempt is made to summarize the recent data, with special reference to Cb1 functioning as a regulator of tyrosine kinase receptor endocytosis.