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PubMed2001

Signal transduction pathways and the modification of chromatin structure.

Mechanical and chemical signaling pathways are involved in transmitting information from the exterior of a cell to its chromatin. The mechanical signaling pathway consists of a tissue matrix system that links together the three-dimensional skeletal networks, the extracellular matrix, cytoskeleton, and karyoskeleton. The tissue matrix system governs cell and nuclear shape and forms a structural and functional connection between the cell periphery and chromatin. Further, this mechanical signaling pathway has a role in controlling cell cycle progression and gene expression. Chemical signaling pathways such as the Ras/mitogen-activated protein kinase (MAPK) pathway can stimulate the activity of kinases that modify transcription factors, nonhistone chromosomal proteins, and histones. Activation of the Ras/MAPK pathway results in the alteration of chromatin structure and gene expression. The tissue matrix and chemical signaling pathways are not independent and one signaling pathway can affect the other. In this chapter, we will review chromatin organization, histone variants and modifications, and the impact that signaling pathways have on chromatin structure and function.

Acetyltransferases↗

PubMed2002

Visualizing selective neural pathways with WGA transgene: combination of neuroanatomy with gene technology.

Functional logic employed by the nervous system for information processing resides mainly in the wiring patterns among specific types of neurons. Therefore, detailed knowledge on neuronal networks is essential for understanding a wide range of brain functions. A powerful and long-awaited method for analyzing the neuronal connectivity patterns would be to deliver tracers selectively to specific types of neurons and at the same time to label transsynaptically their axonal target neurons. For this purpose, we took advantage of a unique property of plant lectin, wheat germ agglutinin (WGA), which has been used as a transsynaptic tracer in classical neuroanatomical studies. We developed a novel genetic strategy that employs WGA cDNA as a transgene, for the visualization of selective and functional neural pathways in the nervous system. In this article, I will introduce several examples of neural pathways visualized with the WGA transgene and discuss about its further refinement and applications.

Animals↗

PubMed2004

Initiation of a teleradiotherapeutic network for patients in German lymphoma studies.

PURPOSE: Deviations of radiation treatment portals and dose from prospective treatment plans are unfavorable prognostic factors for lymphoma patients. Therefore, an extensive radiotherapy quality assurance program is used in the ongoing German lymphoma studies. The introduction of teleradiotherapy offered the opportunity to optimize and simplify the workflow of these quality assurance programs. The purpose of this report was to evaluate the feasibility of teleradiotherapy and to describe our experiences with these innovative tools. METHODS AND MATERIALS: During this pilot phase, five radiotherapy centers were equipped with the hardware and software that guarantees a rapid and high-quality transfer of imaging data, as well as real-time teleconferences. The workstation consists of standard PCs with Windows NT as the operating system and the commercial telemedicine software Hipax. RESULTS: As a first step, imaging communication between the radiotherapy reference centers in Cologne and Homburg/Saar was established. Subsequently, three additional radiotherapy departments (Universities of Berlin, Münster, and Munich) with large numbers of lymphoma patients were connected. Other study centers delivered digital imaging on mobile data carriers or via an Integrated Services Digital Network point-to-point connection. Communication units were completed for interactive teleconferences. A facility for central online documentation was installed. Telemedical functions were integrated into the ongoing radiotherapy quality assurance program. Since the introduction of a teleradiotherapeutic workstation in the radiotherapy reference center in Cologne in January 2001, the images of 10% (n = 228 patients) of all reviewed cases of the ongoing Hodgkin's disease 10-12 trials were delivered digitally. The amount of digitally available imaging is continuously increasing. CONCLUSION: The introduction of teleradiotherapy improved the dialog between the radiotherapy reference centers and study centers and thus contributed toward high radiotherapy quality for lymphoma patients in Germany.

Feasibility Studies↗

PubMed2006

GLP-2 receptor localizes to enteric neurons and endocrine cells expressing vasoactive peptides and mediates increased blood flow.

BACKGROUND & AIMS: Glucagon-like peptide-2 (GLP-2) is a nutrient-responsive hormone that exerts diverse actions in the gastrointestinal tract, including enhancing epithelial cell survival and proliferation, mucosal blood flow, and nutrient uptake and suppressing gastric motility and secretion. These actions are mediated by the G-protein-coupled receptor, GLP-2R. Cellular localization of the GLP-2R and the nature of its signaling network in the gut, however, are poorly defined. Thus, our aim was to establish cellular localization of GLP-2R and functional connection to vascular action of GLP-2 in the gut. METHODS: Intestinal cellular GLP-2R localization was determined with real-time, quantitative reverse-transcription polymerase chain reaction (qRT-PCR) of laser capture microdissected subtissue and fluorescence in situ hybridization and also with double and/or triple immunostaining of human and pig tissue using a validated GLP-2R polyclonal antibody. Superior mesenteric arterial blood flow and intestinal eNOS expression and phosphorylation were measured in TPN-fed pigs acutely (4 h) infused with GLP-2. RESULTS: We show that the porcine GLP-2R mRNA was expressed in the villus epithelium and myenteric plexus. GLP-2R protein was co-localized by confocal immunohistochemistry with serotonin in enteroendocrine cells and also with endothelial nitric oxide synthase (eNOS)-expressing and vasoactive intestinal polypeptide-positive enteric neurons. In neonatal pigs, GLP-2 infusion dose-dependently stimulated intestinal blood flow and coordinately upregulated the expression of intestinal eNOS mRNA, protein, and phosphorylation (eNOS-Ser1117). CONCLUSIONS: We conclude that the GLP-2-induced stimulation of blood flow is mediated by vasoactive neurotransmitters that are colocalized with GLP-2R in 2 functionally distinct cell types within the gastrointestinal tract.

Animals↗

PubMed2002

Retrograde trans-synaptic transfer of green fluorescent protein allows the genetic mapping of neuronal circuits in transgenic mice.

The function of the nervous system is a consequence of the intricate synaptic connectivity of its neurons. Our understanding of these highly complex networks has profited enormously from methods used over the past two decades that are based on the mechanical injection of tracer molecules into brain regions. We have developed a genetic system for the mapping of synaptic connections during development of the mammalian central nervous system and in the mature brain. It is based on the transsynaptic transfer of green fluorescent protein (GFP) in the brains of mice using a fusion protein with a nontoxic fragment of tetanus toxin (TTC) expressed in defined neurons. These transgenic mice allowed us to visualize neurons, at single-cell resolution, that are in synaptic contact by the detection of GFP in interconnected circuits. Targeted genetic expression with a specific promoter permitted us to transfer GFP to defined subsets of neurons and brain regions. GFP-TTC is coexpressed with a lacZ reporter gene to discriminate neurons that produce the tracer from cells that have acquired it transneuronally. The marker shows selective transfer in the retrograde direction. We have used electron microscopic detection of GFP to define the ultrastructural features of the system. Our work opens up a range of possibilities for brain slice and in vivo studies taking advantage of the fluorescence of GFP. We point the way toward the use of powerful multiphoton technology and set the stage for the transsynaptic transfer of other proteins in the brains of mice.

Animals↗

PubMed2006

The evolutionary rate of a protein is influenced by features of the interacting partners.

Rates of protein evolution are thought to be influenced by features of protein-protein interaction (PPI). However, the most important features of interaction for determining the evolutionary rate are poorly understood. Here, we consider four categories for PPIs in Saccharomyces cerevisiae. Properties we consider are the extent to which proteins interact with proteins of the same function or different function (DF) and the extent to which these interactions involve connections in the dense part or sparse part (SP) of a PPI network. Our findings are that proteins with DF-SP interactions evolve at the slowest rate of all the proteins examined.

Cluster Analysis↗

PubMedDate not supplied

Plasticity of GABAergic synapses in the neonatal rat hippocampus.

While the development and plasticity of excitatory synaptic connections have been studied into detail, little is known about the development of inhibitory synapses. As proposed for excitatory synapses, recent studies have indicated that activity-dependent forms of synaptic plasticity, such as long-term potentiation and long-term depression, may play a role in the establishment of functional inhibitory synaptic connections. Here, I review these different forms of plasticity and focus on their possible role in the developing neuronal network.

Animals↗

PubMed2006

Deciphering the underlying mechanism of specification and differentiation: the sea urchin gene regulatory network.

The regulatory genome functions as a vast information processor through development. It processes the initial conditions that are set by asymmetric distributions of cellular components in the egg and translates them into the onset of spatially localized specification states. It regulates the timely differential activation of signaling molecules and transcription factors that divide the emerging domains into subdomains. It also governs the activation of groups of differentiation genes, the genes that encode, at the protein level, the functional and the structural properties of a cell type. The sea urchin endomesoderm gene regulatory network provides a window into the different levels of the regulatory apparatus. It demonstrates how the static physical genomic components define functional connections between the various regulatory genes that act together to conduct the dynamical developmental program.

Animals↗

PubMed1985

Representation of cooperative firing activity among simultaneously recorded neurons.

Simultaneous and separable extracellular recording of substantial populations of neurons under chronic and behavioral conditions is becoming experimentally feasible. We have recently described a conceptual transformation of such multiple spike train data that allows the experimenter to analyze the entire network of observed neurons as an entity rather than as a summation of neuron pairs. The basic transformation represents each of N neurons as a particle in an N-space. Each particle is given a "charge" that is related to the spike train of the corresponding neuron. The resulting forces on the N particles cause aggregation of those particles that represent neurons with time-related firing. The present paper extends the visualization and possibilities of this way of analyzing properties of neuronal assemblies. Data are taken from computer-simulated neuronal networks in order to provide known properties. We demonstrate projection of particle positions from the N space to a plane. Under the right conditions the spatial arrangement of the particles forms a Venn diagram of functional relationships in the entire neural network. We introduce revised force rules in the transformation that allow detection and study of inhibitory connections among the observed neurons. Sensitivity is lower than for excitatory connections. We introduce revised "charge" rules that improve "signal-to-noise" properties and in addition allow inference of directed connectivity. The original transformation only allows identification of neurons with time-related firing. The two-charge transformation allows explicit identification of presynaptic and postsynaptic neurons. Finally we examine sensitivity of the transformation to individual and near-coincident firing rates. Some criteria are presented for choice of charge normalization rules in the transformation.

Action Potentials↗

PubMed1998

Models of neuronal transient synchrony during propagation of activity through neocortical circuitry.

Stereotypic paroxysmal discharges that propagate in neocortical tissues after electrical stimulations are used as a probe for studying cortical circuitry. I use modeling to investigate the effects of sparse connectivity, heterogeneity of intrinsic neuronal properties, and synaptic noise on synchronization of evoked propagating neuronal discharges in a network of excitatory, regular spiking neurons with spatially decaying connectivity. The global coherence of the traveling discharge is characterized by the correlation function between spike trains of neurons, averaged over all the pairs of neurons in the system at the same distance. Local coherence of two neurons is characterized by their correlation function averaged over many trials or, for persistent activity, over a long time interval. Spike synchronization between neurons emerges as a result of the transient activity; if activity is persistent, there is no synchrony, and cross-correlation functions are flat. During discharge propagation, system-average cross-correlation between neurons does not depend on their mutual distance except for a time shift. Spike synchronization occurs only when the average number of synapses M a cell receives is large enough. As M increases, there is a cross-over from an asynchronized to a synchronized discharge. Synaptic depression appears to help synchrony; it reduces the M value at the cross-over. The strengths of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) and N-methyl-D-aspartate (NMDA) conductances affect synchrony only weakly. Spike synchronization is robust even with large levels of heterogeneity. Synaptic noise reduces synchrony, but strong synchrony is observed at a noise level that cannot evoke spontaneous discharges. System-average spike synchronization is determined by the levels of sparseness, heterogeneity, and noise, whereas trial-average spike synchronization is determined only by the noise level. Therefore, I predict that experiments will reveal local, two-cell spike synchrony, but not global synchrony.

Animals↗

PubMed2006

Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria.

BACKGROUND: Chloroplasts descended from cyanobacteria and have a drastically reduced genome following an endosymbiotic event. Many genes of the ancestral cyanobacterial genome have been transferred to the plant nuclear genome by horizontal gene transfer. However, a selective set of metabolism pathways is maintained in chloroplasts using both chloroplast genome encoded and nuclear genome encoded enzymes. As an organelle specialized for carrying out photosynthesis, does the chloroplast metabolic network have properties adapted for higher efficiency of photosynthesis? We compared metabolic network properties of chloroplasts and prokaryotic photosynthetic organisms, mostly cyanobacteria, based on metabolic maps derived from genome data to identify features of chloroplast network properties that are different from cyanobacteria and to analyze possible functional significance of those features. RESULTS: The properties of the entire metabolic network and the sub-network that consists of reactions directly connected to the Calvin Cycle have been analyzed using hypergraph representation. Results showed that the whole metabolic networks in chloroplast and cyanobacteria both possess small-world network properties. Although the number of compounds and reactions in chloroplasts is less than that in cyanobacteria, the chloroplast's metabolic network has longer average path length, a larger diameter, and is Calvin Cycle -centered, indicating an overall less-dense network structure with specific and local high density areas in chloroplasts. Moreover, chloroplast metabolic network exhibits a better modular organization than cyanobacterial ones. Enzymes involved in the same metabolic processes tend to cluster into the same module in chloroplasts. CONCLUSION: In summary, the differences in metabolic network properties may reflect the evolutionary changes during endosymbiosis that led to the improvement of the photosynthesis efficiency in higher plants. Our findings are consistent with the notion that since the light energy absorption, transfer and conversion is highly efficient even in photosynthetic bacteria, the further improvements in photosynthetic efficiency in higher plants may rely on changes in metabolic network properties.

Arabidopsis↗

PubMed1996

Unilateral spatial neglect recovery after sequential strokes.

We describe a patient who had sequential strokes in both hemispheres with a severe unilateral spatial neglect after a first right-sided parietal infarct and abrupt disappearance of the neglect after a second left-sided frontal infarct. The first lesion involve the caudalmost right angular gyrus (area 39), whereas the second lesion involved the left frontal eye field (area 8) and surrounding cortex. Those two cortical areas are assumed to have a pivotal role in modulating both shifts of attention within extrapersonal space and saccadic eye movements through their connections with subcortical structures, in particular, superior colliculi and thalamic nuclei. Our case supports the existence of a distributed anatomic-functional network in subserving directed spatial attention.

Aged↗

PubMed1986

Development of cultured cardiac cells and difference of their structures in vivo.

Some interesting features in the morphological study of rat cardiac cells were obtained by use of the light and phase-contrast microscopy. The histological approach and comparison of the ultrastructures of the cultured cardiac cells with uncultured cells were included in the studies as a control. Four main points are discussed: the process of single beating cells that eventually constitutes the cell cluster and network, the function and histological content of the network, the mechanisms of synchronized beating cells, the substance of the cell surface coat and intercellular connection.

Animals↗

PubMed2004

Networks of local minima in optical system optimization.

We discuss a surprising new feature of the merit function landscape in optical system design. When certain conditions are satisfied, the local minima form a network in which all nodes are connected. Each link between two neighboring minima contains a saddle point with a Morse index of 1. For a simple global optimization search (the symmetric Cooke triplet), the network of the corresponding set of local minima is presented.

Journal Article↗

PubMed2000

PepTool and GeneTool: platform-independent tools for biological sequence analysis.

Although we are unable to discuss all of the functionality available in PepTool and GeneTool, it should be evident from this brief review that both packages offer a great deal in terms of functionality and ease-of-use. Furthermore, a number of useful innovations including platform-independent GUI design, networked parallelism, direct internet connectivity, database compression, and a variety of enhanced or improved algorithms should make these two programs particularly useful in the rapidly changing world of biological sequence analysis. More complete descriptions of the programs, algorithms and operation of PepTool and GeneTool are available on the BioTools web site (www.biotools.com), in the associated program user manuals and in the on-line Help pages.

Amino Acid Sequence↗

PubMed1993

[Biochemical profile of proteoglycans and glucosaminoglycans of the mammalian tectorial membrane].

The tectorial membrane is an acellular connective tissue which plays an essential role in cochlear function. While a comparatively large amount of information is available on the collagen network of the tectorial membrane, studies on the biochemical nature of this highly hydrated matrix, which is composed of proteoglycans (PGs) and glycosaminoglycans (GAGs), have been quite limited. Previous reports on the biochemical analysis of the tectorial membrane have failed to detect uronic acid, which is present in large amounts in all mammalian GAGs except keratan sulfate. Applying a colorimetric assay based on the binding of GAGs to cationic dye Safranin-0 in combination with enzymatic techniques, we were able to measure GAGs in the murine tectorial membrane. Approximately 0.3% uronic acid-containing GAGs (mainly in the form of chondroitin/dermatan sulfate) and 0.17% keratan sulfate were detected in the tectorial membrane (both on a wet weight basis). In addition, various types of electrophoresis revealed one large PG with a molecular mass similar to that of the large type cartilage PGs and three small PGs, containing chondroitin sulfate and keratan sulfate side chains, respectively. Judging by coelution of standards, one of the small PGs seemed to correspond to fibromodulin, which has at least one keratan sulfate side chain, and binds to type I and type II collagen to regulate collagen organization in tissues. Our results suggest: (1) Donnan equilibrium is established in the tectorial membrane because sulfated GAGs are highly negatively charged and consequently bring about an influx of large amounts of water and cations into the matrix.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed2006

"Missing links" in borderline personality disorder: loss of neural synchrony relates to lack of emotion regulation and impulse control.

OBJECTIVE: Symptoms of borderline personality disorder (BPD) may reflect distinct breakdowns in the integration of posterior and frontal brain networks. We used a high temporal resolution measure (40-Hz gamma phase synchrony) of brain activity to examine the connectivity of brain function in BPD. METHODS: Unmedicated patients with BPD (n = 15) and age-and sex-matched healthy control subjects (n = 15) undertook a task requiring discrimination of salient from background tones. In response to salient stimuli, the magnitude and latency of peak gamma phase synchrony for early (0-150 ms post stimulus) and late (250-500 ms post stimulus) phases were calculated for frontal and posterior regions and for left and right hemispheres. We recorded skin conductance responses (SCRs) and reaction time (RT) simultaneously to examine the contribution of arousal and performance. RESULTS: Compared with controls, patients with BPD had a significant delay in early posterior gamma synchrony and a reduction in right hemisphere late gamma synchrony in response to salient stimuli. Both SCR onset and RT were also delayed in BPD, but independently from differences in synchrony. The delay in posterior synchrony was associated with cognitive symptoms, and reduced right hemisphere synchrony was associated with impulsivity. CONCLUSIONS: These findings suggest that distinct impairments in the functional connectivity of neural systems for orienting to salient input underlie core dimensions of cognitive disturbance and poor impulse control in BPD.

Adult↗

PubMed1987

[Regulation and dysregulations of immunoglobulin E synthesis].

Compared to other isotypes of immunoglobulins, IgE antibodies are present in exceedingly low concentrations in normal serum, because their synthesis is maintained under the strict control of several intricate regulatory mechanisms. These normally unapparent mechanisms become accessible to investigations in a number of pathological dysregulations. One may distinguish three orders of controls. An elementary isotypic circuit, constructed on the interactions between IgE Fc portions and IgE-binding molecules, directly regulates IgE synthesis by IgE-secreting B cells. IgE-binding molecules are themselves controlled by several lymphokine cascades, depending on external and genetic factors. The functioning of the IgE isotypic circuit is coordinated with other circuits, corresponding to other immunoglobulin isotypes, by means of an isotypic network, connected to other homeostatic systems of the organism. The dissection of these regulatory mechanisms and an understanding of their interactions are potentially useful for new therapeutic approaches.

Humans↗