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A human keratin 14 "knockout": the absence of K14 leads to severe epidermolysis bullosa simplex and a function for an intermediate filament protein.

Since their discovery, the function of intermediate filaments (IFs) has remained obscure. In skin, epidermal cells have extensive cytoskeletal architectures of IFs, composed of type I and type II keratin heterodimers. Clues to possible functions of these proteins have come from recent studies showing that several autosomal-dominant, blistering skin disorders are caused by defects in genes that encode epidermal keratins. These diseases all exhibit cell degeneration and keratin network perturbations in cells that express the particular mutant keratin gene. However, it is not clear from these studies whether cytolysis arises from the presence of large insoluble keratin aggregates that compromise cellular physiology or from the absence of an extensive keratin filament network, which jeopardizes mechanical integrity. We report here the analysis of an extremely rare case of severe recessive epidermolysis bullosa simplex (EBS), where the patient lacks a discernible keratin filament network in basal epidermal cells. Genetic analyses revealed a homozygous point mutation that yielded a premature termination codon in the major basal type I keratin gene and caused complete ablation of K14. The consanguineous parents were normal, each harboring one copy of the null K14 mutation. Analysis of cultured keratinocytes enabled us to document that the loss of K14 is not compensated for by the up-regulation of any other type I keratin. When taken together with the in vivo studies showing the presence of cell fragility generated from the lack of an extensive basal keratin network, these findings provide the first clear demonstration of loss of function associated with the absence of an IF protein in vivo.

Amino Acid Sequence↗

The physiological functions of prion protein.

Prion proteins are mentioned predominantly as unprecedented infectious pathogens in the context of transmissible spongiform encephalopathies. Since prions are devoid of nucleic acids, disease transmission must be mediated by an entirely novel mechanism. The general accepted theory proposes the conversion of cellular prion protein (PrP(C)) into the pathological isoform solely through conformational changes. This process favors the development of insoluble protein aggregates in the central nervous system typical for prion diseases. However, progress to elucidate the physiological functions of PrP(C) is still slow besides recent indications of a multifaceted network, in which PrP(C) seems to play a fundamental role. Possible contributions of interrupted or disturbed physiological signaling events due to the pathological prion protein isoform are presented in terms of recent findings.

Animals↗

Regulation of gene expression in flux balance models of metabolism.

Genome-scale metabolic networks can now be reconstructed based on annotated genomic data augmented with biochemical and physiological information about the organism. Mathematical analysis can be performed to assess the capabilities of these reconstructed networks. The constraints-based framework, with flux balance analysis (FBA), has been used successfully to predict time course of growth and by-product secretion, effects of mutation and knock-outs, and gene expression profiles. However, FBA leads to incorrect predictions in situations where regulatory effects are a dominant influence on the behavior of the organism. Thus, there is a need to include regulatory events within FBA to broaden its scope and predictive capabilities. Here we represent transcriptional regulatory events as time-dependent constraints on the capabilities of a reconstructed metabolic network to further constrain the space of possible network functions. Using a simplified metabolic/regulatory network, growth is simulated under various conditions to illustrate systemic effects such as catabolite repression, the aerobic/anaerobic diauxic shift and amino acid biosynthesis pathway repression. The incorporation of transcriptional regulatory events in FBA enables us to interpret, analyse and predict the effects of transcriptional regulation on cellular metabolism at the systemic level.

Amino Acids↗

Cartilage stresses in the human hip joint.

The total surface stress measured in vitro on acetabular cartilage when step-loaded by an instrumented hemiprosthesis are partitioned into fluid and cartilage network stresses using a finite element model of the cartilage layer and measurements of the layer consolidation. The finite element model is based on in situ measurements of cartilage geometry and constitutive properties. Unique instrumentation was employed to collect the geometry and constitutive properties and pressure and consolidation data. When loaded, cartilage consolidates and exudes its interstitial fluid through and from its solid network into the inter-articular gap. The finite element solutions include the spatial distributions of fluid and network stresses, the normal flow velocities into the gap, and the contact network stresses at the cartilage surface, all versus time. Even after long-duration application of physiological-level force, fluid pressure supports 90 percent of the load with the cartilage network stresses remaining well below the drained modulus of cartilage. The results support the "weeping" mechanism of joint lubrication proposed by McCutchen.

Anthropometry↗

Tissue endostatin correlates inversely with capillary network in rat heart and skeletal muscles.

The role of angiostatic factors, including endostatin, in regulating physiological angiogenesis is poorly understood. We used normal adult rats under physiological resting conditions to examine the relationship between tissue endostatin, VEGF, and capillary density (CD) in the heart (high metabolic activity) versus the skeletal muscle (relatively low metabolic activity). The heart (left ventricle, LV) and skeletal muscle (anterior tibialis, AT) were dissected from 12-week-old male Sprague-Dawley rats. Transverse cryosections of LV and AT were stained with FITC-conjugated GS-I-lectin. CD was determined by analysis of randomly acquired digital images of the cryosections using Optimas software. Tissue protein levels of endostatin and VEGF were determined by ELISA assays. Tissue endostatin levels were lower in the LV and higher in the AT (135 +/- 39 vs. 663 +/- 114 pg/mg) and VEGF levels were higher in the LV and lower in the AT (41 +/- 3 vs. 27 +/- 4 pg/mg), respectively (n = 7, P < 0.01). CD in LV and AT were 3632 +/- 428 and 437 +/- 44/mm2, respectively (P < 0.01). We demonstrated that an 8.3-fold greater capillary density is related to a 4.9-fold lower level of tissue endostatin and a 1.5-fold higher level of tissue VEGF in the heart (LV) versus the skeletal muscle (AT) of normal rats under physiological resting conditions. Also, exercise training increased capillary density, decreased tissue endostatin and increased tissue VEGF in the skeletal muscle (AT). These findings suggest that tissue endostatin content correlates inversely with capillary network in the muscle tissues with different metabolic activity, and that tissue endostatin may play a very important role in the metabolic control of angiogenesis under physiological conditions.

Animals↗

Propagation of synchronous spiking activity in feedforward neural networks.

'Synfire' activity has been proposed as a model for the experimentally observed accurate spike patterns in cortical activity. We investigated the structural and dynamical aspects of this theory. To quantify the degree of synchrony in neural activity, we introduced the concept of 'pulse packets'. This enabled us to derive a novel neural transmission function which was used to assess the role of the single neuron dynamics and to characterize the stability conditions for propagating synfire activity. Thus, we could demonstrate that the cortical network is able to sustain synchronous spiking activity using local feedforward (synfire) connections. This new approach opens the way for a quantitative description of neural network dynamics, and enables us to test the synfire hypothesis on physiological data.

Action Potentials↗

Differential sensitivity of exchange vessel hydraulic conductivity to atrial natriuretic peptide.

Acute plasma volume reduction by atrial natriuretic peptide (ANP) may be mediated, at least in part, by increased exchange vessel water conductivity (Lp). The present study tests the hypothesis that physiological levels of ANP acutely and reversibly elevate single capillary Lp. Paired, in situ measurements of Lp were obtained using the modified Landis technique in individually perfused mesenteric capillaries of the frog, Rana pipiens. Control Lp measurements ranged from 0.1 to 40 x 10(-7) cm.s-1.cmH2O-1 (with a median value of 2.5 x 10(-7] in 81 microvessels perfused with frog Ringer solution containing dialyzed bovine serum albumin. Vessels were recannulated and perfused with one or more concentrations of human ANP (hANP) spanning the physiopathological range: 0.01, 0.1, 1, 10, and 100 nM. When possible, a final recannulation and Lp determination was performed in the absence of hANP. A median 2.2-fold rapid Lp increase was observed compared with control at each peptide concentration. Lp changes persisted for the duration of exposure to hANP, returning to control levels on withdrawal of the peptide. True and venular capillaries exhibited similar Lp responses: median 2.2- and 2.4-fold elevations, respectively. Sixty percent of true and venular capillaries exhibited twofold or greater hANP-induced increases in Lp, whereas only 25% of arteriolar capillaries exhibited such a response. Thus a differential sensitivity to the peptide exists across the exchange vessel network. The observations of this study demonstrate that physiological levels of ANP are capable of modulating exchange vessel Lp, one means by which the peptide may acutely alter plasma volume.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

Unraveling the cerebellar cortex: cytology and cellular physiology of large-sized interneurons in the granular layer.

Neuronal network behaviors emerge from complex interactions between excitatory relay cells, principal cells and inhibitory interneurons. Therefore, characterizing homogeneous cell types and their properties is an essential step towards understanding information processing in the brain. The cerebellar cortex is generally described as a repetitive circuit composed of only five cell types. However, recent studies have revealed an unexpected diversity in the morphological, neurochemical and electrophysiological properties of the large-sized granular layer interneurons. These data are reviewed here with an emphasis on the synaptic interactions of the different cell types within the cerebellar cortex. The existence of a complex network of excitatory and inhibitory interneurons controlling the spatial and temporal pattern of granule cell firing is documented, providing insights into the cellular and synaptic processes underlying oscillations and synchronization in the cerebellar cortex.

Animals↗

Principal cell-specific antigen and hormonal regulatory network in RC.SVtsA58 cell line.

We used a dual immunomorphological and physiological approach to demonstrate that the RC.SVtsA58 rabbit cortical cell line exhibits features of highly differentiated cortical collecting tubule (CCT) principal cells (PC). First, we raised monoclonal antibodies against RC.SVtsA58 cells and screened their reactivity with the rabbit kidney: three were specific for the basolateral domain of CCT PC and bound to 100% of RC.SVtsA58 cells. Second, we showed that bradykinin, atrial natriuretic peptide, and prostaglandin E2 increased intracellular Ca2+, guanosine 3',5'-cyclic monophosphate, and adenosine 3',5'-cyclic monophosphate (cAMP), respectively. In addition, 10 nM bradykinin inhibited desmopressin-elicited cAMP production by > or = 40%; this effect was suppressed by 10 microM of indomethacin and was reproduced with 1 nM of prostaglandin E2, indicating the conservation of arginine vasopressin-related regulatory loops described in microdissected CCT and freshly isolated cells. However, RC.SVtsA58 cells also express intercalated cell markers even after repeated cloning, which suggests that tsA58, a temperature-sensitive strain of simian virus-40, has transformed a multipotent type of PC in keeping with the cell interconversion hypothesis.

Animals↗

A physiological mechanism for Hebb's postulate of learning.

Hebb's postulate of learning envisages that activation or inactivation of extant synaptic contacts in plastic neural networks depends on the synchronous impulse activity of pre- and postsynaptic nerve cells. The physiological mechanism proposed here for this process posits that at synapses acting according to Hebb's postulate, the receptors for the neurotransmitter are eliminated from the postsynaptic membrane by the transient reversals of the sign of membrane polarization that occur during action potential impulses in the postsynaptic cell. But, since the release of neurotransmitter drives the membrane potential of the synaptic zone towards a level about half-way between the negative-inside resting potential and the positive-inside action potential, it would follow that the membrane patches surrounding the receptors of a synapse whose activity has contributed to setting off the postsynaptic impulse would be spared the full extent of the noxious polarity reversal. This mechanism can account for a neurophysiologically documented example of the operation of Hebb's postulate, namely the plasticity of the connections between fourth- and fifth-order neurons in the visual cortex of cats.

Action Potentials↗

Reconstructing metabolic flux vectors from extreme pathways: defining the alpha-spectrum.

The move towards genome-scale analysis of cellular functions has necessitated the development of analytical (in silico) methods to understand such large and complex biochemical reaction networks. One such method is extreme pathway analysis that uses stoichiometry and thermodynamic irreversibly to define mathematically unique, systemic metabolic pathways. These extreme pathways form the edges of a high-dimensional convex cone in the flux space that contains all the attainable steady state solutions, or flux distributions, for the metabolic network. By definition, any steady state flux distribution can be described as a nonnegative linear combination of the extreme pathways. To date, much effort has been focused on calculating, defining, and understanding these extreme pathways. However, little work has been performed to determine how these extreme pathways contribute to a given steady state flux distribution. This study represents an initial effort aimed at defining how physiological steady state solutions can be reconstructed from a network's extreme pathways. In general, there is not a unique set of nonnegative weightings on the extreme pathways that produce a given steady state flux distribution but rather a range of possible values. This range can be determined using linear optimization to maximize and minimize the weightings of a particular extreme pathway in the reconstruction, resulting in what we have termed the alpha-spectrum. The alpha-spectrum defines which extreme pathways can and cannot be included in the reconstruction of a given steady state flux distribution and to what extent they individually contribute to the reconstruction. It is shown that accounting for transcriptional regulatory constraints can considerably shrink the alpha-spectrum. The alpha-spectrum is computed and interpreted for two cases; first, optimal states of a skeleton representation of core metabolism that include transcriptional regulation, and second for human red blood cell metabolism under various physiological, non-optimal conditions.

Computer Simulation↗

Taste receptors in the gastrointestinal tract. V. Acid sensing in the gastrointestinal tract.

Luminal acidity is a physiological challenge in the foregut, and acidosis can occur throughout the gastrointestinal tract as a result of inflammation or ischemia. These conditions are surveyed by an elaborate network of acid-governed mechanisms to maintain homeostasis. Deviations from physiological values of extracellular pH are monitored by multiple acid sensors expressed by epithelial cells and sensory neurons. Acid-sensing ion channels are activated by moderate acidification, whereas transient receptor potential ion channels of the vanilloid subtype are gated by severe acidosis. Some ionotropic purinoceptor ion channels and two-pore domain background K(+) channels are also sensitive to alterations of extracellular pH.

Acid Sensing Ion Channels↗

Relation of cognitive reserve and task performance to expression of regional covariance networks in an event-related fMRI study of nonverbal memory.

Cognitive reserve (CR) has been established as a mechanism that can explain individual differences in the clinical manifestation of neural changes associated with aging or neurodegenerative diseases. CR may represent individual differences in how tasks are processed (i.e., differences in the component processes), or in the underlying neural circuitry (of the component processes). CR may be a function of innate differences or differential life experiences. To investigate to what extent CR can account for individual differences in brain activation and task performance, we used fMRI to image healthy young individuals while performing a nonverbal memory task. We used IQ estimates as a proxy for CR. During both study and test phase of the task, we identified regional covariance patterns whose change in subject expression across two task conditions correlated with performance and CR. Common brain regions in both activation patterns were suggestive of a brain network previously found to underlie overt and covert shifts of spatial attention. After partialing out the influence of task performance variables, this network still showed an association with the CR, i.e., there were reserve-related physiological differences that presumably would persist were there no subject differences in task performance. This suggests that this network may represent a neural correlate of CR.

Adult↗

Cytokines: is there biological meaning?

In the immune system, amidst the bewildering array of cytokine functions, it is sometimes difficult to discern the relative physiological importance of functions that have been determined in tissue culture. Cytokine functions are indeed complex, but the analysis of relatively simple regulatory networks suggests that activities determined in vitro are highly relevant to genuine physiological functions.

Animals↗

Serotonin, cerebral blood flow, and cerebral metabolic rate in geriatric major depression and normal aging.

While there is substantial evidence for abnormalities in serotonin (5-HT) neurotransmission in major depressive disorder (MDD), almost all of the findings derive from studies of young adults. Moreover, relatively little research has assessed brain 5-HT transmission in vivo. Neuroendocrine studies do not permit evaluation of a range of brain regions, but only the limited circuitry associated with hormone release. Data from autopsy studies are limited by the difficulties of assessment of the acute clinical picture before death, and by post-mortem artifacts. In vivo neuroimaging techniques overcome many of the methodological limitations of both these approaches. There is a large body of imaging data indicating regional cerebral blood flow (rCBF) and cerebral metabolic rate (rCMR) decrements both with aging and in patients with MDD. While the physiological bases for these phenomena are largely unknown, changes in brain 5-HT function may be involved. Neuroanatomical studies have revealed an intricate network of 5-HT-containing neurons within the cerebral microvasculature, with physiological evidence for serotonergic control of both rCBF and rCMR. Acute pharmacological challenges are available to probe brain 5-HT function. Such paradigms, using neuroendocrine responses as endpoints, have been of some utility in predicting outcome with antidepressant treatment. The role of 5-HT dysregulation in geriatric MDD takes on more importance given concerns regarding putative reduced efficacy of serotonin-specific reuptake inhibitors (SSRIs) in this population. If this is due to diminished responsivity of 5-HT systems, then the ability to identify antidepressant nonresponders via 5-HT challenge in combination with neuroimaging measures may have important clinical utility.

Aged↗

EH and UIM: endocytosis and more.

Exogenously and endogenously originated signals are propagated within the cell by functional and physical networks of proteins, leading to numerous biological outcomes. Many protein-protein interactions take place between binding domains and short peptide motifs. Frequently, these interactions are inducible by upstream signaling events, in which case one of the two binding surfaces may be created by a posttranslational modification. Here, we discuss two protein networks. One, the EH-network, is based on the Eps15 homology (EH) domain, which binds to peptides containing the sequence Asp-Pro-Phe (NPF). The other, which we define as the monoubiquitin (mUb) network, relies on monoubiquitination, which is emerging as an important posttranslational modification that regulates protein function. Both networks were initially implicated in the control of plasma membrane receptor endocytosis and in the regulation of intracellular trafficking routes. The ramifications of these two networks, however, appear to extend into many other aspects of cell physiology as well, such as transcriptional regulation, actin cytoskeleton remodeling, and DNA repair. The focus of this review is to integrate available knowledge of the EH- and mUb networks with predictions of genetic and physical interactions stemming from functional genomics approaches.

Adaptor Proteins, Signal Transducing↗

Modeling allosteric regulation of de novo pyrimidine biosynthesis in Escherichia coli.

With the emergence of multifaceted bioinformatics-derived data, it is becoming possible to merge biochemical and physiological information to develop a new level of understanding of the metabolic complexity of the cell. The biosynthetic pathway of de novo pyrimidine nucleotide metabolism is an essential capability of all free-living cells, and it occupies a pivotal position relative to metabolic processes that are involved in the macromolecular synthesis of DNA, RNA and proteins, as well as energy production and cell division. This regulatory network in all enteric bacteria involves genetic, allosteric, and physiological control systems that need to be integrated into a coordinated set of metabolic checks and balances. Allosterically regulated pathways constitute an exciting and challenging biosynthetic system to be approached from a mathematical perspective. However, to date, a mathematical model quantifying the contribution of allostery in controlling the dynamics of metabolic pathways has not been proposed. In this study, a direct, rigorous mathematical model of the de novo biosynthesis of pyrimidine nucleotides is presented. We corroborate the simulations with experimental data available in the literature and validate it with derepression experiments done in our laboratory. The model is able to faithfully represent the dynamic changes in the intracellular nucleotide pools that occur during metabolic transitions of the de novo pyrimidine biosynthetic pathway and represents a step forward in understanding the role of allosteric regulation in metabolic control.

Allosteric Regulation↗

Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms.

MOTIVATION: Information from fully sequenced genomes makes it possible to reconstruct strain-specific global metabolic network for structural and functional studies. These networks are often very large and complex. To properly understand and analyze the global properties of metabolic networks, methods for rationally representing and quantitatively analyzing their structure are needed. RESULTS: In this work, the metabolic networks of 80 fully sequenced organisms are in silico reconstructed from genome data and an extensively revised bioreaction database. The networks are represented as directed graphs and analyzed by using the 'breadth first searching algorithm to identify the shortest pathway (path length) between any pair of the metabolites. The average path length of the networks are then calculated and compared for all the organisms. Different from previous studies the connections through current metabolites and cofactors are deleted to make the path length analysis physiologically more meaningful. The distribution of the connection degree of these networks is shown to follow the power law, indicating that the overall structure of all the metabolic networks has the characteristics of a small world network. However, clear differences exist in the network structure of the three domains of organisms. Eukaryotes and archaea have a longer average path length than bacteria. AVAILABILITY: The reaction database in excel format and the programs in VBA (Visual Basic for Applications) are available upon request. SUPPLEMENTARY MATERIAL: Bioinformatics Online.

Archaea↗